NASA Space Engineering Research Center for VLSI systems design

This annual review reports the center's activities and findings on very large scale integration (VLSI) systems design for 1990, including project status, financial support, publications, the NASA Space Engineering Research Center (SERC) Symposium on VLSI Design, research results, and outreach programs. Processor chips completed or under development are listed. Research results summarized include a design technique to harden complementary metal oxide semiconductors (CMOS) memory circuits against single event upset (SEU); improved circuit design procedures; and advances in computer aided design (CAD), communications, computer architectures, and reliability design. Also described is a high school teacher program that exposes teachers to the fundamentals of digital logic design

Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies

<p>Abstract</p> <p>Background</p> <p>In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding antibody maturation but also for promoting the potential engineering of the therapeutic antibodies. To date, several tools have been developed to perform such "trace-back" calculations. Yet, the predicting ability and processing volume of those tools vary significantly for different sets of data. Moreover, none of them give a confidence for immunoglobulin heavy diversity (IGHD) identification. Developing fast, efficient and enhanced tools is always needed with the booming of immunological data.</p> <p>Results</p> <p>Here, a program named Ab-origin is presented. It is designed by batch query against germline databases based on empirical knowledge, optimized scoring scheme and appropriate parameters. Special efforts have been paid to improve the identification accuracy of the short and volatile region, IGHD. In particular, a threshold score for certain sensitivity and specificity is provided to give the confidence level of the IGHD identification.</p> <p>Conclusion</p> <p>When evaluated using different sets of both simulated data and experimental data, Ab-origin outperformed all the other five popular tools in terms of prediction accuracy. The features of batch query and confidence indication of IGHD identification would provide extra help to users. The program is freely available at <url>http://mpsq.biosino.org/ab-origin/supplementary.html</url>.</p

Methods in Computational Biology

Modern biology is rapidly becoming a study of large sets of data. Understanding these data sets is a major challenge for most life sciences, including the medical, environmental, and bioprocess fields. Computational biology approaches are essential for leveraging this ongoing revolution in omics data. A primary goal of this Special Issue, entitled “Methods in Computational Biology”, is the communication of computational biology methods, which can extract biological design principles from complex data sets, described in enough detail to permit the reproduction of the results. This issue integrates interdisciplinary researchers such as biologists, computer scientists, engineers, and mathematicians to advance biological systems analysis. The Special Issue contains the following sections:•Reviews of Computational Methods•Computational Analysis of Biological Dynamics: From Molecular to Cellular to Tissue/Consortia Levels•The Interface of Biotic and Abiotic Processes•Processing of Large Data Sets for Enhanced Analysis•Parameter Optimization and Measuremen

In silico strategies to improve insight in breast cancer

In clinical practice, breast cancer is currently divided into subtypes based on immunohistochemical expression of the estrogen receptor and human epidermal growth factor receptor 2. These subtypes are crucial for treatment choice and outcome. However, even within these subgroups there is great variability in tumor behavior. This variability within breast cancer subtypes should presumably have clinical implications for treatment decision-making and the potential of novel therapeutic targets. However, conducting trials to investigate treatment efficacy and validate diagnostics are costly, labor-intensive and time-consuming. Therefore, it takes a long time to translate the knowledge regarding tumor variability within breast cancer subtypes into clinical implications for patients. To speed up this translation, using low-cost tools for hypothesis-generation could be very convenient. In this thesis, we used a large database of publicly available gene expression profiles as a low-cost tool to gain insight into how to improve patient selection for systemic therapy and to explore potential new therapeutic targets for difficult to treat subtypes of breast cancer. This has led to the generation of multiple hypotheses which require further study in sets of tumors from patients participating in larger prospective, preferably randomized trials. Ultimately, these findings could contribute to the further improvement of patient outcome in early-stage breast cancer

