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The article reviews the web site the Papers of George Washington Digital Edition, which can be found at http://rotunda.upress.virginia.edu:8080/pgwde, and the George Washington Papers at the Library of Congress, 1741-1799, which is available at http://memory.loc.gov/ammem/gwhtml/gwhome.html.

Discusses biases toward citing scientific literature both before and after the widespread use of computerized databses for literature searches. Predictions and approaches; Citation patterns; Summary.

Motivation: The past decade has seen the introduction of new technologies that lowered the cost of genomic sequencing increasingly. We can even observe that the cost of sequencing is dropping significantly faster than the cost of storage and transmission. The latter motivates a need for continuous improvements in the area of genomic data compression, not only at the level of effectiveness (compression rate), but also at the level of functionality (e.g. random access), configurability (effectiveness versus complexity, coding tool set . . .) and versatility (support for both sequenced reads and assembled sequences). In that regard, we can point out that current approaches mostly do not support random access, requiring full files to be transmitted, and that current approaches are restricted to either read or sequence compression. Results: We propose AFRESh, an adaptive framework for no-reference compression of genomic data with random access functionality, targeting the effective representation of the raw genomic symbol streams of both reads and assembled sequences. AFRESh makes use of a configurable set of prediction and encoding tools, extended by a Context-Adaptive Binary Arithmetic Coding scheme (CABAC), to compress raw genetic codes. To the best of our knowledge, our paper is the first to describe an effective implementation CABAC outside of its’ original application. By applying CABAC, the compression effectiveness improves by up to 19% for assembled sequences and up to 62% for reads. By applying AFRESh to the genomic symbols of the MPEG genomic compression test set for reads, a compression gain is achieved of up to 51% compared to SCALCE, 42% compared to LFQC and 44% compared to ORCOM. When comparing to generic compression approaches, a compression gain is achieved of up to 41% compared to GNU Gzip and 22% compared to 7-Zip at the Ultra setting. Additionaly, when compressing assembled sequences of the Human Genome, a compression gain is achieved up to 34% compared to GNU Gzip and 16% compared to 7-Zip at the Ultra setting. [ABSTRACT FROM AUTHOR]

One of the benefits of web-based research is the capacity to deliver video content directly to individual survey participants. However, yet to be investigated is whether the participant demographic and attitudinal characteristics are distorted when respondents are asked to view and respond to videos on their personal computers. To address this question, this research paper focuses on two potential types of selection bias introduced into web-based studies with video content: (1) that resulting from respondents’ differential ability to view videos; and (2) that resulting from demographic and motivational influences of adequate exposure to video content. Through a secondary analysis of two studies focusing on adult cigarette smokers living in the United States, this research paper investigates whether the ability to view videos differs between demographic groups, whether respondents who do not view videos for their full duration differ from those who view videos for an appropriate amount of time, and whether video characteristics influenced this relationship. Results show that age, education, sex, household internet access, and work status influence the likelihood of a respondent reporting an inability to view videos. In addition, age, employment status, and congeniality of and interest in issue topic affect adequate video viewing times. These outcomes suggest that although web-based studies offer many advantages, the inclusion of videos within these surveys has the potential to undermine the accuracy of study findings and distort the representative nature of the study sample. Recommendations for minimizing potential distortions are presented. [ABSTRACT FROM PUBLISHER]

The article discusses the historiography of U.S. President Abraham Lincoln and the themes explored in Lincoln studies. The author cites the book "Lincoln," by Professor David Herbert Donald and explains that since its publication in 1995, there have been about 20 books a year published on Lincoln. The author also cites the essay: "Has the Lincoln Theme Been Exhausted?," by J.G. Randall. Subjects of the article also include the release of Lincoln's personal and presidential papers in 1947, the professional era in Lincoln studies, and the studies of Lincoln's relationship with Ann Rutledge. Works mentioned in the article include "The Young Eagle," by Kenneth J. Winkle, "Honor's Voice," by Douglas Wilson, and "Lincoln's Melancholy," by Joshua Wolf Shenk. Technological sources are also detailed.

