bluuebunny/crossref_metadata_2025_split huggingface dataset:
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles
Authors: Franceschini Andrea , Lin Jianyi , von Mering Christian , Jensen Lars Juhl 
Published: November 2015

Abstract
Summary: A successful approach for predicting functional associations between non-homologous genes is to compare their phylogenetic distributions. We have devised a phylogenetic profiling algorithm, SVD-Phy, which uses truncated singular value decomposition to address the problem of uninformative profiles giving rise to false positive predictions. Benchmarking the algorithm against the KEGG pathway database, we found that it has substantially improved performance over existing phylogenetic profiling methods.
Availability and implementation: The software is available under the open-source BSD license at https://bitbucket.org/andrea/svd-phy
Contact: lars.juhl.jensen@cpr.ku.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
MetaQUAST: evaluation of metagenome assemblies
Authors: Mikheenko Alla , Saveliev Vladislav , Gurevich Alexey 
Published: November 2015

Abstract
Summary: During the past years we have witnessed the rapid development of new metagenome assembly methods. Although there are many benchmark utilities designed for single-genome assemblies, there is no well-recognized evaluation and comparison tool for metagenomic-specific analogues. In this article, we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (i) unknown species content by detecting and downloading reference sequences, (ii) huge diversity by giving comprehensive reports for multiple genomes and (iii) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets.
Availability and implementation: http://bioinf.spbau.ru/metaquast.
Contact: aleksey.gurevich@spbu.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
Mechanics and thermal management of stretchable inorganic electronics
Authors: Song Jizhou , Feng Xue , Huang Yonggang 
Published: November 2015

Abstract
Stretchable electronics enables lots of novel applications ranging from wearable electronics, curvilinear electronics to bio-integrated therapeutic devices that are not possible through conventional electronics that is rigid and flat in nature. One effective strategy to realize stretchable electronics exploits the design of inorganic semiconductor material in a stretchable format on an elastomeric substrate. In this review, we summarize the advances in mechanics and thermal management of stretchable electronics based on inorganic semiconductor materials. The mechanics and thermal models are very helpful in understanding the underlying physics associated with these systems, and they also provide design guidelines for the development of stretchable inorganic electronics.
Suzaku study on the ejecta of the supernova remnant G272.2−3.2
Authors: Kamitsukasa Fumiyoshi , Koyama Katsuji , Nakajima Hiroshi , Hayashida Kiyoshi , Mori Koji , Katsuda Satoru , Uchida Hiroyuki , Tsunemi Hiroshi 
Published: November 2015

Abstract
We report reanalyses of the Suzaku observations of the Galactic supernova remnant (SNR) G272.2−3.2, for which previous studies were limited below 3 keV. With careful data reduction and background subtraction, we discover the K-shell lines of Ar, Ca, and Fe above 3 keV. The X-ray spectrum of G272.2−3.2 consists of two components, a low-temperature collisional ionization equilibrium (CIE) plasma (kTe ∼ 0.2 keV) and a high-temperature non-equilibrium ionization (NEI) plasma (kTe = 0.6–3 keV). The CIE plasma has solar abundances over the entire area, hence it originates from the interstellar medium. On the other hand, the abundances of the NEI plasma increase toward the inner region, suggesting ejecta origin. The line center energy of the Fe K-shell emission (∼6.4 keV) suggests that the ejecta are recently heated by reverse shock, a common feature in Type Ia SNRs.
BAGEL: A computational framework for identifying essential genes from pooled library screens
Authors: Hart Traver , Moffat Jason 
Published: November 2015

