bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-existence of three-dimensional travelling water waves with constant non-zero vorticity
Authors: Wahlén E. 
Published: April 2014

AbstractWe prove that there are no three-dimensional bounded travelling gravity waves with constant non-zero vorticity on water of finite depth. The result also holds for gravity–capillary waves under a certain condition on the pressure at the surface, which is satisfied by sufficiently small waves. The proof relies on unique continuation arguments and Liouville-type results for elliptic equations.
Language universals at birth
Authors: Gómez David Maximiliano , Berent Iris , Benavides-Varela Silvia , Bion Ricardo A. H. , Cattarossi Luigi , Nespor Marina , Mehler Jacques 
Published: April 2014

SignificanceIt is well known that across languages, certain structures are preferred to others. For example, syllables likeblifare preferred to syllables likebdifandlbif. But whether such regularities reflect strictly historical processes, production pressures, or universal linguistic principles is a matter of much debate. To address this question, we examined whether some precursors of these preferences are already present early in life. The brain responses of newborns show that, despite having little to no linguistic experience, they reacted to syllables likeblif, bdif,andlbifin a manner consistent with adults’ patterns of preferences. We conjecture that this early—possibly universal—bias helps shaping language acquisition.
Trait-mediated assembly processes predict successional changes in community diversity of tropical forests
Authors: Lasky Jesse R. , Uriarte María , Boukili Vanessa K. , Chazdon Robin L. 
Published: April 2014

Significance
The assembly of ecological communities results from multiple mechanisms acting concurrently. Disentangling their relative importance represents a major challenge. Our study quantifies the relative importance of four trait-mediated mechanisms and associated changes in functional diversity over succession. We leverage the rapid community assembly in tropical successional forests and the rich information in functional trait data and spatially explicit long-term tree demographic data. Trait correlations with average species survival rates were the most important processes affecting survival and linked to a decrease in wood trait diversity during succession. Simultaneously, evidence for stabilizing niche differences associated with leaf traits was reflected in increasing leaf functional diversity. Our results suggest mechanisms by which individual performance affects successional change in community-wide diversity.
Neural representations of ethologically relevant hand/mouth synergies in the human precentral gyrus
Authors: Desmurget Michel , Richard Nathalie , Harquel Sylvain , Baraduc Pierre , Szathmari Alexandru , Mottolese Carmine , Sirigu Angela 
Published: April 2014

Significance
The motor repertoire of infants is narrow. Yet newborns can accurately bring their hands toward their mouth for self-feeding, thumb-sucking, or perioral exploration, thus showing fine coordinated movement synergies between the hand and mouth. Here, we show that these gestures of high ethological value are selectively encoded in the human brain and represented as integrated primitives within the precentral gyrus, a key region for sensorimotor processing. These findings have major implications for our understanding of the organization and phylogenesis of motor functions in primates.
Compound facial expressions of emotion
Authors: Du Shichuan , Tao Yong , Martinez Aleix M. 
Published: April 2014

Significance
Though people regularly recognize many distinct emotions, for the most part, research studies have been limited to six basic categories—happiness, surprise, sadness, anger, fear, and disgust; the reason for this is grounded in the assumption that only these six categories are differentially represented by our cognitive and social systems. The results reported herein propound otherwise, suggesting that a larger number of categories is used by humans.
Bypass of the pre-60S ribosomal quality control as a pathway to oncogenesis
Authors: Sulima Sergey O. , Patchett Stephanie , Advani Vivek M. , De Keersmaecker Kim , Johnson Arlen W. , Dinman Jonathan D. 
Published: April 2014

SignificanceRibosomopathies are paradoxical: They first appear as diseases caused by too few cells but later present as diseases caused by too many. Here, we show that the presence of too few cells is caused by a quality control system that eliminates mutant ribosomes before they are allowed to translate mRNAs. Genetic suppression of this quality control system increases the amount of ribosomes available to cells. However, this 60S subunit deficiency results in release of defective ribosomes into the translationally active pool. A genetic model is presented describing how these types of defects may result in cancer, resolving the ribosomopathy paradox.
Trash journals in China
Authors: Lin SONGQING , Zhan LIJUAN 
Published: March 2014

ABSTRACTOver the last two decades, China has seen an enormous rise in the number of scientific journals, second only to the USA. However, their overall academic level has not been high as expected. In fact the frequent occurrence of ‘trash’ journals has been a very negative development. In this regard, we will define trash journals and analyze their characteristics. In addition, we explore how such journals come into existence and look at their relationship with ‘legal’ journals. The development of trash journals is directly associated with market demand and profit, and a flawed academic evaluation system. We advocate action by government departments to purge academia of trash journals and give examples of how this could be done.
flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies
Authors: Rambaldi Davide , Pece Salvatore , Di Fiore Pier Paolo 
Published: March 2014