The world has seen three waves of property. The first hark back centuries and relate to `real and personal property' such as land and chattel, also known as immovable and movable property. The second gained recognition around the nineteenth century and relates to propertization of the `labours of the mind' or `intellectual property'. The third wave came within a much shorter period and starting to gain recognition and it is what is known as `virtual property'. The law and policy-makers have had to surmount not only a steep learning curve but also in some cases a foundation that is wrought with mistakes when it comes to the treatment that should be given to virtual property. The Domain Name System (DNS) is the best example of a form of virtual property that has given rise to challenges in law making and administration. The `land grab' of domain names in the World Wide Web (WWW) have given rise to a virtual tsunami of registrations and this has led to the subsequent erection of levees in the form of a challenge regime. This paper will identify and consider the problems that the DNS is facing and suggest the changes that have to be made to it in order for it to withstand the forces of what will be an increasingly rising sea of domain names on the WWW. This paper will begin with a look at the fissures in the seabed of the DNS by comparing how the management and policies relating to domain name registration and challenge have shifted and diverged in different jurisdictions as well as by examining the inadequacies of the original registration regime (ICANN) and challenge policy (UDRP). After identifying the problem, suggestions will be made to resolve them in the best possible way, which require a revisit of the stakeholder and policy interests in the Internet and the ownership and control of domain names that essentially function as an important gateway to the WWW in order to rebalance these interests in an attempt to achieve greatest equilibrium. Amendments will be proposed to both the registration and challenge regimes as well as to the structure and hierarchy of domain name administration which should be a globally coordinated effort just as the DNS is a common entryway to the global property that is the WWW. [ABSTRACT FROM AUTHOR]

Real-time response (RTR) measurement is an important technique for analyzing human processing of electronic media stimuli. Although it has been demonstrated that RTR data are reliable and internally valid, some argue that they lack external validity. The reason for this is that RTR measurement is restricted to a laboratory environment due to its technical requirements. This paper introduces a smartphone app that 1) captures real-time responses using the dial technique and 2) provides a solution for one of the most important problems in RTR measurement, the (automatic) synchronization of RTR data. In addition, it explores the reliability and validity of mobile RTR measurement by comparing the real-time reactions of two samples of young and welleducated voters to the 2013 German televised debate. Whereas the first sample participated in a classical laboratory study, the second sample was equipped with our mobile RTR system and watched the debate at home. Results indicate that the mobile RTR system yields similar results to the lab-based RTR measurement, providing evidence that laboratory studies using RTR are externally valid. In particular, the argument that the artificial reception situation creates artificial results has to be questioned. In addition, we conclude that RTR measurement outside the lab is possible. Hence, mobile RTR opens the door for large-scale studies to better understand the processing and impact of electronic media content. [ABSTRACT FROM AUTHOR]

In this paper, we investigate whether and to what extent exposure to a company's social media activities over time is beneficial for corporate reputation, and whether conversational human voice mediates this relation. In a two-wave longitudinal survey among 1969 respondents, we assessed consumers' exposure to an international airline's social media activities, perceived level of conversational human voice and perception of corporate reputation. The results show that consumers' level of exposure to company social media activities precedes perceptions of corporate reputation. Also, conversational human voice mediates the relation between consumers' level of exposure to company social media activities and perceptions of corporate reputation. We discuss the implications of the results for the presence of organizations in social media. [ABSTRACT FROM AUTHOR]

This study focuses on second screening for news, a hybrid media process that combines watching news on television and a second, web-connected screen (i.e., smart-phone, laptop). Based on U.S.-national, 2-wave panel data, the paper (a) examines people's motivations to engage in second screen use, and then (b) advances the relationship between second screening and online political behaviors. Discussing and pursuing further information are both central motivations for second screen use. Furthermore, results suggest second screening for news is a significant predictor of online political participation and a key link between TV news and political engagement as this relationship is fully mediated. The study advances theoretically and empirically ways in which an informed public opinion may partake of a more engaged democracy. [ABSTRACT FROM AUTHOR]

This section offers information on the American Society of Mammalogists (ASM) including an invitation for research papers to be submitted for oral and poster presentation at the 91st Annual Meeting, an encouragement for the nominations for the C. Hart Merriam Award and the online access for "Journal of Mammalogy and Mammalian Species."

