bluuebunny/crossref_metadata_2025_split huggingface dataset:
PinaColada: peptide–inhibitor ant colony ad-hoc design algorithm
Authors: Zaidman Daniel , Wolfson Haim J. 
Published: March 2016

Abstract
Motivation: Design of protein–protein interaction (PPI) inhibitors is a major challenge in Structural Bioinformatics. Peptides, especially short ones (5–15 amino acid long), are natural candidates for inhibition of protein–protein complexes due to several attractive features such as high structural compatibility with the protein binding site (mimicking the surface of one of the proteins), small size and the ability to form strong hotspot binding connections with the protein surface. Efficient rational peptide design is still a major challenge in computer aided drug design, due to the huge space of possible sequences, which is exponential in the length of the peptide, and the high flexibility of peptide conformations.
Results: In this article we present PinaColada, a novel computational method for the design of peptide inhibitors for protein–protein interactions. We employ a version of the ant colony optimization heuristic, which is used to explore the exponential space (20n) of length n peptide sequences, in combination with our fast robotics motivated PepCrawler algorithm, which explores the conformational space for each candidate sequence. PinaColada is being run in parallel, on a DELL PowerEdge 2.8 GHZ computer with 20 cores and 256 GB memory, and takes up to 24 h to design a peptide of 5-15 amino acids length.
Availability and implementation: An online server available at: http://bioinfo3d.cs.tau.ac.il/PinaColada/.
Contact: danielza@post.tau.ac.il; wolfson@tau.ac.il
ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database
Authors: Yang Ying , Jiang Xiaotao , Chai Benli , Ma Liping , Li Bing , Zhang Anni , Cole James R. , Tiedje James M. , Zhang Tong 
Published: March 2016

Abstract
Motivation: Environmental dissemination of antibiotic resistance genes (ARGs) has become an increasing concern for public health. Metagenomics approaches can effectively detect broad profiles of ARGs in environmental samples; however, the detection and subsequent classification of ARG-like sequences are time consuming and have been severe obstacles in employing metagenomic methods. We sought to accelerate quantification of ARGs in metagenomic data from environmental samples.
Results: A Structured ARG reference database (SARG) was constructed by integrating ARDB and CARD, the two most commonly used databases. SARG was curated to remove redundant sequences and optimized to facilitate query sequence identification by similarity. A database with a hierarchical structure (type-subtype-reference sequence) was then constructed to facilitate classification (assigning ARG-like sequence to type, subtype and reference sequence) of sequences identified through similarity search. Utilizing SARG and a previously proposed hybrid functional gene annotation pipeline, we developed an online pipeline called ARGs-OAP for fast annotation and classification of ARG-like sequences from metagenomic data. We also evaluated and proposed a set of criteria important for efficiently conducting metagenomic analysis of ARGs using ARGs-OAP.
Availability and Implementation: Perl script for ARGs-OAP can be downloaded from https://github.com/biofuture/Ublastx_stageone. ARGs-OAP can be accessed through http://smile.hku.hk/SARGs.
Contact: zhangt@hku.hk or tiedjej@msu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
D3M: detection of differential distributions of methylation levels
Authors: Matsui Yusuke , Mizuta Masahiro , Ito Satoshi , Miyano Satoru , Shimamura Teppei 
Published: March 2016

AbstractMotivation: DNA methylation is an important epigenetic modification related to a variety of diseases including cancers. We focus on the methylation data from Illumina’s Infinium HumanMethylation450 BeadChip. One of the key issues of methylation analysis is to detect the differential methylation sites between case and control groups. Previous approaches describe data with simple summary statistics or kernel function, and then use statistical tests to determine the difference. However, a summary statistics-based approach cannot capture complicated underlying structure, and a kernel function-based approach lacks interpretability of results.Results: We propose a novel method D3M, for detection of differential distribution of methylation, based on distribution-valued data. Our method can detect the differences in high-order moments, such as shapes of underlying distributions in methylation profiles, based on the Wasserstein metric. We test the significance of the difference between case and control groups and provide an interpretable summary of the results. The simulation results show that the proposed method achieves promising accuracy and shows favorable results compared with previous methods. Glioblastoma multiforme and lower grade glioma data from The Cancer Genome Atlas show that our method supports recent biological advances and suggests new insights.Availability and Implementation: R implemented code is freely available from https://github.com/ymatts/D3M/.Contact: ymatsui@med.nagoya-u.ac.jp or shimamura@med.nagoya-u.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.
On genomic repeats and reproducibility
Authors: Firtina Can , Alkan Can 
Published: March 2016

