Diversity and Seasonality of Bioluminescent Vibrio Cholerae Populations in Chesapeake Bay - Zo,Young-Gun; Chokesajjawatee,Nipa; Grim,Christopher; Arakawa,Eiji; Watanabe,Haruo; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2009)
Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of Vibrio cholerae isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types. V. cholerae O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by stn) and the membrane protein associated with bile resistance (encoded by ompU) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of V. cholerae occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent V. cholerae strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent V. cholerae is concluded to be related to its interaction with copepods and related crustacean species.

Energy loss in MEMS resonators and the impact on inertial and RF devices - Weinberg,M.; Candler,R.; Chandorkar,S.; Varsanik,J.; Kenny,T.; Duwel,A. (2009)
In this paper, we review the current understanding of energy loss mechanisms in micromachined (MEMS and NEMS) devices. We describe the importance of high quality factor (Q) to the performance of MEMS gyros and MEMS resonators used in radio-frequency applications.
Keywords: energy loss; gyroscopes; inertial devices; MEMS gyros; MEMS resonators; micromachined devices; micromechanical resonators; NEMS devices; Q-factor; quality factor; radiofrequency applications; RF devices

Enforcing integrability by error correction using ℓ1-minimization - Reddy, D.; Agrawal,A.; Chellapa, Rama (Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on, 2009)
Surface reconstruction from gradient fields is an important final step in several applications involving gradient manipulations and estimation. Typically, the resulting gradient field is non-integrable due to linear/non-linear gradient manipulations, or due to presence of noise/outliers in gradient estimation. In this paper, we analyze integrability as error correction, inspired from recent work in compressed sensing, particulary lscr0 - lscr1 equivalence. We propose to obtain the surface by finding the gradient field which best fits the corrupted gradient field in lscr1 sense. We present an exhaustive analysis of the properties of lscr1 solution for gradient field integration using linear algebra and graph analogy. We consider three cases: (a) noise, but no outliers (b) no-noise but outliers and (c) presence of both noise and outliers in the given gradient field. We show that lscr1 solution performs as well as least squares in the absence of outliers. While previous lscr0 - lscr1 equivalence work has focused on the number of errors (outliers), we show that the location of errors is equally important for gradient field integration. We characterize the lscr1 solution both in terms of location and number of outliers, and outline scenarios where lscr1 solution is equivalent to lscr0 solution. We also show that when lscr1 solution is not able to remove outliers, the property of local error confinement holds: i.e., the errors do not propagate to the entire surface as in least squares. We compare with previous techniques and show that lscr1 solution performs well across all scenarios without the need for any tunable parameter adjustments.
Keywords: -; algebra; lscr0; algebra; minimisation; analogy; integrability; least; compressed; correction; gradient; equivalence; lscr1-minimization; noise-outlier; surface; estimation; gradient; field; integration; gradient; lscr1; manipulation; graph; methods; graph; reconstruction; error; reconstruction; linear; sensing; error; squares; linear; theory; image

Enhancing sparsity using gradients for compressive sensing - Patel, Vishal M.; Easley,G. R; Chellapa, Rama; Healy,D. M (Image Processing (ICIP), 2009 16th IEEE International Conference on, 2009)
In this paper, we propose a reconstruction method that recovers images assumed to have a sparse representation in a gradient domain by using partial measurement samples that are collected in the Fourier domain. A key improvement of this technique is that it makes use of a robust generalized Poisson solver that greatly aids in achieving a significantly improved performance over similar proposed methods. Experiments provided also demonstrate that this new technique is more flexible to work with either random or restricted sampling scenarios better than its competitors.
Keywords: analysis; gradient; domain; compressive; domain; image; Fourier; generalized; measurement; methods; methods; image; Poisson; reconstruction; image; reconstruction; partial; representation; Fourier; representation; sampling; samples; robust; scenarios; sparse; sensing; enhancing; solver; sampling; sparsity; gradient

Evaluating Attack Resiliency for Host Intrusion Detection Systems - Molina,J.; Michel Cukier (Journal of Information Assurance and Security, 2009)
Host intrusion detection systems (HIDSs) areimportant tools used to provide security to computer systems. Many HIDSs exist and security practitioners need a way to determine the optimal security solution for their environment. Current evaluations of HIDSs focus on detection accuracy and typically do not account for the possibility that an adversary may subvert the HIDS and modify the outcome. As some elements from the HIDS need to reside within the system under supervi- sion, evaluating the strength against HIDS subversion is critical. This paper defines HIDS subversion and presents HIDS resiliency as a metric of HIDS strength in the event of an attack against the system being supervised. To estimate HIDS resiliency, we evaluated the inde- pendency between the system being supervised and the HIDS. Then we integrated resiliency into current frame- works to evaluate detection accuracy.

Evaluating Files to Audit for Detecting Intrusions in FileSystem Data - Molina,J.; Michel Cukier (2009)
Monitoring filesystem data is a common method used to detect intrusions. Once a computer is compromised, an attacker may alter files, add new files or delete existing files. The changes that attackers make may target any part of the filesystem, including metadata along with files (e.g., permissions, ownerships and inodes). The accuracy of detecting an intrusion depends on the data audited: if an intrusion does not manifest in the data, the intrusion will not be detected. Moreover, not all files, which contain filesystem activity, are suitable to detect intrusions, as some may fail to provide useful information. In this paper, we describe an empirical study that focused on filesystem attack activity after a SSH compromise. Three types of attacker action are considered: reconnaissance, password modification, and malware download. For each type of action, we evaluated the files to audit using metrics derived from the field of information theory and estimated with the empirical SSH compromise data.
Keywords: authorisation; Bayes methods; Bayesian metric; data auditing; empirical SSH compromise data; Entropy; entropy-based metric; file evaluation; file organisation; filesystem attack activity; filesystem data monitoring; honeypot; information theory; intrusion detection system; invasive software; malware download; meta data; optimisation; optimization problem; password modification; probability; reconnaissance action; unauthorized user

An evaluation of connection characteristics for separating network attacks - Berthier,Robin; Michel Cukier (International Journal of Security and Networks, 2009)
The goal of this paper is to evaluate the efficiency of connection characteristics to separate different attack families that target a single TCP port. Identifying the most relevant characteristics might allow statistically separating attack families without systematically using forensics. This study is based on a dataset collected over 117 days using a test-bed of two high interaction honeypots. The results indicated that to separate unsuccessful from successful attacks in malicious traffic: the number of bytes is a relevant characteristic; time-based characteristics are poor characteristics; using combinations of characteristics does not improve the efficiency of separating attacks.

Evidence for Bidentate Substrate Binding as the Basis for the K48 Linkage Specificity of Otubain 1 - Wang,Tao; Yin,Luming; Cooper,Eric M.; Lai,Ming-Yih; Dickey,Seth; Pickart,Cecile M.; Fushman, David; Wilkinson,Keith D.; Cohen,Robert E.; Wolberger,Cynthia (Journal of Molecular Biology, 2009)
Otubain 1 belongs to the ovarian tumor (OTU) domain class of cysteine protease deubiquitinating enzymes. We show here that human otubain 1 (hOtu1) is highly linkage-specific, cleaving Lys48 (K48)-linked polyubiquitin but not K63-, K29-, K6-, or K11-linked polyubiquitin, or linear α-linked polyubiquitin. Cleavage is not limited to either end of a polyubiquitin chain, and both free and substrate-linked polyubiquitin are disassembled. Intriguingly, cleavage of K48-diubiquitin by hOtu1 can be inhibited by diubiquitins of various linkage types, as well as by monoubiquitin. NMR studies and activity assays suggest that both the proximal and distal units of K48-diubiquitin bind to hOtu1. Reaction of Cys23 with ubiquitin-vinylsulfone identified a ubiquitin binding site that is distinct from the active site, which includes Cys91. Occupancy of the active site is needed to enable tight binding to the second site. We propose that distinct binding sites for the ubiquitins on either side of the scissile bond allow hOtu1 to discriminate among different isopeptide linkages in polyubiquitin substrates. Bidentate binding may be a general strategy used to achieve linkage-specific deubiquitination.
Keywords: deubiquitination; isopeptide; linkage specificity; otubain; polyubiquitin

Evidence for Coregulation of Myocardial Gene Expression by MEF2 and NFAT in Human Heart Failure / CLINICAL PERSPECTIVE - Putt,Mary E.; Hannenhalli, Sridhar; Lu,Yun; Haines,Philip; Chandrupatla,Hareesh R.; Morrisey,Edward E.; Margulies,Kenneth B.; Cappola,Thomas P. (Circulation: Cardiovascular Genetics, 2009)
Background— Pathological stresses induce heart failure in animal models through activation of multiple cardiac transcription factors (TFs) working cooperatively. However, interactions among TFs in human heart failure are less understood. Here, we use genomic data to examine the evidence that 5 candidate TF families coregulate gene expression in human heart failure.Methods and Results— RNA isolates from failing (n=86) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays. For each gene on the array, we determined conserved MEF2, NFAT, NKX , GATA , and FOX binding motifs within the −1-kb promoter region using human-murine sequence alignments and the TRANSFAC database. Across 9076 genes expressed in the heart, TF-binding motifs tended to cluster together in nonrandom patterns within promoters of specific genes (P values ranging from 10−2 to 10−21), suggesting coregulation. We then modeled differential expression as a function of TF combinations present in promoter regions. Several combinations predicted increased odds of differential expression in the failing heart, with the highest odds ratios noted for genes containing both MEF2 and NFAT binding motifs together in the same promoter region (peak odds ratio, 3.47; P=0.005).Conclusions— These findings provide genomic evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure. In doing so, they extend the paradigm of combinatorial regulation of gene expression to the human heart and identify new target genes for mechanistic study. More broadly, we demonstrate how integrating diverse sources of genomic data yields novel insight into human cardiovascular disorders.

Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development - Takala,S. L; Coulibaly,D.; Thera,M. A; Batchelor,A. H; Cummings, Michael P.; Escalante,A. A; Ouattara,A.; Traoré,K.; Niangaly,A.; Djimdé,A. A; Doumbo,OK; Plowe,CV (Sci Transl Med, 2009)
Vaccines directed against the blood stages of Plasmodium falciparum malaria are intended to prevent the parasite from invading and replicating within host cells. No blood-stage malaria vaccine has shown clinical efficacy in humans. Most malaria vaccine antigens are parasite surface proteins that have evolved extensive genetic diversity, and this diversity could allow malaria parasites to escape vaccine-induced immunity. We examined the extent and within-host dynamics of genetic diversity in the blood-stage malaria vaccine antigen apical membrane antigen-1 in a longitudinal study in Mali. Two hundred and fourteen unique apical membrane antigen-1 haplotypes were identified among 506 human infections, and amino acid changes near a putative invasion machinery binding site were strongly associated with the development of clinical symptoms, suggesting that these residues may be important to consider in designing polyvalent apical membrane antigen-1 vaccines and in assessing vaccine efficacy in field trials. This extreme diversity may pose a serious obstacle to an effective polyvalent recombinant subunit apical membrane antigen-1 vaccine.

Face Recognition from Video - Zhou,Shaohua Kevin; Chellapa, Rama; Aggarwal,Gaurav (The Essential Guide to Video Processing (Second Edition)The Essential Guide to Video Processing (Second Edition), 2009)

First Steps to Netviz Nirvana: Evaluating Social Network Analysis with NodeXL - Bonsignore,E. M; Dunne,C.; Rotman,D.; Smith,M.; Capone,T.; Hansen,D. L; Shneiderman, Ben (International Conference on Computational Science and Engineering, 2009. CSE '09, 2009)
Social Network Analysis (SNA) has evolved as a popular, standard method for modeling meaningful, often hidden structural relationships in communities. Existing SNA tools often involve extensive pre-processing or intensive programming skills that can challenge practitioners and students alike. NodeXL, an open-source template for Microsoft Excel, integrates a library of common network metrics and graph layout algorithms within the familiar spreadsheet format, offering a potentially low-barrier-to-entry framework for teaching and learning SNA. We present the preliminary findings of 2 user studies of 21 graduate students who engaged in SNA using NodeXL. The majority of students, while information professionals, had little technical background or experience with SNA techniques. Six of the participants had more technical backgrounds and were chosen specifically for their experience with graph drawing and information visualization. Our primary objectives were (1) to evaluate NodeXL as an SNA tool for a broad base of users and (2) to explore methods for teaching SNA. Our complementary dual case-study format demonstrates the usability of NodeXL for a diverse set of users, and significantly, the power of a tightly integrated metrics/visualization tool to spark insight and facilitate sense-making for students of SNA.
Keywords: Computer science; computer science education; data visualisation; Data visualization; Educational institutions; graph drawing; graph layout algorithm; Information services; Information Visualization; Internet; Libraries; Microsoft Excel open-source template; MILC; multi-dimensional in-depth long-term case studies; Netviz Nirvana; NodeXL; Open source software; Programming profession; SNA; social network analysis; Social network services; social networking (online); spreadsheet programs; structural relationship; teaching; visual analytics; visualization tool; Web sites

Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo - Shah,Rachana; Lu,Yun; Hinkle,Christine C; McGillicuddy,Fiona C; Kim,Roy; Hannenhalli, Sridhar; Cappola,Thomas P.; Heffron,Sean; Wang,XingMei; Mehta,Nehal N; Putt,Mary; Reilly,Muredach P (DiabetesDiabetes, 2009)
OBJECTIVE Adipose inflammation plays a central role in obesity-related metabolic and cardiovascular complications. However, few human adipose-secreted proteins are known to mediate these processes. We hypothesized that microarray mRNA profiling of human adipose during evoked inflammation could identify novel adipocytokines.RESEARCH DESIGN AND METHODS Healthy human volunteers (n = 14) were treated with intravenous endotoxin (3 ng/kg lipopolysaccharide [LPS]) and underwent subcutaneous adipose biopsies before and after LPS. On Affymetrix U133Plus 2.0 arrays, adipose mRNAs modulated >1.5-fold (with P < 0.00001) were selected. SignalP 3.0 and SecretomeP 2.0 identified genes predicted to encode secreted proteins. Of these, 86 candidates were chosen for validation in adipose from an independent human endotoxemia protocol (N = 7, with 0.6 ng/kg LPS) and for exploration of cellular origin in primary human adipocytes and macrophages in vitro. RESULTS Microarray identified 776 adipose genes modulated by LPS; 298 were predicted to be secreted. Of detectable prioritized genes, 82 of 85 (96% [95% CI 90–99]) were upregulated (fold changes >1.0) during the lower-dose (LPS 0.6 ng/kg) validation study and 51 of 85 (59% [49–70]) were induced greater than 1.5-fold. Treatment of primary adipocytes with LPS and macrophage polarization to M1 proinflammatory phenotype increased expression by 1.5-fold for 58 and 73% of detectable genes, respectively. CONCLUSIONS We demonstrate that evoked inflammation of human adipose in vivo modulated expression of multiple genes likely secreted by adipocytes and monocytes. These included established adipocytokines and chemokines implicated in recruitment and activation of lymphocytes, adhesion molecules, antioxidants, and several novel genes with unknown function. Such candidates may represent biomarkers and therapeutic targets for obesity-related complications.

Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains - Brettin,Thomas S[Los Alamos National Laboratory; Bruce,David C[Los Alamos National Laboratory; Challacombe,Jean F[Los Alamos National Laboratory; Detter,John C[Los Alamos National Laboratory; Han,Cliff S[Los Alamos National Laboratory; Munik,A. C[Los Alamos National Laboratory; Chertkov,Olga[Los Alamos National Laboratory; Meincke,Linda[Los Alamos National Laboratory; Saunders,Elizabeth[Los Alamos National Laboratory; Choi,Seon Y[SEOUL NATL UNIV; Haley,Bradd J[U MARYLAND; Taviani,Elisa[U MARYLAND; et al. (Nature, 2009)
Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the 6th and the current 7th pandemics, respectively. Cholera researchers continually face newly emerging and re-emerging pathogenic clones carrying combinations of new serogroups as well as of phenotypic and genotypic properties. These genotype and phenotype changes have hampered control of the disease. Here we compare the complete genome sequences of 23 strains of V. cholerae isolated from a variety of sources and geographical locations over the past 98 years in an effort to elucidate the evolutionary mechanisms governing genetic diversity and genesis of new pathogenic clones. The genome-based phylogeny revealed 12 distinct V. cholerae phyletic lineages, of which one, designated the V. cholerae core genome (CG), comprises both O1 classical and EI Tor biotypes. All 7th pandemic clones share nearly identical gene content, i.e., the same genome backbone. The transition from 6th to 7th pandemic strains is defined here as a 'shift' between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages within the CG clade. In contrast, transition among clones during the present 7th pandemic period can be characterized as a 'drift' between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V.cholerae serogroup O139 and V.cholerae O1 El Tor hybrid clones that produce cholera toxin of classical biotype. Based on the comprehensive comparative genomics presented in this study it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.
Keywords: 59; CHOLERA; GENES; GENETICS; GENOTYPE; ISLANDS; ORIGIN; PHENOTYPE; PUBLIC HEALTH; RECOMBINATION; STRAINS; TOXINS

The Genus Vibrio and Related Genera - Rita R Colwell; Chun,J. (Practical handbook of microbiologyPractical handbook of microbiology, 2009)

How would you look as you age ? - Ramanathan,N.; Chellapa, Rama (Image Processing (ICIP), 2009 16th IEEE International Conference on, 2009)
Facial appearances change with increase in age. While generic growth patterns that are characteristic of different age groups can be identified, facial growth is also observed to be influenced by individual-specific attributes such as one's gender, ethnicity, life-style etc. In this paper, we propose a facial growth model that comprises of transformation models for facial shape and texture. We collected empirical data pertaining to facial growth from a database of age-separated face images of adults and used the same in developing the aforementioned transformation models. The proposed model finds applications in predicting one's appearance across ages and in performing face verification across ages.
Keywords: age-separated; appearances; facial; database; face; Face; growth; image; model; face; model; facial; models; facial; recognition; image; SHAPE; TEXTURE; texture; transformation; verification; facial

HydroSense: infrastructure-mediated single-point sensing of whole-home water activity - Jon Froehlich; Larson,E.; Campbell,T.; Haggerty,C.; Fogarty,J.; Patel,S.N. (Proceedings of the 11th international conference on Ubiquitous computing, September, 2009)

Implicit authentication for mobile devices - Jakobsson, Markus; Elaine Shi; Golle, Philippe; Chow, Richard (USENIX Association, 2009)
We introduce the notion of implicit authentication - the ability to authenticate mobile users based on actions they would carry out anyway. We develop a model for how to perform implicit authentication, and describe experiments aimed at assessing the benefits of our techniques. Our preliminary findings support that this is a meaningful approach, whether used to increase usability or increase security.

Improved Non-committing Encryption with Applications to Adaptively Secure Protocols - Choi, Seung Geol; Dana Dachman-Soled; Malkin, Tal; Wee, Hoeteck (Advances in Cryptology – ASIACRYPT 2009, 2009)
We present a new construction of non-committing encryption schemes. Unlike the previous constructions of Canetti et al. (STOC ’96) and of Damgård and Nielsen (Crypto ’00), our construction achieves all of the following properties: Optimal round complexity. Our encryption scheme is a 2-round protocol, matching the round complexity of Canetti et al. and improving upon that in Damgård and Nielsen. Weaker assumptions. Our construction is based on trapdoor simulatable cryptosystems, a new primitive that we introduce as a relaxation of those used in previous works. We also show how to realize this primitive based on hardness of factoring. Improved efficiency. The amortized complexity of encrypting a single bit is O(1) public key operations on a constant-sized plaintext in the underlying cryptosystem. As a result, we obtain the first non-committing public-key encryption schemes under hardness of factoring and worst-case lattice assumptions; previously, such schemes were only known under the CDH and RSA assumptions. Combined with existing work on secure multi-party computation, we obtain protocols for multi-party computation secure against a malicious adversary that may adaptively corrupt an arbitrary number of parties under weaker assumptions than were previously known. Specifically, we obtain the first adaptively secure multi-party protocols based on hardness of factoring in both the stand-alone setting and the UC setting with a common reference string.
Keywords: adaptive corruption; Algorithm Analysis and Problem Complexity; Applications of Mathematics; Data Encryption; Data Structures, Cryptology and Information Theory; Discrete Mathematics in Computer Science; non-committing encryption; public-key encryption; secure multi-party computation; Systems and Data Security

Improved statistical machine translation using monolingually-derived paraphrases - Marton,Y.; Callison-Burch,C.; Resnik, Philip (Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1-Volume 1, 2009)

Incremental covering array failure characterization in large configuration spaces - Fouché,S.; Cohen,M. B; Porter, Adam (Proceedings of the eighteenth international symposium on Software testing and analysis, 2009)

Information Visualization - Card,Stuart (Human-Computer InteractionHuman-Computer Interaction, 2009)

The Ins and Outs of Home Networking: The Case for Useful and Usable Domestic Networking - Grinter, Rebecca E.; Edwards, W. Keith; Marshini Chetty; Poole, Erika S.; Sung, Ja-Young; Yang, Jeonghwa; Crabtree, Andy; Tolmie, Peter; Rodden, Tom; Greenhalgh, Chris; Benford, Steve (ACM Trans. Comput.-Hum. Interact., 2009)
Householders are increasingly adopting home networking as a solution to the demands created by the presence of multiple computers, devices, and the desire to access the Internet. However, current network solutions are derived from the world of work (and initially the military) and provide poor support for the needs of the home. We present the key findings to emerge from empirical studies of home networks in the UK and US. The studies reveal two key kinds of work that effective home networking relies upon: one, the technical work of setting up and maintaining the home network, and the other, the collaborative and socially organized work of the home which the network is embedded in and supports. The two are thoroughly intertwined and rely upon one another for their realization, yet neither is adequately supported by current networking technologies and applications. Explication of the “work to make the home network work” opens up the design space for the continued integration of the home network in domestic life and elaboration of future support. Key issues for development include the development of networking facilities that do not require advanced networking knowledge, that are flexible and support the local social order of the home and the evolution of its routines, and which ultimately make the home network visible and accountable to household members.
Keywords: home networking; Human computer interaction

Interacting with eHealth: towards grand challenges for HCI - André,P.; White,R.; Tan,D.; Berners-Lee,T.; Consolvo,S.; Jacobs,R.; Kohane,I.; Le Dantec,C.A.; Mamykina,L.; Marsden,G. (Proceedings of the 27th international conference extended abstracts on Human factors in computing systems, 2009)
While health records are increasingly stored electronically, we, as citizens, have little access to this data about ourselves. We are not used to thinking of these official records either as ours or as useful to us. We increasingly turn to the Web, however, to query any ache, pain or health goal we may have before consulting with health care professionals. Likewise, for proactive health care such as nutrition or fitness, or to find fellow-sufferers for post diagnosis support, we turn to online resources. There is a potential disconnect between points at which professional and lay eHealth data and resources intersect for preventative or proactive health care. Such gaps in information sharing may have direct impact on practices we decide to take up, the care we seek, or the support professionals offer. In this panel, we consider several places within proactive, preventative health care in particular HCI has a role towards enhancing health knowledge discovery and health support interaction. Our goal is to demonstrate how now is the time for eHealth to come to the forefront of the HCI research agenda.