This review summarizes infection prevention resources on the Internet. Web sites are presented in 8 categories: guidelines, policies, and regulatory bodies; health care-associated infection and multidrug-resistant organisms; surveillance, reporting, and initiatives; antibiotic use; employee health; long-term care facilities; facility and environmental infection control; and professional societies, educational opportunities, and listserves. For example, links to the National Surgical Quality Improvement Program and National Healthcare Safety Network reports are provided among resources for infection surveillance, reporting, and initiatives. A link to guidelines for infection prevention in health care workers is listed with other information regarding employee health. The Web address for the Society for Healthcare Epidemiology of America guidelines for infection control in long-term care facilities is listed with resources for long-term care facilities. Guidelines for construction and environmental services are summarized with other information regarding facility and environmental infection control. This review summarizes the most useful and up-to-date infection prevention resources on the Internet and will simplify the search for pertinent information. [ABSTRACT FROM AUTHOR]

Turnover in online communities is very high, with most people who initially post a message to an online community never contributing again. In this paper, we test whether the responses that newcomers receive to their first posts influence the extent to which they continue to participate. The data come from initial posts made by 2,777 newcomers to six public newsgroups. We coded the content and valence of the initial post and its first response, if it received one, to see if these factors influenced newcomers’ likelihood of posting again. Approximately 61% of newcomers received a reply to their initial post, and those who got a reply were 12% more likely to post to the community again; their probability of posting again increased from 44% to 56%. They were more likely to receive a response if they asked a question or wrote a longer post. Surprisingly, the quality of the response they received—its emotional tone and whether it answered a newcomer’s question—did not influence the likelihood of the newcomer’s posting again. [ABSTRACT FROM AUTHOR]

The article highlights the growing online access of the journal "Occupational Medicine" by developing countries. It cites the advantages of using electronic communication by a journal, such as immediate paper submission and review process and in-depth information for people who read beyond abstract. Through the Oxford University Press (OUP), any not-for-profit educational institution from countries like India and South Africa will be given free access to the journal. OUP is working with entities like the World Health Organization (WHO) for this project.

Web pages typically include many visual elements such as header and footer to support interaction with the user. However, if web pages do not comply with web accessibility guidelines, and these visual elements are not explicitly encoded in the underlying source code, they become inaccessible in alternative presentations, such as audio. This article presents an automatic role detection approach to identify visual elements in web pages and their roles. The system architecture has three major components: automatic identification of visual elements in web pages; automatic generation of heuristic rules from the knowledge base; and application of these rules for automatic annotation of visual elements with their roles. This article first explains the system architecture in detail and then presents both technical and user evaluations of the proposed approach. Our user evaluation shows that the automatic role detection approach has around 70% receptive accuracy, but the proposed knowledge base could be further improved for better results. Our technical evaluation shows that the complexity is an important performance factor in role detection - required resources and execution time increases when the web page has more complex structure. [ABSTRACT FROM AUTHOR]

Motivation: Validation and reproducibility of results is a central and pressing issue in genomics. Several recent embarrassing incidents involving the irreproducibility of high-profile studies have illustrated the importance of this issue and the need for rigorous methods for the assessment of reproducibility.Results: Here, we describe an existing statistical model that is very well suited to this problem. We explain its utility for assessing the reproducibility of validation experiments, and apply it to a genome-scale study of adenosine deaminase acting on RNA (ADAR)-mediated RNA editing in Drosophila. We also introduce a statistical method for planning validation experiments that will obtain the tightest reproducibility confidence limits, which, for a fixed total number of experiments, returns the optimal number of replicates for the study.Availability: Downloadable software and a web service for both the analysis of data from a reproducibility study and for the optimal design of these studies is provided at http://ccmbweb.ccv.brown.edu/reproducibility.htmlContact: Charles_Lawrence@Brown.eduSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]

The article reviews several web sites including the National Constitution Center, located at www.constitutioncenter.org, the Gilder Lehrman Center for the Study of Slavery, Resistance, and Abolition, located at www.yale.edu/glc/index.htm, and Detroit Publishing Company: Photographer to the World, located at www.thehenryford.org/exhibits/dpc/default.asp.

