bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ontodog: a web-based ontology community view generation tool
Authors: Zheng Jie , Xiang Zuoshuang , Stoeckert Christian J. , He Yongqun 
Published: January 2014

Abstract
Summary: Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users, it is desirable to have community-based labels rather than the labels generated by ontology developers. Ontodog is a web-based system that can generate an ontology subset based on Excel input, and support generation of an ontology community view, which is defined as the whole or a subset of the source ontology with user-specified annotations including user-preferred labels. Ontodog allows users to easily generate community views with minimal ontology knowledge and no programming skills or installation required. Currently &gt;100 ontologies including all OBO Foundry ontologies are available to generate the views based on user needs. We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology.
Availability: http://ontodog.hegroup.org/
Contact: yongqunh@umich.edu
Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting
Authors: Planatscher Hannes , Weiß Frederik , Eisen David , van den Berg B.H.J. , Zell Andreas , Joos Thomas , Poetz Oliver 
Published: January 2014

Abstract
Motivation: Mass spectrometry-based protein profiling has become a key technology in biomedical research and biomarker discovery. Sample preparation strategies that reduce the complexity of tryptic digests by immunoaffinity substantially increase throughput and sensitivity in proteomic mass spectrometry. The scarce availability of peptide-specific capture antibodies limits these approaches. Recently antibodies directed against short terminal motifs were found to enrich subsets of peptides with identical terminal sequences. This approach holds the promise of a significant gain in efficiency. TXP (Triple X Proteomics) and context-independent motif specific/global proteome survey binders are variants of this concept. Principally the binding motifs of such antibodies have to be elucidated after generating these antibodies. This entails a substantial effort in the lab, as it requires synthetic peptide libraries and numerous mass spectrometry experiments.
Results: We present an algorithm for predicting the antibody-binding motif in a mass spectrum obtained from a tryptic digest of a common cell line after immunoprecipitation. The epitope prediction, based on peptide mass fingerprinting, reveals the most enriched terminal epitopes. The tool provides a P-value for each potential epitope, estimated by sampling random spectra from a peptide database. The second algorithm combines the predicted sequences to more complex binding motifs. A comparison with library screenings shows that the predictions made by the novel methods are reliable and reproducible indicators of the binding properties of an antibody.
Availability: Mass spectrum data, predictions, sampling tables, consensus peptide databases and the applied protocols are available as Supplementary Material. TXP-Terminus Enrichment Analysis (TEA) and MATERICS (Mass-spectrometric Analysis of Terminal Epitope Enrichment in Complex Samples) are available as web services at http://webservices.nmi.de/materics.
Contact: hannes.planatscher@nmi.de
Supplementary information: Supplementary data are available at Bioinformatics online.
CGARS: cancer genome analysis by rank sums
Authors: Lu Xin , Thomas Roman K. , Peifer Martin 
Published: January 2014

Abstract
Motivation: Cancer genomes are characterized by the accumulation of point mutations and structural alterations such as copy-number alterations and genomic rearrangements. Among structural changes, systematic analyses of copy-number alterations have provided deeper insight into the architecture of cancer genomes and had led to new potential treatment opportunities. During the course of cancer genome evolution, selection mechanisms are leading to a non-random pattern of mutational events contributing to fitness benefits of the cancer cells. We therefore developed a new method to dissect random from non-random patterns in copy-number data and thereby to assess significantly enriched somatic copy-number aberrations across a set of tumor specimens or cell lines. In contrast to existing approaches, the method is invariant to any strictly monotonous transformation of the input data which results to an insensitivity of differences in tumor purity, array saturation effects and copy-number baseline levels.
Results: We applied our approach to recently published datasets of small-cell lung cancer and squamous cell lung cancer and validated its performance by comparing the results to an orthogonal approach. In addition, we found a new deletion peak containing the HLA-A gene in squamous cell lung cancer.
Availability: The CGARS program package is available for download at http://www.translational-genomics.uni-koeln.de/scientific-resources/ Documentation and examples are available together with the package.
Contact: mpeifer@uni-koeln.de
Supplementary Information: Supplementary information is available at Bioinformatics online.
Prediction of nuclear export signals using weighted regular expressions (Wregex)
Authors: Prieto Gorka , Fullaondo Asier , Rodriguez Jose A. 
Published: January 2014