Abstract
Summary: Herein we introduce flowFit, a Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The software, distributed as an R Bioconductor library, is based on a mathematical model that takes into account the height of each peak, the size and position of the parental population (labeled but not proliferating) and the estimated distance between the brightness of a cell and the brightness of its daughter (in which the dye is assumed to undergo a 2-fold dilution). Although the algorithm does not make any inference on cell types, rates of cell divisions or rates of cell death, it deconvolutes the actual collected data into a set of peaks, whereby each peak corresponds to a subpopulation of cells that have divided N times. We validated flowFit by retrospective analysis of published proliferation-tracking experiments and demonstrated that the algorithm predicts the same percentage of cells/generation either in samples with discernible peaks (in which the peaks are visible in the collected raw data) or in samples with non-discernible peaks (in which the peaks are fused together). To the best of our knowledge, flowFit represents the first open-source algorithm in its category and might be applied to numerous areas of cell biology in which quantitative deconvolution of tracking dye-based experiments is desired, including stem cell research.
Availability and implementation: http://www.bioconductor.org/packages/devel/bioc/html/flowFit.html
(Bioconductor software page). http://www.bioconductor.org/packages/2.13/bioc/vignettes/flowFit/inst/doc/HowTo-flowFit.pdf (package vignette). http://rpubs.com/tucano/flowFit (online tutorial).
Contact: pierpaolo.difiore@ifom.eu or davide.rambaldi@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Census 2: isobaric labeling data analysis
Authors: Park Sung Kyu Robin , Aslanian Aaron , McClatchy Daniel B. , Han Xuemei , Shah Harshil , Singh Meha , Rauniyar Navin , Moresco James J. , Pinto Antonio F.M. , Diedrich Jolene K. , Delahunty Claire , Yates John R. 
Published: March 2014

Abstract
Motivation: We introduce Census 2, an update of a mass spectrometry data analysis tool for peptide/protein quantification. New features for analysis of isobaric labeling, such as Tandem Mass Tag (TMT) or Isobaric Tags for Relative and Absolute Quantification (iTRAQ), have been added in this version, including a reporter ion impurity correction, a reporter ion intensity threshold filter and an option for weighted normalization to correct mixing errors. TMT/iTRAQ analysis can be performed on experiments using HCD (High Energy Collision Dissociation) only, CID (Collision Induced Dissociation)/HCD (High Energy Collision Dissociation) dual scans or HCD triple-stage mass spectrometry data. To improve measurement accuracy, we implemented weighted normalization, multiple tandem spectral approach, impurity correction and dynamic intensity threshold features.
Availability and implementation: Census 2 supports multiple input file formats including MS1/MS2, DTASelect, mzXML and pepXML. It requires JAVA version 6 or later to run. Free download of Census 2 for academic users is available at http://fields.scripps.edu/census/index.php .
Contact: jyates@scripps.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies
Authors: Thangakani A. Mary , Kumar Sandeep , Nagarajan R. , Velmurugan D. , Gromiha M. Michael 
Published: March 2014

Abstract
Motivation: Distinguishing between amyloid fibril-forming and amorphous β-aggregating aggregation-prone regions (APRs) in proteins and peptides is crucial for designing novel biomaterials and improved aggregation inhibitors for biotechnological and therapeutic purposes.
Results: Adjacent and alternate position residue pairs in hexapeptides show distinct preferences for occurrence in amyloid fibrils and amorphous β-aggregates. These observations were converted into energy potentials that were, in turn, machine learned. The resulting tool, called Generalized Aggregation Proneness (GAP), could successfully distinguish between amyloid fibril-forming and amorphous β-aggregating hexapeptides with almost 100 percent accuracies in validation tests performed using non-redundant datasets.
Conclusion: Accuracies of the predictions made by GAP are significantly improved compared with other methods capable of predicting either general β-aggregation or amyloid fibril-forming APRs. This work demonstrates that amino acid side chains play important roles in determining the morphological fate of β-mediated aggregates formed by short peptides.
Availability and implementation: http://www.iitm.ac.in/bioinfo/GAP/ .
Contact: gromiha@iitm.ac.in
Supplementary information: Supplementary data are available at Bioinformatics online.
Krill, climate, and contrasting future scenarios for Arctic and Antarctic fisheries
Authors: McBride Margaret M. , Dalpadado Padmini , Drinkwater Kenneth F. , Godø Olav Rune , Hobday Alistair J. , Hollowed Anne B. , Kristiansen Trond , Murphy Eugene J. , Ressler Patrick H. , Subbey Sam , Hofmann Eileen E. , Loeng Harald 
Published: March 2014