The article discusses technological resources concerning U.S. history during the time of U.S. President Abraham Lincoln, and how to interpret them. The author discusses patterns within primary sources of this period, including newspapers and telegraphs, which help researchers understand public opinion. The article details the most commonly used words in four Northern and Southern newspapers between April 1861 and April 1865. The article provides several photographic examples of language patterns during the U.S. Civil War.

Keys are traditionally created from data gathered from real observations, which can be a complex and time-consuming process. With a large number of texts containing written descriptions of species, data needed for the creation of a key are already available. A number of published works on Drosera were chosen and the data in these were used to create an interactive, web-based key. The types of data used were evaluated for ease of use and accuracy and the effectiveness of purely literature-based data was tested. The resulting key highlighted a number of problems of using characters and states which have not been observed, as well as showing that literature-based research can lead to a workable key. [ABSTRACT FROM PUBLISHER]

Summary: We present ClicO Free Service, an online web-service based on Circos, which provides a user-friendly, interactive web-based interface with configurable features to generate Circos circular plots. Availability and implementation: Online web-service is freely available at http://clicofs.codoncloud.com. [ABSTRACT FROM AUTHOR]

As computers have increasingly provided new channels of communication, scholars have taken an interest in computer-mediated communication (CMC) in general and the impact of personality traits and other antecedents of preference for face-to-face or computer channels. Research is hampered, however, by the lack of standardized measures of CMC-related concepts. Three studies (N = 914) were undertaken to develop and validate a measure of affect for using communication channels. Findings of the studies provide strong evidence of the internal consistency and both construct and predictive validity of the scale. [ABSTRACT FROM AUTHOR]

This study examines how employees in a distributed work group use email copies in networks of collaboration. It studies the audience design of messages with multiple recipients, analyzing explicit and implicit addressing devices used to appoint recipients as primary and secondary participants in the interaction. Copying in recipients serves to share knowledge of ongoing projects and to build up a common information pool. Furthermore, it is used to facilitate multi-party interaction and to build personal identity and alliances. Copies to third parties may also be used for reasons of social control, for instance in order to gain compliance or to put pressure on the addressee to conform to social norms of conduct. [ABSTRACT FROM AUTHOR]

Features 'America Unbound,' an electronic textbook on history published by the Digital Learning Interactive. Impact of electronic media on history teaching; Advantages of 'America Unbound'; Primary sources used in the textbook; Limitation of the textbook.

Focuses on some of the general trends in the history of the Web and its emergence as an online archive of primary and secondary sources. Strength of the grass-roots history Web; Information conglomerates and Internet startups on the private history Web; Access and control on the private history Web.

SUMMARY In this paper the author discusses systems for on-line statistical analysis, and describes a particular program written for an IBM 1620 computer. [ABSTRACT FROM AUTHOR]

The article reviews the web site America's Historical Newspapers, located at http://infoweb.newsbank.com/best/academiceanall, created and maintained by Readex.

The article discusses the paper "Adjuvant radiation therapy and chemotherapy in Merkel cell carcinoma: Survival analyses of 6908 cases from the National Cancer Data Base," from S. Bhatia and colleagues. Topics discussed include the advantages of adjuvant radiotherapy in the treatment of patien with merkel cell carcinoma (MCC), the impact of surgical modality in adjuvant radiotherapy and overall survival, and the survival outcomes of patients with MCC.

