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Bacterial pathogens have evolved numerous strategies to corrupt, hijack or mimic cellular processes in order to survive and proliferate. Among those strategies, Type IV effectors (T4Es) are proteins secreted by pathogenic bacteria to manipulate host cell processes during infection. They are delivered into eukaryotic cells in an ATP-dependent manner via the type IV secretion system, a specialized multiprotein complex. T4Es contain a wide spectrum of features including eukaryotic-like domains, localization signals or a C-terminal translocation signal. A combination of these features enables prediction of T4Es in a given bacterial genome. In this study, we developed a web-based comprehensive suite of tools with a user-friendly graphical interface. This version 2.0 of S4TE (Searching Algorithm for Type IV Effector Proteins; ) enables accurate prediction and comparison of T4Es. Search parameters and threshold can be customized by the user to work with any genome sequence, whether publicly available or not. Applications range from characterizing effector features and identifying potential T4Es to analyzing the effectors based on the genome G+C composition and local gene density. S4TE 2.0 allows the comparison of putative T4E repertoires of up to four bacterial strains at the same time. The software identifies T4E orthologs among strains and provides a Venn diagram and lists of genes for each intersection. New interactive features offer the best visualization of the location of candidate T4Es and hyperlinks to NCBI and Pfam databases. S4TE 2.0 is designed to evolve rapidly with the publication of new experimentally validated T4Es, which will reinforce the predictive power of the algorithm. The computational methodology can be used to identify a wide spectrum of candidate bacterial effectors that lack sequence conservation but have similar amino acid characteristics. This approach will provide very valuable information about bacterial host-specificity and virulence factors and help identify host targets for the development of new anti-bacterial molecules. [ABSTRACT FROM AUTHOR]

The omnibus test is commonly applied to evaluate the overall disparity between group means in ANOVA. Alternatively, linear contrasts are more informative in detecting specific pattern of mean differences that cannot be obtained via the omnibus test. This article concerns power and sample size calculations for contrast analysis with heterogeneous variances and budget concerns. Optimal allocation procedures for the Welch-Satterthwaite tests of standardized and unstandardized contrasts are presented to minimize the total sample size with the designated ratios, to meet a desirable power level for the least cost, and to attain the maximum power performance under a fixed cost. Currently available methods rely exclusively on simple allocation formula and direct rounding rule. The proposed allocation strategies combine the computing techniques of nonlinear optimization search and iterative screening process. Numerical assessments of a randomized control trial for the overcoming depression on the Internet are conducted to demonstrate and confirm that the approximate procedures do not guarantee optimal solution. The suggested approaches extend and outperform the existing findings in methodological soundness and overall performance. The corresponding computer algorithms are developed to implement the recommended power and sample size calculations for optimal contrast analysis. [ABSTRACT FROM AUTHOR]

Test oracles are commonly used in software testing to determine the correctness of the execution results of test cases. However, the testing of many software systems faces the test oracle problem: a test oracle may not always be available, or it may be available but too expensive to apply. One such software system is a system involving abundant business processes. This paper focuses on the testing of business-process-based software systems and proposes a metamorphic testing approach for event sequences, called MTES, to alleviate the oracle problem. We utilized event sequences to represent business processes and then applied the technique of metamorphic testing to test the system without using test oracles. To apply metamorphic testing, we studied the general rules for identifying metamorphic relations for business processes and further demonstrated specific metamorphic relations for individual case studies. Three case studies were conducted to evaluate the effectiveness of our approach. The experimental results show that our approach is feasible and effective in testing the applications with rich business processes. In addition, this paper summarizes the experimental findings and proposes guidelines for selecting good metamorphic relations for business processes. [ABSTRACT FROM AUTHOR]

Authorship is the currency of an academic career for which the number of papers researchers publish demonstrates creativity, productivity, and impact. To discourage coercive authorship practices and inflated publication records, journals require authors to affirm and detail their intellectual contributions but this strategy has been unsuccessful as authorship lists continue to grow. Here, we surveyed close to 6000 of the top cited authors in all science categories with a list of 25 research activities that we adapted from the National Institutes of Health (NIH) authorship guidelines. Responses varied widely from individuals in the same discipline, same level of experience, and same geographic region. Most researchers agreed with the NIH criteria and grant authorship to individuals who draft the manuscript, analyze and interpret data, and propose ideas. However, thousands of the researchers also value supervision and contributing comments to the manuscript, whereas the NIH recommends discounting these activities when attributing authorship. People value the minutiae of research beyond writing and data reduction: researchers in the humanities value it less than those in pure and applied sciences; individuals from Far East Asia and Middle East and Northern Africa value these activities more than anglophones and northern Europeans. While developing national and international collaborations, researchers must recognize differences in peoples values while assigning authorship. [ABSTRACT FROM AUTHOR]

In this paper, a computationally efficient algorithm for Bayesian joint change point detection (CPD) in multiple time series is presented. The data generation model includes a number of change configurations (CC), each affecting a unique subset of the time series, which introduces correlation between the positions of change points (CPs) in the monitored time series. The inference objective is to identify joint changes and the associated CC. The algorithm consists of two stages: First, a univariate CPD algorithm is applied separately to each of the involved time series. The outcomes of this step are maximum a posteriori (MAP) detected CPs and posterior distributions of CPs conditioned on the MAP CPs. These outcomes are used in combination to approximate the posterior for the CCs. In the second algorithm stage, dynamic programming is used to find the maxima of this approximate CC posterior. The algorithm is applied to synthetic data, and it is shown to be both significantly faster and more accurate compared to a previously proposed algorithm designed to solve similar problems. Also, the initial algorithm is extended with steps from the maximization–maximization algorithm, which allows the hyperparameters of the data generation model to be estimated jointly with the CCs, and we show that these estimates coincide with estimates obtained from a Markov chain Monte Carlo algorithm. [ABSTRACT FROM AUTHOR]