Abstract
Motivation: Leucine-rich nuclear export signals (NESs) are short amino acid motifs that mediate binding of cargo proteins to the nuclear export receptor CRM1, and thus contribute to regulate the localization and function of many cellular proteins. Computational prediction of NES motifs is of great interest, but remains a significant challenge.
Results: We have developed a novel approach for amino acid motif searching that can be used for NES prediction. This approach, termed Wregex (weighted regular expression), combines regular expressions with a position-specific scoring matrix (PSSM), and has been implemented in a web-based, freely available, software tool. By making use of a PSSM, Wregex provides a score to prioritize candidates for experimental testing. Key features of Wregex include its flexibility, which makes it useful for searching other types of protein motifs, and its fast execution time, which makes it suitable for large-scale analysis. In comparative tests with previously available prediction tools, Wregex is shown to offer a good rate of true-positive motifs, while keeping a smaller number of potential candidates.
Availability: Wregex is free, open-source software available from http://wregex.ehubio.es
Contact: gorka.prieto@ehu.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Random effect estimation of time-varying factors in Stock Synthesis
Authors: Thorson James T. , Hicks Allan C. , Methot Richard D. 
Published: January 2014

AbstractBiological processes such as fishery selectivity, natural mortality, and somatic growth can vary over time, but it is challenging to estimate the magnitude of time-variation of demographic parameters in population dynamics models, particularly when using penalized-likelihood estimation approaches. Random-effect approaches can estimate the variance, but are computationally infeasible or not implemented for many models and software packages. We show that existing models and software based on penalized-likelihood can be used to calculate the Laplace approximation to the marginal likelihood of parameters representing variability over time, and specifically demonstrate this approach via application to Stock Synthesis. Using North Sea cod and Pacific hake models as case studies, we show that this method has little bias in estimating variances for simulated data. It also provides a similar estimate of variability in hake recruitment (log-SD = 1.43) to that obtained from Markov chain Monte Carlo (MCMC) methods (log-SD = 1.68), and the method estimates a non-trivial magnitude (log-SD = 0.07) of variation in growth for North Sea cod. We conclude by discussing the generality of the proposed method and by recommending future research regarding its performance relative to MCMC, particularly when estimating multiple variances simultaneously.
Organization of the human mitochondrial transcription initiation complex
Authors: Yakubovskaya Elena , Guja Kip E. , Eng Edward T. , Choi Woo Suk , Mejia Edison , Beglov Dmitri , Lukin Mark , Kozakov Dima , Garcia-Diaz Miguel 
Published: January 2014

AbstractInitiation of transcription in human mitochondria involves two factors, TFAM and TFB2M, in addition to the mitochondrial RNA polymerase, POLRMT. We have investigated the organization of the human mitochondrial transcription initiation complex on the light-strand promoter (LSP) through solution X-ray scattering, electron microscopy (EM) and biochemical studies. Our EM results demonstrate a compact organization of the initiation complex, suggesting that protein–protein interactions might help mediate initiation. We demonstrate that, in the absence of DNA, only POLRMT and TFAM form a stable interaction, albeit one with low affinity. This is consistent with the expected transient nature of the interactions necessary for initiation and implies that the promoter DNA acts as a scaffold that enables formation of the full initiation complex. Docking of known crystal structures into our EM maps results in a model for transcriptional initiation that strongly correlates with new and existing biochemical observations. Our results reveal the organization of TFAM, POLRMT and TFB2M around the LSP and represent the first structural characterization of the entire mitochondrial transcriptional initiation complex.
Binary recombinase systems for high-resolution conditional mutagenesis
Authors: Hermann Mario , Stillhard Patrick , Wildner Hendrik , Seruggia Davide , Kapp Viktor , Sánchez-Iranzo Héctor , Mercader Nadia , Montoliu Lluís , Zeilhofer Hanns Ulrich , Pelczar Pawel 
Published: January 2014

Abstract
Conditional mutagenesis using Cre recombinase expressed from tissue specific promoters facilitates analyses of gene function and cell lineage tracing. Here, we describe two novel dual-promoter-driven conditional mutagenesis systems designed for greater accuracy and optimal efficiency of recombination. Co-Driver employs a recombinase cascade of Dre and Dre-respondent Cre, which processes loxP-flanked alleles only when both recombinases are expressed in a predetermined temporal sequence. This unique property makes Co-Driver ideal for sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types. Co-InCre was designed for highly efficient intersectional conditional transgenesis. It relies on highly active trans-splicing inteins and promoters with simultaneous transcriptional activity to reconstitute Cre recombinase from two inactive precursor fragments. By generating native Cre, Co-InCre attains recombination rates that exceed all other binary SSR systems evaluated in this study. Both Co-Driver and Co-InCre significantly extend the utility of existing Cre-responsive alleles.
SIANN: Strain Identification by Alignment to Near Neighbors
Authors: Minot Samuel S. , Turner Stephen D. , Ternus Krista L. , Kadavy Dana R. 
Published: January 2014