Credibility analysis of textual claims with explainable evidence

Despite being a vast resource of valuable information, the Web has been polluted by the spread of false claims. Increasing hoaxes, fake news, and misleading information on the Web have given rise to many fact-checking websites that manually assess these doubtful claims. However, the rapid speed and large scale of misinformation spread have become the bottleneck for manual verification. This calls for credibility assessment tools that can automate this verification process. Prior works in this domain make strong assumptions about the structure of the claims and the communities where they are made. Most importantly, black-box techniques proposed in prior works lack the ability to explain why a certain statement is deemed credible or not. To address these limitations, this dissertation proposes a general framework for automated credibility assessment that does not make any assumption about the structure or origin of the claims. Specifically, we propose a feature-based model, which automatically retrieves relevant articles about the given claim and assesses its credibility by capturing the mutual interaction between the language style of the relevant articles, their stance towards the claim, and the trustworthiness of the underlying web sources. We further enhance our credibility assessment approach and propose a neural-network-based model. Unlike the feature-based model, this model does not rely on feature engineering and external lexicons. Both our models make their assessments interpretable by extracting explainable evidence from judiciously selected web sources. We utilize our models and develop a Web interface, CredEye, which enables users to automatically assess the credibility of a textual claim and dissect into the assessment by browsing through judiciously and automatically selected evidence snippets. In addition, we study the problem of stance classification and propose a neural-network-based model for predicting the stance of diverse user perspectives regarding the controversial claims. Given a controversial claim and a user comment, our stance classification model predicts whether the user comment is supporting or opposing the claim.Das Web ist eine riesige Quelle wertvoller Informationen, allerdings wurde es durch die Verbreitung von Falschmeldungen verschmutzt. Eine zunehmende Anzahl an Hoaxes, Falschmeldungen und irreführenden Informationen im Internet haben viele Websites hervorgebracht, auf denen die Fakten überprüft und zweifelhafte Behauptungen manuell bewertet werden. Die rasante Verbreitung großer Mengen von Fehlinformationen sind jedoch zum Engpass für die manuelle Überprüfung geworden. Dies erfordert Tools zur Bewertung der Glaubwürdigkeit, mit denen dieser Überprüfungsprozess automatisiert werden kann. In früheren Arbeiten in diesem Bereich werden starke Annahmen gemacht über die Struktur der Behauptungen und die Portale, in denen sie gepostet werden. Vor allem aber können die Black-Box-Techniken, die in früheren Arbeiten vorgeschlagen wurden, nicht erklären, warum eine bestimmte Aussage als glaubwürdig erachtet wird oder nicht. Um diesen Einschränkungen zu begegnen, wird in dieser Dissertation ein allgemeines Framework für die automatisierte Bewertung der Glaubwürdigkeit vorgeschlagen, bei dem keine Annahmen über die Struktur oder den Ursprung der Behauptungen gemacht werden. Insbesondere schlagen wir ein featurebasiertes Modell vor, das automatisch relevante Artikel zu einer bestimmten Behauptung abruft und deren Glaubwürdigkeit bewertet, indem die gegenseitige Interaktion zwischen dem Sprachstil der relevanten Artikel, ihre Haltung zur Behauptung und der Vertrauenswürdigkeit der zugrunde liegenden Quellen erfasst wird. Wir verbessern unseren Ansatz zur Bewertung der Glaubwürdigkeit weiter und schlagen ein auf neuronalen Netzen basierendes Modell vor. Im Gegensatz zum featurebasierten Modell ist dieses Modell nicht auf Feature-Engineering und externe Lexika angewiesen. Unsere beiden Modelle machen ihre Einschätzungen interpretierbar, indem sie erklärbare Beweise aus sorgfältig ausgewählten Webquellen extrahieren. Wir verwenden unsere Modelle zur Entwicklung eines Webinterfaces, CredEye, mit dem Benutzer die Glaubwürdigkeit einer Behauptung in Textform automatisch bewerten und verstehen können, indem sie automatisch ausgewählte Beweisstücke einsehen. Darüber hinaus untersuchen wir das Problem der Positionsklassifizierung und schlagen ein auf neuronalen Netzen basierendes Modell vor, um die Position verschiedener Benutzerperspektiven in Bezug auf die umstrittenen Behauptungen vorherzusagen. Bei einer kontroversen Behauptung und einem Benutzerkommentar sagt unser Einstufungsmodell voraus, ob der Benutzerkommentar die Behauptung unterstützt oder ablehnt

Computer Science and Technology Series : XV Argentine Congress of Computer Science. Selected papers

CACIC'09 was the fifteenth Congress in the CACIC series. It was organized by the School of Engineering of the National University of Jujuy. The Congress included 9 Workshops with 130 accepted papers, 1 main Conference, 4 invited tutorials, different meetings related with Computer Science Education (Professors, PhD students, Curricula) and an International School with 5 courses. CACIC 2009 was organized following the traditional Congress format, with 9 Workshops covering a diversity of dimensions of Computer Science Research. Each topic was supervised by a committee of three chairs of different Universities. The call for papers attracted a total of 267 submissions. An average of 2.7 review reports were collected for each paper, for a grand total of 720 review reports that involved about 300 different reviewers. A total of 130 full papers were accepted and 20 of them were selected for this book.Red de Universidades con Carreras en Informática (RedUNCI

Command & Control: Understanding, Denying and Detecting - A review of malware C2 techniques, detection and defences

In this survey, we first briefly review the current state of cyber attacks, highlighting significant recent changes in how and why such attacks are performed. We then investigate the mechanics of malware command and control (C2) establishment: we provide a comprehensive review of the techniques used by attackers to set up such a channel and to hide its presence from the attacked parties and the security tools they use. We then switch to the defensive side of the problem, and review approaches that have been proposed for the detection and disruption of C2 channels. We also map such techniques to widely-adopted security controls, emphasizing gaps or limitations (and success stories) in current best practices.Comment: Work commissioned by CPNI, available at c2report.org. 38 pages. Listing abstract compressed from version appearing in repor