Motivation: The use of prior knowledge to improve gene regulatory network modelling has often been proposed. In this article we present the first research on the massive incorporation of prior knowledge from literature for Bayesian network learning of gene networks. As the publication rate of scientific papers grows, updating online databases, which have been proposed as potential prior knowledge in past research, becomes increasingly challenging. The novelty of our approach lies in the use of gene-pair association scores that describe the overlap in the contexts in which the genes are mentioned, generated from a large database of scientific literature, harnessing the information contained in a huge number of documents into a simple, clear format. Results: We present a method to transform such literature-based gene association scores to network prior probabilities, and apply it to learn gene sub-networks for yeast, Escherichia coli and Human organisms. We also investigate the effect of weighting the influence of the prior knowledge. Our findings show that literature-based priors can improve both the number of true regulatory interactions present in the network and the accuracy of expression value prediction on genes, in comparison to a network learnt solely from expression data. Networks learnt with priors also show an improved biological interpretation, with identified subnetworks that coincide with known biological pathways. Contact: emma.steele@brunel.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

In order to serve as an antidote to extremist messages, counter-messages (CM) are placed in the same online environment as extremist content. Often, they are even tagged with similar keywords. Given that automated algorithms may define putative relationships between videos based on mutual topics, CM can appear directly linked to extremist content. This poses severe challenges for prevention programs using CM. This study investigates the extent to which algorithms influence the interrelatedness of counter-and extremist messages. By means of two exemplary information network analyses based on YouTube videos of two CM campaigns, we demonstrate that CM are closely--or even directly--connected to extremist content. The results hint at the problematic role of algorithms for prevention campaigns. [ABSTRACT FROM AUTHOR]

Motivation: Planarians are emerging as a model organism to study regeneration in animals. However, the little available data of protein--protein interactions hinders the advances in understanding the mechanisms underlying its regenerating capabilities. Results: We have developed a protocol to predict protein--protein interactions using sequence homology data and a reference Human interactome. This methodology was applied on 11 Schmidtea mediterranea transcriptomic sequence datasets. Then, using Neo4j as our database manager, we developed PlanNET, a web application to explore the multiplicity of networks and the associated sequence annotations. By mapping RNA-seq expression experiments onto the predicted networks, and allowing a transcript-centric exploration of the planarian interactome, we provide researchers with a useful tool to analyse possible pathways and to design new experiments, as well as a reproducible methodology to predict, store, and explore protein interaction networks for non-model organisms. [ABSTRACT FROM AUTHOR]

This article conceptualizes algorithmically-governed platforms as the outcomes of a structuration process involving three types of actors: platform owners/developers, platform users, and machine learning algorithms. This threefold conceptualization informs media effects research, which still struggles to incorporate algorithmic influence. It invokes insights into algorithmic governance from platform studies and (critical) studies in the political economy of online platforms. This approach illuminates platforms' underlying technological and economic logics, which allows to construct hypotheses on how they appropriate algorithmic mechanisms, and how these mechanisms function. The present study tests the feasibility of experience sampling to test such hypotheses. The proposed methodology is applied to the case of mobile dating app Tinder. [ABSTRACT FROM AUTHOR]

This research focuses on the identification of social roles and an investigation of their influence in online context. Relying on a systemic approach for role conceptualization, we investigate member's activity, shared content and position in the network within a consumer to consumer social media-based community (SMC) around a product. This investigation led to the identification of ten core roles, based on three key elements: object of interest (product, practice, and community), main contribution type (sharing information and seeking information), individual orientation (factual, emotional). We propose an explanation about how these roles, through their positioning, participate in the community dynamics and how they contribute to the creation and diffusion of cookery as a social practice, shaping the periphery around this practice. [ABSTRACT FROM AUTHOR]

As one of the most important tasks in protein sequence analysis, protein remote homology detection is critical for both basic research and practical applications. Here, we present an effective web server for protein remote homology detection called ProtDec-LTR2.0 by combining ProtDec-Learning to Rank (LTR) and pseudo protein representation. Experimental results showed that the detection performance is obviously improved. The web server provides a user-friendly interface to explore the sequence and structure information of candidate proteins and find their conserved domains by launching a multiple sequence alignment tool. [ABSTRACT FROM AUTHOR]

The article presents information on the American Institute of Biological Sciences' annual meeting at the University of Illinois on August 20, 1965.