AbstractNext-generation sequencing is increasingly being used to study samples composed of mixtures of organisms, such as in clinical applications where the presence of a pathogen at very low abundance may be highly important. We present an analytical method (SIANN: Strain Identification by Alignment to Near Neighbors) specifically designed to rapidly detect a set of target organisms in mixed samples that achieves a high degree of species- and strain-specificity by aligning short sequence reads to the genomes of near neighbor organisms, as well as that of the target. Empirical benchmarking alongside the current state-of-the-art methods shows an extremely high Positive Predictive Value, even at very low abundances of the target organism in a mixed sample. SIANN is available as an Illumina BaseSpace app, as well as through Signature Science, LLC. SIANN results are presented in a streamlined report designed to be comprehensible to the non-specialist user, providing a powerful tool for rapid species detection in a mixed sample. By focusing on a set of (customizable) target organisms and their near neighbors, SIANN can operate quickly and with low computational requirements while delivering highly accurate results.
Ecological and Evolutionary Oscillations in Host-Parasite Population Dynamics, and The Red Queen
Authors: Rabajante Jomar F. 
Published: January 2014

AbstractIn a host-parasite system, the constitutive interaction among the species, regulated by the growth rates and functional response, may induce populations to approach equilibrium or sometimes to exhibit simple cycles or peculiar oscillations, such as chaos. A large carrying capacity coupled with appropriate parasitism effectiveness frequently drives long-term apparent oscillatory dynamics in population size. We name these oscillations due to the structure of the constitutive interaction among species asecological.On the other hand, there are also exceptional cases when the evolving quantitative traits of the hosts and parasites induce oscillating population size, which we call asevolutionary. This oscillatory behavior is dependent on the speed of evolutionary adaptation and degree of evolutionary trade-off. A moderate level of negative trade-off is essential for the existence of oscillations. Evolutionary oscillations due to the host-parasite coevolution (known as the Red Queen) can be observed beyond the ecological oscillations, especially when there are more than two competing species involved.One Sentence SummaryWe investigate several cases yielding to oscillating host-parasite populations, and we found that the Red Queen hypothesis can explain some of the exceptional cases.Graphical Abstract:
Opposing Microtubule Motors Control Motility, Morphology, and Cargo Segregation During ER-to-Golgi Transport
Authors: Brown Anna K. , Hunt Sylvie D. , Stephens David J. 
Published: January 2014

SummaryWe recently demonstrated that dynein and kinesin motors drive multiple aspects of endosomal function in mammalian cells. These functions include driving motility, maintaining morphology (notably through providing longitudinal tension to support vesicle fission), and driving cargo sorting. Microtubule motors drive bidirectional motility during traffic between the endoplasmic reticulum (ER) and Golgi. Here, we have examined the role of microtubule motors in transport carrier motility, morphology, and domain organization during ER-to-Golgi transport. We show that consistent with our findings for endosomal dynamics, microtubule motor function during ER-to-Golgi transport of secretory is required for motility, morphology of, and cargo sorting within vesicular tubular carriersen routeto the Golgi. Our data are consistent with previous findings that defined roles for dynein-1 and kinesin-1 (KIF5B) and kinesin-2 in this trafficking step. Our high resolution tracking data identify some intriguing aspects. Depletion of kinesin-1 reduces the number of motile structures seen which is in line with other findings relating to the role of kinesin-1 in ER export. However, those transport carriers that were produced had a much greater run length suggesting that this motor can act as a brake on anterograde motility. Kinesin-2 depletion did not significantly reduce the number of motile transport carriers but did cause a similar increase in run length. These data suggest that kinesins act as negative regulators of ER-to-Golgi transport. Depletion of dynein not only reduced the number of motile carriers formed but also caused tubulation of carriers similar to that seen for SNX-coated early endosomes. Our data indicated that the previously observed anterograde-retrograde polarity of transport carriers in transit to the Golgi from the ER is maintained by microtubule motor function.
Transcriptional Regulation of Fruit Ripening by Tomato FRUITFULL Homologs and Associated MADS Box Proteins
Authors: Fujisawa Masaki , Shima Yoko , Nakagawa Hiroyuki , Kitagawa Mamiko , Kimbara Junji , Nakano Toshitsugu , Kasumi Takafumi , Ito Yasuhiro 
Published: January 2014

AbstractThe tomato (Solanum lycopersicum) MADS box FRUITFULL homologs FUL1 and FUL2 act as key ripening regulators and interact with the master regulator MADS box protein RIPENING INHIBITOR (RIN). Here, we report the large-scale identification of direct targets of FUL1 and FUL2 by transcriptome analysis of FUL1/FUL2 suppressed fruits and chromatin immunoprecipitation coupled with microarray analysis (ChIP-chip) targeting tomato gene promoters. The ChIP-chip and transcriptome analysis identified FUL1/FUL2 target genes that contain at least one genomic region bound by FUL1 or FUL2 (regions that occur mainly in their promoters) and exhibit FUL1/FUL2-dependent expression during ripening. These analyses identified 860 direct FUL1 targets and 878 direct FUL2 targets; this set of genes includes both direct targets of RIN and nontargets of RIN. Functional classification of the FUL1/FUL2 targets revealed that these FUL homologs function in many biological processes via the regulation of ripening-related gene expression, both in cooperation with and independent of RIN. Our in vitro assay showed that the FUL homologs, RIN, and tomato AGAMOUS-LIKE1 form DNA binding complexes, suggesting that tetramer complexes of these MADS box proteins are mainly responsible for the regulation of ripening.
Accuracy of background matching and prey detection: predation by blue tits indicates intense selection for highly matching prey colour pattern
Authors: Merilaita Sami , Dimitrova Marina 
Published: January 2014

