bluuebunny/crossref_metadata_2025_split huggingface dataset:
Children’s referent selection and word learning
Authors: Twomey Katherine E. , Morse Anthony F. , Cangelosi Angelo , Horst Jessica S. 
Published: September 2016

Abstract
It is well-established that toddlers can correctly select a novel referent from an ambiguous array in response to a novel label. There is also a growing consensus that robust word learning requires repeated label-object encounters. However, the effect of the context in which a novel object is encountered is less well-understood. We present two embodied neural network replications of recent empirical tasks, which demonstrated that the context in which a target object is encountered is fundamental to referent selection and word learning. Our model offers an explicit account of the bottom-up associative and embodied mechanisms which could support children’s early word learning and emphasises the importance of viewing behaviour as the interaction of learning at multiple timescales.
Frankfurt and Cohen on bullshit, bullshiting, deception, lying, and concern with the truth of what one says
Authors: Carson Thomas L. 
Published: September 2016

This paper addresses the following three claims that Frankfurt makes about the concept of bullshit:1. Bullshit requires the intention to deceive others.2. Bullshit does not constitute lying (bullshit is “short of lying”).3. The essence of bullshit is lack of concern with the truth of what one says.I offer counterexamples to all three claims. By way of defending my counterexamples, I examine Cohen’s distinction between bullshiting and bullshit and argue that my examples are indeed cases of bullshiting that Frankfurt’s analysis is intended to cover. My examples of bullshitters who are very concerned to say only things that are true show that Frankfurt is mistaken in claiming that the “essence” of bullshit is lack of concern with the truth of what one says.
Eutectic alloys based on the Al–Zn–Mg–Ca system: Microstructure, phase composition and hardening
Authors: Belov N. , Naumova E. , Akopyan T. 
Published: September 2016

The experimental study of aluminium alloys based on the Al–Ca–Zn–Mg system (3.5% Mg and 2.5% Mg, 0–10% Ca, 0–14% Zn (wt-%)) was combined with Thermo-Calc simulations for the optimisation of the alloy composition. Zinc is distributed between aluminium solid solution and phase (Al,Zn)4Ca. Magnesium was not observed in the intermetallic phase. The eutectic (Al,Zn)4Ca had fine structure and particles of (Al,Zn)4Ca were capable of spheroidisation during the heat treatment at 520°С. The maximum level of hardness observed in calcium-containing alloys was higher than 200 HB, suggesting good strength properties. With an example of the Al–Zn(9%)–Mg(3.5%)–Ca(3%) alloy, the possibility of manufacturing thin rolled sheets based on the (Al)–Ca eutectic was demonstrated. This article is part of a Themed Issue on Aluminium-based materials: processing, microstructure, properties, and recycling.
Educational expansion without equalization: a reappraisal of the ‘Effectively Maintained Inequality’ hypothesis in children's choice of the upper secondary track
Authors: Guetto Raffaele , Vergolini Loris 
Published: September 2016

ABSTRACT
Previous studies of trends in social inequalities in upper secondary track choices in Italy found evidence that, in the period of highest educational expansion, horizontal inequalities increased, consistently with the Effectively Maintained Inequality thesis (EMI). Our paper, focusing on the youngest birth cohorts (1958–1989), documents that enrolments at upper secondary schools have become almost universal and have been followed by a huge expansion of the academic track. Although the latter has also involved children from the lowest social strata, our evidence suggests that their relative disadvantage to attend the academic track, compared to the most privileged social groups, has diminished only slightly. When distinguishing between different curricula within the academic track, we found evidence supporting the EMI hypothesis also among recent cohorts: the expansion of the academic track has gone hand-in-hand with increasing social inequalities in the chances to attend more prestigious curricula. Finally, social class inequalities in the chances of enrolling at the academic track are stronger at high levels of parental education, while they are largely muted among low-educated parents. We suggest the latter as a possible mechanism to explain why educational expansion may not produce a decline in the association between social origins and educational attainment.
LAMSA: fast split read alignment with long approximate matches
Authors: Liu Bo , Gao Yan , Wang Yadong 
Published: September 2016