It's Not Easy Being Green: Understanding Home Computer Power Management - Marshini Chetty; Brush, A.J. Bernheim; Meyers, Brian R.; Johns, Paul (SIGCHI '09, 2009)
Although domestic computer use is increasing, most efforts to reduce energy use through improved power management have focused on computers in the workplace. We studied 20 households to understand how people use power management strategies on their home computers. We saw computers in the home, particularly desktop computers, are left on much more than they are actively used suggesting opportunities for economic and energy savings. However, for most of our participants, the economic incentives were too minor to motivate them to turn off devices when not in use, especially given other frustrations such as long boot up times. We suggest research directions for home computer power management that could help users be more green without having to dramatically change their home computing habits.
Keywords: home computer use; power management; Sustainability

Knowledge Extraction from Surveillance Sensors - Chellapa, Rama; Veeraraghavan,Ashok; Sankaranarayanan,Aswin C. (Wiley Handbook of Science and Technology for Homeland SecurityWiley Handbook of Science and Technology for Homeland Security, 2009)
Keywords: multi‐camera tracking; multi‐modal fusion; recognition; sensor networks; Surveillance

Learning Facial Aging Models: A Face Recognition Perspective - Ramanathan,N.; Chellapa, Rama (Biometrics: theory, methods, and applications, 2009)

Learning multi-modal densities on Discriminative Temporal Interaction Manifold for group activity recognition - Ruonan Li; Chellapa, Rama; Zhou,S. K (Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on, 2009)
While video-based activity analysis and recognition has received much attention, existing body of work mostly deals with single object/person case. Coordinated multi-object activities, or group activities, present in a variety of applications such as surveillance, sports, and biological monitoring records, etc., are the main focus of this paper. Unlike earlier attempts which model the complex spatial temporal constraints among multiple objects with a parametric Bayesian network, we propose a Discriminative Temporal Interaction Manifold (DTIM) framework as a data-driven strategy to characterize the group motion pattern without employing specific domain knowledge. In particular, we establish probability densities on the DTIM, whose element, the discriminative temporal interaction matrix, compactly describes the coordination and interaction among multiple objects in a group activity. For each class of group activity we learn a multi-modal density function on the DTIM. A Maximum a Posteriori (MAP) classifier on the manifold is then designed for recognizing new activities. Experiments on football play recognition demonstrate the effectiveness of the approach.
Keywords: a; activities; parametric; activity; analysis; belief; analysis; pattern; Bayesian; classification; image; classifier; multimodal; complex; constraints; data-driven; density; equipment; video; function; multiobject; interaction; manifold; discriminative; matrix; football; MOTION; network; video-based; networks; image; play; posteriori; processing; recognition; recognition; group; recognition; maximum; signal; spatial; strategy; discriminative; temporal

Locally time-invariant models of human activities using trajectories on the grassmannian - Turaga,P.; Chellapa, Rama (Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on, 2009)
Human activity analysis is an important problem in computer vision with applications in surveillance and summarization and indexing of consumer content. Complex human activities are characterized by non-linear dynamics that make learning, inference and recognition hard. In this paper, we consider the problem of modeling and recognizing complex activities which exhibit time-varying dynamics. To this end, we describe activities as outputs of linear dynamic systems (LDS) whose parameters vary with time, or a time-varying linear dynamic system (TV-LDS). We discuss parameter estimation methods for this class of models by assuming that the parameters are locally time-invariant. Then, we represent the space of LDS models as a Grassmann manifold. Then, the TV-LDS model is defined as a trajectory on the Grassmann manifold. We show how trajectories on the Grassmannian can be characterized using appropriate distance metrics and statistical methods that reflect the underlying geometry of the manifold. This results in more expressive and powerful models for complex human activities. We demonstrate the strength of the framework for activity-based summarization of long videos and recognition of complex human actions on two datasets.
Keywords: action; activity; analysis; local; analysis; video; content; dynamic; Estimation; estimation; statistical; Grassmann; indexing; distance; linear; manifold; activity-based; method; statistical; method; surveillance; time-varying; metrics; human; model; parameter; recognition; human; recognition; indexing; parameter; summarization; computer; surveillance; system; computer; time-invariant; vision; consumer; vision; image

Maintaining nets and net trees under incremental motion - Cho,M.; Mount, Dave; Park,E. (Algorithms and Computation, 2009)
The problem of maintaining geometric structures for points in motion has been well studied over the years. Much theoretical work to date has been based on the assumption that point motion is continuous and predictable, but in practice, motion is typically presented incrementally in discrete time steps and may not be predictable. We consider the problem of maintaining a data structure for a set of points undergoing such incremental motion. We present a simple online model in which two agents cooperate to maintain the structure. One defines the data structure and provides a collection of certificates, which guarantee the structure’s correctness. The other checks that the motion over time satisfies these certificates and notifies the first agent of any violations.We present efficient online algorithms for maintaining both nets and net trees for a point set undergoing incremental motion in a space of constant dimension. We analyze our algorithms’ efficiencies by bounding their competitive ratios relative to an optimal algorithm. We prove a constant factor competitive ratio for maintaining a slack form of nets, and our competitive ratio for net trees is proportional to the square of the tree’s height.

Measurement methods for fast and accurate blackhole identification with binary tomography - Cunha,Ítalo; Teixeira,Renata; Feamster, Nick; Diot,Christophe (Proceedings of the 9th ACM SIGCOMM conference on Internet measurement conference, 2009)
Binary tomography - the process of identifying faulty network links through coordinated end-to-end probes - is a promising method for detecting failures that the network does not automatically mask (e.g., network "blackholes"). Because tomography is sensitive to the quality of the input, however, naïve end-to-end measurements can introduce inaccuracies. This paper develops two methods for generating inputs to binary tomography algorithms that improve their inference speed and accuracy. Failure confirmation is a per-path probing technique to distinguish packet losses caused by congestion from persistent link or node failures. Aggregation strategies combine path measurements from unsynchronized monitors into a set of consistent observations. When used in conjunction with existing binary tomography algorithms, our methods identify all failures that are longer than two measurement cycles, while inducing relatively few false alarms. In two wide-area networks, our techniques decrease the number of alarms by as much as two orders of magnitude. Compared to the state of the art in binary tomography, our techniques increase the identification rate and avoid hundreds of false alarms.
Keywords: diagnosis; network tomography; troubleshooting

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays - Bloom, Joshua S.; Zia Khan; Kruglyak, Leonid; Singh, Mona; Caudy, Amy A. (BMC Genomics, 2009)
Background High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression. Results Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of S. cerevisiae. Conclusion Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.
Keywords: Animal Genetics and Genomics; Life Sciences, general; Microarrays; Microbial Genetics and Genomics; Plant Genetics & Genomics; proteomics

Microbial oceanography in a sea of opportunity - Bowler,Chris; Karl,David M.; Rita R Colwell (Nature, 2009)
Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean's response to climate change, improving the predictive power of climate models.
Keywords: Astronomy; astrophysics; Biochemistry; Bioinformatics; Biology; biotechnology; cancer; cell cycle; cell signalling; climate change; Computational Biology; development; developmental biology; DNA; drug discovery; earth science; ecology; environmental science; Evolution; evolutionary biology; functional genomics; Genetics; Genomics; geophysics; immunology; interdisciplinary science; life; marine biology; materials science; medical research; medicine; metabolomics; molecular biology; molecular interactions; nanotechnology; Nature; neurobiology; neuroscience; palaeobiology; pharmacology; Physics; proteomics; quantum physics; RNA; Science; science news; science policy; signal transduction; structural biology; systems biology; transcriptomics

Model-based quality assessment and base-calling for second-generation sequencing data - Irizarry,R. A; Corrada Bravo, Hector (Johns Hopkins University, Dept. of Biostatistics Working Papers, 2009)

Modeling and analysis of ordinal ranking in content fingerprinting - Chuang,Wei-Hong; Varna,A.L.; M. Wu (Information Forensics and Security, 2009. WIFS 2009. First IEEE International Workshop on, 2009)
Content fingerprinting provides a compact representation of multimedia objects for copy detection. This paper analyzes the robustness of the ordinal ranking module frequently used in content fingerprinting by examining the changes in ranks as local variations are introduced in feature values. Closed-form expressions to measure such sensitivity are derived when feature values are jointly Gaussian-distributed. The results show that sensitivity depends on the strength of local variation, the total number of blocks, and the correlations among block-based feature values. Experiments with both synthesized data and image data validate the analysis and provide interesting insights, inspiring an approach to reduce the sensitivity.
Keywords: detection; detection; multimedia; fingerprinting; copy; Gaussian-distributed; content; identification; multimedia; objects; ordinal; processes; fingerprint; ranking; Gaussian; systems; object

Modeling and visualization of human activities for multicamera networks - Sankaranarayanan,A. C; Patro,R.; Turaga,P.; Varshney, Amitabh; Chellapa, Rama (EURASIP Journal on Image and Video Processing, 2009)

Moving Object Verification in Airborne Video Sequences - Yue,Zhanfeng; Guarino, D.; Chellapa, Rama (Circuits and Systems for Video Technology, IEEE Transactions on, 2009)
This paper presents an end-to-end system for moving object verification in airborne video sequences. Using a sample selection module, the system first selects frames from a short sequence and stores them in an exemplar database. To handle appearance change due to potentially large aspect angle variations, a homography-based view synthesis method is then used to generate a novel view of each image in the exemplar database at the same pose as the testing object in each frame of a testing video segment. A rotationally invariant color matcher and a spatial-feature matcher based on distance transforms are combined using a weighted average rule to compare the novel view and the testing object. After looping over all testing frames, the set of match scores is passed to a temporal analysis module to examine the behavior of the testing object, and calculate a final likelihood. Very good verification performance is achieved over thousands of trials for both color and infrared video sequences using the proposed system.
Keywords: airborne; database; homography-based; databases; matcher; color; matcher; image; matching; image; method; infrared; object; sequences; color; sequences; distance; sequences; moving; sequences; video; synthesis; system; exemplar; transforms; end-to-end; verification; spatial-feature; video; view

Multicamera Tracking of Articulated Human Motion Using Shape and Motion Cues - Sundaresan, A.; Chellapa, Rama (Image Processing, IEEE Transactions on, 2009)
We present a completely automatic algorithm for initializing and tracking the articulated motion of humans using image sequences obtained from multiple cameras. A detailed articulated human body model composed of sixteen rigid segments that allows both translation and rotation at joints is used. Voxel data of the subject obtained from the images is segmented into the different articulated chains using Laplacian eigenmaps. The segmented chains are registered in a subset of the frames using a single-frame registration technique and subsequently used to initialize the pose in the sequence. A temporal registration method is proposed to identify the partially segmented or unregistered articulated chains in the remaining frames in the sequence. The proposed tracker uses motion cues such as pixel displacement as well as 2-D and 3-D shape cues such as silhouettes, motion residue, and skeleton curves. The tracking algorithm consists of a predictor that uses motion cues and a corrector that uses shape cues. The use of complementary cues in the tracking alleviates the twin problems of drift and convergence to local minima. The use of multiple cameras also allows us to deal with the problems due to self-occlusion and kinematic singularity. We present tracking results on sequences with different kinds of motion to illustrate the effectiveness of our approach. The pose of the subject is correctly tracked for the duration of the sequence as can be verified by inspection.
Keywords: 2D shape cues; 3D shape cues; algorithms; Anatomic; Models; articulated human motion; automatic algorithm; Biological; Movement; Posture; Skeleton; Video Recording; Computer-Assisted; Models; Eigenvalues and eigenfunctions; human pose estimation; HUMANS; Image motion analysis; IMAGE PROCESSING; image registration; Image segmentation; Image sequences; kinematic singularity; Laplacian eigenmaps; multicamera tracking algorithm; pixel displacement; pose estimation; single-frame registration technique; temporal registration method; tracking

New records of phytoplankton for Bangladesh. 9. Some rare and a new species - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Plant Taxonomy, 2009)
Ten taxa belonging to Chlorophyceae, Cyanophyceae, Bacillariophyceae and Euglenophyceae, and one with an uncertain taxonomic position have been described in this paper. Of these, 10 taxa have been found to be globally rare and new records for Bangladesh, whereas Strombomonas islamii Khondker sp. nov. has been described as new to science.

A phylogenetic mixture model for the evolution of gene expression - Eng,K. H; Corrada Bravo, Hector; Keleş,S. (Molecular biology and evolution, 2009)

Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study - Constantin de Magny,G.; Long,W.; Brown,C. W.; Hood,R. R.; Huq,A.; Murtugudde,R.; Rita R Colwell (EcoHealth, 2009)
Vibrio cholerae, the causative agent of cholera, is a naturally occurring inhabitant of the Chesapeake Bay and serves as a predictor for other clinically important vibrios, including Vibrio parahaemolyticus and Vibrio vulnificus. A system was constructed to predict the likelihood of the presence of V. cholerae in surface waters of the Chesapeake Bay, with the goal to provide forecasts of the occurrence of this and related pathogenic Vibrio spp. Prediction was achieved by driving an available multivariate empirical habitat model estimating the probability of V. cholerae within a range of temperatures and salinities in the Bay, with hydrodynamically generated predictions of ambient temperature and salinity. The experimental predictions provided both an improved understanding of the in situ variability of V. cholerae, including identification of potential hotspots of occurrence, and usefulness as an early warning system. With further development of the system, prediction of the probability of the occurrence of related pathogenic vibrios in the Chesapeake Bay, notably V. parahaemolyticus and V. vulnificus, will be possible, as well as its transport to any geographical location where sufficient relevant data are available.

Prioritizing Vulnerability Remediation by Determining Attacker-Targeted Vulnerabilities - Michel Cukier; Panjwani,S. (Security Privacy, IEEE, 2009)
This article attempts to empirically analyze which vulnerabilities attackers tend to target in order to prioritize vulnerability remediation. This analysis focuses on the link between malicious connections and vulnerabilities, where each connection is considered malicious. Attacks requiring multiple connections are counted as multiple attacks. As the number of connections increases, so does the cost of recovering from the intrusion. The authors deployed four honey pots for four months, each running a different Windows service pack with its associated set of vulnerabilities. They then performed three empirical analyses to determine the relationship between the number of malicious connections and the total number of vulnerabilities, the number of malicious connections and the number of the vulnerabilities for different services, and the number of known successful attacks and the number of vulnerabilities for different services.
Keywords: attacker-targeted vulnerabilities; intrusion detection; malicious connections; security of data; vulnerability remediation; Windows service pack

Promoting social creativity: a component of a national initiative for social participation - Shneiderman, Ben; Churchill,Elizabeth; Fischer,Gerhard; Goldberg,Ken (Proceedings of the seventh ACM conference on Creativity and cognition, 2009)
This panel will discuss group processes that promote social creativity in science, engineering, arts, and humanities. We will offer positive and negative examples of social creativity projects, while suggesting research directions for dramatically increased social participation. The goal is to develop strategies that would expand resources and opportunities for research and education in social creativity. This requires our community to develop a unified position, then reach out to national science funding agencies, while building the case for the importance of this topic beyond our own community. How can social creativity, collaborative discovery, distributed innovation, and collective intelligence be framed as an international priority to cope with the problems of the 21st century and how can we identify a clear set of research challenges? The theme of technology-mediated social participation is outlined in the white paper for a National Initiative for Social Participation (http://iparticipate.wikispaces.com). The white paper suggests that successful research challenges should have three key elements: (1) compelling national need (healthcare, national security, community safety, education, innovation, cultural heritage, energy sustainability, environmental protection, etc.), (2) scientific foundation based on established theories and well-defined research questions (privacy, reciprocity, trust, motivation, recognition, etc.), and (3) computer science research challenges (security, privacy protection, scalability, visualization, end-user development, distributed data handling for massive user-generated content, network analysis of community evolution, cross network comparison, etc.). We seek recommendations for ways to increase the resources and attention for this field. We hope to inspire: universities to change course content, add courses, and offer new degree programs industry to help researchers on social creativity government to support these ideas and try them out in government applications scientists and artists to open themselves to more social/collaborative approaches
Keywords: research agenda; social creativity; social participation

Pushing Enterprise Security Down the Network Stack - Clark,R.; Feamster, Nick; Nayak,A.; Reimers,A. (Georgia Institute of Technology, 2009)
Network security is typically reactive: Networks provide connectivity and subsequently alter this connectivity according to various security policies, as implemented in middleboxes, or at higher layers. This approach gives rise to complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. In this paper, we propose a proactive approach to securing networks, whereby security-related actions (e.g., dropping or redirecting traffic) are embedded into the network fabric itself, leaving only a fixed set of actions to higher layers. We explore this approach in the context of network access control. Our design uses programmable switches to manipulate traffic at lower layers; these switches interact with policy and monitoring at higher layers. We apply our approach to Georgia Tech’s network access control system, show how the new design can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.

Rate-Invariant Recognition of Humans and Their Activities - Veeraraghavan,A.; Srivastava, A.; Roy-Chowdhury, A.K.; Chellapa, Rama (Image Processing, IEEE Transactions on, 2009)
Pattern recognition in video is a challenging task because of the multitude of spatio-temporal variations that occur in different videos capturing the exact same event. While traditional pattern-theoretic approaches account for the spatial changes that occur due to lighting and pose, very little has been done to address the effect of temporal rate changes in the executions of an event. In this paper, we provide a systematic model-based approach to learn the nature of such temporal variations (time warps) while simultaneously allowing for the spatial variations in the descriptors. We illustrate our approach for the problem of action recognition and provide experimental justification for the importance of accounting for rate variations in action recognition. The model is composed of a nominal activity trajectory and a function space capturing the probability distribution of activity-specific time warping transformations. We use the square-root parameterization of time warps to derive geodesics, distance measures, and probability distributions on the space of time warping functions. We then design a Bayesian algorithm which treats the execution rate function as a nuisance variable and integrates it out using Monte Carlo sampling, to generate estimates of class posteriors. This approach allows us to learn the space of time warps for each activity while simultaneously capturing other intra- and interclass variations. Next, we discuss a special case of this approach which assumes a uniform distribution on the space of time warping functions and show how computationally efficient inference algorithms may be derived for this special case. We discuss the relative advantages and disadvantages of both approaches and show their efficacy using experiments on gait-based person identification and activity recognition.
Keywords: Automated; Video Recording; Bayesian algorithm; Monte Carlo sampling; action recognition; activity-specific time warping transformations; computationally efficient inference algorithms; distance measures; execution rate function; function space; gait-based person identification; geodesics; no; Statistical; Monte Carlo Method; Movement; Pattern Recognition

Reading tea leaves: How humans interpret topic models - Chang,J.; Jordan Boyd-Graber; Gerrish,S.; Wang,C.; Blei,D.M. (Proceedings of the 23rd Annual Conference on Neural Information Processing Systems, 2009)
Probabilistic topic models are a popular tool for the unsupervised analysis of text, providing both a predictive model of future text and a latent topic representation of the corpus. Practitioners typically assume that the latent space is semantically meaningful. It is used to check models, summarize the corpus, and guide explo- ration of its contents. However, whether the latent space is interpretable is in need of quantitative evaluation. In this paper, we present new quantitative methods for measuring semantic meaning in inferred topics. We back these measures with large-scale user studies, showing that they capture aspects of the model that are undetected by previous measures of model quality based on held-out likelihood. Surprisingly, topic models which perform better on held-out likelihood may infer less semantically meaningful topics.

Recognition of quantized still face images - Tao Wu; Chellapa, Rama (Biometrics: Theory, Applications, and Systems, 2009. BTAS '09. IEEE 3rd International Conference on, 2009)
In applications such as document understanding, only binary face images may be available as inputs to a face recognition (FR) algorithm. In this paper, we investigate the effects of the number of grey levels on PCA, multiple exemplar discriminant analysis (MEDA) and the elastic bunch graph matching (EBGM) FR algorithms. The inputs to these FR algorithms are quantized images (binary images or images with small number of grey levels) modified by distance and Box-Cox transforms. The performances of PCA and MEDA algorithms are at 87.66% for images in FRGC version 1 experiment 1 after they are thresholded and transformed while the EBGM algorithm achieves only 37.5%. In many document understanding applications, it is also required to verify a degraded low-quality image against a high-quality image, both of which are from the same source. For this problem, the performances of PCA and MEDA are stable when the images were degraded by noise, downsampling or different thresholding parameters.
Keywords: (signal); algorithm; grey; algorithms; face; analysis; quantisation; analysis; quantized; Box-Cox; bunch; component; discriminant; exemplar; Face; FR; graph; images; distance; images; face; levels; multiple; MATCHING; recognition; recognition; principal; transforms; document; transforms; PCA; binary; understanding; elastic

Recognizing coordinated multi-object activities using a dynamic event ensemble model - Ruonan Li; Chellapa, Rama (Acoustics, Speech and Signal Processing, 2009. ICASSP 2009. IEEE International Conference on, 2009)
While video-based activity analysis and recognition has received broad attention, existing body of work mostly deals with single object/person case. Modeling involving multiple objects and recognition of coordinated group activities, present in a variety of applications such as surveillance, sports, biological records, and so on, is the main focus of this paper. Unlike earlier attempts which model the complex spatial temporal constraints among different activities of multiple objects with a parametric Bayesian network, we propose a dynamic dasiaevent ensemblepsila framework as a data-driven strategy to characterize the group motion pattern without employing any specific domain knowledge. In particular, we exploit the Riemannian geometric property of the set of ensemble description functions and develop a compact representation for group activities on the ensemble manifold. An appropriate classifier on the manifold is then designed for recognizing new activities. Experiments on football play recognition demonstrate the effectiveness of the framework.
Keywords: activities; activity; analysis; Bayes; Bayesian; classification; video; description; ensemble; event; framework; dynamic; functions; ensemble; geometric; manifold; football; methods; geometry; image; model; ensemble; multiobject; network; video-based; play; processing; property; classifier; coordinated; recognition; data-driven; recognition; parametric; Riemannian; signal; strategy; dynamic

Recovering Views of Inter-System Interaction Behaviors - Ackermann,Christopher; Lindvall,Mikael; Cleaveland, Rance (Reverse Engineering, Working Conference on, 2009)
This paper presents an approach for recovering application-level views of the interaction behaviors between systems that communicate via networks. Rather than illustrating a single behavior, a sequence diagram is constructed that describes the characteristics of multiple combined behaviors. The approach has several properties that make it particularly suitable for analyzing heterogeneous systems. First, since the interactions are retrieved from observing the network communication, our technique can be applied to systems that are implemented in different languages and run on different platforms. Second, it does not require the availability or modification of source code. After the behaviors are extracted, we employ methods to merge multiple observed behaviors to a single sequence diagram that illustrates the overall behavior.The contributions of this paper are a technique for observing and processing the network communication to derive a model of the behavior. Furthermore, it describes a series of model transformations to construct a sequence diagram view of all observed behaviors.
Keywords: distributed systems; program understanding; reliability

Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians - Qasim,Atif N; Metkus,Thomas S; Tadesse,Mahlet; Lehrke,Michael; Restine,Stephanie; Wolfe,Megan L; Hannenhalli, Sridhar; Cappola,Thomas; Rader,Daniel J; Reilly,Muredach P (Clinical Endocrinology, 2009)
Objective  Resistin causes insulin resistance and diabetes in mice whereas in humans it is linked to inflammation and atherosclerosis. Few human genetic studies of resistin in inflammation and atherosclerosis have been performed. We hypothesized that the –420C>G putative gain-of-function resistin variant would be associated with inflammatory markers and atherosclerosis but not with metabolic syndrome or adipokines in humans.Design and methods  We examined the association of three resistin polymorphisms, –852A>G, –420C>G and +157C>T, and related haplotypes with plasma resistin, cytokines, C-reactive protein (CRP), adipokines, plasma lipoproteins, metabolic syndrome and coronary artery calcification (CAC) in nondiabetic Caucasians (n = 851). Results  Resistin levels were higher, dose-dependently, with the –420G allele (CC 5·9 ± 2·7 ng/ml, GC 6·5 ± 4·0 ng/ml and GG 7·2 ± 4·8 ng/ml, trend P = 0·04) after age and gender adjustment [fold higher for GC + GG vs. CC; 1·07 (1·00–1·15), P < 0·05)]. The –852A>G single nucleotide polymorphism (SNP) was associated with higher soluble tumour necrosis factor-receptor 2 (sol-TNFR2) levels in fully adjusted models [1·06 (95% CI 1·01–1·11), P = 0·01)]. The estimated resistin haplotype (GGT) was associated with sol-TNFR2 (P = 0·04) and the AGT haplotype was related to CRP (P = 0·04) in the fully adjusted models. Resistin SNPs and haplotypes were not associated with body mass index (BMI), fasting glucose, insulin resistance, metabolic syndrome, adipokines or CAC scores. Conclusions  Despite modest associations with plasma resistin and inflammatory biomarkers, resistin 5′ variants were not associated with metabolic parameters or coronary calcification. This suggests that resistin is an inflammatory cytokine in humans but has little influence on adiposity, metabolic syndrome or atherosclerosis.