Summary

Although background matching decreases prey detectability, resemblance between camouflaged prey and their visual background is seldom perfect. This could be because even a moderate resemblance might provide sufficient protection, and additional adjustment of colour pattern might give little benefit. Alternatively, close resemblance to background may not be attained due to trade‐offs or constraints. To understand selection on colour patterns of camouflaged prey and the existence of inaccurate background matching, it is necessary to investigate how detectability of a colour pattern varies with its resemblance to the background.

We trained wild‐caught blue tits (Cyanistes caeruleus) to search for artificial prey. We manipulated the resemblance of the artificial prey items to the visual backgrounds.

For the first half of the twelve repeated prey presentations, we found a nonlinear relationship between resemblance and detectability such that for prey that had high background matching, a change in resemblance resulted in a larger change in detectability than an equal change in resemblance did for prey with lower background matching. However, for the second half of the presentations, this relationship was linear. Moreover, in a two‐patch‐type habitat, a prey pattern that was a compromise between the two different backgrounds did after few initial presentations equally well as the prey pattern that matched highly one of the backgrounds.

Our results indicate an intense selection for close matching in a single background. Yet, in the heterogeneous environment that consisted of two backgrounds, the compromise, which only loosely resembled either background, provided good protection. Therefore, we conclude that cryptic colour patterns that bear only a loose resemblance to a given background, and thus represent inaccurate background matching, may be adaptive outcomes.
Large‐scale movements in European badgers: has the tail of the movement kernel been underestimated?
Authors: Byrne Andrew W. , Quinn John L. , O'Keeffe James J. , Green Stuart , Paddy Sleeman D. , Wayne Martin S. , Davenport John 
Published: January 2014

Summary

Characterizing patterns of animal movement is a major aim in population ecology, and yet doing so at an appropriate spatial scale remains a major challenge. Estimating the frequency and distances of movements is of particular importance when species are implicated in the transmission of zoonotic diseases.

European badgers (Meles meles) are classically viewed as exhibiting limited dispersal, and yet their movements bring them into conflict with farmers due to their potential to spread bovine tuberculosis in parts of their range. Considerable uncertainty surrounds the movement potential of badgers, and this may be related to the spatial scale of previous empirical studies. We conducted a large‐scale mark–recapture study (755 km2; 2008–2012; 1935 capture events; 963 badgers) to investigate movement patterns in badgers, and undertook a comparative meta‐analysis using published data from 15 European populations.

The dispersal movement (>1 km) kernel followed an inverse power‐law function, with a substantial ‘tail’ indicating the occurrence of rare long‐distance dispersal attempts during the study period. The mean recorded distance from this distribution was 2·6 km, the 95 percentile was 7·3 km and the longest recorded was 22·1 km. Dispersal frequency distributions were significantly different between genders; males dispersed more frequently than females, but females made proportionally more long‐distance dispersal attempts than males.

We used a subsampling approach to demonstrate that the appropriate minimum spatial scale to characterize badger movements in our study population was 80 km2, substantially larger than many previous badger studies. Furthermore, the meta‐analysis indicated a significant association between maximum movement distance and study area size, while controlling for population density. Maximum long‐distance movements were often only recorded by chance beyond the boundaries of study areas.

These findings suggest that the tail of the badger movement distribution is currently underestimated. The implications of this for understanding the spatial ecology of badger populations and for the design of disease intervention strategies are potentially significant.
Optimisation of a pilot‐scale spray drying process for probiotic yoghurt, using response surface methodology
Authors: Izadi Masoumeh , Eskandari Mohammad Hadi , Niakousari Mehrdad , Shekarforoush Shahram , Hanifpour Mahammad Amin , Izadi Zahra 
Published: January 2014

The influence of drying air temperatures, drying air flow rate and feed flow rate on percentage survival rate (% SR) of starter and probiotic bacteria, moisture content, water activity and colour of probiotic yoghurt powder produced using a pilot‐scale spray dryer was investigated. Optimisation of spray drying conditions was achieved based on the desirability value. Results showed that inlet air temperature, drying air flow rate, feed flow rate and outlet air temperature of 150 °C, 478 m3/h, 2 L/h and 63.3 °C, respectively, were optimal conditions to produce powder that meets quality specifications and with a satisfactory% SR.