AbstractArctic and Antarctic marine systems have in common high latitudes, large seasonal changes in light levels, cold air and sea temperatures, and sea ice. In other ways, however, they are strikingly different, including their: age, extent, geological structure, ice stability, and foodweb structure. Both regions contain very rapidly warming areas and climate impacts have been reported, as have dramatic future projections. However, the combined effects of a changing climate on oceanographic processes and foodweb dynamics are likely to influence their future fisheries in very different ways. Differences in the life-history strategies of the key zooplankton species (Antarctic krill in the Southern Ocean and Calanus copepods in the Arctic) will likely affect future productivity of fishery species and fisheries. To explore future scenarios for each region, this paper: (i) considers differing characteristics (including geographic, physical, and biological) that define polar marine ecosystems and reviews known and projected impacts of climate change on key zooplankton species that may impact fished species; (ii) summarizes existing fishery resources; (iii) synthesizes this information to generate future scenarios for fisheries; and (iv) considers the implications for future fisheries management. Published studies suggest that if an increase in open water during summer in Arctic and Subarctic seas results in increased primary and secondary production, biomass may increase for some important commercial fish stocks and new mixes of species may become targeted. In contrast, published studies suggest that in the Southern Ocean the potential for existing species to adapt is mixed and that the potential for the invasion of large and highly productive pelagic finfish species appears low. Thus, future Southern Ocean fisheries may largely be dependent on existing species. It is clear from this review that new management approaches will be needed that account for the changing dynamics in these regions under climate change.
Bycatch and discards: from improved knowledge to mitigation programmes
Authors: Rochet Marie-Joëlle , Catchpole Tom , Cadrin Steve 
Published: April 2014

Abstract
Discarding is considered by many as an important problem in world fisheries. In many regions, data collection onboard commercial vessels has intensified, and the understanding of both human and ecological drivers of discards is improving quickly. Discarding patterns vary widely across regions, fisheries, gears, and species. Fishers' responses to regulations and markets explain these complex patterns, on top of resource availability partly driven by environmental fluctuations. This expanded knowledge base provides an appropriate basis for discussing the discard mitigation measures proposed in various settings. In September 2012, a theme session was convened at the ICES Annual Science Conference in Bergen, Norway, to discuss these issues. This themed set of articles includes several of the studies presented at the theme session. Owing to the wide diversity of drivers and reasons for discarding, no single management measure or even framework is expected to address the issue. Rather, discard mitigation measures need to be tailored to each particular fishery, or even species within a fishery, and the effectiveness of solutions is greatest when they are used in combination with other approaches. Bottom-up approaches to bycatch and discard management, which involve incentive-based solutions to bycatch problems, were agreed to be the most promising.
Ghosts of fisheries-induced depletions: do they haunt us still?
Authors: Hutchings Jeffrey A. , Kuparinen Anna 
Published: March 2014

Abstract
The depletion of several North Atlantic gadoids in the 1980s and 1990s stimulated an unprecedented amount of research on the recovery of marine fish. Some of this work addressed long-standing questions of teleost population dynamics: (i) Does per capita population growth rate (r) always increase as abundance declines? (ii) Do teleost fish possess greater intrinsic recovery abilities (as reflected by rmax) than terrestrial vertebrates? (iii) Does the magnitude of population reduction influence the probability of recovery? (iv) If fish evolve in response to fishing, changing average fitness and thus rmax, are the population-dynamic consequences likely to be negative, positive, or neutral? Challenging some long-standing perceptions and beliefs, recent meta-analyses and empirically based model simulations on marine teleost fish support theoretically based postulates that: (i) rmax does not differ from that of terrestrial mammals; (ii) high fecundity has no influence on recovery potential; (iii) Allee effects can be manifest in some depleted populations; (iv) the greater the magnitude of population reduction, the greater the uncertainty of recovery; and (v) the consequences of fisheries-induced evolution for recovery need not always be negative. An emerging imperative of the work examined here is the need to more fully embrace and comprehensively examine the links that exist between fitness and per capita population growth, given that what happens at the level of the individual will have consequences for how populations respond to natural and anthropogenic environment change.
From supernovae to neutron stars
Authors: Suwa Yudai 
Published: March 2014

Abstract
Gravitational collapse, bounce, and explosion of an iron core of an 11.2 M⊙ star are simulated by two-dimensional neutrino-radiation hydrodynamic code. The explosion is driven by the neutrino heating aided by multi-dimensional hydrodynamic effects such as convection. Following the explosion phase, we continue the simulation focusing on the thermal evolution of the protoneutron star up to ∼ 70 s when the crust of the neutron star is formed, using one-dimensional simulation. We find that the crust forms at a high-density region (ρ ∼ 1014 g cm−3) and it proceeds from inside to outside. This is the first self-consistent simulation that successfully follows from the collapse phase to the protoneutron star cooling phase based on multi-dimensional hydrodynamic simulation.
Finitistic Arithmetic and Classical Logic†
Authors: Ganea Mihai 
Published: March 2014