AbstractBackgroundThe adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed.ResultsWe offer BAGEL (Bayesian Analysis of Gene EssentiaLity), a supervised learning method for analyzing gene knockout screens. Coupled with gold-standard reference sets of essential and nonessential genes, BAGEL offers significantly greater sensitivity than current methods, while computational optimizations reduce runtime by an order of magnitude.ConclusionsUsing BAGEL, we identify ~2,000 fitness genes in pooled library knockout screens in human cell lines at 5% FDR, a major advance over competing platforms. BAGEL shows high sensitivity and specificity even across screens with highly variable reagent quality.
Novel Intronic Non-Coding RNAs Contribute to Maintenance of Phenotype inSaccharomyces Cerevisiae
Authors: Hooks Katarzyna B , Naseeb Samina , Griffiths-Jones Sam , Delneri Daniela 
Published: November 2015

ABSTRACTTheSaccharomyces cerevisiaegenome has undergone extensive intron loss during its evolutionary history. It has been suggested that the few remaining introns (in only 5% of protein-coding genes) are retained because of their impact on function under stress conditions. Here, we explore the possibility that novel non-coding RNA structures (ncRNAs) are embedded within intronic sequences and are contributing to phenotype and intron retention in yeast. We employedde novoRNA structure prediction tools to screen intronic sequences inS. cerevisiaeand 36 other fungi. We identified and validated 19 new intronic RNAs via RNAseq and RT-PCR. Contrary to common belief that excised introns are rapidly degraded, we found that, in six cases, the excised introns were maintained intact in the cells. In other two cases we showed that the ncRNAs were further processed from their introns. RNAseq analysis confirmed higher expression of introns in the ribosomial protein genes containing predicted RNA structures. We deleted the novel intronic RNA structure within theGLC7intron and showed that this predicted ncRNA, rather than the intron itself, is responsible for the cell’s ability to respond to salt stress. We also showed a direct association between the presence of the intronic ncRNA andGLC7expression. Overall, these data support the notion that some introns may have been maintained in the genome because they harbour functional ncRNAs.
Unearthing New Genomic Markers of Drug Response by Improved Measurement of Discriminative Power
Authors: Dang Cuong C. , Peón Antonio , Ballester Pedro J. 
Published: November 2015

AbstractBackgroundOncology drugs are only effective in a small proportion of cancer patients. Our current ability to identify these responsive patients before treatment is still poor in most cases. Thus, there is a pressing need to discover response markers for marketed and research oncology drugs in order to improve patient survival, reduce healthcare costs and enhance success rates in clinical trials. Screening these drugs against a large panel of cancer cell lines has been employed to discover new genomic markers ofin vitrodrug response, which can now be further evaluated on more accurate tumour models. However, while the identification of discriminative markers among thousands of candidate drug-gene associations in the data is error-prone, an appraisal of the effectiveness of such detection task is currently lacking.ResultsHere we present a new non-parametric method to measuring the discriminative power of a drug-gene association. This is enabled by the identification of an auxiliary threshold posing this task as a binary classification problem. Unlike parametric statistical tests, the adopted non-parametric test has the advantage of not making strong assumptions about the data distorting the identification of genomic markers. Furthermore, we introduce a new benchmark to further validate these markersin vitrousing more recent data not used to identify the markers. The application of this new methodology has led to the identification of 128 new genomic markers distributed across 61% of the analysed drugs, including 5 drugs without previously known markers, which were missed by the MANOVA test initially applied to analyse data from the Genomics of Drug Sensitivity in Cancer consortium.Abbreviation(WT)wild-type(GDSC)Genomics of Drug Sensitivity in Cancer(TP)true positive(TN)true negative(FP)false positive(FN)false negative(MCC)Matthews Correlation Co-efficient.
Sequenceserver: a modern graphical user interface for custom BLAST databases
Authors: Priyam Anurag , Woodcroft Ben J. , Rai Vivek , Munagala Alekhya , Moghul Ismail , Ter Filip , Gibbins Mark Anthony , Moon HongKee , Leonard Guy , Rumpf Wolfgang , Wurm Yannick 
Published: November 2015