Abstract
Results: Here, we present a comprehensive analysis on the reproducibility of computational characterization of genomic variants using high throughput sequencing data. We reanalyzed the same datasets twice, using the same tools with the same parameters, where we only altered the order of reads in the input (i.e. FASTQ file). Reshuffling caused the reads from repetitive regions being mapped to different locations in the second alignment, and we observed similar results when we only applied a scatter/gather approach for read mapping—without prior shuffling. Our results show that, some of the most common variation discovery algorithms do not handle the ambiguous read mappings accurately when random locations are selected. In addition, we also observed that even when the exact same alignment is used, the GATK HaplotypeCaller generates slightly different call sets, which we pinpoint to the variant filtration step. We conclude that, algorithms at each step of genomic variation discovery and characterization need to treat ambiguous mappings in a deterministic fashion to ensure full replication of results.
Availability and Implementation: Code, scripts and the generated VCF files are available at DOI:10.5281/zenodo.32611.
Contact: calkan@cs.bilkent.edu.tr
Supplementary information: Supplementary data are available at Bioinformatics online.
TreeDom: a graphical web tool for analysing domain architecture evolution
Authors: Haider Christian , Kavic Marina , Sonnhammer Erik L.L. 
Published: March 2016

Abstract
Summary: We present TreeDom, a web tool for graphically analysing the evolutionary history of domains in multi-domain proteins. Individual domains on the same protein chain may have distinct evolutionary histories, which is important to grasp in order to understand protein function. For instance, it may be important to know whether a domain was duplicated recently or long ago, to know the origin of inserted domains, or to know the pattern of domain loss within a protein family. TreeDom uses the Pfam database as the source of domain annotations, and displays these on a sequence tree. An advantage of TreeDom is that the user can limit the analysis to N sequences that are most similar to a query, or provide a list of sequence IDs to include. Using the Pfam alignment of the selected sequences, a tree is built and displayed together with the domain architecture of each sequence.
Availablility and implementation: http://TreeDom.sbc.su.se
Contact: Erik.Sonnhammer@scilifelab.se
FRODOCK 2.0: fast protein–protein docking server
Authors: Ramírez-Aportela Erney , López-Blanco José Ramón , Chacón Pablo 
Published: March 2016

Abstract
Summary: The prediction of protein–protein complexes from the structures of unbound components is a challenging and powerful strategy to decipher the mechanism of many essential biological processes. We present a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein–protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein–protein binding conformations that can be further refined with more computationally demanding strategies.
Availability and Implementation: The server is free and open to all users with no login requirement at http://frodock.chaconlab.org
Contact: pablo@chaconlab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Fish and squid behaviour at the mouth of a drop-chain trawl: factors contributing to capture or escape
Authors: Bayse Shannon M. , Pol Michael V. , He Pingguo 
Published: March 2016