AbstractIt can be argued that only the equational theories of some sub-elementary function algebras are finitistic or intuitive according to a certain interpretation of Hilbert's conception of intuition. The purpose of this paper is to investigate the relation of those restricted forms of equational reasoning to classical quantifier logic in arithmetic. The conclusion reached is that Edward Nelson's ‘predicative arithmetic’ program, which makes essential use of classical quantifier logic, cannot be justified finitistically and thus requires a different philosophical foundation, possibly as a restricted form of logicism.
The Scramble Conversion Tool
Authors: Bonfield James K 
Published: March 2014

ABSTRACTMotivationThe reference CRAM file format implementation is in Java. We present “Scramble”: a new C implementation of SAM, BAM and CRAM file I/O.ResultsThe C API for CRAM is 1.5–1.7x slower than BAM at decoding, but 1.8–2.6x faster at encoding. We see file size savings of 40–50%.AvailabilitySource code is available fromhttp://sourceforge.net/projects/staden/files/io_lib/
Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks
Authors: Morreel Kris , Saeys Yvan , Dima Oana , Lu Fachuang , Van de Peer Yves , Vanholme Ruben , Ralph John , Vanholme Bartel , Boerjan Wout 
Published: April 2014

Abstract
Plant metabolomics is increasingly used for pathway discovery and to elucidate gene function. However, the main bottleneck is the identification of the detected compounds. This is more pronounced for secondary metabolites as many of their pathways are still underexplored. Here, an algorithm is presented in which liquid chromatography–mass spectrometry profiles are searched for pairs of peaks that have mass and retention time differences corresponding with those of substrates and products from well-known enzymatic reactions. Concatenating the latter peak pairs, called candidate substrate-product pairs (CSPP), into a network displays tentative (bio)synthetic routes. Starting from known peaks, propagating the network along these routes allows the characterization of adjacent peaks leading to their structure prediction. As a proof-of-principle, this high-throughput cheminformatics procedure was applied to the Arabidopsis thaliana leaf metabolome where it allowed the characterization of the structures of 60% of the profiled compounds. Moreover, based on searches in the Chemical Abstract Service database, the algorithm led to the characterization of 61 compounds that had never been described in plants before. The CSPP-based annotation was confirmed by independent MSn experiments. In addition to being high throughput, this method allows the annotation of low-abundance compounds that are otherwise not amenable to isolation and purification. This method will greatly advance the value of metabolomics in systems biology.
Translocations of Chromosome End-Segments and Facultative Heterochromatin Promote Meiotic Ring Formation in Evening Primroses
Authors: Golczyk Hieronim , Massouh Amid , Greiner Stephan 
Published: March 2014

AbstractDue to reciprocal chromosomal translocations, many species of Oenothera (evening primrose) form permanent multichromosomal meiotic rings. However, regular bivalent pairing is also observed. Chiasmata are restricted to chromosomal ends, which makes homologous recombination virtually undetectable. Genetic diversity is achieved by changing linkage relations of chromosomes in rings and bivalents via hybridization and reciprocal translocations. Although the structural prerequisite for this system is enigmatic, whole-arm translocations are widely assumed to be the mechanistic driving force. We demonstrate that this prerequisite is genome compartmentation into two epigenetically defined chromatin fractions. The first one facultatively condenses in cycling cells into chromocenters negative both for histone H3 dimethylated at lysine 4 and for C-banding, and forms huge condensed middle chromosome regions on prophase chromosomes. Remarkably, it decondenses in differentiating cells. The second fraction is euchromatin confined to distal chromosome segments, positive for histone H3 lysine 4 dimethylation and for histone H3 lysine 27 trimethylation. The end-segments are deprived of canonical telomeres but capped with constitutive heterochromatin. This genomic organization promotes translocation breakpoints between the two chromatin fractions, thus facilitating exchanges of end-segments. We challenge the whole-arm translocation hypothesis by demonstrating why reciprocal translocations of chromosomal end-segments should strongly promote meiotic rings and evolution toward permanent translocation heterozygosity. Reshuffled end-segments, each possessing a major crossover hot spot, can furthermore explain meiotic compatibility between genomes with different translocation histories.
Global Dissection of Alternative Splicing in Paleopolyploid Soybean
Authors: Shen Yanting , Zhou Zhengkui , Wang Zheng , Li Weiyu , Fang Chao , Wu Mian , Ma Yanming , Liu Tengfei , Kong Ling-An , Peng De-Liang , Tian Zhixi 
Published: March 2014

Abstract
Alternative splicing (AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean (Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS.