bluuebunny/crossref_metadata_2025_split huggingface dataset:
Telicity in typical and impaired acquisition
Authors: Schulz Petra 
Published: July 2018

Abstract
This chapter discusses children’s knowledge of the syntactic-semantic interface of different types of telicity in typical and impaired acquisition. It maintains that telicity can be semantic or pragmatic, depending on whether event completion is entailed or implicated. It further delineates the Event Structural Bootstrapping account, arguing that Endstate Orientation – rather than a Manner Bias – guides children’s acquisition of verb meanings. Findings from studies testing German-speaking children’s early verb production and comprehension are provided as evidence for a strong Endstate Orientation in typical development, but not in Specific Language Impairment. These data speak for modularity in the domain of semantics and for the presence of selective impairments in verb semantics. Cross-linguistic implications for further research are formulated in the conclusion.
Analogical structure mapping and the formation of abstract constructions
Authors: Ambridge Ben , Goldwater Micah B. , Lieven Elena 
Published: July 2018

Abstract
This chapter reports an experimental study in which children aged 4;9–6;1 were taught two novel constructions with meanings of enabling/helping and preventing/stopping with OSV and VOS word order. The aim was to test Tomasello’s (2003) proposal that children form abstract constructions by performing analogical structure mapping across lexically-specific slot-and-frame patterns (e.g., He’s [X]ing it) and/or particular sentences that instantiate them. All surface cues were minimized, such that successful learning of the construction required children to align the relational structure (i.e., helper-action-helpee or preventer-action-preventee, as appropriate) of the training sentences. A forced-choice pointing test revealed that children did not successfully learn either the constructions’ global meanings or argument linking patterns (though a control group of adults succeeded at the latter task).
The labeling problem in syntactic bootstrapping
Authors: White Aaron Steven , Hacquard Valentine , Lidz Jeffrey 
Published: July 2018

Abstract
In English, the distinction between belief verbs, such as think, and desire verbs, such as want, is tracked by tense found in the subordinate clauses of those verbs. This suggests that subordinate clause tense might be a useful cue for learning the meanings of these verbs via syntactic bootstrapping. However, the correlation between tense and the belief v. desire distinction is not cross-linguistically robust; yet the acquisition profile of these verbs is similar cross-linguistically. Our proposal in this chapter is that, instead of using concrete cues like subordinate clause tense, learners may utilize more abstract syntactic cues that must be tuned to the syntactic distinctions present in a particular language. We present computational modeling evidence supporting the viability of this proposal.
Perspectives on truth
Authors: de Villiers Jill G. 
Published: July 2018

Abstract
Many theorists take language – vocabulary, mental verbs, syntax, counterfactuals, discourse – to be a significant help in the development of explicit Theory of Mind. Does conversation, with all its point-of-view indicators, betray another’s perspective? By comparing how different linguistic markers behave across clausal environments, I demonstrate that they fall into distinct classes, only one of which – tense – patterns with the truth of the clause in terms of perspective. Sentences with embedded finite complements thus have a special role in representing the truth or falsity of others’ beliefs. Children who master embedded sentential complements can then more readily reason about others’ false beliefs.
Four-year-old children compute scalar implicatures in absence of epistemic reasoning
Authors: Barner David , Hochstein Lara K. , Rubenson Miriam P. , Bale Alan 
Published: July 2018

Abstract
Children exhibit sophisticated mental state (epistemic) reasoning abilities from an early age, but it remains unclear what role these abilities play in the development of pragmatic inference in language acquisition. Here, we examined the role of epistemic reasoning in scalar implicature. Experiment 1 found that most 4-year-olds successfully computed a sub-type of scalar implicature (ad hoc implicatures), despite failing to compute so-called “ignorance implicatures”, a type of epistemic inference that Gricean models of pragmatics deem necessary for scalar implicature. In Experiment 2, we tested 4- and 5-year-old children, and replicated the finding that children compute ad hoc implicatures more readily than ignorance implicatures, and that children’s difficulties with ignorance implicature are unrelated to performance on Theory of Mind tasks.
Generality and Causal Interdependence in Ecology
Authors: Elliott-Graves Alkistis 
Published: July 2018

AbstractA hallmark of ecological research is dealing with complexity in the systems under investigation. One strategy is to diminish this complexity by constructing models and theories that are general. Alternatively, ecologists can constrain the scope of their generalizations to particular phenomena or types of systems. However, research employing the second strategy is often met with scathing criticism. I offer a theoretical argument in support of moderate generalizations in ecological research, based on the notions of interdependence and causal heterogeneity and their effect on the trade-off between generality and realism.
The Time of Data: Timescales of Data Use in the Life Sciences
Authors: Leonelli Sabina 
Published: July 2018