Resonance: dynamic access control for enterprise networks - Nayak,Ankur Kumar; Reimers,Alex; Feamster, Nick; Clark,Russ (Proceedings of the 1st ACM workshop on Research on enterprise networking, 2009)
Enterprise network security is typically reactive, and it relies heavily on host security and middleboxes. This approach creates complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. We argue that imbuing the network layer with mechanisms for dynamic access control can remedy these ills. We propose Resonance, a system for securing enterprise networks, where the network elements themselves enforce dynamic access control policies based on both flow-level information and real-time alerts. Resonance uses programmable switches to manipulate traffic at lower layers; these switches take actions (e.g., dropping or redirecting traffic) to enforce high-level security policies based on input from both higherlevel security policies and distributed monitoring and inference systems. We describe the design of Resonance, apply it to Georgia Tech's network access control system, show how it can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.
Keywords: Access control; enterprise networks; programmable networks

RNA Colony Blot Hybridization Method for Enumeration of Culturable Vibrio Cholerae and Vibrio Mimicus Bacteria - Grim,Christopher J.; Zo,Young-Gun; Hasan,Nur A.; Ali,Afsar; Chowdhury,Wasimul B.; Islam,Atiqul; Rashid,Mohammed H.; Alam,Munirul; Morris,J. Glenn; Huq,Anwar; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2009)
A species-specific RNA colony blot hybridization protocol was developed for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria in environmental water samples. Bacterial colonies on selective or nonselective plates were lysed by sodium dodecyl sulfate, and the lysates were immobilized on nylon membranes. A fluorescently labeled oligonucleotide probe targeting a phylogenetic signature sequence of 16S rRNA of V. cholerae and V. mimicus was hybridized to rRNA molecules immobilized on the nylon colony lift blots. The protocol produced strong positive signals for all colonies of the 15 diverse V. cholerae-V. mimicus strains tested, indicating 100% sensitivity of the probe for the targeted species. For visible colonies of 10 nontarget species, the specificity of the probe was calculated to be 90% because of a weak positive signal produced by Grimontia (Vibrio) hollisae, a marine bacterium. When both the sensitivity and specificity of the assay were evaluated using lake water samples amended with a bioluminescent V. cholerae strain, no false-negative or false-positive results were found, indicating 100% sensitivity and specificity for culturable bacterial populations in freshwater samples when G. hollisae was not present. When the protocol was applied to laboratory microcosms containing V. cholerae attached to live copepods, copepods were found to carry approximately 10,000 to 50,000 CFU of V. cholerae per copepod. The protocol was also used to analyze pond water samples collected in an area of cholera endemicity in Bangladesh over a 9-month period. Water samples collected from six ponds demonstrated a peak in abundance of total culturable V. cholerae bacteria 1 to 2 months prior to observed increases in pathogenic V. cholerae and in clinical cases recorded by the area health clinic. The method provides a highly specific and sensitive tool for monitoring the dynamics of V. cholerae in the environment. The RNA blot hybridization protocol can also be applied to detection of other gram-negative bacteria for taxon-specific enumeration.

Robust Estimation of Albedo for Illumination-Invariant Matching and Shape Recovery - Biswas,S.; Aggarwal,G.; Chellapa, Rama (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2009)
We present a nonstationary stochastic filtering framework for the task of albedo estimation from a single image. There are several approaches in the literature for albedo estimation, but few include the errors in estimates of surface normals and light source direction to improve the albedo estimate. The proposed approach effectively utilizes the error statistics of surface normals and illumination direction for robust estimation of albedo, for images illuminated by single and multiple light sources. The albedo estimate obtained is subsequently used to generate albedo-free normalized images for recovering the shape of an object. Traditional shape-from-shading (SFS) approaches often assume constant/piecewise constant albedo and known light source direction to recover the underlying shape. Using the estimated albedo, the general problem of estimating the shape of an object with varying albedo map and unknown illumination source is reduced to one that can be handled by traditional SFS approaches. Experimental results are provided to show the effectiveness of the approach and its application to illumination-invariant matching and shape recovery. The estimated albedo maps are compared with the ground truth. The maps are used as illumination-invariant signatures for the task of face recognition across illumination variations. The recognition results obtained compare well with the current state-of-the-art approaches. Impressive shape recovery results are obtained using images downloaded from the Web with little control over imaging conditions. The recovered shapes are also used to synthesize novel views under novel illumination conditions.
Keywords: albedo estimation; error statistics; face recognition; illumination-invariant matching; nonstationary stochastic filtering; robust estimation; shape recovery; shape-from-shading approach; error statistics; face recognition; filtering theory; image matching; Algorithm; Automated; Photometry; Reproducibility of Results; Sensitivity and Specificity; Computer-Assisted; Imaging; Three-Dimensional; Lighting; Pattern Recognition

Robust human detection under occlusion by integrating face and person detectors - Schwartz, W.R.; Gopalan,R.; Chellapa, Rama; Davis, Larry S. (Proceedings of the Third International Conference on Advances in Biometrics, 2009)
Human detection under occlusion is a challenging problemin computer vision. We address this problem through a framework which integrates face detection and person detection. We first investigate how the response of a face detector is correlated with the response of a person detector. From these observations, we formulate hypotheses that capture the intuitive feedback between the responses of face and person detectors and use it to verify if the individual detectors’ outputs are true or false. We illustrate the performance of our integration framework on challeng- ing images that have considerable amount of occlusion, and demonstrate its advantages over individual face and person detectors.

Salient Clustering for View-dependent Multiresolution Rendering - Barni,R.; Comba,J.; Varshney, Amitabh (Computer Graphics and Image Processing (SIBGRAPI), 2009 XXII Brazilian Symposium on, 2009)
Perceptual information is quickly gaining importance in mesh representation, analysis and rendering. User studies, eye tracking and other techniques are able to provide ever more useful insights for many user-centric systems, which form the bulk of computer graphics applications. In this work we build upon the concept of Mesh Saliency - an automatic measure of visual importance for triangle meshes based on models of low-level human visual attention - applying it to the problem of mesh segmentation and view-dependent rendering. We introduce a technique for segmentation that partitions an object into a set of face clusters, each encompassing a group of locally interesting features; Mesh Saliency is incorporated in a propagative mesh clustering framework, guiding cluster seed selection and triangle propagation costs and leading to a convergence of face clusters around perceptually important features. We compare our technique with different fully automatic segmentation algorithms, showing that it provides similar or better segmentation without the need for user input. We illustrate application of our clustering results through a saliency-guided view-dependent rendering system, achieving significant frame rate increases with little loss of visual detail.
Keywords: (computer; algorithms; cluster; analysis; mesh; attention; mesh; AUTOMATIC; centred; clustering; clustering; rendering; clustering; user-centric; clusters; low-level; dependent; design; framework; salient; graphics); user; graphics; face; human; information; propagative; mesh; multiresolution; rendering; image; representation; mesh; resolution; image; saliency; mesh; seed; segmentation; segmentation; pattern; segmentation; perceptual; selection; computer; system; view; visual

Scope error detection and handling concerning software estimation models - Sarcia,Salvatore Alessandro; Basili, Victor R.; Cantone,Giovanni (Proceedings of the 2009 3rd International Symposium on Empirical Software Engineering and Measurement, 2009)
Over the last 25+ years, the software community has been searching for the best models for estimating variables of interest (e.g., cost, defects, and fault proneness). However, little research has been done to improve the reliability of the estimates. Over the last decades, scope error and error analysis have been substantially ignored by the community. This work attempts to fill this gap in the research and enhance a common understanding within the community. Results provided in this study can eventually be used to support human judgment-based techniques and be an addition to the portfolio. The novelty of this work is that, we provide a way of detecting and handling the scope error arising from estimation models. The answer whether or not scope error will occur is a pre-condition to safe use of an estimation model. We also provide a handy procedure for dealing with outliers as to whether or not to include them in the training set for building a new version of the estimation model. The majority of the work is empirically based, applying computational intelligence techniques to some COCOMO model variations with respect to a publicly available cost estimation data set in the PROMISE repository.

Semantically informed machine translation (SIMT) - Baker,K.; Bethard,S.; Bloodgood,M.; Brown,R.; Callison-Burch,C.; Coppersmith,G.; Dorr, Bonnie J; Filardo,W.; Giles,K.; Irvine,A.; others (SCALE summer workshop final report, Human Language Technology Center Of Excellence, 2009)

Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh - Alam,Munirul; Chowdhury,Wasimul B.; Bhuiyan,N. A.; Islam,Atiqul; Hasan,Nur A.; Nair,G. Balakrish; Watanabe,H.; Siddique,A. K.; Huq,Anwar; Sack,R. Bradley; Akhter,M. Z.; Grim,Christopher J.; et al. (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2009)
Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., “clonal cluster,” as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.

Sikuli: using GUI screenshots for search and automation - Tom Yeh; Chang,Tsung-Hsiang; Miller,Robert C. (Proceedings of the 22nd annual ACM symposium on User interface software and technology, 2009)
We present Sikuli, a visual approach to search and automation of graphical user interfaces using screenshots. Sikuli allows users to take a screenshot of a GUI element (such as a toolbar button, icon, or dialog box) and query a help system using the screenshot instead of the element's name. Sikuli also provides a visual scripting API for automating GUI interactions, using screenshot patterns to direct mouse and keyboard events. We report a web-based user study showing that searching by screenshot is easy to learn and faster to specify than keywords. We also demonstrate several automation tasks suitable for visual scripting, such as map navigation and bus tracking, and show how visual scripting can improve interactive help systems previously proposed in the literature.
Keywords: Automation; image search; online help

Simple, Black-Box Constructions of Adaptively Secure Protocols - Choi, Seung Geol; Dana Dachman-Soled; Malkin, Tal; Wee, Hoeteck (Theory of Cryptography, 2009)
We present a compiler for transforming an oblivious transfer (OT) protocol secure against an adaptive semi-honest adversary into one that is secure against an adaptive malicious adversary. Our compiler achieves security in the universal composability framework, assuming access to an ideal commitment functionality, and improves over previous work achieving the same security guarantee in two ways: it uses black-box access to the underlying protocol and achieves a constant multiplicative overhead in the round complexity. As a corollary, we obtain the first constructions of adaptively secure protocols in the stand-alone model using black-box access to a low-level primitive.
Keywords: Algorithm Analysis and Problem Complexity; computers and society; Data Encryption; Discrete Mathematics in Computer Science; Management of Computing and Information Systems; Systems and Data Security

Sparsity inspired selection and recognition of iris images - Pillai,J.K.; Patel, Vishal M.; Chellapa, Rama (Biometrics: Theory, Applications, and Systems, 2009. BTAS '09. IEEE 3rd International Conference on, 2009)
Iris images acquired from a partially cooperating subject often suffer from blur, occlusion due to eyelids, and specular reflections. The performance of existing iris recognition systems degrade significantly on these images. Hence it is essential to select good images from the incoming iris video stream, before they are input to the recognition algorithm. In this paper, we propose a sparsity based algorithm for selection of good iris images and their subsequent recognition. Unlike most existing algorithms for iris image selection, our method can handle segmentation errors and a wider range of acquisition artifacts common in iris image capture. We perform selection and recognition in a single step which is more efficient than devising separate specialized algorithms for the two. Recognition from partially cooperating users is a significant step towards deploying iris systems in a wide variety of applications.
Keywords: biometrics (access control); image recognition; Image segmentation; iris image recognition; iris image selection; iris video stream; sparsity inspired selection; video signal processing; video streaming

Speaking through pictures: images vs. icons - Ma,Xiaojuan; Jordan Boyd-Graber; Nikolova,Sonya; Cook,Perry R. (Proceedings of the 11th international ACM SIGACCESS conference on Computers and accessibility, 2009)
People with aphasia, a condition that impairs the ability to understand or generate written or spoken language, are aided by assistive technology that helps them communicate through a vocabulary of icons. These systems are akin to language translation systems, translating icon arrangements into spoken or written language and vice versa. However, these icon-based systems have little vocabulary breadth or depth, making it difficult for people with aphasia to apply their usage to multiple real world situations. Pictures from the web are numerous, varied, and easily accessible and thus, could potentially address the small size issues of icon-based systems. We present results from two studies that investigate this potential and demonstrate that images can be as effective as icons when used as a replacement for English language communication. The first study uses elderly subjects to investigate the efficacy of images vs. icons in conveying word meaning; the second study examines the retention of word-level meaning by both images and icons with a population of aphasics. We conclude that images collected from the web are as functional as icons in conveying information and thus, are feasible to use in assistive technology that supports people with aphasia.
Keywords: aphasia; computerized visual communication (C-VIC); visual communication (VIC)

The Story of One: Humanity scholarship with visualization and text analysis - Clement,T.; Plaisant, Catherine; Vuillemot,R. (Relation, 2009)

Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13 - Zhang,Naixia; Wang,Qinghua; Ehlinger,Aaron; Randles,Leah; Lary,Jeffrey W.; Kang,Yang; Haririnia,Aydin; Storaska,Andrew J.; Cole,James L.; Fushman, David; Walters,Kylie J. (Molecular Cell, 2009)
SummaryDegradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of one ubiquitin subunit (the “proximal” one) is covalently bonded to G76 of the other (the “distal” subunit). We demonstrate that S5a's UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains.
Keywords: Proteins

Surface reconstruction from gradient fields via gradient transformations - Agrawal,A.; Raskar, R.; Chellapa, Rama (International Journal of Computer Vision, 2009)

Tampering identification using Empirical Frequency Response - Chuang,Wei-Hong; Swaminathan,A.; M. Wu (Acoustics, Speech and Signal Processing, 2009. ICASSP 2009. IEEE International Conference on, 2009)
With the widespread popularity of digital images and the presence of easy-to-use image editing software, content integrity can no longer be taken for granted, and there is a strong need for techniques that not only detect the presence of tampering but also identify its type. This paper focusses on tampering-type identification and introduces a new approach based on the empirical frequency response (EFR) to address this problem. We show that several types of tampering operations, both linear shift invariant (LSI) and non-LSI, can be characterized consistently and distinctly by their EFRs. We then extend the approach to estimate the EFR for scenarios where only the final image is available. Theoretical reasoning supported by experimental results verify the effectiveness of this method for identifying the type of a tampering operation.
Keywords: aproach; JPEG; coding; multimedia; compression; frequency; compression; LSI; computing; security; data; editing; EFR; forensics; tampering-type; Frequency; identification; data; image; invariant; multimedia; of; response; image; response; linear; shift; software; empirical; system; digital

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. - Ward, Naomi L; Challacombe, Jean F; Janssen, Peter H; Henrissat, Bernard; Coutinho, Pedro M; Wu, Martin; Xie, Gary; Haft, Daniel H; Sait, Michelle; Badger, Jonathan; Barabote, Ravi D; Bradley, Brent; et al. (Appl Environ Microbiol, 2009)
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
Keywords: Anti-Bacterial Agents; bacteria; Biological Transport; Carbohydrate Metabolism; Cyanobacteria; DNA, Bacterial; Fungi; Genome, Bacterial; Macrolides; Molecular Sequence Data; Nitrogen; Phylogeny; Proteobacteria; Sequence Analysis, DNA; sequence homology; Soil Microbiology

Together, Rpn10 and Dsk2 Can Serve as a Polyubiquitin Chain-Length Sensor - Zhang,Daoning; Chen,Tony; Ziv,Inbal; Rosenzweig,Rina; Matiuhin,Yulia; Bronner,Vered; Glickman,Michael H.; Fushman, David (Molecular Cell, 2009)
SummaryAs a signal for substrate targeting, polyubiquitin meets various layers of receptors upstream to the 26S proteasome. We obtained structural information on two receptors, Rpn10 and Dsk2, alone and in complex with (poly)ubiquitin or with each other. A hierarchy of affinities emerges with Dsk2 binding monoubiquitin tighter than Rpn10 does, whereas Rpn10 prefers the ubiquitin-like domain of Dsk2 to monoubiquitin, with increasing affinities for longer polyubiquitin chains. We demonstrated the formation of ternary complexes of both receptors simultaneously with (poly)ubiquitin and found that, depending on the ubiquitin chain length, the orientation of the resulting complex is entirely different, providing for alternate signals. Dynamic rearrangement provides a chain-length sensor, possibly explaining how accessibility of Dsk2 to the proteasome is limited unless it carries a properly tagged cargo. We propose a mechanism for a malleable ubiquitin signal that depends both on chain length and combination of receptors to produce tetraubiquitin as an efficient signal threshold.
Keywords: Proteins; signaling

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study - Regier,J. C; Zwick,A.; Cummings, Michael P.; Kawahara,A. Y; Cho,S.; Weller,S.; Roe,A.; Baixeras,J.; Brown,J. W; Parr,C.; Davis,DR; Epstein,M; et al. (BMC Evol Biol, 2009)
BACKGROUND: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS: Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION: Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.

Towards Dynamic Adaptive Automated Test Generation for Graphical User Interfaces - Xun Yuan; Cohen,M. B; Memon, Atif M. (Software Testing, Verification and Validation Workshops, 2009. ICSTW '09. International Conference on, 2009)
Graphical user interfaces (GUIs) present an enormous number of potential event sequences to users. During testing it is necessary to cover this space, however the complexity of modern GUIs has made this an increasingly difficult task. Our past work has demonstrated that it is important to incorporate "context” into GUI test cases, in terms of event combinations, event sequence length, and by considering all possible starting and ending positions for each event. Despite the use of our most refined modeling techniques, many of the generated test cases remain unexecutable. In this paper, we posit that due to the dynamic state-based nature of GUIs, it is important to incorporate feedback from the execution of tests into test case generation algorithms. We propose the use of an evolutionary algorithm to generate test suites with fewer unexecutable test cases and higher event interaction coverage.
Keywords: adaptive automated test generation; computational complexity; event sequence length; evolutionary algorithm; evolutionary computation; graphical user interface; Graphical user interfaces; GUI test case; program testing

Tree-Based Encoding for Cancellations on Morse Complexes - Čomić,L.; De Floriani, Leila (Combinatorial Image Analysis, 2009)
A scalar function f, defined on a manifold M, can be simplified by applying a sequence of removal and contraction operators, which eliminate its critical points in pairs, and simplify the topological representation of M, provided by Morse complexes of f. The inverse refinement operators, together with a dependency relation between them, enable a construction of a multi-resolution representation of such complexes. Here, we encode a sequence of simplification operators in a data structure called an augmented cancellation forest, which will enable procedural encoding of the inverse refinement operators, and reduce the dependency relation between modifications of the Morse complexes. In this way, this representation will induce a high flexibility of the hierarchical representation of the Morse complexes, producing a large number of Morse complexes at different resolutions that can be obtained from the hierarchy.

UbiGreen: investigating a mobile tool for tracking and supporting green transportation habits - Jon Froehlich; Dillahunt,Tawanna; Klasnja,Predrag; Mankoff,Jennifer; Consolvo,Sunny; Harrison,Beverly; Landay,James A. (Proceedings of the 27th international conference on Human factors in computing systems, 2009)
Keywords: ambient displays; mobile phones; sensing; Sustainability; transportation; ubicomp

Unsupervised view and rate invariant clustering of video sequences - Turaga,Pavan; Veeraraghavan,Ashok; Chellapa, Rama (Computer Vision and Image Understanding, 2009)
Videos play an ever increasing role in our everyday lives with applications ranging from news, entertainment, scientific research, security and surveillance. Coupled with the fact that cameras and storage media are becoming less expensive, it has resulted in people producing more video content than ever before. This necessitates the development of efficient indexing and retrieval algorithms for video data. Most state-of-the-art techniques index videos according to the global content in the scene such as color, texture, brightness, etc. In this paper, we discuss the problem of activity-based indexing of videos. To address the problem, first we describe activities as a cascade of dynamical systems which significantly enhances the expressive power of the model while retaining many of the computational advantages of using dynamical models. Second, we also derive methods to incorporate view and rate-invariance into these models so that similar actions are clustered together irrespective of the viewpoint or the rate of execution of the activity. We also derive algorithms to learn the model parameters from a video stream and demonstrate how a single video sequence may be clustered into different clusters where each cluster represents an activity. Experimental results for five different databases show that the clusters found by the algorithm correspond to semantically meaningful activities.
Keywords: Affine invariance; Cascade of linear dynamical systems; Rate invariance; Summarization; Surveillance; Video clustering; View invariance

Using formal specifications to support testing - Hierons,Robert M.; Krause,Paul; Lüttgen,Gerald; Simons,Anthony J. H.; Vilkomir,Sergiy; Woodward,Martin R.; Zedan,Hussein; Bogdanov,Kirill; Bowen,Jonathan P.; Cleaveland, Rance; Derrick,John; Dick,Jeremy; et al. (ACM Computing Surveys, 2009)

Using Satellite Images of Environmental Changes to Predict Infectious Disease Outbreaks - Ford,Timothy E.; Rita R Colwell; Rose,Joan B.; Morse,Stephen S.; Rogers,David J.; Yates,Terry L. (Emerging Infectious DiseasesEmerg Infect Dis, 2009)
A strong global satellite imaging system is essential for predicting outbreaks., Recent events clearly illustrate a continued vulnerability of large populations to infectious diseases, which is related to our changing human-constructed and natural environments. A single person with multidrug-resistant tuberculosis in 2007 provided a wake-up call to the United States and global public health infrastructure, as the health professionals and the public realized that today’s ease of airline travel can potentially expose hundreds of persons to an untreatable disease associated with an infectious agent. Ease of travel, population increase, population displacement, pollution, agricultural activity, changing socioeconomic structures, and international conflicts worldwide have each contributed to infectious disease events. Today, however, nothing is larger in scale, has more potential for long-term effects, and is more uncertain than the effects of climate change on infectious disease outbreaks, epidemics, and pandemics. We discuss advances in our ability to predict these events and, in particular, the critical role that satellite imaging could play in mounting an effective response.