Abstract

Motivation
Read length is continuously increasing with the development of novel high-throughput sequencing technologies, which has enormous potentials on cutting-edge genomic studies. However, longer reads could more frequently span the breakpoints of structural variants (SVs) than that of shorter reads. This may greatly influence read alignment, since most state-of-the-art aligners are designed for handling relatively small variants in a co-linear alignment framework. Meanwhile, long read alignment is still not as efficient as that of short reads, which could be also a bottleneck for the upcoming wide application.

Results
We propose long approximate matches-based split aligner (LAMSA), a novel split read alignment approach. It takes the advantage of the rareness of SVs to implement a specifically designed two-step strategy. That is, LAMSA initially splits the read into relatively long fragments and co-linearly align them to solve the small variations or sequencing errors, and mitigate the effect of repeats. The alignments of the fragments are then used for implementing a sparse dynamic programming-based split alignment approach to handle the large or non-co-linear variants. We benchmarked LAMSA with simulated and real datasets having various read lengths and sequencing error rates, the results demonstrate that it is substantially faster than the state-of-the-art long read aligners; meanwhile, it also has good ability to handle various categories of SVs.

Availability and Implementation
LAMSA is available at https://github.com/hitbc/LAMSA

Supplementary information
Supplementary data are available at Bioinformatics online.
cMapper: gene-centric connectivity mapper for EBI-RDF platform
Authors: Shoaib Muhammad , Ansari Adnan Ahmad , Ahn Sung-Min 
Published: September 2016

Abstract

Motivation
In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language. To overcome this practical limitation of the EBI-RDF platform, we developed cMapper, a web-based tool that enables biologists to search the EBI-RDF databases in a gene-centric manner without a thorough knowledge of RDF and SPARQL.

Results
cMapper allows biologists to search data entities in the EBI-RDF platform that are connected to genes or small molecules of interest in multiple biological contexts. The input to cMapper consists of a set of genes or small molecules, and the output are data entities in six independent EBI-RDF databases connected with the given genes or small molecules in the user's query. cMapper provides output to users in the form of a graph in which nodes represent data entities and the edges represent connections between data entities and inputted set of genes or small molecules. Furthermore, users can apply filters based on database, taxonomy, organ and pathways in order to focus on a core connectivity graph of their interest. Data entities from multiple databases are differentiated based on background colors. cMapper also enables users to investigate shared connections between genes or small molecules of interest. Users can view the output graph on a web browser or download it in either GraphML or JSON formats.

Availability and Implementation
cMapper is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on Tomcat server. We developed the user interface using HTML5, JQuery and the Cytoscape Graph API. cMapper can be accessed at http://cmapper.ewostech.net. Readers can download the development manual from the website http://cmapper.ewostech.net/docs/cMapperDocumentation.pdf. Source Code is available at https://github.com/muhammadshoaib/cmapper.

Supplementary information
Supplementary data are available at Bioinformatics online.
Detecting subnetwork-level dynamic correlations
Authors: Yan Yan , Qiu Shangzhao , Jin Zhuxuan , Gong Sihong , Bai Yun , Lu Jianwei , Yu Tianwei 
Published: September 2016

Abstract

Motivation
The biological regulatory system is highly dynamic. The correlations between many functionally related genes change over different biological conditions. Finding dynamic relations on the existing biological network may reveal important regulatory mechanisms. Currently no method is available to detect subnetwork-level dynamic correlations systematically on the genome-scale network. Two major issues hampered the development. The first is gene expression profiling data usually do not contain time course measurements to facilitate the analysis of dynamic relations, which can be partially addressed by using certain genes as indicators of biological conditions. Secondly, it is unclear how to effectively delineate subnetworks, and define dynamic relations between them.