Abstract
Underwater video recordings in the mouth of a squid trawl were used to evaluate the effectiveness of a trawl configured with drop-chain groundgear to catch longfin inshore squid (Doryteuthis pealeii) and reduce bycatch of finfish in the Nantucket Sound squid fishery off Cape Cod, Massachusetts, USA. Entrance through the trawl mouth or escape underneath the fishing line and between drop chains was quantified for targeted squid, and two major bycatch species, summer flounder (Paralichthys dentatus) and skates (family Rajidae). Additionally, contact and impingement between animals and groundgear were also quantified. Fish and squid swimming behaviours, positions, orientations, and time in the trawl mouth were quantified and related to capture or escape at the trawl mouth. Squid entered the trawl singly and in schools, and no squid were observed escaping under the fishing line. Most squid entered the trawl in the upper portion of the trawl mouth; mantle orientated away from the trawl and swimming in the same direction, and were gradually overtaken, not actively attempting to escape. Summer flounder and skates were observed to remain on or near the seabed, orientated, and swimming in the same direction as the approaching trawl. The majority (60.5%) of summer flounder entered the trawl above the fishing line. Summer flounder that changed their orientation and turned 180° were significantly more likely to enter the trawl (p &lt; 0.05). Most skates (89.7%) avoided trawl entrance and escaped under the fishing line. Neither squid nor summer flounder were observed to make contact or become impinged to the groundgear; however, 35.4% of skates had substantial contact with groundgear, with 12.3% becoming impinged. Video analysis results showed that the drop-chain trawl is effective at retaining targeted squid while allowing skates to escape. However, it is ineffective at avoiding the capture of summer flounder.
Pulse trawl fishing: characteristics of the electrical stimulation and the effect on behaviour and injuries of Atlantic cod (Gadus morhua)
Authors: de Haan D. , Fosseidengen J. E. , Fjelldal P. G. , Burggraaf D. , Rijnsdorp A. D. 
Published: March 2016

Abstract
In the North Sea flatfish fishery, electric pulse trawls have been introduced to replace the conventional mechanical method. Pulse trawls reduce the fuel consumption, reduce adverse impact on the ecosystem but cause injuries in gadoids. We describe the design and electrical properties of pulse trawls currently in use and study the behavioural response and injuries in cod exposed to electrical pulses under controlled conditions. Pulse trawls operate at an average power of 0.7 kW m−1 beam length and a duty cycle of ∼2%. The electric field is heterogeneous with highest field strength occurring close to the conductors. Cod were exposed to three different pulse types for a range of field strengths, frequencies, and duty cycles. Two size classes were tested representing cod that escape through the meshes (11–17 cm) and market-sized cod that are retained in the net (34–56 cm). Cod exposed to a field strength of ≥37 V m−1 responded by moderate-to-strong muscular contractions. Some of the large cod (n = 260) developed haemorrhages and fractures in the spine, and haemal and neural arches in the tail part of the body. The probability of injuries increased with field strength and decreased when frequency was increased from 100 to 180 Hz. None of the small cod (n = 132) were injured and all survived. The field strength at the lateral boundaries of the trawl was too low to inflict injuries in cod.
Spectral distortion of the CMB by the cumulative CO emission from galaxies throughout cosmic history
Authors: Mashian Natalie , Loeb Abraham , Sternberg Amiel 
Published: March 2016

Abstract
We show that the cumulative CO emission from galaxies throughout cosmic history distorts the spectrum of the cosmic microwave background at a level that is well above the detection limit of future instruments, such as the Primordial Inflation Explorer. The modelled CO signal has a prominent bump in the frequency interval 100–200 GHz, with a characteristic peak intensity of ∼2 × 10−23 W m−2 Hz−1 sr−1. Most of the CO foreground originates from modest redshifts, z ∼ 2–5, and needs to be efficiently removed for more subtle distortions from the earlier Universe to be detected.
Evaluation of Serum Creatinine Changes With Integrase Inhibitor Use in Human Immunodeficiency Virus-1 Infected Adults
Authors: Lindeman Tara A. , Duggan Joan M. , Sahloff Eric G. 
Published: March 2016

Abstract
This retrospective chart review evaluated changes in serum creatinine and creatinine clearance (CrCl) after initiation of an integrase inhibitor (INSTI)-based regimen as initial treatment in human immunodeficiency virus-infected adults. Serum creatinine and CrCl changes were similar to those seen in clinical trials for INSTIs. No renal-related serious adverse events or discontinuations occurred.
Middle Palaeolithic Diets
Authors: Morin Eugène , Speth John D. , Lee-Thorp Julia 
Published: March 2016

