RDF and RDF Schema are two W3C standards aimed at enriching the Web with machine-processable semantic data.

We provide formal definitions and efficient secure techniques for • turning noisy information into keys usable for any cryptographic application, and, in particular, • reliably and securely authenticating biometric data. Our techniques apply not just to biometric information, but to any keying material that, unlike traditional cryptographic keys, is (1) not reproducible precisely and (2) not distributed uniformly. We propose two primitives: a fuzzy extractor reliably extracts nearly uniform randomness R from its input; the extraction is error-tolerant in the sense that R will be the same even if the input changes, as long as it remains reasonably close to the original. Thus, R can be used as a key in a cryptographic application. A secure sketch produces public information about its input w that does not reveal w, and yet allows exact recovery of w given another value that is close to w. Thus, it can be used to reliably reproduce error-prone biometric inputs without incurring the security risk inherent in storing them. We define the primitives to be both formally secure and versatile, generalizing much prior work. In addition, we provide nearly optimal constructions of both primitives for various measures of “closeness” of input data, such as Hamming distance, edit distance, and set difference.

Recently Viola et al. [5] have introduced a rapid object detection scheme based on a boosted cascade of simple feature classifiers. In this paper we introduce a novel set of rotated haar-like features. These novel features significantly enrich the simple features of [5] and can also be calculated

Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of cDNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analysis of mappings of sequence reads to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing (AS), ∼86 % with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that a majority of AS and of alternative cleavage and polyadenylation (APA) events vary between tissues, while variation between individuals was ∼2- to 3-fold less common. Extreme or ‘switch-like ’ regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of AS and APA were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3′ UTRs suggested common involvement of specific factors in tissue-level regulation of both

Summary: The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape’s versatile visualization environment to produce an intuitive and customizable visual representation of the results.

PVS is a prototype system for writing specifications and constructing proofs. Its development has been shaped by our experiences studying or using several other systems and performing a number of rather substantial formal verifications (e.g., [5,6,8]). PVS is fully implemented and freely available. It has been used to construct proofs of nontrivial difficulty with relatively modest amounts of human effort. Here, we describe some of the motivation behind PVS and provide some details of the system. Automated reasoning systems typically fall in one of two classes: those that provide powerful automation for an impoverished logic, and others that feature expressive logics but only limited automation. PVS attempts to tread the middle ground between these two classes by providing mechanical assistance to support clear and abstract specifications, and readable yet sound proofs for difficult theorems. Our goal is to provide mechanically-checked specificati

Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metage-nomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK

Finite-state verification techniques, such as model checking, have shown promise as a cost-effective means for finding defects in hardware designs. To date, the application of these techniques to software has been hindered by several obstacles. Chief among these is the problem of constructing a finite-state model that approximates the executable behavior of the software system of interest. Current best-practice involves handconstruction of models which is expensive (prohibitive for all but the smallest systems), prone to errors (which can result in misleading verification results), and difficult to optimize (which is necessary to combat the exponential complexity of verification algorithms). In this paper, we describe an integrated collection of program analysis and transformation components, called Bandera, that enables the automatic extraction of safe, compact finite-state models from program source code. Bandera takes as input Java source code and generates a program model in the input language of one of several existing verification tools; Bandera also maps verifier outputs back to the original source code. We discuss the major components of Bandera and give an overview of how it can be used to model check correctness properties of Java programs.

Abstract not found

We present a broad extension of the conventional formalism of state machines and state diagrams, that is relevant to the specification and design of complex discrete-event systems, such as multi-computer real-time systems, communication protocols and digital control units. Our diagrams, which we call statecharts, extend conventional state-transition diagrams with essentially three olements, dealing, respectively, with the notions of hierarchy, concurrency and communication. These transform the language of state diagrams into a highly structured' and economical description language. Statecharts are thus compact and expressive--small diagrams can express complex behavior--as well as compositional and modular. When coupled with the capabilities of computerized graphics, statecharts enable viewing the description at different levels of detail, and make even very large specifications manageable and comprehensible. In fact, we intend to demonstrate here that statecharts counter many of the objections raised against conventional state diagrams, and thus appear to render specification by diagrams an attractive and plausible approach. Statecharts can be used either as a stand-alone behavioral description or as part of a more general design methodology that deals also with the system's other aspects, such as functional decomposition and data-flow specification. We also discuss some practical experience that was gained over the last three years in applying the statechart formalism to the specification of a particularly complex system.