Results
Here we propose a new method named LANDD (Liquid Association for Network Dynamics Detection) to find subnetworks that show substantial dynamic correlations, as defined by subnetwork A is concentrated with Liquid Association scouting genes for subnetwork B. The method produces easily interpretable results because of its focus on subnetworks that tend to comprise functionally related genes. Also, the collective behaviour of genes in a subnetwork is a much more reliable indicator of underlying biological conditions compared to using single genes as indicators. We conducted extensive simulations to validate the method’s ability to detect subnetwork-level dynamic correlations. Using a real gene expression dataset and the human protein-protein interaction network, we demonstrate the method links subnetworks of distinct biological processes, with both confirmed relations and plausible new functional implications. We also found signal transduction pathways tend to show extensive dynamic relations with other functional groups.

Availability and Implementation
The R package is available at https://cran.r-project.org/web/packages/LANDD.

Supplementary information
Supplementary data are available at Bioinformatics online.
Systemic Age-Associated DNA Hypermethylation of ELOVL2 Gene:
In Vivo and In Vitro Evidences of a Cell Replication Process
Authors: Bacalini Maria Giulia , Deelen Joris , Pirazzini Chiara , De Cecco Marco , Giuliani Cristina , Lanzarini Catia , Ravaioli Francesco , Marasco Elena , van Heemst Diana , Suchiman H. Eka D. , Slieker Roderick , Giampieri Enrico , Recchioni Rina , Mercheselli Fiorella , Salvioli Stefano , Vitale Giovanni , Olivieri Fabiola , Spijkerman Annemieke M. W. , Dollé Martijn E. T. , Sedivy John M. , Castellani Gastone , Franceschi Claudio , Slagboom Pieternella E. , Garagnani Paolo 
Published: September 2016

Abstract
Epigenetic remodeling is one of the major features of the aging process. We recently demonstrated that DNA methylation of ELOVL2 and FHL2 CpG islands is highly correlated with age in whole blood. Here we investigated several aspects of age-associated hypermethylation of ELOVL2 and FHL2. We showed that ELOVL2 methylation is significantly different in primary dermal fibroblast cultures from donors of different ages. Using epigenomic data from public resources, we demonstrated that most of the tissues show ELOVL2 and FHL2 hypermethylation with age. Interestingly, ELOVL2 hypermethylation was not found in tissues with very low replication rate. We demonstrated that ELOVL2 hypermethylation is associated with in vitro cell replication rather than with senescence. We confirmed intra-individual hypermethylation of ELOVL2 and FHL2 in longitudinally assessed participants from the Doetinchem Cohort Study. Finally we showed that, although the methylation of the two loci is not associated with longevity/mortality in the Leiden Longevity Study, ELOVL2 methylation is associated with cytomegalovirus status in nonagenarians, which could be informative of a higher number of replication events in a fraction of whole-blood cells. Collectively, these results indicate that ELOVL2 methylation is a marker of cell divisions occurring during human aging.
Article 102 TFEU
Authors: Jones Alison , Sufrin Brenda 
Published: September 2016

Abstract
Article 102 only applies to undertakings in a dominant position. Thus, whether or not an undertaking holds a ‘dominant position’ is of central importance to Article 102. This chapter discusses the definition of a dominant position in the case law of the Court and its relation to the concept of substantial market power, including the Commission’s treatment of it in the Guidance Paper. It explains how a dominant position is established. The chapter therefore deals with the definition of the relevant market for the purposes of Article 102, including issues of demand and supply substitution, the cellophane fallacy, and aftermarkets; the role of market share in establishing dominance; and barriers to entry and other factors indicating dominance; and dominant positions in the new economy.
Horizontal Cooperation Agreements
Authors: Jones Alison , Sufrin Brenda 
Published: September 2016