Following the nudging perspective, this research investigates how technology interface could cue heuristics that influence decisions. A field study showed that interface cues on a food-ordering website signaling the amount of food other users consume could trigger an anchoring heuristic and induce individuals to model that amount when deciding their own consumption volume. A laboratory experiment further showed that the anchoring cue tends to induce the modeling behavior of individuals without them being aware of its influence, and such an influence was especially pronounced when resources for cognitive deliberation were limited. Altogether, this research suggests that interface cues could function as nudges and influence decisions at a relatively automatic level. Implications for technology design and intervention are discussed. [ABSTRACT FROM AUTHOR]

This study draws on communication infrastructure theory (CIT) to examine the extent to which expressive uses of Internet and mobile devices moderate the relationship between integrated connectedness to a storytelling network (ICSN) and offline and online civic participation. Data collected through a Web survey of a U.S. national online panel ( N = 1201) reveal that the relationships of ICSN with offline and online civic participation are conditioned by locality-oriented expressive uses of Internet and mobile media. With these findings, this study discusses theoretical insights, policy implications, and practical applications. [ABSTRACT FROM AUTHOR]

This qualitative and quantitative content analysis examines 46 African and African American museum websites. Merelman's cultural projection concept serves as a foundation to explain the societal importance of Black cultural expression. The analysis reviews how the African- and African American-centric organizations communicate Black and organizational identities on their digital platforms. Described are images, sound, and visual dynamism. The findings add to the literature on counterstereotypes and digital cultural expression, linking visual communication research with intercultural communication and strategic communication. [ABSTRACT FROM AUTHOR]

Motivation: Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. [ABSTRACT FROM AUTHOR]

Background. Since 2010, the Champlain BASE (Building Access to Specialist Advice through eConsultation) has allowed primary care providers (PCPs) to submit clinical questions to specialists through a secure web service. The study objectives are to describe questions asked to Infectious Diseases specialists through eConsultation and assess impact on physician behaviors. Methods. eConsults completed through the Champlain BASE service from April 15, 2013 to January 29, 2015 were characterized by the type of question asked and infectious disease content. Usage data and PCP responses to a closeout survey were analyzed to determine eConsult response time, change in referral plans, and change in planned course of action. Results. Of the 224 infectious diseases eConsults, the most common question types were as follows: interpretation of a clinical test 18.0% (41), general management 16.5% (37), and indications/goals of treating a particular condition 16.5% (37). The most frequently consulted infectious diseases were as follows: tuberculosis 14.3% (32), Lyme disease 14.3% (32), and parasitology 12.9% (29). Within 24 hours, 63% of cases responded to the questions, and 82% of cases took under 15 minutes to complete. In 32% of cases, a face-to-face referral was originally planned by the PCP but was no longer needed. In 8% of cases, the PCP referred the patient despite originally not planning to make a referral. In 55% of cases, the PCP either received new information or changed their course of action. Conclusions. An eConsult service provides PCPs with timely access to infectious disease specialists' advice that often results in a change in plans for a face-to-face referral. [ABSTRACT FROM AUTHOR]

The article reviews the web site U.S. Department of State: Office of the Historian, located at http://history.state.gov/, created and maintained by the Bureau of Public Affairs, U.S. Department of State, Washington, D.C.

The author comments that the Internet has created opportunities in distance learning for people who are studying medicine in Great Britain. In the past, online limitations included the types of media utilized and their accessibility and delivery, but the author states that these limitations no longer exist. With new technology it has become possible for distance learners to access more than just text and images and a wide range of media is available such as video conferencing and videostreaming.

The author comments on the issue of creating an open-source online network of ecological data. It has been suggested that reproducibility should not be required of ecological studies. According to the author, this means ecological journals should not require authors to publish data as a requirement of publication, nor should reviewers insist on it. Interest in using the Semantic Web as a framework for the exchange of data is said to be growing.

A wide variety of large-scale data have been produced in bioinformatics. In response, the need for efficient handling of biomedical big data has been partly met by parallel computing. However, the time demand of many bioinformatics programs still remains high for large-scale practical uses because of factors that hinder acceleration by parallelization. Recently, new generations of storage devices have emerged, such as NAND flash-based solid-state drives (SSDs), and with the renewed interest in near-data processing, they are increasingly becoming acceleration methods that can accompany parallel processing. In certain cases, a simple drop-in replacement of hard disk drives by SSDs results in dramatic speedup. Despite the various advantages and continuous cost reduction of SSDs, there has been little review of SSD-based profiling and performance exploration of important but time-consuming bioinformatics programs. For an informative review, we perform indepth profiling and analysis of 23 key bioinformatics programs using multiple types of devices. Based on the insight we obtain from this research, we further discuss issues related to design and optimize bioinformatics algorithms and pipelines to fully exploit SSDs. The programs we profile cover traditional and emerging areas of importance, such as alignment, assembly, mapping, expression analysis, variant calling and metagenomics. We explain how acceleration by parallelization can be combined with SSDs for improved performance and also how using SSDs can expedite important bioinformatics pipelines, such as variant calling by the Genome Analysis Toolkit and transcriptome analysis using RNA sequencing. We hope that this review can provide useful directions and tips to accompany future bioinformatics algorithm design procedures that properly consider new generations of powerful storage devices. [ABSTRACT FROM AUTHOR]

Nongovernmental organization ( NGO) hyperlink networks are institutionalized connective public goods. They influence which actors and what aspects of social issues are made visible to the public in search engine results. To understand how contextual forces and institutional pressures influence who hyperlinks to whom online, this research examines a hyperlink network of 410 NGOs with various social missions operating across China. It suggests that institutional factors external to the network impact the structure of NGO hyperlink networks. In particular, institutional convener and legal registration status induce homophily hyperlinking effects among organizations, controlling for network interdependencies and other organizational attributes. Implications for hyperlink networks, institutional homophily, NGO collective action, and the development of civil society in China are drawn from the results. [ABSTRACT FROM AUTHOR]

The current study investigates how different types of company website designs influence first impressions, aesthetic evaluations and memory performance. We implemented an online study with a between-subjects design to examine differences between three design categories identified by ten experts in a pretest: strong colours of one colour family (SCOFA), large pictures (LAPIC) and same amount of pictures and text (SAPAT). The data of 458 participants (52.2% female) reveal that (i) after an exposure time of 5 s, response times for website-related attributes differ between the categories, (ii) LAPIC and SAPAT are perceived as more aesthetic than SCOFA and (iii) memory performance is best on SAPAT sites. These results underline the importance of first impressions of a site's appearance and provide practical guidance for web designers by showing what users associate with certain designs, which designs they prefer, and which sites are the most memorable. [ABSTRACT FROM AUTHOR]

Motivation: Recent advancements in molecular methods have made it possible to capture physical contacts between multiple chromatin fragments. The resulting association matrices provide a noisy estimate for average spatial proximity that can be used to gain insights into the genome organization inside the nucleus. However, extracting topological information from these data is challenging and their integration across resolutions is still poorly addressed. Recent findings suggest that a hierarchical approach could be advantageous for addressing these challenges. Results: We present an algorithmic framework, which is based on hierarchical block matrices (HBMs), for topological analysis and integration of chromosome conformation capture (3C) data. We first describe chromoHBM, an algorithm that compresses high-throughput 3C (HiT-3C) data into topological features that are efficiently summarized with an HBM representation. We suggest that instead of directly combining HiT-3C datasets across resolutions, which is a difficult task, we can integrate their HBM representations, and describe chromoHBM-3C, an algorithm which merges HBMs. Since three-dimensional (3D) reconstruction can also benefit from topological information, we further present chromoHBM-3D, an algorithm which exploits the HBM representation in order to gradually introduce topological constraints to the reconstruction process. We evaluate our approach in light of previous image microscopy findings and epigenetic data, and show that it can relate multiple spatial scales and provide a more complete view of the 3D genome architecture. Availability and implementation: The presented algorithms are available from: https://github.com/yolish/hbm. [ABSTRACT FROM AUTHOR]