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Haplotype-based methods compete with “one-SNP-at-a-time” approaches on being preferred for association studies. Chromosome 6 contains most of the known genetic biomarkers for rheumatoid arthritis (RA) disease. Therefore, chromosome 6 serves as a benchmark for the haplotype methods testing. The aim of this study is to test the North American Rheumatoid Arthritis Consortium (NARAC) dataset to find out if haplotype block methods or single-locus approaches alone can sufficiently provide the significant single nucleotide polymorphisms (SNPs) associated with RA. In addition, could we be satisfied with only one method of the haplotype block methods for partitioning chromosome 6 of the NARAC dataset? In the NARAC dataset, chromosome 6 comprises 35,574 SNPs for 2,062 individuals (868 cases, 1,194 controls). Individual SNP approach and three haplotype block methods were applied to the NARAC dataset to identify the RA biomarkers. We employed three haplotype partitioning methods which are confidence interval test (CIT), four gamete test (FGT), and solid spine of linkage disequilibrium (SSLD). P-values after stringent Bonferroni correction for multiple testing were measured to assess the strength of association between the genetic variants and RA susceptibility. Moreover, the block size (in base pairs (bp) and number of SNPs included), number of blocks, percentage of uncovered SNPs by the block method, percentage of significant blocks from the total number of blocks, number of significant haplotypes and SNPs were used to compare among the three haplotype block methods. Individual SNP, CIT, FGT, and SSLD methods detected 432, 1,086, 1,099, and 1,322 associated SNPs, respectively. Each method identified significant SNPs that were not detected by any other method (Individual SNP: 12, FGT: 37, CIT: 55, and SSLD: 189 SNPs). 916 SNPs were discovered by all the three haplotype block methods. 367 SNPs were discovered by the haplotype block methods and the individual SNP approach. The P-values of these 367 SNPs were lower than those of the SNPs uniquely detected by only one method. The 367 SNPs detected by all the methods represent promising candidates for RA susceptibility. They should be further investigated for the European population. A hybrid technique including the four methods should be applied to detect the significant SNPs associated with RA for chromosome 6 of the NARAC dataset. Moreover, SSLD method may be preferred for its favored benefits in case of selecting only one method. [ABSTRACT FROM AUTHOR]

Recent changes in institutional cyberinfrastructure and collections data storage methods have dramatically improved accessibility of specimen-based data through the use of digital databases and data aggregators. This analysis of digitized fish collections in the U.S. demonstrates how information from data aggregators, in this case iDigBio, can be extracted and analyzed. Data from U.S. institutional fish collections in iDigBio were explored through a strictly programmatic approach using the ridigbio package and fishfindR web application. iDigBio facilitates the aggregation of collections data on a purely voluntary fashion that requires collection staff to consent to sharing of their data. Not all collections are sharing their data with iDigBio, but the data harvested from 38 of the 143 known fish collections in the U.S. that are in iDigBio account for the majority of fish specimens housed in U.S. collections. In the 22 years since publication of the last survey providing information on these 38 collections, 1,219,168 specimen records (lots), 15,225,744 specimens, 3,192 primary types, and 32,868 records of secondary types have been added. This is an increase of 65.1% in the number of cataloged records and an increase of 56.1% in the number of specimens. In addition to providing specimen-based data for research, education, and various outreach activities, data that are accessible via data aggregators can be used to develop accurate, up-to-date reports of information on institutional collections. Such reports present collections data in an organized and accessible fashion and can guide targeted efforts by collections personnel to meet discipline-specific needs and make data more transparent to downstream users. Data from this survey will be updated and published regularly in a dynamic web application that will aid collections staff in communicating collections value while simultaneously giving stakeholders a way to explore collections holdings as they relate to the institutions in which they are housed. It is through this resource that collections will be able to leverage their data against those of similar collections to aid in the procurement of financial and institutional support. [ABSTRACT FROM AUTHOR]

The article offers author's opinion on development life sciences repositories, databases, and archives. It is mentioned representational state transfer (REST) API and HTTP standard could be used for development of such databases to manage information in real-time. The article also discusses that these databases would help in managing various biological questions and offering solutions to various problems.

This paper proposes a power-system protection device designed to be integrated in smart environments based on Internet-of-Things technologies. The proposed system enhances electrical safety by fast disconnection of the power supply in case of fault events like leakage current, electrical arc, overcurrent or overvoltage and has been designed with the goal to be integrated in smart environments like smart homes or smart cities for protecting the electrical equipment. The system also enables real-time monitoring and notification events through an advanced communication interface using a data concentrator architecture. This paper provides an extended description of the proposed system’s design and implementation, as well as the experimental validation results. [ABSTRACT FROM AUTHOR]

Digital convergence promises universal access to information, new spaces of communicative interaction and performing tasks typical of other areas. This research focuses on mobile applications such as exponent of this digital convergence. We analyze a sample of young segment as consumers of leading franchise companies in the fast-food sector, because the young people are the main users of these devices. The methodology combines the bibliographic review with a descriptive analysis. The results reveal an underutilization of the possibilities of the smartphones and consequently a little innovation in the communication through the. In the same way it concludes the lack of use by the brands of the social tendencies related to their main activity. [ABSTRACT FROM AUTHOR]