AbstractThe dramatic drop in DNA sequencing costs has created many opportunities for novel biological research. These opportunities largely rest upon the ability to effectively compare newly obtained and previously known sequences. This is commonly done with BLAST, yet using BLAST directly on new datasets requires substantial technical skills or helpful colleagues. Furthermore, graphical interfaces for BLAST are challenging to install and largely mimic underlying computational processes rather than work patterns of researchers.We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver (http://sequenceserver.com), a modern graphical user interface for BLAST. Sequenceserver substantially increases the efficiency of researchers working with sequence data. This is due to innovations at three levels. First, our software can be installed and used on custom datasets extremely rapidly for personal and shared applications. Second, based on analysis of user input and simple algorithms, Sequenceserver reduces the amount of decisions the user must make, provides interactive visual feedback, and prevents common potential errors that would otherwise cause erroneous results. Finally, Sequenceserver provides multiple highly visual and text-based output options that mirror the requirements and work patterns of researchers. Together, these features greatly facilitate BLAST analysis and interpretation and thus substantially enhance researcher productivity.
Meiotic interactors of a mitotic geneTAO3revealed by functional analysis of its rare variant
Authors: Gupta Saumya , Radhakrishnan Aparna , Nitin Rachana , Raharja-Liu Pandu , Lin Gen , Steinmetz Lars M. , Gagneur Julien , Sinha Himanshu 
Published: November 2015

ABSTRACTStudying the molecular consequences of rare genetic variants has the potential of identifying novel and hereto uncharacterized pathways causally contributing to phenotypic variation. Here we characterize the functional consequences of a rare coding variant ofTAO3, previously reported to significantly contribute to sporulation efficiency variation inSaccharomyces cerevisiae. During mitosisTAO3interacts withCBK1, a conserved NDR kinase and a component of RAM network. The RAM network genes are involved in regulation cell separation and polarization. We demonstrate that the role of the rare alleleTAO3(4477C)in meiosis is distinct from its role in mitosis by being independent ofACE2, which is a RAM network target gene. By quantitatively measuring cell morphological dynamics and conditionally expressingTAO3(4477C)allele during sporulation, we show thatTAO3has an early role in meiosis. This early role ofTAO3coincides with entry of cells into meiotic division. Time-resolved transcriptome analyses during early sporulation phase identified regulators of carbon and lipid metabolic pathways as candidate mediators. We experimentally show that during sporulation theTAO3allele genetically interacts withERT1andPIP2, the regulators of tricarboxylic acid cycle and gluconeogenic enzymes, respectively. We thus uncover meiotic functions ofTAO3, a mitotic gene and proposeERT1andPIP2as novel regulators of sporulation efficiency. Our results demonstrate that study of causal effects of genetic variation on the underlying molecular network has the potential to provide more extensive comprehension of the pathways driving a complex trait. This can help identify prospective personalized targets for intervention in complex diseases.
Sex‐specific and individual preferences for hunting strategies in white sharks
Authors: Towner Alison V. , Leos‐Barajas Vianey , Langrock Roland , Schick Robert S. , Smale Malcolm J. , Kaschke Tami , Jewell Oliver J. D. , Papastamatiou Yannis P. 
Published: November 2015

Summary

Fine‐scale predator movements may be driven by many factors including sex, habitat and distribution of resources. There may also be individual preferences for certain movement strategies within a population which can be hard to quantify.

Within top predators, movements are also going to be directly related to the mode of hunting, for example sit‐and‐wait or actively searching for prey. Although there is mounting evidence that different hunting modes can cause opposing trophic cascades, there has been little focus on the modes used by top predators, especially those in the marine environment.

Adult white sharks (Carcharhodon carcharias) are well known to forage on marine mammal prey, particularly pinnipeds. Sharks primarily ambush pinnipeds on the surface, but there has been less focus on the strategies they use to encounter prey.

We applied mixed hidden Markov models to acoustic tracking data of white sharks in a coastal aggregation area in order to quantify changing movement states (area‐restricted searching (ARS) vs. patrolling) and the factors that influenced them. Individuals were re‐tracked over multiple days throughout a month to see whether state‐switching dynamics varied or if individuals preferred certain movement strategies.