Abstract
This chapter discusses EU competition policy towards horizontal cooperation agreements. It covers joint ventures; the contents of the 2010 Guidelines; the general approach to horizontal cooperation agreements in the Guidelines; information agreements; research and development agreements, including the block emption, Regulation 1217/2010; production agreements, including the block exemption on specialisation agreements, Regulation 1218/2010 ; purchasing agreements; commercialisation agreements; standardisation agreements; and agreements in particular sectors, such as the joint buying or selling of media rights to sports events.
Licensing Agreements and other Agreements Involving Intellectual Property Rights
Authors: Jones Alison , Sufrin Brenda 
Published: September 2016

Abstract
This chapter examines some of the different types of intellectual property rights (IPRs) before outlining the relationship between intellectual property and both EU competition law and the EU free movement rules. It focuses, however, on IP licensing agreements and their treatment under Article 101. The chapter is organized as follows. Section 3 traces the development of EU competition policy to IP licensing agreements. Sections 4 and 5 examine the current Technology Transfer Block Exemption, Regulation 316/2014 (TTBER) and the Guidelines in detail. Sections 6, 7, and 8 deal with trade mark licences, trade mark delimitation agreements, and copyright (other than software) licences not covered by the TTBER and Guidelines. Section 9 outlines issues arising in cases involving IPRs under Article 102, while Section 10 concludes.
Private Enforcement
Authors: Jones Alison , Sufrin Brenda 
Published: September 2016

Abstract
This chapter focuses on the private civil enforcement of EU antitrust rules through claims made by private litigants in the national courts and tribunals of the individual Member States. The discussions cover the principle of direct effect and national procedural autonomy; why there has been relatively little antitrust litigation in the EU; the relationship between public and private enforcement; the Commission's policy towards private enforcement, the initiatives it has taken to encourage private litigation, particularly the 2014 Damages Directive, and mechanisms for cooperation between the Commission and national courts; and the obligations of national courts when dealing with cases that raise the issue of whether a contract in violation of Article 101 or Article 102 is enforceable and whether, and if so when, damages and injunctions should be available to remedy such violations.
Title: Time to wake up: Studying neurovascular coupling and brain-wide circuit function in the un-anesthetized animal
Authors: Gao Yu-Rong , Ma Yuncong , Zhang Qingguang , Winder Aaron T. , Liang Zhifeng , Antinori Lilith , Drew Patrick J. , Zhang Nanyin 
Published: September 2016

AbstractFunctional magnetic resonance imaging (fMRI) has allowed the noninvasive study of task-based and resting-state brain dynamics in humans by inferring neural activity from blood-oxygenation-level dependent (BOLD) signal changes. An accurate interpretation of the hemodynamic changes that underlie fMRI signals depends on the understanding of the quantitative relationship between changes in neural activity and changes in cerebral blood flow, oxygenation and volume. While there has been extensive study of neurovascular coupling in anesthetized animal models, anesthesia causes large disruptions of brain metabolism, neural responsiveness and cardiovascular function. Here, we review work showing that neurovascular coupling and brain circuit function in the awake animal are profoundly different from those in the anesthetized state. We argue that the time is right to study neurovascular coupling and brain circuit function in the awake animal to bridge the physiological mechanisms that underlie animal and human neuroimaging signals, and to interpret them in light of underlying neural mechanisms. Lastly, we discuss recent experimental innovations that have enabled the study of neurovascular coupling and brain-wide circuit function in un-anesthetized and behaving animal models.
Traumatic brain injury causes retention of long introns in metabolic genes via regulation of intronic Histone 3 lysine 36 methylation levels in the sub-acute phase of injury
Authors: Sen Arko , Qu Wen , Nuga Oluwademi Okikiolu , Liu Jenney , Burl Rayanne , Gurdziel Katherine , Pique-Regi Roger , Hüttemann Maik , Ruden Douglas. M. 
Published: September 2016

AbstractTraumatic brain injury (TBI) can cause persistent pathological alteration of neurons. This may lead to cognitive dysfunctions, depression, and even increased susceptibility to life threatening diseases, such as epilepsy and Alzheimer’s Disease. To investigate the underlying genetic and molecular basis of TBI, Wasserman and colleagues developed an inexpensive and reproducible model for simulating TBI inDrosophila melanogaster(Fruit Fly). Using a modified version of this high impact trauma (HIT) device, we subjected w1118fruit flies to mild closed head trauma. To determine the transcriptomic changes that contribute to survival post TBI, we collected fly heads from the survivors at 2 time points; 4 hours and 24 hours’ post-trauma. Mild TBI had limited impact on the steady state RNA levels but showed large perturbations in alternative splicing (AS) 24 hours’ post-trauma. Classification of these AS changes showed selective retention (RI) of long introns (>81bps), with a mean size of ~3000bps. Some of these RI genes also showed a significant reduction in transcript abundance and were specifically enriched in genes involved in mitochondrial metabolism. The RI are enriched in ACACACA motifs known to bind to Smooth (SM), an hnRNPL class of splicing factor. Mutating SM (sm4/Df) resulted in reversal of RI observed 24 hours’ post-trauma, and in some cases, elimination of basal levels of RI in long introns. This observation suggests that SM is critical regulator of RI and that this process is enhanced by TBI. Interestingly, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) for histone 3 lysine 36 trimethylation (H3K36me3) revealed increased levels of this histone modification in retained introns post-trauma. Consistent with this observation, mutations in lysine specific demethylase 4A (KDM4A), which de-methylate H3K36me3, increased RI in many of the same long introns affected by TBI. Additionally, higher H3K36me3 levels are observed around intronic SM-binding motifs post-trauma, suggesting interaction between H3K36me3 and SM binding to intronic splicing suppressor sites might be responsible for increasing RI of metabolic genes as a novel mechanism to improve survival after TBI.
Multidimensional stimulus-response correlation reveals supramodal neural responses to naturalistic stimuli
Authors: Dmochowski Jacek P. , Ki Jason , DeGuzman Paul , Sajda Paul , Parra Lucas C. 
Published: September 2016

AbstractIn neuroscience, stimulus-response relationships have traditionally been analyzed using either encoding or decoding models. Here we combined both techniques by decomposing neural activity into multiple components, each representing a portion of the stimulus. We tested this hybrid approach on encephalographic responses to auditory and audiovisual narratives identically experienced across subjects, as well as uniquely experienced video game play. The highest stimulus-response correlations (SRC) were detected for dynamic visual features. During narratives both auditory and visual SRC were modulated by attention and tracked correlations between subjects. During video game play, SRC was modulated by task difficulty and attentional state. Importantly, the strongest component extracted for visual and auditory features had nearly identical spatial distributions, suggesting that the predominant encephalographic response to naturalistic stimuli is supramodal. The variety of novel findings demonstrates the utility of measuring multidimensional stimulus-response correlations.
RIblast: An ultrafast RNA-RNA interaction prediction system for comprehensive lncRNA interaction analysis
Authors: Fukunaga Tsukasa , Hamada Michiaki 
Published: September 2016

AbstractLong non-coding RNAs (lncRNAs) play important roles in various biological processes. Although more than 58,000 human lncRNA genes have been discovered, most known lncRNAs are still poorly characterised. One approach to understanding the functions of lncRNAs is the detection of the interacting RNA target of each lncRNA. Because experimental detection of comprehensive lncRNA-RNA interactions are difficult, computational prediction of lncRNA-RNA interactions is an indispensable technique. However, the high computational costs of existing RNA-RNA interaction prediction tools prevents their application to large-scale lncRNA datasets. Here, we present “RIblast”, an ultrafast RNA-RNA interaction prediction method based on the seed-and-extension approach. RIblast discovers seed regions using suffix arrays and subsequently extends seed regions based on an RNA secondary structure energy model. Computational experiments indicate that RIblast achieves a level of prediction accuracy similar to those of existing programs, but at speeds over 64 times faster than existing programs.