Using Stereo Matching with General Epipolar Geometry for 2D Face Recognition across Pose - Castillo,C. D; Jacobs, David W. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2009)
Face recognition across pose is a problem of fundamental importance in computer vision. We propose to address this problem by using stereo matching to judge the similarity of two, 2D images of faces seen from different poses. Stereo matching allows for arbitrary, physically valid, continuous correspondences. We show that the stereo matching cost provides a very robust measure of similarity of faces that is insensitive to pose variations. To enable this, we show that, for conditions common in face recognition, the epipolar geometry of face images can be computed using either four or three feature points. We also provide a straightforward adaptation of a stereo matching algorithm to compute the similarity between faces. The proposed approach has been tested on the CMU PIE data set and demonstrates superior performance compared to existing methods in the presence of pose variation. It also shows robustness to lighting variation.
Keywords: 2D face recognition; CMU PIE data set; computer vision; continuous correspondences; general epipolar geometry; lighting variation; pose variation; stereo matching; computer vision; face recognition; geometry; image matching; pose estimation; stereo image processing; Al; Automated; Computer-Assisted; Pattern Recognition

Using uncertainty as a model selection and comparison criterion - Sarcia',Salvatore Alessandro; Basili, Victor R.; Cantone,Giovanni (Proceedings of the 5th International Conference on Predictor Models in Software Engineering, 2009)
Over the last 25+ years, software estimation research has been searching for the best model for estimating variables of interest (e.g., cost, defects, and fault proneness). This research effort has not lead to a common agreement. One problem is that, they have been using accuracy as the basis for selection and comparison. But accuracy is not invariant; it depends on the test sample, the error measure, and the chosen error statistics (e.g., MMRE, PRED, Mean and Standard Deviation of error samples). Ideally, we would like an invariant criterion. In this paper, we show that uncertainty can be used as an invariant criterion to figure out which estimation model should be preferred over others. The majority of this work is empirically based, applying Bayesian prediction intervals to some COCOMO model variations with respect to a publicly available cost estimation data set coming from the PROMISE repository.
Keywords: accuracy; Bayesian prediction intervals; Calibration; cost estimation; cost model; model evaluation; model selection; prediction interval; Uncertainty

Validating Automotive Control Software Using Instrumentation-Based Verification - Ray,Arnab; Morschhaeuser,Iris; Ackermann,Chris; Cleaveland, Rance; Shelton,Charles; Martin,Chris (Automated Software Engineering, International Conference on, 2009)
This paper discusses the results of an application of a formally based verification technique, called Instrumentation-Based Verification (IBV), to a production automotive lighting controller. The goal of the study is to assess, from both a tools as well as a methodological perspective, the performance of IBV in an industrial setting. The insights obtained as a result of the project include a refinement of a previously developed architecture for requirements specifications; observations about changes to model-based design workflows; insights into the role of requirements during development; and the capability of automated verification to detect inconsistencies among requirements as well as between requirements and design models.

Vehicle Speed Estimation Using Acoustic Wave Patterns - Cevher, V.; Chellapa, Rama; McClellan, J.H. (Signal Processing, IEEE Transactions on, 2009)
We estimate a vehicle's speed, its wheelbase length, and tire track length by jointly estimating its acoustic wave pattern with a single passive acoustic sensor that records the vehicle's drive-by noise. The acoustic wave pattern is determined using the vehicle's speed, the Doppler shift factor, the sensor's distance to the vehicle's closest-point-of-approach, and three envelope shape (ES) components, which approximate the shape variations of the received signal's power envelope. We incorporate the parameters of the ES components along with estimates of the vehicle engine RPM, the number of cylinders, and the vehicle's initial bearing, loudness and speed to form a vehicle profile vector. This vector provides a fingerprint that can be used for vehicle identification and classification. We also provide possible reasons why some of the existing methods are unable to provide unbiased vehicle speed estimates using the same framework. The approach is illustrated using vehicle speed estimation and classification results obtained with field data.
Keywords: acoustic; Doppler; estimation; passive; estimation; road; estimation; wheelbase; factor; acoustic; identification; vehicle; length; Doppler; length; vehicle; likelihood; patterns; envelope; processing; maximum; profile; sensor; tire; shape; maximum; shift; shift; acoustic; signal; speed; track; vector; vehicle; vehicles; wave

Viable but not cultivable bacteria - Rita R Colwell (Uncultivated Microorganisms, 2009)
A well-studied, long-term survival mechanism employed by Gram-positive bacteria is formation of endospores. For Gram-negative bacteria, the assumption has been that a survival state does not exist. However, a dormancy state has been described for Gram-negative bacteria and designated as the viable but nonculturable (VBNC) strategy of nonspore-forming cells. A variety of environmental factors are involved in induction of the viable but nonculturable state and Vibrio cholerae provides a useful paradigm for the VBNC phenomenon. It is now accepted that plate counts cannot be relied upon to enumerate or detect VBNC cells. Therefore, direct methods employing fluorescent staining, molecular genetic probes, and other molecular methods have proven both useful and reliable in detecting and enumerating both culturable and nonculturable cells. A predictive model for cholera has been developed, based on ground truth data gathered using these molecular methods and combining them with data obtained by remote sensing, employing satellites. It is clear that microbiology in the twenty-first century has been enhanced by these new tools and paradigms.

Video-Based Face Recognition Algorithms - Chellapa, Rama; Bicego, M.; Turaga,P. (Handbook of Remote Biometrics, 2009)
Traditional face recognition systems have relied on a gallery of still images for learning and a probe of still images for recognition. While the advantage of using motion information in face videos has been widely recognized, computational models for video-based face recognition have only recently gained attention. This chapter reviews some recent advances in this novel framework. In particular, the utility of videos in enhancing performance of image-based tasks (such as recognition or localization) will be summarized. Subsequently, spatiotemporal video-based face recognition systems based on particle filters, hidden Markov models , and system theoretic approaches will be presented. Further, some useful face databases employable by researchers interested in this field will be described. Finally, some open research issues will be proposed and discussed.

Video-based Lane Detection using Boosting Principles - Gopalan,R.; Hong, T.; Shneier, M.; Chellapa, Rama (Snowbird, 2009)
Autonomous navigation of road vehicles is a challenging problem that has widespread applications in intelligent systems, and robotics. An integral componentof such a system is to understand how the road is structured. Detection of road lane markings assumes importance in this regard, and this problem has been approached with different visual input- based inference algorithms ([1], [2]), besides other sensing modalities such as the GPS sensor and the internal vehicle- state sensors. But the challenge still remains when there is considerable amount of shadows on the road, variations in outdoor lighting conditions of the scene (transition from day to night), among others. To address such issues, we propose a machine learning approach based on Real Adaboost [3], and train linear classifiers for both the appearance and edge cues of the training examplars. Additionally, we incorporate prior knowledge about the relative importance of the training samples by computing their weights using kernel discriminant analysis [4], before learning the classification function through boosting. The regions identified as lane markings are then analyzed for gradient direction consistency before making the final detection decision. We illustrate the effectiveness of our algorithm on challenging daylight and night- time road scenarios.

Visual Tracking by Continuous Density Propagation in Sequential Bayesian Filtering Framework - Han,Bohyung; Zhu,Ying; Comaniciu, D.; Davis, Larry S. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2009)
Particle filtering is frequently used for visual tracking problems since it provides a general framework for estimating and propagating probability density functions for nonlinear and non-Gaussian dynamic systems. However, this algorithm is based on a Monte Carlo approach and the cost of sampling and measurement is a problematic issue, especially for high-dimensional problems. We describe an alternative to the classical particle filter in which the underlying density function has an analytic representation for better approximation and effective propagation. The techniques of density interpolation and density approximation are introduced to represent the likelihood and the posterior densities with Gaussian mixtures, where all relevant parameters are automatically determined. The proposed analytic approach is shown to perform more efficiently in sampling in high-dimensional space. We apply the algorithm to real-time tracking problems and demonstrate its performance on real video sequences as well as synthetic examples.
Keywords: Automated; Reproducibility of Results; Sensitivity and Specificity; Signal Processing; Computer-Assisted; Pattern Recognition; Computer-Assisted; Subtraction Technique; Monte Carlo approach; continuous density propagation; density approximation; density interpolation; nonGaussian dynamic systems; nonlinear dynamic systems; particle filtering; probability density functions; sequential Bayesian filtering framework; video sequences

What's being said near "Martha"? Exploring name entities in literary text collections - Vuillemot,R.; Clement,T.; Plaisant, Catherine; Kumar,A. (Visual Analytics Science and Technology, 2009. VAST 2009. IEEE Symposium on, 2009)
A common task in literary analysis is to study characters in a novel or collection. Automatic entity extraction, text analysis and effective user interfaces facilitate character analysis. Using our interface, called POSvis, the scholar uses word clouds and self-organizing graphs to review vocabulary, to filter by part of speech, and to explore the network of characters located near characters under review. Further, visualizations show word usages within an analysis window (i.e. a book chapter), which can be compared with a reference window (i.e. the whole book). We describe the interface and report on an early case study with a humanities scholar.
Keywords: analysis; humanities; analysis; literary; analysis; user; clouds; word; collection; name; entity; entity; part-of-speech; extraction; character; filtering; linguistics; text; filtering; self-organizing; graph; text; interface; vocabulary; word; interfaces; vocabulary; POSvis; automatic; scholar; literary; text; usage; data; visualisation; information

Within epsilon of optimal play in the cultaptation social learning game - Carr,Ryan; Raboin,Eric; Parker,Austin; Nau, Dana S. (International Foundation for Autonomous Agents and Multiagent Systems, 2009)
Social learning, in which members of a society learn by observing the behavior of others, is an important foundation for human culture, and is observed in many other species as well. It seems natural to assume that social learning evolved due to the inherent superiority of copying others' success rather than learning on one's own via trial-and-error innovation. However, there has also been substantial work questioning this intuition [3, 5, 1, 6, 4]. For example, blindly copying information from others is not useful if the information is wrong---or if it once was right but has since become outdated. Under what conditions does social learning outperform trial-and-error learning, and what kinds of social-learning strategies are likely to perform well?

3D shape-encoded particle filter for object tracking and its application to human body tracking - Moon, H.; Chellapa, Rama (J. Image Video Process., 2008)
We present a nonlinear state estimation approach using particle filters, for tracking objects whose approximate 3D shapes are known. The unnormalized conditional density for the solution to the nonlinear filtering problem leads to the Zakai equation, and is realized by the weights of the particles. The weight of a particle represents its geometric and temporal fit, which is computed bottom-up from the raw image using a shape-encoded filter. The main contribution of the paper is the design of smoothing filters for feature extraction combined with the adoption of unnormalized conditional density weights. The "shape filter" has the overall form of the predicted 2D projection of the 3D model, while the cross-section of the filter is designed to collect the gradient responses along the shape. The 3D-model-based representation is designed to emphasize the changes in 2D object shape due to motion, while de-emphasizing the variations due to lighting and other imaging conditions. We have found that the set of sparse measurements using a relatively small number of particles is able to approximate the high-dimensional state distribution very effectively. As a measure to stabilize the tracking, the amount of random diffusion is effectively adjusted using a Kalman updating of the covariance matrix. For a complex problem of human body tracking, we have successfully employed constraints derived from joint angles and walking motion.

Activity Modeling Using Event Probability Sequences - Cuntoor, N.P.; Yegnanarayana,B.; Chellapa, Rama (Image Processing, IEEE Transactions on, 2008)
Changes in motion properties of trajectories provide useful cues for modeling and recognizing human activities. We associate an event with significant changes that are localized in time and space, and represent activities as a sequence of such events. The localized nature of events allows for detection of subtle changes or anomalies in activities. In this paper, we present a probabilistic approach for representing events using the hidden Markov model (HMM) framework. Using trained HMMs for activities, an event probability sequence is computed for every motion trajectory in the training set. It reflects the probability of an event occurring at every time instant. Though the parameters of the trained HMMs depend on viewing direction, the event probability sequences are robust to changes in viewing direction. We describe sufficient conditions for the existence of view invariance. The usefulness of the proposed event representation is illustrated using activity recognition and anomaly detection. Experiments using the indoor University of Central Florida human action dataset, the Carnegie Mellon University Credo Intelligence, Inc., Motion Capture dataset, and the outdoor Transportation Security Administration airport tarmac surveillance dataset show encouraging results.
Keywords: Automated; Reproducibility of Results; Sensitivity and Specificity; Video Recording; Biological; Models; Carnegie Mellon University; Credo Intelligence; Computer-Assisted; Models; Inc.; Motion Capture dataset; Transportation Security Administration; University Central Florida; airport tarmac surveillance dataset; anomaly detection; event probability sequence; event representation; hidden Markov model; human action dataset; human activity rec; Statistical; Motor Activity; Movement; Pattern Recognition

Activity representation using 3D shape models - Abdelkader,Mohamed F.; Roy-Chowdhury,Amit K.; Chellapa, Rama; Akdemir,Umut (J. Image Video Process., 2008)
We present a method for characterizing human activities using 3D deformable shape models. The motion trajectories of points extracted from objects involved in the activity are used to build models for each activity, and these models are used for classification and detection of unusual activities. The deformable models are learnt using the factorization theorem for nonrigid 3D models. We present a theory for characterizing the degree of deformation in the 3D models from a sequence of tracked observations. This degree, termed as deformation index (DI), is used as an input to the 3D model estimation process. We study the special case of ground plane activities in detail because of its importance in video surveillance applications. We present results of our activity modeling approach using videos of both high-resolution single individual activities and ground plane surveillance activities.

Activity sensing in the wild: a field trial of ubifit garden - Consolvo,S.; McDonald,D.W.; Toscos,T.; Chen,M.Y.; Jon Froehlich; Harrison,B.; Klasnja,P.; LaMarca,A.; LeGrand,L.; Libby,R.; others (Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems, 2008)

Adopting Curvilinear Component Analysis to Improve Software Cost Estimation Accuracy. Model, Application Strategy, and an Experimental Verification - Sarcia,Salvatore A.; Cantone,Giovanni; Basili, Victor R. (In G. Visaggio (Ed.), 12 th International Conference on Evaluation and Assessment in Software Engineering. BCS eWIC, 2008)
Cost estimation is a critical issue for software organizations. Good estimates can help us make more informed decisions (controlling and planning software risks), if they are reliable (correct) and valid (stable). In this study, we apply a variable reduction technique (based on auto-associative feed--forward neural networks – called Curvilinear component analysis) to log-linear regression functions calibrated with ordinary least squares. Based on a COCOMO 81 data set, we show that Curvilinear component analysis can improve the estimation model accuracy by turning the initial input variables into an equivalent and more compact representation. We show that, the models obtained by applying Curvilinear component analysis are more parsimonious, correct, and reliable.

Advancing social science research by applying computational linguistics - Cheng,A.S.; Fleischmann,K.R.; Wang,P.; Oard, Douglas (Proceedings of the American Society for Information Science and Technology, 2008)

Algorithmic and Architectural Optimizations for Computationally Efficient Particle Filtering - Sankaranarayanan,A. C; Srivastava, A.; Chellapa, Rama (Image Processing, IEEE Transactions on, 2008)
In this paper, we analyze the computational challenges in implementing particle filtering, especially to video sequences. Particle filtering is a technique used for filtering nonlinear dynamical systems driven by non-Gaussian noise processes. It has found widespread applications in detection, navigation, and tracking problems. Although, in general, particle filtering methods yield improved results, it is difficult to achieve real time performance. In this paper, we analyze the computational drawbacks of traditional particle filtering algorithms, and present a method for implementing the particle filter using the Independent Metropolis Hastings sampler, that is highly amenable to pipelined implementations and parallelization. We analyze the implementations of the proposed algorithm, and, in particular, concentrate on implementations that have minimum processing times. It is shown that the design parameters for the fastest implementation can be chosen by solving a set of convex programs. The proposed computational methodology was verified using a cluster of PCs for the application of visual tracking. We demonstrate a linear speedup of the algorithm using the methodology proposed in the paper.
Keywords: Automated; Reproducibility of Results; Sensitivity and Specificity; Signal Processing; Computer-Assisted; Models; Computer-Assisted; Video Recording; convex program; independent Metropolis Hastings sampler; nonGaussian noise process; nonlinear dynamical system filtering; particle filtering algorithm; pipelined architectural optimization; video sequences; visual tracking; convex programming; image sequences; opti; Statistical; Pattern Recognition

Analysis of Computer Security Incident Data Using Time Series Models - Condon,E.; He,A.; Michel Cukier (2008)
Organizations face increasing challenges in addressing and preventing computer and network security incidents. There are financial consequences from security incidents. These include lost time and resources used during recovery, possible theft of personal and/or proprietary information, and reputational damage that may negatively impact stock prices or reduce consumer confidence in a company. Being able to understand and predict trends in computer and network security incidents can aid an organization with resource allocation for prevention of such incidents, as well as evaluation of mitigation strategies. We look at using time series models with a large set of security incident data. We examine appropriateness of the data for modeling and consider needed transformations. Parameter search and model selection criteria are discussed. Then, forecasts from time series models are compared to forecasts from Non-Homogeneous Poisson Process (NHPP) software reliability growth (SRG) models.
Keywords: Computer networks; computer security incident data; NETWORK SECURITY; resource allocation; security of data; telecommunication security; time series; time series model

Approximation Algorithms for Computing Capacity of Wireless Networks with SINR Constraints - Chafekar,D.; Kumart,V. S.A; Marathe,M. V; Parthasarathy,S.; Srinivasan, Aravind (IEEE INFOCOM 2008. The 27th Conference on Computer Communications, 2008)
A fundamental problem in wireless networks is to estimate its throughput capacity - given a set of wireless nodes, and a set of connections, what is the maximum rate at which data can be sent on these connections. Most of the research in this direction has focused on either random distributions of points, or has assumed simple graph-based models for wireless interference. In this paper, we study capacity estimation problem using the more general Signal to Interference Plus Noise Ratio (SINR) model for interference, on arbitrary wireless networks. The problem becomes much harder in this setting, because of the non-locality of the SINR model. Recent work by Moscibroda et al. (2006) has shown that the throughput in this model can differ from graph based models significantly. We develop polynomial time algorithms to provably approximate the total throughput in this setting.
Keywords: Algorithm design and analysis; approximation algorithm; Approximation algorithms; approximation theory; Computer networks; Computer science; graph theory; graph-based model; Interference constraints; polynomial time algorithm; Propagation losses; Protocols; radio networks; radiofrequency interference; signal to interference plus noise ratio; Signal to noise ratio; Throughput; wireless interference; wireless network; Wireless networks

Arabic/English Multi-document Summarization with CLASSYThe Past and the Future - Schlesinger,Judith D.; O'Leary, Dianne P.; Conroy,John M. (Computational Linguistics and Intelligent Text Processing, Lecture Notes in Computer Science Volume 4919Computational Linguistics and Intelligent Text Processing, Lecture Notes in Computer Science Volume 4919, 2008)

An assessment of systems and software engineering scholars and institutions (2001–2005) - Wong,W. Eric; Tse,T.H.; Glass,Robert L.; Basili, Victor R.; Chen,T.Y. (Journal of Systems and Software, 2008)
This paper presents the findings of a five-year study of the top scholars and institutions in the systems and software engineering field, as measured by the quantity of papers published in the journals of the field in 2001–2005. The top scholar is Magne Jørgensen of Simula Research Laboratory, Norway, and the top institution is Korea Advanced Institute of Science and Technology, Korea.This paper is part of an ongoing study, conducted annually, that identifies the top 15 scholars and institutions in the most recent five-year period.
Keywords: Research publications; Systems and software engineering; Top institutions; Top scholars

Biofilms in water, its role and impact in human disease transmission - Huq,Anwar; Whitehouse,Chris A.; Grim,Christopher J.; Alam,Munirul; Rita R Colwell (Current Opinion in Biotechnology, 2008)
Understanding the mechanism of biofilm formation is the first step in determining its function and, thereby, its impact and role in the environment. Extensive studies accomplished during the past few years have elucidated the genetics and biochemistry of biofilm formation. Cell-to-cell communication, that is, quorum sensing, is a key factor in the initiation of biofilm. Occurrence of viable but nonculturable bacteria, including Vibrio cholerae in biofilms has been reported and most likely such cells were overlooked previously because appropriate methods of detection were not employed. For this reason discovery and investigation of this important bacterial ecological niche in the environment were impeded.

Black-Box Construction of a Non-malleable Encryption Scheme from Any Semantically Secure One - Choi, Seung Geol; Dana Dachman-Soled; Malkin, Tal; Wee, Hoeteck (Theory of Cryptography, 2008)
We show how to transform any semantically secure encryption scheme into a non-malleable one, with a black-box construction that achieves a quasi-linear blow-up in the size of the ciphertext. This improves upon the previous non-black-box construction of Pass, Shelat and Vaikuntanathan (Crypto ’06). Our construction also extends readily to guarantee non-malleability under a bounded-CCA2 attack, thereby simultaneously improving on both results in the work of Cramer et al. (Asiacrypt ’07). Our construction departs from the oft-used paradigm of re-encrypting the same message with different keys and then proving consistency of encryptions; instead, we encrypt an encoding of the message with certain locally testable and self-correcting properties. We exploit the fact that low-degree polynomials are simultaneously good error-correcting codes and a secret-sharing scheme.
Keywords: Algorithm Analysis and Problem Complexity; black-box constructions; computers and society; Data Encryption; Discrete Mathematics in Computer Science; Management of Computing and Information Systems; non-malleability; public-key encryption; semantic security; Systems and Data Security

Cancellation of critical points in 2D and 3D Morse and Morse-Smale complexes - Čomić,L.; De Floriani, Leila (Discrete Geometry for Computer Imagery, 2008)
Morse theory studies the relationship between the topology of a manifold M and the critical points of a scalar function f defined on M. The Morse-Smale complex associated with f induces a subdivision of M into regions of uniform gradient flow, and represents the topology of M in a compact way. Function f can be simplified by cancelling its critical points in pairs, thus simplifying the topological representation of M, provided by the Morse-Smale complex. Here, we investigate the effect of the cancellation of critical points of f in Morse-Smale complexes in two and three dimensions by showing how the change of connectivity of a Morse-Smale complex induced by a cancellation can be interpreted and understood in a more intuitive and straightforward way as a change of connectivity in the corresponding ascending and descending Morse complexes. We consider a discrete counterpart of the Morse-Smale complex, called a quasi-Morse complex, and we present a compact graph-based representation of such complex and of its associated discrete Morse complexes, showing also how such representation is affected by a cancellation.

Capacity of Asynchronous Random-Access Scheduling in Wireless Networks - Chafekar,D.; Levin,D.; Kumar,V. S.A; Marathe,M. V; Parthasarathy,S.; Srinivasan, Aravind (IEEE INFOCOM 2008. The 27th Conference on Computer Communications, 2008)
We study the throughput capacity of wireless networks which employ (asynchronous) random-access scheduling as opposed to deterministic scheduling. The central question we answer is: how should we set the channel-access probability for each link in the network so that the network operates close to its optimal throughput capacity? We design simple and distributed channel-access strategies for random-access networks which are provably competitive with respect to the optimal scheduling strategy, which is deterministic, centralized, and computationally infeasible. We show that the competitiveness of our strategies are nearly the best achievable via random-access scheduling, thus establishing fundamental limits on the performance of random- access. A notable outcome of our work is that random access compares well with deterministic scheduling when link transmission durations differ by small factors, and much worse otherwise. The distinguishing aspects of our work include modeling and rigorous analysis of asynchronous communication, asymmetry in link transmission durations, and hidden terminals under arbitrary link-conflict based wireless interference models.
Keywords: asynchronous random-access scheduling; channel access probability; Computer networks; Computer science; Educational institutions; Interference; Optimal scheduling; Peer to peer computing; probability; Processor scheduling; radio link; radio links; radio networks; Routing; scheduling; Throughput; throughput capacity; wireless channels; Wireless networks

On the Comparison of Network Attack Datasets: An Empirical Analysis - Berthier,R.; Korman,D.; Michel Cukier; Hiltunen,M.; Vesonder,G.; Sheleheda,D. (2008)
Network malicious activity can be collected and reported by various sources using different attack detection solutions. The granularity of these solutions provides either very detailed information (intrusion detection systems, honeypots) or high-level trends (CAIDA, SANS). The problem for network security operators is often to select the sources of information to better protect their network. How much information from these sources is redundant and how much is unique? The goal of this paper is to show empirically that while some global attack events can be correlated across various sensors, the majority of incoming malicious activity has local specificities. This study presents a comparative analysis of four different attack datasets offering three different levels of granularity: 1) two high interaction honeynets deployed at two different locations (i.e., a corporate and an academic environment); 2) ATLAS which is a distributed network telescope from Arbor; and 3) Internet Protecttrade which is a global alerting service from AT amp;T.
Keywords: ATLAS; distributed network telescope; Internet; intrusion detection systems; network attack datasets; network malicious activity; network security operators; security of data

The Complete Genome Sequence of Thermococcus Onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism - Lee,Hyun Sook; Kang,Sung Gyun; Bae,Seung Seob; Lim,Jae Kyu; Cho,Yona; Kim,Yun Jae; Jeon,Jeong Ho; Cha,Sun-Shin; Kwon,Kae Kyoung; Kim,Hyung-Tae; Park,Cheol-Joo; Lee,Hee-Wook; et al. (Journal of BacteriologyJ. Bacteriol., 2008)
Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus.