Sharks were more likely to use ARS movements in the morning and during periods of chumming by ecotourism operators. Furthermore, the proportion of time individuals spent in the two different states and the state‐switching frequency, differed between the sexes and between individuals.

Predation attempts/success on pinnipeds were observed for sharks in both ARS and patrolling movement states and within all random effects groupings. Therefore, white sharks can use both a ‘sit‐and‐wait’ (ARS) and ‘active searching’ (patrolling) movements to ambush pinniped prey on the surface.

White sharks demonstrate individual preferences for fine‐scale movement patterns, which may be related to their use of different hunting modes. Marine top predators are generally assumed to use only one type of hunting mode, but we show that there may be a mix within populations. As such, individual variability should be considered when modelling behavioural effects of predators on prey species.
Silicon in aquatic vegetation
Authors: Schoelynck Jonas , Struyf Eric 
Published: November 2015

Summary

Silicon (Si) use by plants has not always received the research attention of other elements. Yet today, the importance of Si for plant functioning is slowly becoming better understood. Si is a crucial element for many terrestrial plant species (especially grasses), yet a recent surge of research has shown that some species of aquatic plants contain significant amounts of Si too.

We argue that degree of Si accumulation is a functional trait in aquatic vegetation, with plants adapting to environmental conditions. Aquatic vegetation can show apparent plasticity regarding Si uptake, adaptive to water and wind dynamics, light interception, herbivory and nutrient stress. Beyond a plant physiological viewpoint, high Si uptake results in high BSi in plant litter, which can impact on aquatic decomposition processes. Si content in aquatic vegetation shows intriguing relations with other strength components such as cellulose and lignin. Si content has also been linked to fungal and microbial community, litter stoichiometry and invertebrate shredders: all factors that potentially influence organic turnover in aquatic sediments.

Uptake of Si by aquatic vegetation is thus not only an important transient sink for Si in the global biogeochemical Si cycle, it can also affect carbon turnover in aquatic ecosystems. Experimental and field studies should be conducted to elucidate controls on aquatic plant Si uptake, especially focusing on interactive effects of multiple biotic and abiotic factors. This review provides an overview of the state‐of‐the‐art knowledge on silicon in aquatic vegetation.
Above‐ground and below‐ground responses to long‐term nutrient addition across a retrogressive chronosequence
Authors: Wardle David A. , Jonsson Micael , Mayor Jordan R. , Metcalfe Daniel B. 
Published: November 2015

Summary

There is much interest in understanding ecosystem responses to local‐scale soil fertility variation, which has often been studied using retrogressive chronosequences that span thousands of years and show declining fertility and plant productivity over time. There have been few attempts to experimentally test how plant nutrient limitation changes during retrogression.

We studied a well‐characterized system of 30 forested lake islands in northern Sweden that collectively represent a 5350‐year post‐fire retrogressive chronosequence, with fertility and productivity decreasing as time since fire increases. For each island, we set up four plots on understorey vegetation, each subjected to a different fertilizer treatment over 6 years: no additions, nitrogen (N) only, phosphorus (P) only and N + P.

We found that both N and P additions reduced feather moss and thus total plant biomass. Meanwhile, the three dominant vascular plant species showed contrasting biomass responses, but similar responses of foliar nutrient concentrations to nutrient additions. Fertilization reduced most microbial groups and altered CO2 fluxes, most likely through feather moss reduction. Against expectations, the majority of interactive effects of N and P were antagonistic.

Changes in effects of nutrient additions during retrogression were usually modest. Empetrum hermaphroditum biomass was increasingly promoted by P and N + P addition, while vascular plant N‐to‐P ratios were increasingly reduced by P addition, indicating increasing plant limitation by nutrients (notably P) during retrogression. Below‐ground, positive effects of N addition on soil mineral N increased, while negative effects of N addition on soil fungi decreased during retrogression; no other below‐ground effects of fertilization changed along the gradient.