Abstract
This chapter examines the evidence for diet amongst Middle Palaeolithic foragers in Europe and south-west Asia from c. 300,000 to 40,000 years ago, concentrating on faunal and isotopic approaches. Published faunal evidence shows that Middle Palaeolithic hominins in both regions hunted a relatively narrow range of medium- to large-sized ungulates, with occasional exploitation of megaherbivores more evident in open sites than in caves and rockshelters. Broader diets have been documented in southern Europe, although regular consumption of fast, small-sized taxa emerged only later during the Upper Palaeolithic. Stable light isotope data, often interpreted as indicating that European Neanderthals were top-level predators preferring either megaherbivores, or bovids and horses, only partly accords with the faunal evidence. Taphonomic considerations suggest that energy procurement, especially as fat, and the effects of transport constraints have so far not been sufficiently considered when assessing the dietary composition of Middle Palaeolithic hominins.
Coptic
Authors: Orlandi Tito 
Published: March 2016

AbstractCoptic literature was born together with the Coptic language in Roman Egypt, around the third century, inside the Christian Church. It developed following the exigencies of the Church, together with a parallel literature in Greek: after biblical translations, and Gnosticizing (and Manichaean) treatises, homilies, canons, historical, and monastic texts were produced. After the Chalcedonian crisis, Coptic texts acquired a new autonomy, replacing Greek texts and supporting the life of the anti-Chalcedonian Church.
Shocking Behavior: Random Wealth in Antebellum Georgia and Human Capital Across Generations
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Authors: Bleakley Hoyt , Ferrie Joseph 
Published: March 2016

Abstract
Does the lack of wealth constrain parents’ investments in the human capital of their descendants? We conduct a nearly 50-year follow-up of an episode in which such constraints would have been plausibly relaxed by a random allocation of substantial wealth to families. We track descendants of participants in Georgia’s Cherokee Land Lottery of 1832, in which nearly every adult white male in the state took part. Winners received close to the median level of wealth—a large financial windfall orthogonal to participants’ underlying characteristics that might have also affected their children’s human capital. Although winners had slightly more children than did nonwinners, they did not send them to school more. Sons of winners have no better adult outcomes (wealth, income, literacy) than the sons of nonwinners, and winners’ grandchildren do not have higher literacy or school attendance than nonwinners’ grandchildren. We can reject effects implied by the cross-sectional gradient of child outcomes by paternal wealth. This suggests only a limited role for family financial resources in the formation of human capital in the next generations in this environment and a potentially more important role for other factors that persist through family lines.
Innovation, Competition, and Investment Timing
Authors: Koskinen Yrjö , Maeland Joril 
Published: March 2016

AbstractIn our model multiple innovators compete against each other by submitting investment proposals to an investor. The investor chooses the least expensive proposal and the timing of the investment. Innovators privately learn the cost of investing. The investor has to compensate the innovators for their reservation wages, but competition makes screening easier and helps to erode innovators’ informational rents. Consequently, competition leads to faster innovation, because the investor has less need to delay expensive investments. With an endogenous number of innovators investment timing becomes first best.Received June 5, 2013; accepted February 26, 2016 by Editor Paolo Fulghieri.
Neural Pattern Change During Encoding of a Narrative Predicts Retrospective Duration Estimates
Authors: Lositsky Olga , Chen Janice , Toker Daniel , Honey Christopher J. , Poppenk Jordan L. , Hasson Uri , Norman Kenneth A. 
Published: March 2016