Compressed sensing for multi-view tracking and 3-D voxel reconstruction - Reddy, D.; Sankaranarayanan,A. C; Cevher, V.; Chellapa, Rama (Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on, 2008)
Compressed sensing (CS) suggests that a signal, sparse in some basis, can be recovered from a small number of random projections. In this paper, we apply the CS theory on sparse background-subtracted silhouettes and show the usefulness of such an approach in various multi-view estimation problems. The sparsity of the silhouette images corresponds to sparsity of object parameters (location, volume etc.) in the scene. We use random projections (compressed measurements) of the silhouette images for directly recovering object parameters in the scene coordinates. To keep the computational requirements of this recovery procedure reasonable, we tessellate the scene into a bunch of non-overlapping lines and perform estimation on each of these lines. Our method is scalable in the number of cameras and utilizes very few measurements for transmission among cameras. We illustrate the usefulness of our approach for multi-view tracking and 3-D voxel reconstruction problems.
Keywords: 3D; background-subtracted; coding; Estimation; image; problems; multi-view; projections; silhouette; reconstruction; CS; reconstruction; video; sensing; multi-view; silhouettes; image; sparsity; sparse; theory; compressed; tracking; random; voxel

Compressive sensing for background subtraction - Cevher, V.; Sankaranarayanan, A.; Duarte, M.; Reddy, D.; Baraniuk, R.; Chellapa, Rama (Computer Vision–ECCV 2008, 2008)
Compressive sensing (CS) is an emerging field that provides a framework for image recovery using sub-Nyquist sampling rates. The CS theory shows that a signal can be reconstructed from a small set of random projections, provided that the signal is sparse in some basis, e.g., wavelets. In this paper, we describe a method to directly recover background subtracted images using CS and discuss its applications in some communication constrained multi-camera computer vision problems. We show how to apply the CS theory to recover object silhouettes (binary background subtracted images) when the objects of interest occupy a small portion of the camera view, i.e., when they are sparse in the spatial domain. We cast the background subtraction as a sparse approximation problem and provide different solutions based on convex optimization and total variation. In our method, as opposed to learning the background, we learn and adapt a low dimensional compressed representation of it, which is sufficient to determine spatial innovations; object silhouettes are then estimated directly using the compressive samples without any auxiliary image reconstruction. We also discuss simultaneous appearance recovery of the objects using compressive measurements. In this case, we show that it may be necessary to reconstruct one auxiliary image. To demonstrate the performance of the proposed algorithm, we provide results on data captured using a compressive single-pixel camera. We also illustrate that our approach is suitable for image coding in communication constrained problems by using data captured by multiple conventional cameras to provide 2D tracking and 3D shape reconstruction results with compressive measurements.

Compressive wireless arrays for bearing estimation - Cevher, V.; Gurbuz, A.C.; McClellan, J.H.; Chellapa, Rama (Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on, 2008)
Joint processing of sensor array outputs improves the performance of parameter estimation and hypothesis testing problems beyond the sum of the individual sensor processing results. When the sensors have high data sampling rates, arrays are tethered, creating a disadvantage for their deployment and also limiting their aperture size. In this paper, we develop the signal processing algorithms for randomly deployable wireless sensor arrays that are severely constrained in communication bandwidth. We focus on the acoustic bearing estimation problem and show that when the target bearings are modeled as a sparse vector in the angle space, low dimensional random projections of the microphone signals can be used to determine multiple source bearings by solving an l 1-norm minimization problem. Field data results are shown where only 10 bits of information is passed from each microphone to estimate multiple target bearings.
Keywords: acoustic; algorithms; sparse; arrays; acoustic; arrays; hypothesis; bandwidth; compressive; bearing; Estimation; estimation; signal; estimation; sparse; matrices; vectors; wireless; minimization; networks; problem; communication; problem; microphone; problems; joint; PROCESSING; processing; array; processing; direction-of-arrival; processing; l1-norm; sensor; signal; signals; parameter; Testing; vector; wireless; wireless

Computational Vision Approaches for Event Modeling - Chellapa, Rama; Cuntoor, N.P.; Joo, S.W.; V.S. Subrahmanian; Turaga,P. (Understanding Events, 2008)
Event modeling systems provide a semantic interpretation of sequences of pixels that are captured by a video camera. The design of a practical system has to take into account the following three main factors: low-level preprocessing limitations, computational and storage complexity of the event model, and user interaction. The hidden Markov model (HMM) and its variants have been widely used to model both speech and video signals. Computational efficiency of the Baum-Welch and the Viterbi algorithms has been a leading reason for the popularity of the HMM. Since the objective is to detect events in video sequences that are meaningful to humans, one might want to provide space in the design loop for a user who can specify events of interest. This chapter explores this using semantic approaches that not only use features extracted from raw video streams but also incorporate metadata and ontologies of activities. It presents three approaches for applications such as event recognition: anomaly detection, temporal segmentation, and ontology evaluation. The three approaches discussed are statistical methods based on HMMs, formal grammars, and ontologies. The effectiveness of these approaches is illustrated using video sequences captured both indoors and outdoors: the indoor UCF human action dataset, the TSA airport tarmac surveillance dataset, and the bank monitoring dataset.

A Constrained Probabilistic Petri Net Framework for Human Activity Detection in Video - Albanese, M.; Chellapa, Rama; Moscato, V.; Picariello, A.; V.S. Subrahmanian; Turaga,P.; Udrea,O. (Multimedia, IEEE Transactions on, 2008)
Recognition of human activities in restricted settings such as airports, parking lots and banks is of significant interest in security and automated surveillance systems. In such settings, data is usually in the form of surveillance videos with wide variation in quality and granularity. Interpretation and identification of human activities requires an activity model that a) is rich enough to handle complex multi-agent interactions, b) is robust to uncertainty in low-level processing and c) can handle ambiguities in the unfolding of activities. We present a computational framework for human activity representation based on Petri nets. We propose an extension-Probabilistic Petri Nets (PPN)-and show how this model is well suited to address each of the above requirements in a wide variety of settings. We then focus on answering two types of questions: (i) what are the minimal sub-videos in which a given activity is identified with a probability above a certain threshold and (ii) for a given video, which activity from a given set occurred with the highest probability? We provide the PPN-MPS algorithm for the first problem, as well as two different algorithms (naive PPN-MPA and PPN-MPA) to solve the second. Our experimental results on a dataset consisting of bank surveillance videos and an unconstrained TSA tarmac surveillance dataset show that our algorithms are both fast and provide high quality results.
Keywords: activity; dataset; automated; detection; human; interactions; security; net; human; nets; image; Petri; probabilistic; processing; multiagent; processing; video; representation; low-level; representation; video; signal; Surveillance; surveillance; systems; constrained; systems; surveillance; tarmac; TSA; videos; Petri

Context and observation driven latent variable model for human pose estimation - Gupta,A.; Chen,T.; Chen,F.; Kimber,D.; Davis, Larry S. (Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on, 2008)
Current approaches to pose estimation and tracking can be classified into two categories: generative and discriminative. While generative approaches can accurately determine human pose from image observations, they are computationally expensive due to search in the high dimensional human pose space. On the other hand, discriminative approaches do not generalize well, but are computationally efficient. We present a hybrid model that combines the strengths of the two in an integrated learning and inference framework. We extend the Gaussian process latent variable model (GPLVM) to include an embedding from observation space (the space of image features) to the latent space. GPLVM is a generative model, but the inclusion of this mapping provides a discriminative component, making the model observation driven. Observation Driven GPLVM (OD-GPLVM) not only provides a faster inference approach, but also more accurate estimates (compared to GPLVM) in cases where dynamics are not sufficient for the initialization of search in the latent space. We also extend OD-GPLVM to learn and estimate poses from parameterized actions/gestures. Parameterized gestures are actions which exhibit large systematic variation in joint angle space for different instances due to difference in contextual variables. For example, the joint angles in a forehand tennis shot are function of the height of the ball (Figure 2). We learn these systematic variations as a function of the contextual variables. We then present an approach to use information from scene/objects to provide context for human pose estimation for such parameterized actions.
Keywords: estimation; estimation; image; Gaussian; gestures; pose; latent; learning; parameterized; model; human; observations; integrated; pose; process; processes; gesture; processing; pose; recognition; image; tracking; Gaussian; variable

Covariability of Vibrio Cholerae Microdiversity and Environmental Parameters - Zo,Young-Gun; Chokesajjawatee,Nipa; Arakawa,Eiji; Watanabe,Haruo; Huq,Anwar; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2008)
Fine-scale diversity of natural bacterial assemblages has been attributed to neutral radiation because correspondence between bacterial phylogenetic signals in the natural environment and environmental parameters had not been detected. Evidence that such correspondence occurs is provided for Vibrio cholerae, establishing a critical role for environmental parameters in bacterial diversity.

The Deployment of a Darknet on an Organization-Wide Network: An Empirical Analysis - Berthier,R.; Michel Cukier (2008)
Darknet sensors have the interesting property of collecting only suspicious traffic, including misconfiguration, backscatter and malicious traffic. The type of traffic collected highly depends on two parameters: the size and the location of the darknet sensor. The goals of this paper are to study empirically the relationship between these two parameters and to try to increase the volume of attackers detected by a given darknet sensor. Our empirical results reveal that on average, on a daily basis, 485 distinct external source IP addresses perform a TCP scan on one of the two /16 networks of our organizationpsilas network. Moreover, a given darknet sensor of 77 IP addresses deployed in the same /16 network collects on average attack traffic from 26% of these attackers.
Keywords: attack traffic; backscatter; darknet sensors; external source IP address; malicious traffic; organization network; organization-wide network; TCP scan; telecommunication congestion control; transmission control protocol; Transport protocols

Determination of Clonality and Relatedness of Vibrio Cholerae Isolates by Genomic Fingerprinting, Using Long-Range Repetitive Element Sequence-Based PCR - Chokesajjawatee,Nipa; Zo,Young-Gun; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2008)
A high-throughput method which is applicable for rapid screening, identification, and delineation of isolates of Vibrio cholerae, sensitive to genome variation, and capable of providing phylogenetic inferences enhances environmental monitoring of this bacterium. We have developed and optimized a method for genomic fingerprinting of V. cholerae based on long-range PCR. The method uses a primer set directed to enterobacterial repetitive intergenic consensus sequences, a high-fidelity DNA polymerase, and analysis via conventional agarose gel electrophoresis. Long (∼10 kb), highly reproducible amplicons were generated from V. cholerae isolates, including those from different geographical locations and historical strains isolated during the period 1931-2000. The amplicons yielded reduced variability in their densitometric band patterns to ≤10% and clonal distinction at <90% similarity. Rapid band-matching analysis was accomplished for fingerprints with ≥90% similarity, discriminating O serotypes and biotypes (classical versus El Tor) as well as pathogenic and nonpathogenic strains. Compared to genome similarity measured by DNA-DNA hybridization, the results showed good correlation (r = 0.7; P < 0.001), with five times less measurement error and without bias. The method permits both phylogenetic inference and clonal differentiation of individual V. cholerae strains, enables robust, high-throughput analysis, and does not require specialized equipment to perform. With access to a curated public database furnished with appropriate analytical software applications, the method should prove useful in large-scale multilaboratory surveys, especially those designed to detect specific pathogens in the natural environment.

Distinguishing persistent failures from transient losses - Cunha,Ítalo; Teixeira,Renata; Feamster, Nick; Diot,Christophe (Proceedings of the 2008 ACM CoNEXT Conference, 2008)
Network tomography is a promising technique to identify the location of of IP faults. The goal of tomography is to infer the status of network internal characteristics based on end-to-end observations. In particular, binary tomography identifies the set of failed links from end-to-end path meausrments. Upon detecting the failure of one or more of the monitored paths, a monitor sends its measurements to a central coordinator. The coordinator then runs the binary tomography algorithm, which takes as input the topology of the network and the status (i.e., up or down) of all monitored paths and finds the minimum set of links that explain the observations.

Dual role colonization factors connecting Vibrio cholerae's lifestyles in human and aquatic environments open new perspectives for combating infectious diseases - Vezzulli,Luigi; Guzmán,Carlos A; Rita R Colwell; Pruzzo,Carla (Current Opinion in Biotechnology, 2008)
Vibrio cholerae exhibits two distinctive lifestyles, one inside the milieu of the human intestine and the other in the aquatic environment. Recently, the existence of V. cholerae ligands involved in colonization of both human intestine and environmental chitin surfaces via the same binding specificity has been shown. Such molecules, here named ‘dual role colonization factors (DRCFs)’, are example of a tight connection between the two V. cholerae's lifestyles. It is suggested that DRCFs and, more generally, bacterial factors and pathways having roles in pathogenesis and in the out of the human body life may be promising targets for development of novel prophylactic or therapeutic interventions that may also affect V. cholerae fitness in its environmental reservoirs.

Dynamic Resource Allocation for Robust Distributed Multi-Point Video Conferencing - Chen,Meng; Su,Guan-Ming; M. Wu (Multimedia, IEEE Transactions on, 2008)
This paper proposes a distributed multi-point video conferencing system over packet erasure channels, where the aggregation of multiple video streams and resource allocation are performed in a distributed manner. Video stream combiners, which are located in different geographical areas and serve as portals for conferees, aggregate incoming streams supplied by local users with other streams aggregated from nearby video stream combiners. A packet-division multiple-access (PDMA)-based error protection scheme is proposed to be performed at each video stream combiner to minimize the maximal expected video distortion among aggregated streams. The proposed error protection scheme for multi-stream aggregation also supports user preference. In order to deliver video streams to end users with different preferred quality, a consensus algorithm is proposed to adaptively perform resource allocation based on user preference. Simulation results show that the proposed multi-stream aggregation and error protection scheme has significant gains over traditional multi-stream error protection schemes for a multi-point video conferencing system.
Keywords: allocation; error; channels; packet-division; communication; conferencing; conferencing; multi-access; distributed; dynamic; erasure; error; multiple-access-based; multipoint; Protection; resource; scheme; multi-point; scheme; robust; schemes; packet; streams; multistream; system; multiple; systems; teleconferencing; video; video

Effective Visualization of File System Access-Control - Heitzmann, Alexander; Palazzi, Bernardo; Charalampos Papamanthou; Tamassia, Roberto (Visualization for Computer Security, 2008)
In this paper, we present a visual representation of access control permissions in a standard hierarchical file system. Our visualization of file permissions leverages treemaps, a popular graphical representation of hierarchical data. In particular, we present a visualization of access control for the NTFS file system that can help a non-expert user understand and manipulate file system permissions in a simple and effective way. While our examples are based on NTFS, our approach can be used for many other hierarchical file systems as well.
Keywords: Computer Communication Networks; Computer Imaging, Vision, Pattern Recognition and Graphics; data mining and knowledge discovery; Data Structures, Cryptology and Information Theory; Visualization

Embedding and similarity search for point sets under translation - Cho,Minkyoung; Mount, Dave (Proceedings of the twenty-fourth annual symposium on Computational geometry, 2008)
Pattern matching in point sets is a well studied problem with numerous applications. We assume that the point sets may contain outliers (missing or spurious points) and are subject to an unknown translation. We define the distance between any two point sets to be the minimum size of their symmetric difference over all translations of one set relative to the other. We consider the problem in the context of similarity search. We assume that a large database of point sets is to be preprocessed so that given any query point set, the closest matches in the database can be computed efficiently. Our approach is based on showing that there is a randomized algorithm that computes a translation-invariant embedding of any point set of size at most n into the L_1 metric, so that with high probability, distances are subject to a distortion that is O(log2 n).
Keywords: EMBEDDING; point pattern matching; randomized algorithms; Similarity Search

Enhancing In-Car Navigation Systems with Personal Experience - Bederson, Benjamin B.; Clamage,Aaron; Plaisant, Catherine (Transportation Research Record: Journal of the Transportation Research Board, 2008)
Computers are extremely powerful for data processing but less adept at handling problems that involve subjective reasoning. People, on the other hand, are good at such tasks. A framework is presented for adding subjective human experience to in-car navigation systems. People often rely on personal experience when planning trips, choosing the route that is fastest, prettiest, or recommended by a friend. A set of methods was developed to help people record personal driving history, add textual annotations describing subjective experiences, and share data with friends and family or even the broader community. Users can then learn from personal data or harness the multiplicity of individual experiences to enjoy new routes. This approach can be used in conjunction with traditional in-car navigation systems.

Environmental signatures associated with cholera epidemics - Constantin de Magny,G.; Murtugudde,R.; Sapiano,M. R. P.; Nizam,A.; Brown,C. W.; Busalacchi,A. J.; Yunus,M.; Nair,G. B.; Gil,A. I.; Lanata,C. F.; Rita R Colwell (Proceedings of the National Academy of Sciences, 2008)
The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998–2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.ecology epidemiology microbiology remote sensing

Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons - Taviani,Elisa; Ceccarelli,Daniela; Lazaro,Nivalda; Bani,Stefania; Cappuccinelli,Piero; Rita R Colwell; Colombo,Mauro M. (FEMS Microbiology Ecology, 2008)
Circulation of mobile genetic elements linked to drug resistance spread was studied in Vibrio strains isolated from surface urban water (river and sea) and shellfish samples in 2002–2003 in Maputo, Mozambique. Class 1 integrons and integrating conjugative elements (ICE) were investigated by PCR and mating experiments in strains of major health interest: 10 Vibrio cholerae, six Vibrio parahaemolyticus, two Vibrio alginolyticus and one Vibrio fluvialis. Resistance to at least two antibiotics (predominantly β-lactams) was detected in all the strains, with additional resistances to sulfamethoxazole, spectinomycin, streptomycin and/or trimethoprim. Class 1 integrons contributed partially to the expression of drug resistance and were found in five isolates: four V. cholerae (blaP1 cassette, one strain also contained the dfrA15 cassette) and one V. alginolyticus (aadA2 cassette). ICEs, apparently devoid of resistance genes, were found in eight V. cholerae, three V. parahaemolyticus and one V. fluvialis isolates. A wide variability was observed by molecular characterization of ICEs. Five ICEs were included in the SXT/R391 family and seven ICEs were not classified. Our results indicate that the SXT/R391 family and related ICEs comprise a large class of polymorphic genetic elements widely circulating in environmental Vibrio strains in Africa, beside those evidently linked to drug resistance in clinical isolates.
Keywords: ICE; integron; Mozambique; Vibrio

Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming with an Application to Phylogenetic Analysis of Gene Expression - Corrada Bravo, Hector; Eng,K. H; Keles,S.; Wahba,G.; Wright,S. (Department of Statistics, University of Wisconsin, 2008)
We present a novel method for estimating tree-structured covariance matrices directly fromobserved continuous data. A representation of these classes of matrices as linear combinations of rank-one matrices indicating object partitions is used to formulate estimation as instances of well-studied numerical optimization problems. In particular, we present estimation based on projection where the covariance estimate is the nearest tree-structured covariance matrix to an observed sample covariance matrix. The problem is posed as a linear or quadratic mixed-integer program (MIP) where a setting of the integer variables in the MIP specifies a set of tree topologies of the structured covariance matrix. We solve these problems to optimality using efficient and robust existing MIP solvers. We also show that the least squares distance method of Fitch and Margoliash (1967) can be formulated as a quadratic MIP and thus solved exactly using existing, robust branch-and-bound MIP solvers. Our motivation for this method is the discovery of phylogenetic structure directly from gene expression data. Recent studies have adapted traditional phylogenetic comparative anal- ysis methods to expression data. Typically, these methods first estimate a phylogenetic tree from genomic sequence data and subsequently analyze expression data. A covariance matrix constructed from the sequence-derived tree is used to correct for the lack of independence in phy- logenetically related taxa. However, recent results have shown that the hierarchical structure of sequence-derived tree estimates are highly sensitive to the genomic region chosen to build them. To circumvent this difficulty, we propose a stable method for deriving tree-structured covariance matrices directly from gene expression as an exploratory step that can guide investigators in their modelling choices for these types of comparative analysis. We present a case study in phylogenetic analysis of expression in yeast gene families. Our method is able to corroborate the presence of phylogenetic structure in the response of expression in a subset of the gene families under particular experimental conditions. Additionally, when used in conjunction with transcription factor occupancy data, our methods show that alternative modelling choices should be considered when creating sequence-derived trees for this comparative analysis.