Synthesis. Our results show that forest understorey communities on islands of different fire history and thus stages of retrogression show relatively modest differences in how they respond to nutrient addition despite large changes in ecosystem productivity and soil fertility, probably because of high species turnover and adaptation of communities to infertile conditions. While increased nutrient availability (as expected through global change) may have important ecological consequences, these effects are likely, especially below‐ground, to be rather similar across ecosystems that differ greatly in nutrient availability and productivity.
Effects of spatial plant–soil feedback heterogeneity on plant performance in monocultures
Authors: Wubs E. R. Jasper , Bezemer T. Martijn 
Published: November 2015

Summary

Plant–soil feedback (PSF) effects have almost exclusively been quantified on homogeneous soils, but as different plant species will influence their local soil differently, in reality PSF effects will be spatially heterogeneous. Whether plant performance in soils with spatially heterogeneous PSF can be predicted from pot experiments with homogeneous soils is unclear.

In a glasshouse experiment, we tested the response of monocultures of six grassland species (two grasses, two legumes and two forbs) to three spatially explicit treatments (fine‐grained heterogeneity, coarse‐grained heterogeneity and homogeneous). Sixteen patches of conditioned soil (˜6 × 6 cm) were placed within each container. For homogeneous treatments, all patches contained the same conditioned soil within a container. The fine‐grained heterogeneous treatment contained four differently conditioned soils that were applied following a Latin square design, while for the coarse‐grained heterogeneous treatment, four contiguous square blocks of four cells each were created in each container.

In general, species grew worse on soil conditioned by conspecifics. However, when the biomass production on all homogeneous soil treatments (own and foreign soils) was averaged and compared to the heterogeneous treatments, we found that biomass production was lower than expected in the heterogeneous soils. This effect of heterogeneity depended on both the conditioning and test species, but most heterogeneity effects were negative. The grain of the heterogeneity (coarse vs. fine: at the chosen spatial scale) did not affect plant performance.

We hypothesize that a more diverse soil community is present in spatially heterogeneous soils. This increases (i) the chance of plants to encounter its antagonists, which may then rapidly increase in numbers; and (ii) the scope for synergistic co‐infections. Together, this may lead to non‐additive responses of plants to spatial heterogeneity in PSF.

Synthesis. Plant performance was lower in spatially heterogeneous soils than predicted by spatially homogeneous soils. In natural grasslands that have mixed plant communities conditioning the soil, plant–soil feedback (PSF) effects on plant performance may therefore be more negative than what is predicted from pot experiments. Our results emphasize the need to incorporate the spatial dynamics of PSF both in empirical and modelling studies if we are to understand the role of PSF in plant–plant interactions and plant community dynamics.
Public Pressure and Corporate Tax Behavior
Authors: DYRENG SCOTT D. , HOOPES JEFFREY L. , WILDE JARON H. 
Published: November 2015

ABSTRACTWe use a shock to the public scrutiny of firm subsidiary locations to investigate whether that scrutiny leads to changes in firms’ disclosure and corporate tax avoidance behavior. ActionAid International, a nonprofit activist group, levied public pressure on noncompliant U.K. firms in the FTSE 100 to comply with a rule requiring U.K. firms to disclose the location of all of their subsidiaries. We use this setting to examine whether the public pressure led scrutinized firms to increase their subsidiary disclosure, decrease tax avoidance, and reduce the use of subsidiaries in tax haven countries compared to other firms in the FTSE 100 not affected by the public pressure. The evidence suggests that the public scrutiny sufficiently changed the costs and benefits of tax avoidance such that tax expense increased for scrutinized firms. The results suggest that public pressure from outside activist groups can exert a significant influence on the behavior of large, publicly traded firms. Our findings extend prior research that has had little success documenting an empirical relation between public scrutiny of tax avoidance and firm behavior.