AbstractThis article considers the temporal dimension of data processing and use and the ways in which it affects the production and interpretation of knowledge claims. I start by distinguishing the time at which data collection, dissemination, and analysis occur (Data time, or Dt) from the time in which the phenomena for which data serve as evidence operate (Phenomena time, or Pt). Building on the analysis of two examples of data reuse from modeling and experimental practices in biology, I then argue that Dt affects how researchers (1) select and interpret data as evidence and (2) identify and understand phenomena.
Broom: application for non-redundant storage of high throughput sequencing data
Authors: Albayrak Levent , Khanipov Kamil , Golovko George , Fofanov Yuriy 
Published: July 2018

Abstract

Motivation
The data generation capabilities of high throughput sequencing (HTS) instruments have exponentially increased over the last few years, while the cost of sequencing has dramatically decreased allowing this technology to become widely used in biomedical studies. For small labs and individual researchers, however, storage and transfer of large amounts of HTS data present a significant challenge. The recent trends in increased sequencing quality and genome coverage can be used to reconsider HTS data storage strategies.

Results
We present Broom, a stand-alone application designed to select and store only high-quality sequencing reads at extremely high compression rates. Written in C++, the application accepts single and paired-end reads in FASTQ and FASTA formats and decompresses data in FASTA format.

Availability and implementation
C++ code available at https://scsb.utmb.edu/labgroups/fofanov/broom.asp.

Supplementary information
Supplementary data are available at Bioinformatics online.
Matt: Unix tools for alternative splicing analysis
Authors: Gohr André , Irimia Manuel 
Published: July 2018

Abstract

Summary
Tracking thousands of alternative splicing (AS) events genome-wide makes their downstream analysis computationally challenging and laborious. Here, we present Matt, the first UNIX command-line toolkit with focus on high-level AS analyses. With 50 commands it facilitates computational AS analyses by (i) expediting repetitive data-preparation tasks, (ii) offering routine high-level analyses, including the extraction of exon/intron features, discriminative feature detection, motif enrichment analysis, and the generation of motif RNA-maps, (iii) improving reproducibility by documenting all analysis steps and (iv) accelerating the implementation of own analysis pipelines by offering users to exploit its modular functionality.

Availability and implementation
matt.crg.eu under GNU LGPLv3, together with comprehensive documentation and application examples. Matt is implemented in Perl and R, invokes pdfLATEX and depends only on Perl Core modules/the R Base package simplifying its installation.

Supplementary information
Supplementary data are available at Bioinformatics online.
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models
Authors: Eriksson Olivia , Jauhiainen Alexandra , Maad Sasane Sara , Kramer Andrei , Nair Anu G , Sartorius Carolina , Hellgren Kotaleski Jeanette 
Published: July 2018

Abstract

Motivation
Dynamical models describing intracellular phenomena are increasing in size and complexity as more information is obtained from experiments. These models are often over-parameterized with respect to the quantitative data used for parameter estimation, resulting in uncertainty in the individual parameter estimates as well as in the predictions made from the model. Here we combine Bayesian analysis with global sensitivity analysis (GSA) in order to give better informed predictions; to point out weaker parts of the model that are important targets for further experiments, as well as to give guidance on parameters that are essential in distinguishing different qualitative output behaviours.

Results
We used approximate Bayesian computation (ABC) to estimate the model parameters from experimental data, as well as to quantify the uncertainty in this estimation (inverse uncertainty quantification), resulting in a posterior distribution for the parameters. This parameter uncertainty was next propagated to a corresponding uncertainty in the predictions (forward uncertainty propagation), and a GSA was performed on the predictions using the posterior distribution as the possible values for the parameters. This methodology was applied on a relatively large model relevant for synaptic plasticity, using experimental data from several sources. We could hereby point out those parameters that by themselves have the largest contribution to the uncertainty of the prediction as well as identify parameters important to separate between qualitatively different predictions. This approach is useful both for experimental design as well as model building.

Availability and implementation
Source code is freely available at https://github.com/alexjau/uqsa.

Supplementary information
Supplementary data are available at Bioinformatics online.
Metagenomic binning through low-density hashing
Authors: Luo Yunan , Yu Yun William , Zeng Jianyang , Berger Bonnie , Peng Jian 
Published: July 2018

Abstract

Motivation
Vastly greater quantities of microbial genome data are being generated where environmental samples mix together the DNA from many different species. Here, we present Opal for metagenomic binning, the task of identifying the origin species of DNA sequencing reads. We introduce ‘low-density’ locality sensitive hashing to bioinformatics, with the addition of Gallager codes for even coverage, enabling quick and accurate metagenomic binning.