Motivation: Whole genome sequencing (WGS) of parent-offspring trios is a powerful approach for identifying disease-associated genes via detecting copy number variations (CNVs). Existing approaches, which detect CNVs for each individual in a trio independently, usually yield low-detection accuracy. Joint modeling approaches leveraging Mendelian transmission within the parent-offspring trio can be an efficient strategy to improve CNV detection accuracy. Results: In this study, we developed TrioCNV, a novel approach for jointly detecting CNVs in parent-offspring trios from WGS data. Using negative binomial regression, we modeled the read depth signal while considering both GC content bias and mappability bias. Moreover, we incorporated the family relationship and used a hidden Markov model to jointly infer CNVs for three samples of a parent-offspring trio. Through application to both simulated data and a triofrom 1000 Genomes Project, we showed that TrioCNV achieved superior performance than existing approaches. Availability and implementation: The software TrioCNV implemented using a combination of Java and R is freely available from the website at https://github.com/yongzhuang/TrioCNV. [ABSTRACT FROM AUTHOR]

Motivation Can we predict protein-protein interactions (PPIs) of a novel virus with its host? Three major problems arise: the lack of known PPIs for that virus to learn from, the cost of learning about its proteins and the sequence dissimilarity among viral families that makes most methods inapplicable or inefficient. We develop DeNovo, a sequence-based negative sampling and machine learning framework that learns from PPIs of different viruses to predict for a novel one, exploiting the shared host proteins. We tested DeNovo on PPIs from different domains to assess generalization. Results: By solving the challenge of generating less noisy negative interactions, DeNovo achieved accuracy up to 81 and 86% when predicting PPIs of viral proteins that have no and distant sequence similarity to the ones used for training, receptively. This result is comparable to the best achieved in single virus-host and intra-species PPI prediction cases. Thus, we can now predict PPIs for virtually any virus infecting human. DeNovo generalizes well; it achieved near optimal accuracy when tested on bacteria-human interactions. Availability and implementation: Code, data and additional supplementary materials needed to reproduce this study are available at: https://bioinformatics.cs.vt.edu/~alzahraa/denovo. [ABSTRACT FROM AUTHOR]

Recent years have seen an increase in the amount of statistics describing different phenomena based on "Big Data." This term includes data characterized not only by their large volume, but also by their variety and velocity, the organic way in which they are created, and the new types of processes needed to analyze them and make inference from them. The change in the nature of the new types of data, their availability, and the way in which they are collected and disseminated is fundamental. This change constitutes a paradigm shift for survey research. There is great potential in Big Data, but there are some fundamental challenges that have to be resolved before its full potential can be realized. This report provides examples of different types of Big Data and their potential for survey research; it also describes the Big Data process, discusses its main challenges, and considers solutions and research needs. [ABSTRACT FROM AUTHOR]

Motivation: High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read-count variability. These estimates are typically based on statistical models such as the negative binomial distribution, which is employed by the tools edgeR, DESeq and cuffdiff. Until now, the validity of these models has usually been tested on either low-replicate RNA-seq data or simulations. Results: A 48-replicate RNA-seq experiment in yeast was performed and data tested against theoretical models. The observed gene read counts were consistent with both log-normal and negative binomial distributions, while the mean-variance relation followed the line of constant dispersion parameter of ~0.01. The high-replicate data also allowed for strict quality control and screening of 'bad' replicates, which can drastically affect the gene read-count distribution. Availability and implementation: RNA-seq data have been submitted to ENA archive with project ID PRJEB5348. [ABSTRACT FROM AUTHOR]

Does adoption of broadband internet in firms enhance labor productivity and increase wages? Is this technological change skill biased or factor neutral? We combine several Norwegian data sets to answer these questions. A public program with limited funding rolled out broadband access points and provides plausibly exogenous variation in the availability and adoption of broadband internet in firms. Our results suggest that broadband internet improves (worsens) the labor market outcomes and productivity of skilled (unskilled) workers. We explore several possible explanations for the skill complementarity of broadband internet. We find suggestive evidence that broadband adoption in firms complements skilled workers in executing nonroutine abstract tasks, and substitutes for unskilled workers in performing routine tasks. Taken together, our findings have important implications for the ongoing policy debate over government investment in broadband infrastructure to encourage productivity and wage growth. [ABSTRACT FROM AUTHOR]