AbstractWhat mechanisms support our ability to estimate durations on the order of minutes? Behavioral studies in humans have shown that changes in contextual features lead to overestimation of past durations. Based on evidence that the medial temporal lobes and prefrontal cortex represent contextual features, we related the degree of fMRI pattern change in these regions with people’s subsequent duration estimates. After listening to a radio story in the scanner, participants were asked how much time had elapsed between pairs of clips from the story. Our ROI analysis found that the neural pattern distance between two clips at encoding was correlated with duration estimates in the right entorhinal cortex and right pars orbitalis. Moreover, a whole-brain searchlight analysis revealed a cluster spanning the right anterior temporal lobe. Our findings provide convergent support for the hypothesis that retrospective time judgments are driven by “drift” in contextual representations supported by these regions.
Beyond clines: lineages and haplotype blocks in hybrid zones
Authors: Sedghifar Alisa , Brandvain Yaniv , Ralph Peter 
Published: March 2016

AbstractHybrid zones formed between recently diverged populations offer an opportunity to study the mechanisms underlying reproductive isolation and the process of speciation. Here, we use a combination of analytical theory and explicit forward simulations to describe how selection against hybrid genotypes impacts patterns of introgression across genomic and geographic space. By describing how lineages move across the hybrid zone, in a model without coalescence, we add to modern understanding of how clines form and how parental haplotypes are broken up during introgression. Working with lineages makes it easy to see that clines form in about 1/sgenerations, where s is the strength of selection against hybrids, and linked clines persist over a genomic scale of 1/T, whereTis the age, in generations, of the hybrid zone. Locally disadvantageous alleles tend to exist as small families, whose lineages trace back to the side from which they originated at speeddispersal distances per generation. The lengths of continuous tracts of ancestry provide an additional source of information: blocks of ancestry surrounding incompatibilities can be substantially longer than the genome-wide average block length at the same spatial location, an observation that might be used to identify candidate targets of selection.
Whole-genome characterization in pedigreed non-human primates using Genotyping-By-Sequencing and imputation
Authors: Bimber Ben N , Raboin Michael J , Letaw John , Nevonen Kimberly , Spindel Jennifer E , McCouch Susan R , Cervera-Juanes Rita , Spindel Eliot , Carbone Lucia , Ferguson Betsy , Vinson Amanda 
Published: March 2016

ABSTRACTBackgroundRhesus macaques are widely used in biomedical research, but the application of genomic information in this species to better understand human disease is still undeveloped. Whole-genome sequence (WGS) data in pedigreed macaque colonies could provide substantial experimental power, but the collection of WGS data in large cohorts remains a formidable expense. Here, we describe a cost-effective approach that selects the most informative macaques in a pedigree for whole-genome sequencing, and imputes these dense marker data into all remaining individuals having sparse marker data, obtained using Genotyping-By-Sequencing (GBS).ResultsWe developed GBS for the macaque genome using a single digest withPstI, followed by sequencing to 30X coverage. From GBS sequence data collected on all individuals in a 16-member pedigree, we characterized an optimal 22,455 sparse markers spaced ~125 kb apart. To characterize dense markers for imputation, we performed WGS at 30X coverage on 9 of the 16 individuals, yielding ~10.2 million high-confidence variants. Using the approach of “Genotype Imputation Given Inheritance” (GIGI), we imputed alleles at an optimized dense set of 4,920 variants on chromosome 19, using 490 sparse markers from GBS. We assessed changes in accuracy of imputed alleles, 1) across 3 different strategies for selecting individuals for WGS, i.e., a) using “GIGI-Pick” to select informative individuals, b) sequencing the most recent generation, or c) sequencing founders only; and 2) when using from 1-9 WGS individuals for imputation. We found that accuracy of imputed alleles was highest using the GIGI-Pick selection strategy (median 92%), and improved very little when using >4 individuals with WGS for imputation. We used this ratio of 4 WGS to 12 GBS individuals to impute an expanded set of ~14.4 million variants across all 20 macaque autosomes, achieving ~85-88% accuracy per chromosome.ConclusionsWe conclude that an optimal tradeoff exists at the ratio of 1 individual selected for WGS using the GIGI-Pick algorithm, per 3-5 relatives selected for GBS, a cost savings of ~67-83% over WGS of all individuals. This approach makes feasible the collection of accurate, dense genome-wide sequence data in large pedigreed macaque cohorts without the need for expensive WGS data on all individuals.