Results
On public benchmarks, Opal halves the error on precision/recall (F1-score) as compared with both alignment-based and alignment-free methods for species classification. We demonstrate even more marked improvement at higher taxonomic levels, allowing for the discovery of novel lineages. Furthermore, the innovation of low-density, even-coverage hashing should itself prove an essential methodological advance as it enables the application of machine learning to other bioinformatic challenges.

Availability and implementation
Full source code and datasets are available at http://opal.csail.mit.edu and https://github.com/yunwilliamyu/opal.

Supplementary information
Supplementary data are available at Bioinformatics online.
CoMSA: compression of protein multiple sequence alignment files
Authors: Deorowicz Sebastian , Walczyszyn Joanna , Debudaj-Grabysz Agnieszka 
Published: July 2018

AbstractMotivationBioinformatics databases grow rapidly and achieve values hardly to imagine a decade ago. Among numerous bioinformatics processes generating hundreds of GB is multiple sequence alignments of protein families. Its largest database, i.e. Pfam, consumes 40–230 GB, depending of the variant. Storage and transfer of such massive data has become a challenge.ResultsWe propose a novel compression algorithm, CoMSA, designed especially for aligned data. It is based on a generalization of the positional Burrows–Wheeler transform for non-binary alphabets. CoMSA handles FASTA, as well as Stockholm files. It offers up to six times better compression ratio than other commonly used compressors, i.e. gzip. Performed experiments resulted in an analysis of the influence of a protein family size on the compression ratio.Availability and implementationCoMSA is available for free at https://github.com/refresh-bio/comsa and http://sun.aei.polsl.pl/REFRESH/comsa.Supplementary materialSupplementary data are available at Bioinformatics online.
DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters
Authors: Lu Xinguo , Qian Xin , Li Xing , Miao Qiumai , Peng Shaoliang 
Published: July 2018

AbstractMotivationFunctional somatic mutations within coding amino acid sequences confer growth advantage in pathogenic process. Most existing methods for identifying cancer-related mutations focus on the single amino acid or the entire gene level. However, gain-of-function mutations often cluster in specific protein regions instead of existing independently in the amino acid sequences. Some approaches for identifying mutation clusters with mutation density on amino acid chain have been proposed recently. But their performance in identification of mutation clusters remains to be improved.ResultsHere we present a Data-adaptive Mutation Clustering Method (DMCM), in which kernel density estimate (KDE) with a data-adaptive bandwidth is applied to estimate the mutation density, to find variable clusters with different lengths on amino acid sequences. We apply this approach in the mutation data of 571 genes in over twenty cancer types from The Cancer Genome Atlas (TCGA). We compare the DMCM with M2C, OncodriveCLUST and Pfam Domain and find that DMCM tends to identify more significant clusters. The cross-validation analysis shows DMCM is robust and cluster cancer type enrichment analysis shows that specific cancer types are enriched for specific mutation clusters.Availability and implementationDMCM is written in Python and analysis methods of DMCM are written in R. They are all released online, available through https://github.com/XinguoLu/DMCM.Supplementary informationSupplementary data are available at Bioinformatics online.
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC
Authors: Cheng Xiang , Lin Wei-Zhong , Xiao Xuan , Chou Kuo-Chen 
Published: July 2018

Abstract

Motivation
A cell contains numerous protein molecules. One of the fundamental goals in cell biology is to determine their subcellular locations, which can provide useful clues about their functions. Knowledge of protein subcellular localization is also indispensable for prioritizing and selecting the right targets for drug development. With the avalanche of protein sequences emerging in the post-genomic age, it is highly desired to develop computational tools for timely and effectively identifying their subcellular localization based on the sequence information alone. Recently, a predictor called ‘pLoc-mAnimal’ was developed for identifying the subcellular localization of animal proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with the multi-label systems in which some proteins, called ‘multiplex proteins’, may simultaneously occur in two or more subcellular locations. Although it is indeed a very powerful predictor, more efforts are definitely needed to further improve it. This is because pLoc-mAnimal was trained by an extremely skewed dataset in which some subset (subcellular location) was about 128 times the size of the other subsets. Accordingly, such an uneven training dataset will inevitably cause a biased consequence.

Results
To alleviate such biased consequence, we have developed a new and bias-reducing predictor called pLoc_bal-mAnimal by quasi-balancing the training dataset. Cross-validation tests on exactly the same experiment-confirmed dataset have indicated that the proposed new predictor is remarkably superior to pLoc-mAnimal, the existing state-of-the-art predictor, in identifying the subcellular localization of animal proteins.

Availability and implementation
To maximize the convenience for the vast majority of experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc_bal-mAnimal/, by which users can easily get their desired results without the need to go through the complicated mathematics.