Evaluating Visual Analytics at the 2007 VAST Symposium Contest - Plaisant, Catherine; Grinstein,G.; Scholtz,J.; Whiting,M.; O'Connell,T.; Laskowski,S.; Chien,L.; Tat,A.; Wright,W.; Gorg,C.; Zhicheng Liu; Parekh,N.; et al. (Computer Graphics and Applications, IEEE, 2008)
In this article, we report on the contest's data set and tasks, the judging criteria, the winning tools, and the overall lessons learned in the competition. We believe that by organizing these contests, we're creating useful resources for researchers and are beginning to understand how to better evaluate VA tools. Competitions encourage the community to work on difficult problems, improve their tools, and develop baselines for others to build or improve upon. We continue to evolve a collection of data sets, scenarios, and evaluation methodologies that reflect the richness of the many VA tasks and applications.
Keywords: 2007; analytics; analytics; data; and; Contest; Visual; Science; Symposium; Technology; data; VAST; visualisation; visualization; visual

Executable Specifications for Real-Time Distributed Systems - Ray,Arnab; Cleaveland, Rance (Electronic Notes in Theoretical Computer Science, 2008)
One of the challenges in designing distributed, embedded systems is the paucity of formal, executable specification notations that provide support for both real-time and asynchronous communication. This paper describes a timed architecture design language (Timed Architecture Interaction Diagrams or TAID) that, by virtue of its formal, executable semantics, combines the benefits of synchronous specification notations with the advantages of traditional architecture description languages. In addition, TAID provides support for a variety of temporal inter-process communication (IPC) primitives as a native feature of the language, so that the encapsulated communication behavior (captured by real-time â€œbusesâ€ in TAID) may be re-used across designs and serve as specifications for more detailed model implementations.
Keywords: distributed systems; Formal Methods; real-time; Simulations; Software architecture

Expanding the reach of Grid computing: combining Globus- and BOINC-based systems - Myers,D. S; Bazinet,A. L; Cummings, Michael P. (Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology, 2008)

Experiences with building an intrusion-tolerant group communication system - Ramasamy,HariGovind V.; Pandey,Prashant; Michel Cukier; Sanders,William H. (Software: Practice and Experience, 2008)
There are many group communication systems (GCSs) that provide consistent group membership and reliable, ordered multicast properties in the presence of crash faults. However, relatively few GCS implementations are able to provide these properties in the presence of malicious faults resulting from intrusions. We describe the systematic transformation of a crash-tolerant GCS, namely C-Ensemble, into an intrusion-tolerant GCS, the ITUA GCS. To perform the transformation, we devised intrusion-tolerant versions of key group communication protocols. We then inserted implementations of the protocols into C-Ensemble and made significant changes to the rest of the C-Ensemble protocol stack to make the stack intrusion tolerant. We quantify the cost of providing intrusion-tolerant group communication in two ways. First, we quantify the implementation effort by presenting a detailed analysis of the amount of change required to the original C-Ensemble system. In doing so, we provide insight into the choice of building an intrusion-tolerant GCS from scratch versus building one by leveraging a crash-tolerant implementation. Second, we quantify the run-time performance cost of tolerating intrusions by presenting results from an experimental evaluation of the main intrusion-tolerant microprotocols. The results are analyzed to identify the parts that contribute the most overhead while providing intrusion tolerance during both normal operation and recovery from intrusions. Copyright © 2007 John Wiley & Sons, Ltd.
Keywords: distributed protocols; experimental evaluation; Fault tolerance; Group communication; intrusion tolerance

Fable: A Language for Enforcing User-defined Security Policies - Swamy,N.; Corcoran,B.J.; Hicks, Michael W. (IEEE Symposium on Security and Privacy, 2008. SP 2008, 2008)
This paper presents FABLE, a core formalism for a programming language in which programmers may specify security policies and reason that these policies are properly enforced. In FABLE, security policies can be expressed by associating security labels with the data or actions they protect. Programmers define the semantics of labels in a separate part of the program called the enforcement policy. FABLE prevents a policy from being circumvented by allowing labeled terms to be manipulated only within the enforcement policy; application code must treat labeled values abstractly. Together, these features facilitate straightforward proofs that programs implementing a particular policy achieve their high-level security goals. FABLE is flexible enough to implement a wide variety of security policies, including access control, information flow, provenance, and security automata. We have implemented FABLE as part of the LINKS web programming language; we call the resulting language SELlNKS. We report on our experience using SELlNKS to build two substantial applications, a wiki and an on-line store, equipped with a combination of access control and provenance policies. To our knowledge, no existing framework enables the enforcement of such a wide variety of security policies with an equally high level of assurance.
Keywords: Access control; Automata; Collaborative work; Communication system security; Computer languages; computer security; Data security; enforcement policy; FABLE; Government; high-level security goals; information flow; Information security; Language-based security; programming languages; Programming profession; provenance; security automata; security labels; security of data; user-defined security policies; verified enforcement; Web programming language

Factorized variational approximations for acoustic multi source localization - Cevher, V.; Sankaranarayanan,A. C; Chellapa, Rama (Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on, 2008)
Estimation based on received signal strength (RSS) is crucial in sensor networks for sensor localization, target tracking, etc. In this paper, we present a Gaussian approximation of the Chi distribution that is applicable to general RSS source localization problems in sensor networks. Using our Gaussian approximation, we provide a factorized variational Bayes (VB) approximation to the location and power posterior of multiple sources using a sensor network. When the source signal and the sensor noise have uncorrelated Gaussian distributions, we demonstrate that the envelope of the sensor output can be accurately modeled with a multiplicative Gaussian noise model. In turn, our factorized VB approximations decrease the computational complexity and provide computational robustness as the number of targets increases. Simulations are provided to demonstrate the effectiveness of the proposed approximations.
Keywords: approximation; acoustic; approximation; Bayes; approximation; multisensor; approximation; variational; Bayes; Chi; detection; wireless; distribution; Gaussian; localization; factorized; localization; sensor; methods; Gaussian; multisource; networks; networks; stochastic; processes; acoustic; sensor; signal; strength; sensor; systems; object; tracking; received; variational

Fast, easy, and cheap: Construction of statistical machine translation models with MapReduce - Dyer,C.; Cordova,A.; Mont,A.; Jimmy Lin (Proceedings of the Third Workshop on Statistical Machine Translation, 2008)
In recent years, the quantity of parallel train-ing data available for statistical machine trans- lation has increased far more rapidly than the performance of individual computers, re- sulting in a potentially serious impediment to progress. Parallelization of the model- building algorithms that process this data on computer clusters is fraught with challenges such as synchronization, data exchange, and fault tolerance. However, the MapReduce programming paradigm has recently emerged as one solution to these issues: a powerful functional abstraction hides system-level de- tails from the researcher, allowing programs to be transparently distributed across potentially very large clusters of commodity hardware. We describe MapReduce implementations of two algorithms used to estimate the parame- ters for two word alignment models and one phrase-based translation model, all of which rely on maximum likelihood probability esti- mates. On a 20-machine cluster, experimental results show that our solutions exhibit good scaling characteristics compared to a hypo- thetical, optimally-parallelized version of cur- rent state-of-the-art single-core tools.

Finding Corrupted Computers Using Imperfect Intrusion Prevention System Event Data - Chrun,Danielle; Michel Cukier; Sneeringer,Gerry (Computer Safety, Reliability, and Security, 2008)
With the increase of attacks on the Internet, a primary concern for organizations is how to protect their network. The objectives of a security team are 1) to prevent external attackers from launching successful attacks against organization computers that could become compromised, 2) to ensure that organization computers are not vulnerable (e.g., fully patched) so that in either case the organization computers do not start launching attacks. The security team can monitor and block malicious activity by using devices such as intrusion prevention systems. However, in large organizations, such monitoring devices could record a high number of events. The contributions of this paper are 1) to introduce a method that ranks potentially corrupted computers based on imperfect intrusion prevention system event data, and 2) to evaluate the method based on empirical data collected at a large organization of about 40,000 computers. The evaluation is based on the judgment of a security expert of which computers were indeed corrupted. On the one hand, we studied how many computers classified as of high concern or of concern were indeed corrupted (i.e., true positives). On the other hand, we analyzed how many computers classified as of lower concern were in fact corrupted (i.e., false negatives).
Keywords: Computer science

Flowers or a robot army?: encouraging awareness & activity with personal, mobile displays - Consolvo,Sunny; Klasnja,Predrag; McDonald,David W.; Avrahami,Daniel; Jon Froehlich; LeGrand,Louis; Libby,Ryan; Mosher,Keith; Landay,James A. (Proceedings of the 10th international conference on Ubiquitous computing, 2008)
Personal, mobile displays, such as those on mobile phones, are ubiquitous, yet for the most part, underutilized. We present results from a field experiment that investigated the effectiveness of these displays as a means for improving awareness of daily life (in our case, self-monitoring of physical activity). Twenty-eight participants in three experimental conditions used our UbiFit system for a period of three months in their day-to-day lives over the winter holiday season. Our results show, for example, that participants who had an awareness display were able to maintain their physical activity level (even during the holidays), while the level of physical activity for participants who did not have an awareness display dropped significantly. We discuss our results and their general implications for the use of everyday mobile devices as awareness displays.
Keywords: ambient display; awareness; calm technology; field experiment; fitness; glanceable display; mobile phone; personal mobile display; persuasive technology; physical activity

A Framework for Software Engineering Experimental Replications - Mendonca,M.G.; Maldonado,J.C.; de Oliveira,M.C.F.; Carver, J.; Fabbri,C.P.F.; Shull, F.; Travassos,G.H.; Hohn,E.N.; Basili, Victor R. (Engineering of Complex Computer Systems, 2008. ICECCS 2008. 13th IEEE International Conference on, 2008)
Experimental replications are very important to the advancement of empirical software engineering. Replications are one of the key mechanisms to confirm previous experimental findings. They are also used to transfer experimental knowledge, to train people, and to expand a base of experimental evidence. Unfortunately, experimental replications are difficult endeavors. It is not easy to transfer experimental know-how and experimental findings. Based on our experience, this paper discusses this problem and proposes a Framework for Improving the Replication of Experiments (FIRE). The FIRE addresses knowledge sharing issues both at the intra-group (internal replications) and inter-group (external replications) levels. It encourages coordination of replications in order to facilitate knowledge transfer for lower cost, higher quality replications and more generalizable results.
Keywords: engineering; engineering; evidence; experimental; experimental; Experiments; experimental; for; Framework; Improving; knowledge; of; replication; replication; software; sharing; software; the; transfer; knowledge

From Videos to Verbs: Mining Videos for Activities using a cascade of dynamical systems (Supplemental Material) - Turaga, P.K.; Veeraraghavan,A.; Chellapa, Rama (Relation, 2008)

A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE - Cummings, Michael P.; Neel,Maile C; Shaw,Kerry L (Evolution, 2008)
We introduce a statistic, the genealogical sorting index (gsi), for quantifying the degree of exclusive ancestry of labeled groups on a rooted genealogy and demonstrate its application. The statistic is simple, intuitive, and easily calculated. It has a normalized range to facilitate comparisons among different groups, trees, or studies and it provides information on individual groups rather than a composite measure for all groups. It naturally handles polytomies and accommodates measures of uncertainty in phylogenetic relationships. We use coalescent simulations to explore the behavior of the gsi across a range of divergence times, with the mean value increasing to 1, the maximum value when exclusivity within a group reached monophyly. Simulations also demonstrate that the power to reject the null hypothesis of mixed genealogical ancestry increased markedly as sample size increased, and that the gsi provides a statistically more powerful measure of divergence than FST. Applications to data from published studies demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic. Although we describe this statistic in the context of divergence, it is more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree.
Keywords: Ancestral polymorphism; congruence; exclusivity; genealogy; lineage sorting; monophyly; paraphyly; Phylogeny; polyphyly; speciation; species

Getting to Green: Understanding Resource Consumption in the Home - Marshini Chetty; Tran, David; Grinter, Rebecca E. (UbiComp '08, 2008)
Rising global energy demands, increasing costs and limited natural resources mean that householders are more conscious about managing their domestic resource consumption. Yet, the question of what tools Ubicomp researchers can create for residential resource management remains open. To begin to address this omission, we present a qualitative study of 15 households and their current management practices around the water, electricity and natural gas systems in the home. We find that in-the-moment resource consumption is mostly invisible to householders and that they desire more real-time information to help them save money, keep their homes comfortable and be environmentally friendly. Designing for domestic sustainability therefore turns on improving the visibility of resource production and consumption costs as well as supporting both individuals and collectives in behavior change. Domestic sustainability also highlights the caveat of potentially creating a green divide by making resource management available only to those who can afford the technologies to support being green. Finally, we suggest that the Ubicomp community can contribute to the domestic and broader sustainability agenda by incorporating green values in designs and highlight the challenge of collecting data on being green.
Keywords: domestic conservation; residential resource consumption; Sustainability

Global impact of Vibrio cholerae interactions with chitin - Pruzzo,Carla; Vezzulli,Luigi; Rita R Colwell (Environmental Microbiology, 2008)
The interaction of Vibrio cholerae with chitin exemplifies for microbial ecology a successful bacteria–substrate interaction with complex and significant influence on the lifestyle of the bacterium. Chitin is one of the most abundant polymers on earth and possibly the most abundant in the aquatic environment, where its association with V. cholerae has provided the microorganism with a number of advantages, including food availability, adaptation to environmental nutrient gradients, tolerance to stress and protection from predators. Emergent properties of V. cholerae–chitin interactions occur at multiple hierarchical levels in the environment and include cell metabolic and physiological responses e.g. chemotaxis, cell multiplication, induction of competence, biofilm formation, commensal and symbiotic relationship with higher organisms, cycling of nutrients, and pathogenicity for humans and aquatic animals. As factors mediating virulence of V. cholerae for humans and aquatic animals derive from mechanisms of adaptation to its environment, at different levels of hierarchical scale, V. cholerae interactions with chitin represent a useful model for examination of the role of primary habitat selection in the development of traits that have been identified as virulence factors in human disease.

Hardware and Software Systems for Image and Video Processing-Algorithmic and Architectural Optimizations for Computationally Efficient Particle Filtering - Sankaranarayanan,A. C; Srivastava, A.; Chellapa, Rama (IEEE Transactions on Image Processing, 2008)

Hci for community and international development - Thomas, John; Dearden, Andy; Dray, Susan; Light, Ann; Best, Michael; Arkin, Nuray; Maunder, Andrew; Kam, Mathew; Marshini Chetty; Sambasivan, Nithya; Buckhalter, Celeste; Krishnan, Gaurishankar (SIGCHI EA '08, 2008)
This workshop explores the challenges in applying, extending and inventing appropriate methods and contributions of Human Computer Interaction (HCI) to International economic and community Development. We address interaction design for parts of the world that are often marginalized by the Global North as well as people in the Global North who are themselves similarly marginalized by poverty or other barriers. We hope to extend the boundaries of the field of Human Computer Interaction by spurring a discussion on how existing methods and practices can be adapted and modified, and how new practices can be developed, to deal with the unique challenges posed by these contexts.
Keywords: community design; ict4d; information and communication technology; international development; participatory design; ucd4id; User centered design

Improved approximation bounds for planar point pattern matching - Cho,M.; Mount, Dave (Algorithmica, 2008)
We analyze the performance of simple algorithms for matching two planar point sets under rigid transformations so as to minimize the directed Hausdorff distance between the sets. This is a well studied problem in computational geometry. Goodrich, Mitchell, and Orletsky presented a very simple approximation algorithm for this problem, which computes transformations based on aligning pairs of points. They showed that their algorithm achieves an approximation ratio of 4. We introduce a modification to their algorithm, which is based on aligning midpoints rather than endpoints. This modification has the same simplicity and running time as theirs, and we show that it achieves a better approximation ratio of roughly 3.14. We also analyze the approximation ratio in terms of a instance-specific parameter that is based on the ratio between diameter of the pattern set to the optimum Hausdorff distance. We show that as this ratio increases (as is common in practical applications) the approximation ratio approaches 3 in the limit. We also investigate the performance of the algorithm by Goodrich et al. as a function of this ratio, and present nearly matching lower bounds on the approximation ratios of both algorithms.

Indexing planar point quartets via geometric attributes - Cranston,Charles B.; Samet, Hanan (Proceedings of the 16th ACM SIGSPATIAL international conference on Advances in geographic information systems, 2008)
An index is devised to support position-independent search for images containing quartets of icons. Point quartets exist that do not unambiguously map to quadrilaterals, however, four points do unambiguously determine a set of six interpoint line segments. Values for the "size", "shape", and "orientation" attributes of an icon quartet can be derived as functions of this interpoint line set, and can be used to construct a point-based index, in which each point quartet maps to a single point in the resulting hyperdimensional index space. Orientation can be represented by a single, spatially closed dimension. However, assignment of a reference direction for quartets possessing a k-fold rotational symmetry presents a significant challenge. Methods are described for determining shape and orientation attributes for point quartets, and for mapping these attributes onto a set of attribute axes to form a combined index. The orientation computation supplies, as a byproduct, one component of the shape attribute. All attributes are continuous with respect to small variations in the indexed point quartets.

An instrumentation-based approach to controller model validation - Cleaveland, Rance; Smolka,S.; Sims,S. (Model-Driven Development of Reliable Automotive Services, 2008)

A Java3D framework for inspecting and segmenting 3D models - De Floriani, Leila; Papaleo,Laura; Carissimi,Nicoló (Proceedings of the 13th international symposium on 3D web technology, 2008)
Models of 3D objects have become widely accessible in several disciplines within academia and industry, spanning from scientific visualization to entertainment. In the last few years, 3D models are often organized into digital libraries accessible over the network, and thus semantic annotation of such models becomes an important issue. A fundamental step in annotating a 3D model is to segment it into meaningful parts. In this work, we present a Java3D framework for inspecting and segmenting 3D objects represented in X3D format. In particular, we present a combination of segmentation and merging techniques for producing a feasible decomposition of the boundary of a 3D object. We represent such decomposition as a graph, that we call the segmentation graph which is the basis for semantic annotation. We describe also the interface we have developed to allow visualization and browsing of both the decomposition and the segmentation graph in order to understand the topological structure of the resulting decomposition.
Keywords: Java3D; object manipulation; Object segmentation; shape semantics; X3D

The Lattice Project: a Grid research and production environment combining multiple Grid computing models - Bazinet,A. L; Cummings, Michael P. (Distributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting CommunitiesDistributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting Communities, 2008)

Learning action dictionaries from video - Turaga,P.; Chellapa, Rama (Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on, 2008)
Summarizing the contents of a video containing human activities is an important problem in computer vision and has important applications in automated surveillance systems. Summarizing a video requires one to identify and learn a 'vocabulary' of action-phrases corresponding to specific events and actions occurring in the video. We propose a generative model for dynamic scenes containing human activities as a composition of independent action-phrases - each of which is derived from an underlying vocabulary. Given a long video sequence, we propose a completely unsupervised approach to learn the vocabulary. Once the vocabulary is learnt, a video segment can be decomposed into a collection of phrases for summarization. We then describe methods to learn the correlations between activities and sequentiality of events. We also propose a novel method for building invariances to spatial transforms in the summarization scheme.
Keywords: (artificial; action; action-phrases; learning; automated; decomposition; video; dictionaries; spatial; intelligence); video; segment; segmentation; learning; sequence; computer; Surveillance; surveillance; systems; computer; transforms; video; vision; image; vision; independent

Machine Recognition of Human Activities: A Survey - Turaga,P.; Chellapa, Rama; V.S. Subrahmanian; Udrea,O. (Circuits and Systems for Video Technology, IEEE Transactions on, 2008)
The past decade has witnessed a rapid proliferation of video cameras in all walks of life and has resulted in a tremendous explosion of video content. Several applications such as content-based video annotation and retrieval, highlight extraction and video summarization require recognition of the activities occurring in the video. The analysis of human activities in videos is an area with increasingly important consequences from security and surveillance to entertainment and personal archiving. Several challenges at various levels of processing-robustness against errors in low-level processing, view and rate-invariant representations at midlevel processing and semantic representation of human activities at higher level processing-make this problem hard to solve. In this review paper, we present a comprehensive survey of efforts in the past couple of decades to address the problems of representation, recognition, and learning of human activities from video and related applications. We discuss the problem at two major levels of complexity: 1) "actions" and 2) "activities." "Actions" are characterized by simple motion patterns typically executed by a single human. "Activities" are more complex and involve coordinated actions among a small number of humans. We will discuss several approaches and classify them according to their ability to handle varying degrees of complexity as interpreted above. We begin with a discussion of approaches to model the simplest of action classes known as atomic or primitive actions that do not require sophisticated dynamical modeling. Then, methods to model actions with more complex dynamics are discussed. The discussion then leads naturally to methods for higher level representation of complex activities.
Keywords: activity; low-level; annotation; human; cameras; video; content-based; factors; image; processing; machine; processing; rate-invariant; recognition; image; recognition; midlevel; representation; image; representation; video; representations; semantic; retrieval; human; sequences; summarization; content-based; video

The marine environment and human health: the cholera model - Rita R Colwell (Global Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease EmergenceGlobal Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease Emergence, 2008)

The Maryland Large-Scale Integrated Neurocognitive Architecture - Reggia, James A.; Tagamets,M.; Contreras-Vidal,J.; Jacobs, David W.; Weems,S.; Naqvi,W.; Yang,C. (University of Maryland College Park, 2008)
Recent progress in neural computation, high performance computing, neuroscience and cognitive science suggests that an effort to produce a general-purpose, adaptive machine intelligence is likely to yield a qualitatively more powerful system than those currently existing. Here we outline our progress in developing a framework for creating such a large-scale machine intelligence, or neurocognitive architecture that is based on the modularity, dynamics and plasticity of the human brain. We successfully implemented three intermediate-scale parts of such a system, and these are described. Based on this experience, we concluded that for the short term, optimal results would be obtained by using a hybrid design including neural, symbolic AI, and artificial life methods. We propose a three-tiered architecture that integrates these different methods, and describe a prototype mini-Roboscout that we implemented and evaluated based on this architecture. We also examined, via computational experiments, the effectiveness of genetic programming as a design tool for recurrent neural networks, and the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for proceeding.
Keywords: *COMPUTATIONS; *HYBRID SYSTEMS; *NEURAL NETS; *NEUROCOGNITIVE ARCHITECTURE; ADAPTIVE SYSTEMS; Artificial intelligence; BRAIN; Cognition; COMPUTER PROGRAMMING; COMPUTER PROGRAMMING AND SOFTWARE; HYBRID AI; Machine intelligence; MECHANICAL ORGANS; MODULAR CONSTRUCTION; NERVOUS SYSTEM; PE61101E; PLASTIC PROPERTIES; PROCESSING EQUIPMENT; RECURRENT NEURAL NETWORK

Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development - Wan,Le-Ben; Pan,Hua; Hannenhalli, Sridhar; Cheng,Yong; Ma,Jun; Fedoriw,Andrew; Lobanenkov,Victor; Latham,Keith E.; Schultz,Richard M.; Bartolomei,Marisa S. (Development, 2008)
CTCF is a multifunctional nuclear factor involved in epigenetic regulation. Despite recent advances that include the systematic discovery of CTCF-binding sites throughout the mammalian genome, the in vivo roles of CTCF in adult tissues and during embryonic development are largely unknown. Using transgenic RNAi, we depleted maternal stores of CTCF from growing mouse oocytes, and identified hundreds of misregulated genes. Moreover, our analysis suggests that CTCF predominantly activates or derepresses transcription in oocytes. CTCF depletion causes meiotic defects in the egg, and mitotic defects in the embryo that are accompanied by defects in zygotic gene expression, and culminate in apoptosis. Maternal pronuclear transfer and CTCF mRNA microinjection experiments indicate that CTCF is a mammalian maternal effect gene, and that persistent transcriptional defects rather than persistent chromosomal defects perturb early embryonic development. This is the first study detailing a global and essential role for CTCF in mouse oocytes and preimplantation embryos.

Mixed state models for automatic target recognition and behavior analysis in video sequences - Chellapa, Rama; Sankaranarayanan,Aswin C.; Veeraraghavan,Ashok (Proceedings of SPIE, 2008)
Mixed state or hybrid state space systems are useful tools for various problems in computer vision. These systems model complicated system dynamics as a mixture of inherently simple sub-systems, with an additional mechanism to switch between the sub-systems. This approach of modeling using simpler systems allows for ease in learning the parameters of the system and in solving the inference problem. In this paper, we study the use of such mixed state space systems for problems in recognition and behavior analysis in video sequences. We begin with a dynamical system formulation for recognition of faces from a video. This system is used to introduce the simultaneous tracking and recognition paradigm that allows for improved performance in both tracking and recognition. We extend this framework to design a second system for verification of vehicles across non-overlapping views using structural and textural fingerprints for characterizing the identity of the target. Finally, we show the use of such modeling for tracking and behavior analysis of bees from video.

Model Based Design Verification: A Monitor Based Approach - Ackermann,Chris; Ray,Arnab; Cleaveland, Rance; Heit,Jürgen; Martin,Christopher; Shelton,Charles (SAE International, 2008)
This paper assesses the utility of an automated functional verification methodology in the design of a body electronics application. The use of design models as detailed specifications for software is gaining steady acceptance in the automotive industry because of the advantages it offers in terms of rapid system prototyping and automatic code generation. This paper argues that such modeling effort can also be used to provide support for design verification, so that errors may be pinpointed before they find their way into code, when they become much harder and more expensive to isolate, diagnose and repair.

Model Driven Segmentation of Articulating Humans in Laplacian Eigenspace - Sundaresan, A.; Chellapa, Rama (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2008)
We propose a general approach using Laplacian Eigenmaps and a graphical model of the human body to segment 3D voxel data of humans into different articulated chains. In the bottom-up stage, the voxels are transformed into a high-dimensional (6D or less) Laplacian Eigenspace (LE) of the voxel neighborhood graph. We show that LE is effective at mapping voxels on long articulated chains to nodes on smooth 1D curves that can be easily discriminated, and prove these properties using representative graphs. We fit 1D splines to voxels belonging to different articulated chains such as the limbs, head and trunk, and determine the boundary between splines using the spline fitting error. A top-down probabilistic approach is then used to register the segmented chains, utilizing their mutual connectivity and individual properties. Our approach enables us to deal with complex poses such as those where the limbs form loops. We use the segmentation results to automatically estimate the human body models. While we use human subjects in our experiments, the method is fairly general and can be applied to voxel-based segmentation of any articulated object composed of long chains. We present results on real and synthetic data that illustrate the usefulness of this approach.
Keywords: 3D voxel data segmentation; algorithms; Anatomic; Pattern Recognition; Artificial intelligence; Automated; Reproducibility of Results; Sensitivity and Specificity; Whole Body Imaging; Computer simulation; Computer-Assisted; Imaging; curve fitting; Eigenvalues and eigenfunctions; graph theory; human articulation; human body graphical model; human motion analysis; HUMANS; Image Enhancement; Image Interpretation; Image motion analysis; image registration; Image segmentation; Laplace transforms; Laplacian eigenspace transform; model driven segmentation; probability; representative graph; skeleton registration; Smoothing methods; solid modelling; spline fitting error; splines (mathematics); Three-Dimensional; Joints; Models; top-down probabilistic approach; voxel neighborhood graph

Modeling shape and textural variations in aging faces - Ramanathan,N.; Chellapa, Rama (Automatic Face Gesture Recognition, 2008. FG '08. 8th IEEE International Conference on, 2008)
We propose a two fold approach towards modeling facial aging in adults. Firstly, we develop a shape transformation model that is formulated as a physically-based parametric muscle model that captures the subtle deformations facial features undergo with age. The model implicitly accounts for the physical properties and geometric orientations of the individual facial muscles. Next, we develop an image gradient based texture transformation function that characterizes facial wrinkles and other skin artifacts often observed during different ages. Facial growth statistics (both in terms of shape and texture) play a crucial role in developing the aforementioned transformation models. From a database that comprises of pairs of age separated face images of many individuals, we extract age-based facial measurements across key fiducial features and further, study textural variations across ages. We present experimental results that illustrate the applications of the proposed facial aging model in tasks such as face recognition and facial appearance prediction across aging.
Keywords: Aging; analysis; faces; image; function; face; gradient; modeling; model; textural; recognition; image; shape; shape; texture; statistical; transformation; variations; texture

A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13 - Kohlsdorf,T; Cummings, Michael P.; Lynch,VJ; Stopper,GF; Takahashi,K; Wagner,GP (J Mol Evol, 2008)
The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with the release of functional constraints caused by limb loss. Fragments of the Hoxa-13 exon 1 were sequenced from 13 species and analyzed, with additional published sequences of the same region, using relative rates and likelihood-ratio tests. Five amino acid sites in exon 1 of Hoxa-13 were detected as evolving under positive selection in the stem lineage of snakes. To further investigate whether there is an association between limb loss and sequence variation in Hoxa-13, we used the random forest method on an alignment that included shark, basal fish lineages, and "eu-tetrapods" such as mammals, turtle, alligator, and birds. The random forest method approaches the problem as one of classification, where we seek to predict the presence or absence of autopodium based on amino acid variation in Hoxa-13 sequences. Different alignments tested were associated with similar error rates (18.42%). The random forest method suggested that phenotypic states (autopodium present and absent) can often be correctly predicted based on Hoxa-13 sequences. Basal, nontetrapod gnat-hostomes that never had an autopodium were consistently classified as limbless together with the snakes, while eu-tetrapods without any history of limb loss in their phylogeny were also consistently classified as having a limb. Misclassifications affected mostly lizards, which, as a group, have a history of limb loss and limb re-evolution, and the urodele and caecilian in our sample. We conclude that a molecular footprint can be detected in Hoxa-13 that is associated with the lack of an autopodium; groups with classification ambiguity (lizards) are characterized by a history of repeated limb loss and possible limb re-evolution.

More Than Meets the Eye: Transforming the User Experience of Home Network Management - Poole, Erika Shehan; Marshini Chetty; Grinter, Rebecca E.; Edwards, W. Keith (Proceedings of the 7th ACM conference on Designing interactive systems, 2008)
As computing migrates from the workplace to the home, householders must tackle problems of home network maintenance. Often they lack the technical knowledge or motivation to complete these tasks, making the user experience of home network maintenance frustrating. In response to these difficulties, many householders rely on handwritten reminders or interactive networking tools that are ill-suited for the home environment. In this paper, we seek to understand how to design better home network management tools through a study of sketches created by 40 people in 18 households. In our study, we obtained information about householders' knowledge, practices and needs with respect to home networking. Based on our results, we present guidelines for transforming the user experience of home network management.
Keywords: home networks; sketching; troubleshooting

Multi-biometric cohort analysis for biometric fusion - Aggarwal,G.; Ratha,N. K; Bolle, R.M.; Chellapa, Rama (Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on, 2008)
Biometric matching decisions have traditionally been made based solely on a score that represents the similarity of the query biometric to the enrolled biometric(s) of the claimed identity. Fusion schemes have been proposed to benefit from the availability of multiple biometric samples (e.g., multiple samples of the same fingerprint) or multiple different biometrics (e.g., face and fingerprint). These commonly adopted fusion approaches rarely make use of the large number of non-matching biometric samples available in the database in the form of other enrolled identities or training data. In this paper, we study the impact of combining this information with the existing fusion methodologies in a cohort analysis framework. Experimental results are provided to show the usefulness of such a cohort-based fusion of face and fingerprint biometrics.
Keywords: (access; analysis; biometrics; biometric; biometrics; fingerprint; biometrics; multi-biometric; cohort; control); face; data; decisions; face; fusion; biometric; identification; security; MATCHING; of; recognition; fingerprint

Multi-Scale 3D Morse Complexes - Comic,L.; De Floriani, Leila (Computational Sciences and Its Applications, 2008. ICCSA '08. International Conference on, 2008)
Morse theory studies the relationship between the topology of a manifold M and the critical points of a scalar function f defined over M. Morse and Morse-Smale complexes, defined by critical points and integral lines of f, induce a subdivision of M into regions of uniform gradient flow, representing the morphology of M in a compact way. Function f can be simplified by canceling its critical points in pairs, thus simplifying the morphological representation of M, given by Morse and Morse-Smale complexes of f. Here, we propose a compact representation for the two Morse complexes in 3D, which is based on encoding the incidence relations of their cells, and on exploiting the duality among the complexes. We define cancellation operations, and their inverse expansion operations, on the Morse complexes and on their dual representation. We propose a multi-scale representation of the Morse complexes which provides a description of such complexes, and thus of the morphology of a 3D scalar field, at different levels of abstraction. This representation allows us also to perform selective refinement operations to extract description of the complexes which varies in different parts of the domain, thus improving efficiency on large data sets, and eliminating the noise in the data through topology simplification.
Keywords: (mathematics); inverse; 3D; analysis; duality; complexes; topology; data; computing; topology; critical; expansion; lines; inverse; morphology; mathematics; Morse; operations; morphology; multi-scale; points; duality; integral; problems; mathematical

New records of phytoplankton for Bangladesh. 2. Cryptophyceae and Synurophyceae - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Botany, 2008)
This study presents two species of Rhodomonas, four species of Chroomonas, six species of Cryptomonas and Cryptochrysis minor, Cyanomonas coeruleus, Chrysodidymus synuroideus and Mallomonas akrokomos. These species have been reported from some ponds of Mathbaria in Pirojpur and Bakerganj of Barisal district in Bangladesh.

New records of phytoplankton for Bangladesh. 5. Euglena, Euglenocapsa - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Plant Taxonomy, 2008)
This study presents 20 taxa of the genus Euglena and one species of the rare euglenoid genus Euglenocapsa. All these taxa are reported for the first time from some pond ecosystems of Mathbaria in Pirojpur and Bakerganj of Barisal districts of Bangladesh.

New records of phytoplankton for Bangladesh. 7. Phacus spp. - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Botany, 2008)
Thirteen species of Phacus hitherto not reported from Bangladesh have been described and illustrated. Freshwater ponds at southern districts of Pirojpur and Barisal revealed these presence of the species.

New records of phytoplankton for Bangladesh. 8. Trachelomonas Ehr. (Euglenophyceae) - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Botany, 2008)
Investigation of pelagic plankton communities from some freshwater ponds of Pirojpur and Barisal districts revealed the presence of 17 species under the genus Trachelomonas Ehr. for the first time in Bangladesh.

A Non-generative Approach for Face Recognition Across Aging - Biswas,S.; Aggarwal,G.; Ramanathan,N.; Chellapa, Rama (Biometrics: Theory, Applications and Systems, 2008. BTAS 2008. 2nd IEEE International Conference on, 2008)
Human faces undergo a lot of change in appearance as they age. Though facial aging has been studied for decades, it is only recently that attempts have been made to address the problem from a computational point of view. Most of these early efforts follow a simulation approach in which matching is performed by synthesizing face images at the target age. Given the innumerable different ways in which a face can potentially age, the synthesized aged image may not be similar to the actual aged image. In this paper, we bypass the synthesis step and directly analyze the drifts of facial features with aging from a purely matching perspective. Our analysis is based on the observation that facial appearance changes in a coherent manner as people age. We provide measures to capture this coherency in feature drifts. Illustrations and experimental results show the efficacy of such an approach for matching faces across age progression.
Keywords: appearance; nongenerative; approach; face; Face; image; matching; recognition; facial; recognition; image; synthesis; face

Object Detection, Tracking and Recognition for Multiple Smart Cameras - Sankaranarayanan,A. C; Veeraraghavan,A.; Chellapa, Rama (Proceedings of the IEEE, 2008)
Video cameras are among the most commonly used sensors in a large number of applications, ranging from surveillance to smart rooms for videoconferencing. There is a need to develop algorithms for tasks such as detection, tracking, and recognition of objects, specifically using distributed networks of cameras. The projective nature of imaging sensors provides ample challenges for data association across cameras. We first discuss the nature of these challenges in the context of visual sensor networks. Then, we show how real-world constraints can be favorably exploited in order to tackle these challenges. Examples of real-world constraints are (a) the presence of a world plane, (b) the presence of a three-dimiensional scene model, (c) consistency of motion across cameras, and (d) color and texture properties. In this regard, the main focus of this paper is towards highlighting the efficient use of the geometric constraints induced by the imaging devices to derive distributed algorithms for target detection, tracking, and recognition. Our discussions are supported by several examples drawn from real applications. Lastly, we also describe several potential research problems that remain to be addressed.
Keywords: algorithm; geometric; analysis; image; association; distributed; camera; visual; cameras; cameras; object; colour; constraints; imaging; data; detection; object; detection; sensor; detection; three-dimiensional; fusion; target; model; video; network; distributed; recognition; object; scene; sensor; sensor; multiple; sensors; geometry; image; sensors; object; smart; texture; intelligent; tracking; target; tracking; video

Occurrence and Expression of Luminescence in Vibrio Cholerae - Grim,Christopher J.; Taviani,Elisa; Alam,Munirul; Huq,Anwar; Sack,R. Bradley; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2008)
Several species of the genus Vibrio, including Vibrio cholerae, are bioluminescent or contain bioluminescent strains. Previous studies have reported that only 10% of V. cholerae strains are luminescent. Analysis of 224 isolates of non-O1/non-O139 V. cholerae collected from Chesapeake Bay, MD, revealed that 52% (116/224) were luminescent when an improved assay method was employed and 58% (130/224) of isolates harbored the luxA gene. In contrast, 334 non-O1/non-O139 V. cholerae strains isolated from two rural provinces in Bangladesh yielded only 21 (6.3%) luminescent and 35 (10.5%) luxA+ isolates. An additional 270 clinical and environmental isolates of V. cholerae serogroups O1 and O139 were tested, and none were luminescent or harbored luxA. These results indicate that bioluminescence may be a trait specific for non-O1/non-O139 V. cholerae strains that frequently occur in certain environments. Luminescence expression patterns of V. cholerae were also investigated, and isolates could be grouped based on expression level. Several strains with defective expression of the lux operon, including natural K variants, were identified.

An ontology based approach for activity recognition from video - Akdemir,Umut; Turaga,Pavan; Chellapa, Rama (Proceedings of the 16th ACM international conference on Multimedia, 2008)
Representation and recognition of human activities is an important problem for video surveillance and security applications. Considering the wide variety of settings in which surveillance systems are being deployed, it is necessary to create a common knowledge-base or ontology of human activities. Most current attempts at ontology design in computer vision for human activities have been empirical in nature. In this paper, we present a more systematic approach to address the problem of designing ontologies for visual activity recognition. We draw on general ontology design principles and adapt them to the specific domain of human activity ontologies. Then, we discuss qualitative evaluation principles and provide several examples from existing ontologies and how they can be improved upon. Finally, we demonstrate quantitatively in terms of recognition performance, the efficacy and validity of our approach for bank and airport tarmac surveillance domains.
Keywords: activity ontologies; visual surveillance

Optimal Multi-View Fusion of Object Locations - Sankaranarayanan,A. C; Chellapa, Rama (Motion and video Computing, 2008. WMVC 2008. IEEE Workshop on, 2008)
In surveillance applications, it is common to have multiple cameras observing targets exhibiting motion on a ground plane. Tracking and estimation of the location of a target on the plane becomes an important inference problem. In this paper, we study the problem of combining estimates of location obtained from multiple cameras. We model the relation between the uncertainty in the location estimation to the position and location of the camera with respect to the plane (which is encoded by a 2D projective transformation). This is addressed by a theoretical study of the properties of a random variable under a projective transformation and analysis of the geometric setting when the moments of the transformed random variable exist. In this context, we prove that ground plane tracking near the horizon line is often inaccurate. Using suitable approximations to compute the moments, a minimum variance estimator is designed to fuse the multi-camera location estimates. Finally, we present experimental results that illustrate the importance of such modeling in location estimation and tracking.
Keywords: control; surveillance; tracking; detection; position; estimates; optimal; estimation; location; estimation; multicamera; estimation; object; estimator; motion; fusion; surveillance; cameras; estimation; location; multiview; theory; motion; tracking; minimum; variance

Pose and Illumination Issues in Face-and Gait-Based Identification - Chellapa, Rama; Aggarwal,G. (Advances in Biometrics, 2008)
Although significant work has been done in the field of face- and gait- based recognition, the performance of the state-of-the-art recognition algorithms is not good enough to be effective in operational systems. Most algorithms do reasonably well for controlled images but are susceptible to changes in illumination conditions and pose. This has shifted the focus of research to more challenging tasks of obtaining better performance for uncontrolled realistic scenarios. In this chapter, we discuss several recent advances made to achieve this goal.

Recognition of Humans and their Activities using Statistical analysis on Stiefel and Grassmann Manifolds - Turaga,P.; Veeraraghavan,A.; Chellapa, Rama (Red, 2008)
Many applications in computer vision involve learning and recognition of patterns from exemplars which lie on certainmanifolds. Given a database of examples and a query, the following two questions are usually addressed – a) what is the ‘closest’ example to the query in the database ? b) what is the ‘most probable’ class to which the query belongs ? The answer to the first question involves study of the geometric properties of the manifold, which then leads to appropriate definitions of distance metrics on the manifold (geodesics etc). The answer to the second question involves statistical modeling of inter- and intra-class variations on the manifold. In this paper, we concern ourselves with two related manifolds that often appear in several vision applications – the Stiefel Manifold and the Grassmann Manifold. We describe statistical modeling and inference tools on these manifolds which result in significant improvements in performance over traditional distance-based classifiers. We illustrate applications to video-based face recognition and activity recognition.

Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence - Regier,J. C; Shultz,J. W; Ganley,A. R.D; Hussey,A.; Shi,D.; Ball,B.; Zwick,A.; Stajich,J. E; Cummings, Michael P.; Martin,J. W; Cunningham,CW (Syst Biol, 2008)
This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations–first codon positions encoding leucine and arginine, which were also compositionally heterogeneous–yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned–fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase support of taxonomic relationships, sequence data from 49 additional taxa for three slow genes (i.e., EF-1 alpha, EF-2, and Pol II) were combined with the various 13-taxon data sets. The 62-taxon analyses supported the results of the 13-taxon analyses and provided increased support for additional pancrustacean clades found in an earlier analysis including only EF-1 alpha, EF-2, and Pol II.

A review of overview+ detail, zooming, and focus+ context interfaces - Cockburn,A.; Karlson,A.; Bederson, Benjamin B. (ACM Computing Surveys (CSUR), 2008)

A Scalable Projective Bundle Adjustment Algorithm using the L infinity Norm - Mitra, K.; Chellapa, Rama (Computer Vision, Graphics Image Processing, 2008. ICVGIP '08. Sixth Indian Conference on, 2008)
The traditional bundle adjustment algorithm for structure from motion problem has a computational complexity of O((m+n)3) per iteration and memory requirement of O(mn(m+n)), where m is the number of cameras and n is the number of structure points. The sparse version of bundle adjustment has a computational complexity of O(m3+mn) per iteration and memory requirement of O(mn). Here we propose an algorithm that has a computational complexity of O(mn(radicm+radicn)) per iteration and memory requirement of O(max(m,n)). The proposed algorithm is based on minimizing the Linfin norm of reprojection error. It alternately estimates the camera and structure parameters, thus reducing the potentially large scale optimization problem to many small scale subproblems each of which is a quasi-convex optimization problem and hence can be solved globally. Experiments using synthetic and real data show that the proposed algorithm gives good performance in terms of minimizing the reprojection error and also has a good convergence rate.
Keywords: adjustment; algorithm; structure; bundle; complexity; convex; complexity; iteration; error; scalable; estimation; estimation; cameras; computational; Linfin; method; large; methods; parameter; norm; camera; computational; OPTIMIZATION; parameter; problem; memory; problem; projection; problem; reprojection; programming; image; projective; reconstruction; iterative; reconstruction; quasiconvex; requirement; motion; scale

Searching the world’s herbaria: A system for visual identification of plant species - Belhumeur,P.; Chen,D.; Feiner,S.; Jacobs, David W.; Kress,W.; Ling,H.; Lopez,I.; Ramamoorthi,R.; Sheorey,S.; White,S. (Computer Vision–ECCV 2008, 2008)
We describe a working computer vision system that aids in the identification of plant species. A user photographs an isolated leaf on a blank background, and the system extracts the leaf shape and matches it to the shape of leaves of known species. In a few seconds, the system displays the top matching species, along with textual descriptions and additional images. This system is currently in use by botanists at the Smithsonian Institution National Museum of Natural History. The primary contributions of this paper are: a description of a working computer vision system and its user interface for an important new application area; the introduction of three new datasets containing thousands of single leaf images, each labeled by species and verified by botanists at the US National Herbarium; recognition results for two of the three leaf datasets; and descriptions throughout of practical lessons learned in constructing this system.

Seasonal Cholera from Multiple Small Outbreaks, Rural Bangladesh - Stine,O. Colin; Alam,Munirul; Tang,Li; Nair,G. Balakrish; Siddique,A. Kasem; Faruque,Shah M.; Huq,Anwar; Rita R Colwell; Sack,R. Bradley; Morris,J. Glenn (Emerging Infectious DiseasesEmerg Infect Dis, 2008)
Clinical and environmental Vibrio cholerae organisms collected from February 2004 through April 2005 were systematically isolated from 2 rural Bangladeshi locales. Their genetic relatedness was evaluated at 5 loci that contained a variable number of tandem repeats (VNTR). The observed minimal overlap in VNTR patterns between the 2 communities was consistent with sequential, small outbreaks from local sources.

Sequence diversity and evolution of multigene families in Trypanosoma cruzi - Cerqueira,Gustavo C.; Bartholomeu,Daniella C.; DaRocha,Wanderson D.; Hou,Lihua; Freitas-Silva,Danielle M.; Machado,Carlos Renato; El‐Sayed, Najib M.; Teixeira,Santuza M.R. (Molecular and Biochemical Parasitology, 2008)
Several copies of genes belonging to three multigene families present in the genome of Trypanosoma cruzi were sequenced and comparatively analyzed across six different strains of the parasite belonging to the T. cruzi I lineage (Colombiana, Silvio X10 and Dm28c), the T. cruzi II lineage (Esmeraldo and JG) and a hybrid strain (CL Brener). For all three gene families analyzed, our results support the division in T. cruzi I and II lineages. Furthermore, in agreement with its hybrid nature, sequences derived from the CL Brener clone clustered together with T. cruzi II sequences as well as with a third group of sequences. Paralogous sequences encoding Amastin, an amastigote surface glycoprotein and TcAG48, an antigenic RNA binding protein, which are clustered in the parasite genome, present higher intragenomic variability in T. cruzi II and CL Brener strains, when compared to T. cruzi I strains. Paralogous sequences derived from the TcADC gene family, which encode various isoforms of adenylyl cyclases and are dispersed throughout the T. cruzi genome, exhibit similar degree of variability in all strains, except in the CL Brener strain, in which the sequences were more divergent. Several factors including mutation rates and gene conversion mechanisms, acting differently within the T. cruzi population, may contribute to create such distinct levels of sequence diversity in multigene families that are clustered in the T. cruzi genome.
Keywords: Amastin; Gene conversion; Genetic diversity; Multigene families; Trypanosoma cruzi

Sequential Kernel Density Approximation and Its Application to Real-Time Visual Tracking - Han,Bohyung; Comaniciu, D.; Zhu,Ying; Davis, Larry S. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2008)
Visual features are commonly modeled with probability density functions in computer vision problems, but current methods such as a mixture of Gaussians and kernel density estimation suffer from either the lack of flexibility by fixing or limiting the number of Gaussian components in the mixture or large memory requirement by maintaining a nonparametric representation of the density. These problems are aggravated in real-time computer vision applications since density functions are required to be updated as new data becomes available. We present a novel kernel density approximation technique based on the mean-shift mode finding algorithm and describe an efficient method to sequentially propagate the density modes over time. Although the proposed density representation is memory efficient, which is typical for mixture densities, it inherits the flexibility of nonparametric methods by allowing the number of components to be variable. The accuracy and compactness of the sequential kernel density approximation technique is illustrated by both simulations and experiments. Sequential kernel density approximation is applied to online target appearance modeling for visual tracking, and its performance is demonstrated on a variety of videos.
Keywords: Automated; Reproducibility of Results; Sensitivity and Specificity; Statistical Distributions; Subtraction Technique; Computer-Assisted; Models; Gaussian estimation; kernel density estimation; mean-shift mode finding algorithm; online target appearance modeling; probability density function; real-time computer vision application; real-time visual tracking; sequential kernel density approximation; visual f; Statistical; Motion; Pattern Recognition

Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure - Fermin,David R.; Barac,Ana; Lee,Sangjin; Polster,Sean P.; Hannenhalli, Sridhar; Bergemann,Tracy L.; Grindle,Suzanne; Dyke,David B.; Pagani,Francis; Miller,Leslie W.; Tan,Sarah; dos Remedios,Cris; et al. (Circulation: Cardiovascular Genetics, 2008)
Background— We report the first comprehensive analysis of gene expression differences by sex and age in left ventricular samples from 102 patients with dilated cardiomyopathy.Methods and Results— Gene expression data (HG-U133A gene chip, Affymetrix) were analyzed from 30 females and 72 males from 3 separate centers. More than 1800 genes displayed sexual dimorphism in the heart (adjusted P value <0.05). A significant number of these genes were highly represented in gene ontology pathways involved in ion transport and G-protein-coupled receptor signaling. Localization of these genes revealed enrichment on both the sex chromosomes as well as chromosomes 3, 4, and 14. The second goal of this study was to determine the effect of age on gene expression. Within the female cohort, >140 genes were differentially expressed in the <55 years age group compared with the >55 years age group. These genes were highly represented in gene ontology pathways involved in DNA damage. In contrast, zero genes in the male cohort <55 years met statistical significance when compared with the >55 years age group.Conclusions— Gene expression in dilated cardiomyopathy displayed evidence of sexual dimorphism similar to other somatic tissues and age dimorphism within the female cohort.

Shape-and-Behavior Encoded Tracking of Bee Dances - Veeraraghavan,A.; Chellapa, Rama; Srinivasan, M. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2008)
Behavior analysis of social insects has garnered impetus in recent years and has led to some advances in fields like control systems and flight navigation. Manual labeling of insect motions required for analyzing the behaviors of insects requires significant investment of time and effort. In this paper, we propose certain general principles that help in simultaneous automatic tracking and behavior analysis, with applications in tracking bees and recognizing specific behaviors that they exhibit. The state space for tracking is defined using the position, orientation, and current behavior of the insect being tracked. The position and the orientation are parameterized using a shape model, whereas the behavior is explicitly modeled using a three-tier hierarchical motion model. The first tier (dynamics) models the local motions exhibited, and the models built in this tier act as a vocabulary for behavior modeling. The second tier is a Markov motion model built on top of the local motion vocabulary, which serves as the behavior model. The third tier of the hierarchy models the switching between behaviors, and this is also modeled as a Markov model. We address issues in learning the three-tier behavioral model, in discriminating between models, and in detecting and modeling abnormal behaviors. Another important aspect of this work is that it leads to joint tracking and behavior analysis instead of the traditional "track-and-then-recognize" approach. We apply these principles for tracking bees in a hive while they are executing the waggle dance and the round dance.
Keywords: Automated; Reproducibility of Results; Sensitivity and Specificity; Social Behavior; Computer-Assisted; Imaging; Markov model; bee dance; behavior analysis; shape model; social insect; three-tier hierarchical motion model; tracking; video sequence; waggle dance; Markov processes; image sequences; optical tracking; video signal processing; zoology; Algorithms; Animal Communication; Three-Dimensional; Information Storage and Retrieval; Male; Pattern Recognition

Silent Sputnik - Rita R Colwell (BioScience, 2008)

A simple binomial test for estimating sequencing errors in public repository 16S rRNA sequences - Zo,Young-Gun; Rita R Colwell (Journal of Microbiological Methods, 2008)
Sequences in public databases may contain a number of sequencing errors. A double binomial model describing the distribution of indel-excluded similarity coefficients (S) among repeatedly sequenced 16S rRNA was previously developed and it produced a confidence interval of S useful for testing sequence identity among sequences of 400-bp length. We characterized patterns in sequencing errors found in nearly complete 16S rRNA sequences of Vibrionaceae as highly variable in reported sequence length and containing a small number of indels. To accommodate these characteristics, a simple binomial model for distribution of the similarity coefficient (H) that included indels was derived from the double binomial model for S. The model showed good fit to empirical data. By using either a pre-determined or bootstrapping estimated standard probability of base matching, we were able to use the exact binomial test to determine the relative level of sequencing error for a given pair of duplicated sequences. A limitation of the method is the requirement that duplicated sequences for the same template sequence be paired, but this can be overcome by using only conserved regions of 16S rRNA sequences and pairing a given sequence with its highest scoring BLAST search hit from the nr database of GenBank.
Keywords: 16S rRNA; Binomial model; Sequence similarity coefficient; Sequencing error; SSU rRNA

Statistical analysis on Stiefel and Grassmann manifolds with applications in computer vision - Turaga,P.; Veeraraghavan,A.; Chellapa, Rama (Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on, 2008)
Many applications in computer vision and pattern recognition involve drawing inferences on certain manifold-valued parameters. In order to develop accurate inference algorithms on these manifolds we need to a) understand the geometric structure of these manifolds b) derive appropriate distance measures and c) develop probability distribution functions (pdf) and estimation techniques that are consistent with the geometric structure of these manifolds. In this paper, we consider two related manifolds - the Stiefel manifold and the Grassmann manifold, which arise naturally in several vision applications such as spatio-temporal modeling, affine invariant shape analysis, image matching and learning theory. We show how accurate statistical characterization that reflects the geometry of these manifolds allows us to design efficient algorithms that compare favorably to the state of the art in these very different applications. In particular, we describe appropriate distance measures and parametric and non-parametric density estimators on these manifolds. These methods are then used to learn class conditional densities for applications such as activity recognition, video based face recognition and shape classification.
Keywords: algorithm; learning; analysis; computer; analysis; statistical; analysis; video; based; classification; image; classification; spatio-temporal; distribution; distributions; Face; functions; shape; Grassmann; invariant; manifold; activity; manifold; Stiefel; matching; inference; matching; spatiotemporal; measures; estimation; modeling; statistical; parameters; pattern; phenomena; statistical; recognition; affine; recognition; computer; recognition; probability; SHAPE; structure; image; technique; geometric; theory; manifold-valued; vision; distance; vision; image

Stochastic fusion of multi-view gradient fields - Sankaranarayanan,A. C; Chellapa, Rama (Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on, 2008)
Image gradients form powerful cues in a host of vision and graphics applications. In this paper, we consider multiple views of a textured planar scene and consider the problem of estimating the scene texture map using these multi-view inputs. Modeling each camera view as a projective transformation of the scene, we show that the problem is equivalent to that of studying the effect of noise (and the projective imaging) on the gradient fields induced by this texture map. We show that these noisy gradient fields can be modeled as complete observers of the scene radiance. Further, the corrupting noise can be shown to be additive and linear, although spatially varying. However, the specific form of the noise term can be exploited to design linear estimators that fuse the gradient fields obtained from each of the individual views. The fused gradient field forms a robust estimate of the scene gradients and can be used for scene reconstruction.
Keywords: application; brightness; cameras; gradient; application; image; camera; estimators; multiview; fields; projective; fusion; image; fusion; textured; gradient; gradients; linear; gradients; scene; imaging; scene; map; stochastic; methods; image; noise; graphics; planar; radiance; scene; reconstruction; image; reconstruction; scene; scene; vision; TEXTURE; texture; view; corrupting

Synthesis of Silhouettes and Visual Hull Reconstruction for Articulated Humans - Yue,Zhanfeng; Chellapa, Rama (Multimedia, IEEE Transactions on, 2008)
In this paper, we propose a complete framework for improved synthesis and understanding of the human pose from a limited number of silhouette images. It combines the active image-based visual hull (IBVH) algorithm and a contour-based body part segmentation technique. We derive a simple, approximate algorithm to decide the extrinsic parameters of a virtual camera, and synthesize the turntable image collection of the person using the IBVH algorithm by actively moving the virtual camera on a properly computed circular trajectory around the person. Using the turning function distance as the silhouette similarity measurement, this approach can be used to generate the desired pose-normalized images for recognition applications. In order to overcome the inability of the visual hull (VH) method to reconstruct concave regions, we propose a contour-based human body part localization algorithm to segment the silhouette images into convex body parts. The body parts observed from the virtual view are generated separately from the corresponding body parts observed from the input views and then assembled together for a more accurate VH reconstruction. Furthermore, the obtained turntable image collection helps to improve the body part segmentation and identification process. By using the inner distance shape context (IDSC) measurement, we are able to estimate the body part locations more accurately from a synthesized view where we can localize the body part more precisely. Experiments show that the proposed algorithm can greatly improve body part segmentation and hence shape reconstruction results.
Keywords: active; algorithm; articulated; algorithm; inner; body; camera; visual; collection; virtual; computation; contour-based; Context; detection; image; distance; distance; turntable; estimation; shape; function; hull; human; image; image; approximate; localization; measurement; silhouette; measurement; turning; part; pose; circular; reality; recognition; virtual; reconstruction; approximation; reconstruction; image; segmentation; segmentation; pose; SHAPE; similarity; synthesis; silhouette; technique; human; theory; cameras; edge; Trajectory

Transesterification activity of a novel lipase from Acinetobacter venetianus RAG-1 - Snellman,E. A.; Rita R Colwell (Antonie van Leeuwenhoek, 2008)
Transesterification activity and the industrial potential of a novel lipase prepared from Acinetobacter ventiatus RAG-1 were evaluated. Purified lipase samples were dialyzed against pH 9.0 buffer in a single optimization step prior to lyophilization. The enzyme and organic phase were pre-equilibrated (separately) to the same thermodynamic water activities (a w) ranging from a w 0.33 to 0.97. Production of 1-octyl butyrate by lipase-catalyzed transesterification of vinyl butyrate with 1-octanol in hexane was monitored by gas chromatography. Production of 1-octyl butyrate and initial rate of reaction depended on water activity. Product synthesis and rate of transesterification increased sharply with increase from a w 0.33 to 0.55. Highest product concentration (218 mM) and rate of reaction (18.7 μmol h−1 · 10 μg protein) were measured at a w 0.86. Transesterification activity in hexane represented 32% of comparable hydrolytic activity in aqueous buffer.

Understanding the High-Performance-Computing Community: A Software Engineer's Perspective - Basili, Victor R.; Carver, J. C; Cruzes, D.; Hochstein, L. M; Hollingsworth, Jeffrey K; Shull, F.; Zelkowitz, Marvin V (Software, IEEE, 2008)
Computational scientists developing software for HPC systems face unique software engineering issues. Attempts to transfer SE technologies to this domain must take these issues into account.
Keywords: community; software; computational; engineering; engineering; software; Science; software; high-performance-computing

On the Use of Security Metrics Based on Intrusion Prevention System Event Data: An Empirical Analysis - Chrun,D.; Michel Cukier; Sneeringer,G. (2008)
With the increasing number of attacks on the Internet, a primary concern for organizations is the protection of their network. To do so, organizations install security devices such as intrusion prevention systems to monitor network traffic. However, data that are collected by these devices are often imperfect. The contribution of this paper is to try to define some practical metrics based on imperfect data collected by an intrusion prevention system. Since attacks greatly differ, we propose to group the attacks into several attack type groups. We then define a set of metrics for each attack type group. We introduce an approach that consists in analyzing the evolution of these metrics per attack type group by focusing on outliers in order to give an insight into an organizationpsilas security. The method is assessed for an organization of about 40,000 computers. The results were encouraging: outliers could be related to security issues that, in some cases, had not been previously flagged.
Keywords: empirical analysis; Internet; Internet attack group; intrusion prevention system event data; network traffic monitoring; organization security metrics; security of data

Vibrio cholerae non‐O1, non‐O139 strains isolated before 1992 from Varanasi, India are multiple drug resistant, contain intSXT, dfr18 and aadA5 genes - Mohapatra,Harapriya; Mohapatra,Saswat S.; Mantri,Chinmay K.; Rita R Colwell; Singh,Durg V. (Environmental Microbiology, 2008)
In this study, we report the presence of the SXT element and Class I integron in Vibrio cholerae non-O1, non-O139 strains isolated from Varanasi, India. Isolates were resistant to cotrimoxazole, trimethoprim and/or streptomycin, furazolidone and ampicillin. None contained plasmids. Polymerase chain reaction (PCR) and DNA sequencing revealed the presence of antibiotic resistance gene cassettes, aadA1, aadA2, aadA5 and dfrA15, in the Class I integron and SXT, an integrative conjugative element containing dfr18, sulII and strAB, in three and six of the isolates respectively. Conjugation experiments, followed by PCR analysis of transconjugants, provided evidence for the transferable nature of intSXT and associated antibiotic resistance gene cassettes. This is the first report of the occurrence of SXT ICE, dfr18, sulII, strAB and aadA5 genes in environmental V. cholerae non-O1, non-O139 strains from Varanasi, India, that had been isolated before 1992.

Video stabilization and mosaicing - Ramachandran, M.; Veeraraghavan,A.; Chellapa, Rama (The Essential Guide to Video Processing,, 2008)

Virtual access points for vehicular networks - Frangiadakis,N.; Câmara,D.; Filali,F.; Loureiro,A. A.F; Roussopoulos, Nick (Proceedings of the 1st international conference on MOBILe Wireless MiddleWARE, Operating Systems, and Applications, 2008)

Visualizing Functional Data with an Application to eBay’s Online Auctions - Chen,Chun-houh; Härdle,Wolfgang; Unwin,Antony; Jank,Wolfgang; Shmueli,Galit; Plaisant, Catherine; Shneiderman, Ben (Handbook of Data VisualizationHandbook of Data Visualization, 2008)
Technological advances in the measurement, collection, and storage of data have led tomore andmore complex data structures. Examples of such structures include measurements of the behavior of individuals over time, digitized two- or three-dimensional images of the brain, and recordings of three- or even four-dimensional movements of objects traveling through space and time. Such data, although recorded in a discrete fashion, are usually thought of as continuous objects that are represented by functional relationships. This gave rise to functional data analysis (FDA), which was made popular by the monographs of Ramsay and Silverman (1997, 2002), where the center of interest is a set of curves, shapes, objects, or, more generally, a set of functional observations , in contrast to classical statistics where interest centers on a set of data vectors. In that sense, functional data is not only different from the data structure studied in classical statistics, but it actually generalizes it. Many of these new data structures require new statistical methods to unveil the information that they carry.

A Weighted GCV Method for Lanczos Hybrid Regularization - Chung,Julianne; Nagy,James G.; O'Leary, Dianne P. (Electronic Transactions on Numerical Analysis, 2008)

Appearance Characterization of Linear Lambertian Objects, Generalized Photometric Stereo, and Illumination-Invariant Face Recognition - Zhou,S. K; Aggarwal,G.; Chellapa, Rama; Jacobs, David W. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2007)
Traditional photometric stereo algorithms employ a Lambertian reflectance model with a varying albedo field and involve the appearance of only one object. In this paper, we generalize photometric stereo algorithms to handle all appearances of all objects in a class, in particular the human face class, by making use of the linear Lambertian property. A linear Lambertian object is one which is linearly spanned by a set of basis objects and has a Lambertian surface. The linear property leads to a rank constraint and, consequently, a factorization of an observation matrix that consists of exemplar images of different objects (e.g., faces of different subjects) under different, unknown illuminations. Integrability and symmetry constraints are used to fully recover the subspace bases using a novel linearized algorithm that takes the varying albedo field into account. The effectiveness of the linear Lambertian property is further investigated by using it for the problem of illumination-invariant face recognition using just one image. Attached shadows are incorporated in the model by a careful treatment of the inherent nonlinearity in Lambert's law. This enables us to extend our algorithm to perform face recognition in the presence of multiple illumination sources. Experimental results using standard data sets are presented
Keywords: albedo field; appearance characterization; generalized photometric stereo algorithms; illumination-invariant face recognition; linear Lambertian objects; observation matrix factorization; face recognition; matrix decomposition; Algorithms; Artificial Intelligence; Automated; Photogrammetry; Reproducibility of Results; Sensitivity and Specificity; Computer-Assisted; Information Storage and Retrieval; Lighting; Linear Models; Pattern Recognition

Applying Software Reliability Models on Security Incidents - Condon,E.; Michel Cukier; He,Tao (2007)
Computer and network security incidents have increasing financial consequences as demand for network accessibility and connectivity to resources continues to rise. These security incidents can lead to direct financial losses either through data theft of personal and/or proprietary information as well as a reputational damage which may negatively impact stock prices or consumer confidence in a company. This paper examines a large set of security incident data using tools from the software reliability community. We look at applying Non-Homogenous Poisson Process (NHPP) models as a method for describing the reliability growth process. We examine the full set of incidents as well as subsets of the data based on incident types. We look at using the Laplace test to guide selection of the appropriate models. Then, based on the trend results, we apply various NHPP models (i.e., Goel-Okumutu, S-Shaped, Duane, and K-Stage Curve) to illustrate the relevance of using these models to fit the incident data and to predict future incidents.
Keywords: computer security incidents; consumer confidence; data theft; network security incidents; nonhomogenous Poisson process; reliability growth process; reputational damage; security of data; software reliability; stock prices

Archetypal behavior in computer security - Rosenfeld,Shalom N.; Rus,Ioana; Michel Cukier (Journal of Systems and Software, 2007)
The purpose of this study is to understand observed behavior and to diagnose and find solutions to issues encountered in organizational computer security using a systemic approach, namely system archetypes. In this paper we show the feasibility of archetypes application and the benefits of simulation. We developed a model and simulation of some aspects of security based on system dynamics principles. The system dynamics simulation model can be used in support of decision-making, training, and teaching regarding the mitigation of computer security risks. In this paper, we combine two archetypes and show the computer security relevance of such combinations. Presented are instances of the archetypes “Escalation”, in which an organization must continuously increase its efforts to counter additional attacker effort; and “Limits to Growth”, in which the gains from an organization’s security efforts plateau or decline due to its limited capacity for security-related tasks. We describe a scenario where these archetypes (individually and combined) can help in diagnosis and understanding, and present simulation of “what-if” scenarios suggesting how an organization might remedy these problems and maximize its gains from security efforts.
Keywords: Attacks and countermeasures; Escalation; Limits to Growth; Organization computer security; System archetypes; System dynamics; System dynamics modeling and simulation

Association of Vibrio Cholerae O1 El Tor and O139 Bengal with the Copepods Acartia Tonsa and Eurytemora Affinis - Rawlings,Tonya K.; Ruiz,Gregory M.; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2007)
The association of Vibrio cholerae with zooplankton has been suggested as an important factor in transmission of human epidemic cholera, and the ability to colonize zooplankton surfaces may play a role in the temporal variation and predominance of the two different serogroups (V. cholerae O1 El Tor and O139) in the aquatic environment. To date, interactions between specific serogroups and species of plankton remain poorly understood. Laboratory microcosm experiments were carried out to compare quantitatively the colonization of two copepod species, Acartia tonsa and Eurytemora affinis, by each of the epidemic serogroups. V. cholerae O1 consistently achieved higher abundances than V. cholerae O139 in colonizing adults of each copepod species as well as the multiple life stages of E. affinis. This difference in colonization may be significant in the general predominance of V. cholerae O1 in cholera epidemics in rural Bangladesh where water supplies are taken directly from the environment.

A Bayesian model for discovering typological implications - Daumé, Hal; Campbell,L. (ANNUAL MEETING-ASSOCIATION FOR COMPUTATIONAL LINGUISTICS, 2007)

Biased data reduce efficiency and effectiveness of conservation reserve networks - Grand,Joanna; Cummings, Michael P.; Rebelo,Tony G; Ricketts,Taylor H; Neel,Maile C (Ecology Letters, 2007)
Complementarity-based reserve selection algorithms efficiently prioritize sites for biodiversity conservation, but they are data-intensive and most regions lack accurate distribution maps for the majority of species. We explored implications of basing conservation planning decisions on incomplete and biased data using occurrence records of the plant family Proteaceae in South Africa. Treating this high-quality database as ‘complete’, we introduced three realistic sampling biases characteristic of biodiversity databases: a detectability sampling bias and two forms of roads sampling bias. We then compared reserve networks constructed using complete, biased, and randomly sampled data. All forms of biased sampling performed worse than both the complete data set and equal-effort random sampling. Biased sampling failed to detect a median of 1–5% of species, and resulted in reserve networks that were 9–17% larger than those designed with complete data. Spatial congruence and the correlation of irreplaceability scores between reserve networks selected with biased and complete data were low. Thus, reserve networks based on biased data require more area to protect fewer species and identify different locations than those selected with randomly sampled or complete data.
Keywords: Bias; biodiversity conservation; complementarity; efficiency; marxan; rarity; reserve networks; reserve selection algorithms; species detection

Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences - Lee,S.; Wang,T. D; Hashmi,N.; Cummings, Michael P. (Future Generation Comp Syst, 2007)
Life science research is becoming evermore computationally intensive. Hence, from a computational resource perspective, Grid computing provides a logical approach to meeting many of the computational needs of life science research. However, there are several barriers to the widespread use of Grid computing in life sciences. In this paper, we attempt to address one particular barrier: the difficulty of using Grid computing by life scientists. Life science research often involves connecting multiple applications together to form a workflow. This process of constructing a workflow is complex. When combined with the difficulty of using Grid services, composing a meaningful workflow using Grid services can present a challenge to life scientists. Our proposed solution is a Semantic Web-enabled computing environment, called Bio-STEER. In BioSTEER, bioinformatics Grid services are mapped to Semantic Web services, described in OWL-S. We also defined an ontology in OWL to model bioinformatics applications. A graphical user interface helps to construct a scientific workflow by showing a list of services that are semantically sound: that is, the output of one service is semantically compatible with the input of the connecting service. Bio-STEER can help users take full advantaue of Grid services through a user-friendly graphical user interface (GUI), which allows them to easily construct the workflows they need. (c) 2006 Elsevier B.V. All rights reserved.
Keywords: client/server; distributed; environments; integrated; interface; management; semantics; services; systems; user; web-base; workflow

Bridging art and science with creativity support tools - Shneiderman, Ben; Rita R Colwell; Diamond,Sara; Greenhalgh,Paul; Wulf,William (Proceedings of the 6th ACM SIGCHI conference on Creativity & cognition, 2007)

Bridging the ROUGE/Human Evaluation Gap in Multi-Document Summarization - Conroy,John M.; Schlesinger,Judith D.; O'Leary, Dianne P. (Document Understanding Conference DUC 2007Document Understanding Conference DUC 2007, 2007)

Chosen-ciphertext security from identity-based encryption - Boneh,D.; Canetti,R.; Halevi,S.; Katz, Jonathan (SIAM Journal on Computing, 2007)
We propose simple and efficient CCA-secure public-key encryption schemes (i.e., schemessecure against adaptive chosen-ciphertext attacks) based on any identity-based encryption (IBE) scheme. Our constructions have ramifications of both theoretical and practical interest. First, our schemes give a new paradigm for achieving CCA-security; this paradigm avoids “proofs of well-formedness” that have been shown to underlie previous constructions. Second, instantiating our construction using known IBE constructions we obtain CCA-secure encryption schemes whose performance is competitive with the most efficient CCA-secure schemes to date. Our techniques extend naturally to give an efficient method for securing IBE schemes (even hierarchical ones) against adaptive chosen-ciphertext attacks. Coupled with previous work, this gives the first efficient constructions of CCA-secure IBE schemes.

Coarse-to-Fine Event Model for Human Activities - Cuntoor, N.P.; Chellapa, Rama (Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on, 2007)
We analyze coarse-to-fine hierarchical representation of human activities in video sequences. It can be used for efficient video browsing and activity recognition. Activities are modeled using a sequence of instantaneous events. Events in activities can be represented in a coarse-to-fine hierarchy in several ways, i.e., there may not be a unique hierarchical structure. We present five criteria and quantitative measures for evaluating their effectiveness. The criteria are minimalism, stability, consistency, accessibility and applicability. It is desirable to develop activity models that rank highly on these criteria at all levels of hierarchy. In this paper, activities are represented as sequence of event probabilities computed using the hidden Markov model framework. Two aspects of hierarchies are analyzed: the effect of reduced frame rate on the accuracy of events detected at a finer scale; and the effect of reduced spatial resolution on activity recognition. Experiments using the UCF indoor human action dataset and the TSA airport tarmac surveillance dataset show encouraging results
Keywords: action; activities; spatial; airport; browsing; video; dataset; activity; dataset; UCF; event; framework; human; human; indoor; Markov; model; model; event; models; image; probabilities; hidden; processing; recognition; coarse-to-fine; reduction; video; representation; image; resolution; resolution; image; sequences; hidden; sequences; stability; video; signal; Surveillance; tarmac; TSA

Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei - Djikeng,A.; Raverdy,S.; Foster, Jeffrey S.; Bartholomeu,D.; Zhang,Y.; El‐Sayed, Najib M.; Carlow,C. (Parasitology research, 2007)

Combining provenance and security policies in a web-based document management system - Corcoran,B.J.; Swamy,N.; Hicks, Michael W. (On-line Proceedings of the Workshop on Principles of Provenance (PrOPr), 2007)