Supplementary information
Supplementary data are available at Bioinformatics online.
Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios
Authors: Curis Emmanuel , Courtin Cindie , Geoffroy Pierre Alexis , Laplanche Jean-Louis , Saubaméa Bruno , Marie-Claire Cynthia 
Published: July 2018

AbstractMotivationRNA quantification experiments result in compositional data, however usual methods for compositional data analysis [additive log ratio (alr), centered log ratio (clr), isometric log ratio (ilr)] do not apply easily and give results difficult to interpret. To handle this, a method based on disjoint subgraphs in a graph whose nodes are the quantified RNAs is proposed. Edges in the graph are defined by lack of change in ratios of the corresponding RNAs between conditions.ResultsThe methods is suited for qRT-PCR and RNA-Seq data analyses, and leads to easy-to-interpret, graphical results and the identification of set of genes that share a similar behavior when the studied condition changes. For qRT-PCR data, it has better statistical properties than the common ΔΔCq method.Availability and implementationConstruction of all pairwise ratio analysis P-values matrix, and conversion into a graph was implemented in an R package, named SARP.compo. It is freely available for download on the CRAN repository. Example R script using the package are provided as Supplementary Material; the R package includes the data needed. One of these scripts reproduces the Figure 2 of this paper.Supplementary informationSupplementary data are available at Bioinformatics online.
Precessional dynamics of black hole triples: binary mergers with near-zero effective spin
Authors: Antonini Fabio , Rodriguez Carl L , Petrovich Cristobal , Fischer Caitlin L 
Published: July 2018

ABSTRACT
The binary black hole mergers detected by Advanced LIGO/Virgo have shown no evidence of large black hole spins. However, because LIGO/Virgo best measures the effective combination of the two spins along the orbital angular momentum (χeff), it is difficult to distinguish between binaries with slowly spinning black holes and binaries with spins lying in the orbital plane. Here, we study the spin dynamics for binaries with a distant black hole companion. For spins initially aligned with the orbital angular momentum of the binary, we find that χeff ‘freezes’ near zero as the orbit decays through the emission of gravitational waves. Through a population study, we show that this process predominantly leads to merging black hole binaries with near-zero χeff. We conclude that if the detected black hole binaries were formed in triples, then this would explain their low χeff without the need to invoke near-zero spins or initially large spin–orbit angles.
Coronal EUV, QFP, and kink waves simultaneously launched during the course of jet–loop interaction
Authors: Shen Yuandeng , Tang Zehao , Li Hongbo , Liu Yu 
Published: July 2018

Abstract
We present the observations of an extreme ultraviolet (EUV) wave, a quasi-periodic fast-propagating (QFP) magnetosonic wave, and a kink wave that were simultaneously associated with the impingement of a coronal jet upon a group of coronal loops. After the interaction, the coronal loop showed obvious kink oscillation that had a period of about 428 s. In the meantime, a large-scale EUV wave and a QFP wave are observed on the west of the interaction position. It is interesting that the QFP wave showed refraction effect during its passing through two strong magnetic regions. The angular extent, speed, and lifetime of the EUV (QFP) wave were about 140° (40°), 423 (322) km s−1, and 6 (26) min, respectively. It is measured that the period of the QFP wave was about 390 ± 100. Based on the observational analysis results, we propose that the kink wave was probably excited by the interaction of the jet; the EUV was probably launched by the sudden expansion of the loop system due to the impingement of the coronal jet; and the QFP wave was possibly formed through the dispersive evolution of the disturbance caused by the jet–loop interaction.
On the [α/Fe]–[Fe/H] relations in early-type galaxies
Authors: Vincenzo Fiorenzo , Kobayashi Chiaki , Taylor Philip 
Published: July 2018

AbstractWe study how the predicted [α/Fe]–[Fe/H] relations in early-type galaxies vary as functions of their stellar masses, ages, and stellar velocity dispersions, by making use of cosmological chemodynamical simulations with feedback from active galactic nuclei. Our model includes a detailed treatment for the chemical enrichment from dying stars, core-collapse supernovae (both Type II and hypernovae) and Type Ia supernovae. At redshift $z$ = 0, we create a catalogue of 526 galaxies, among which we determine 80 early-type galaxies. From the analysis of our simulations, we find [α/Fe]–[Fe/H] relations similar to the Galactic bulge. We also find that, in the oldest galaxies, Type Ia supernovae start to contribute at higher [Fe/H] than in the youngest ones. On the average, early-type galaxies with larger stellar masses (and, equivalently, higher stellar velocity dispersions) have higher [α/Fe] ratios, at fixed [Fe/H]. This is qualitatively consistent with the recent observations of Sybilska et al., but quantitatively there are mismatches, which might require stronger feedback, sub-classes of Type Ia Supernovae, or a variable initial mass function to address.