bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to grow a human
Authors: Corballis Michael C. 
Published: February 2010

AbstractI enlarge on the theme that the brain mechanisms required for languageand other aspects of the human mind evolved through selective changes in the regulatory genes governing growth. Extension of the period of postnatal growth increases the role of the environment in structuring the brain, and spatiotemporal programming (heterochrony) ofgrowth might explain hierarchical representation, hemispheric specialization, and perhaps sex differences.
Sign language and the brain: Apes, apraxia, and aphasia
Authors: Corina David 
Published: February 2010

AbstractThe study of signed languages has inspired scientific' speculation regarding foundations of human language. Relationships between the acquisition of sign language in apes and man are discounted on logical grounds. Evidence from the differential hreakdown of sign language and manual pantomime places limits on the degree of overlap between language and nonlanguage motor systems. Evidence from functional magnetic resonance imaging reveals neural areas of convergence and divergence underlying signed and spoken languages.
Neurobiological approaches to language: Falsehoods and fallacies
Authors: Grodzinsky Yosef 
Published: February 2010

AbstractThe conclusion that language is not really innate or modular is based on several fallacies. I show that the target article confuses communicative skills with linguistic abilities, and that its discussion of brain/language relations is replete with factual errors. I also criticize its attempt to contrast biological and linguistic principles. Finally, I argue that no case is made for the “alternative” approach proposed here.
Evolutionary principles and the emergence of syntax
Authors: Schoenemann P. Thomas , Wang William S.-Y. 
Published: February 2010

AbstractThe belief that syntax is an innate, autonomous, species-specific module is highly questionable. Syntax demonstrates the mosaic nature of evolutionary change, in that it made use of (and led to the enhancement of) numerous preexisting neurocognitive features. It is best understood as an emergent characteristic of the explosion of semantic complexity that occurred during hominid evolution.
Autonomy and its discontents
Authors: Sinha Chris 
Published: February 2010

AbstractMüller's review of the neuroscientific evidence undermines nativist claims for autonomous syntax and the argument from the poverty of the stimulus. Generativists will appeal to data from language acquisition, but here too there is growing evidence against the nativist position. Epigenetic naturalism, the developmental alternative to nativism, can be extended to epigenetic socionaturalism, acknowledging the importance of sociocultural processes in language and cognitive development.
Is human language just another neurobiological specialization?
Authors: Walker Stephen F. 
Published: February 2010

AbstractOne can disagree with Müller that it is neurobiologically questionable to suppose that human language is innate, specialized, and species-specific, yet agree that the precise brain mechanisms controlling language in any individual will be influenced by epigenesis and genetic variability, and that the interplay between inherited and acquired aspects of linguistic capacity deserves to be investigated.
What we have to explain in foreign language learning
Authors: Bley-Vroman Robert 
Published: February 2010

AbstractWhile child language development theory must explain invariant “success,” foreign language learning theory must explain variation and lack of success. The fundamental difference hypothesis (FDH) outlines such a theory. Epstein et al. ignore the explanatory burden, mischaracterize the FDH, and underestimate the resources of human cognition. The field of second language acquisition is not divided into camps by views on “access” to UG.
How adult second language learning differs from child first language development
Authors: Clahsen Harald , Muysken Pieter 
Published: February 2010

AbstractWe argue that the model developed in Epstein et al.'s target article does not explain differences between child first language (LI) acquisition and adult second language (L2) acquisition. We therefore sketch an alternative view, originally developed in Clahsen and Muysken (1989), in the light of new empirical findings and theoretical developments.
UG and SLA: The access question, and how to beg it
Authors: Gregg Kevin R. 
Published: February 2010

AbstractEpstein, Flynn, and Martohardjono trivialize the question of access to universal grammar in second language acquisition by arguing against a straw-man version of the no-access position and by begging the question of how second language (L2) knowledge is represented in the mind/brain of an adult L2 learner. They compound their errors by employing a research methodology that fails to provide any relevant evidence.
In support of the early presence of functional categories in second language acquisition
Authors: Kanno Kazue 
Published: February 2010

AbstractThis commentary focuses on whether the full set of categories is available to beginning L2 learners. After critiquing Epstein et al.'s experimental evidence for the presence of functional categories, I outline the results of an experiment involving English speakers learning Japanese as a second language that does indeed point toward the early presence of fuuctional categories.
To “grow” and what “to grow,” that is one question
Authors: Liceras Juana M. 
Published: February 2010

AbstractL2 learners may access UG principles because these are realized in all natural languages. Since this is not the case for the parametrized aspects of language, parameter setting may be progressively replaced by restructuring mechanisms which are specifically related to the process of representational redescription because L2 learners are not sensitive to the [±] features which define parameters.
Alternative origins of motor images
Authors: Grant Stuart C. , Schmuckler Mark A. 
Published: February 2010

AbstractJeannerod (1994) advocates studying motor images to understand the representation of action. We identify an unsettled issue that complicates the use of motor images to study the representation of action and present some evidence for a clear absence of equivalence between motor imagery and movement preparation. We then elaborate and emphasize the relevance of the mental practice literature, which was introduced in the first round of commentary. Finally, we suggest two methods that will allow motor imagery theorists to address these points.
The language bioprogram hypothesis
Authors: Bickerton Derek 
Published: February 2010

AbstractIt is hypothesized that creole languages are largely invented by children and show fundamental similarities, which derive from a biological program for language. The structures of Hawaiian Pidgin and Hawaiian Creole are contrasted, and evidence is provided to show that the latter derived from the former in a single generation. A realistic model of the processes of Creole formation shows how several specific historical and demographic factors interacted to restrict, in varying degrees, the access of pidgin speakers to the dominant language, and hence the nature of input to the children of those speakers. It is shown that the resulting similarities of Creole languages derive from a single grammar with a restricted list of categories and operations. However, grammars of individual Creoles will differ from this grammar to a varying extent: The degree of difference will correlate very closely with the quantity of dominant-language input, which in turn is controlled by extralinguistic factors. Alternative explanations of the above phenomena are surveyed, in particular, substratum theory and monogenesis: Both are found inadequate to account for the facts. Primary acquisition is examined in light of the general hypothesis, and it is suggested that the bioprogram provides a skeletal model of language which the child can then readily convert into the target language. Cases of systematic error and precocious learning provide indirect support for the hypothesis. Some conjectures are made concerning the evolutionary origins of the bioprogram and what study of Creoles and related topics might reveal about language origins.
Unconscious cerebral initiative and the role of conscious will in voluntary action
Authors: Libet Benjamin 
Published: February 2010

AbstractVoluntary acts are preceded by electrophysiological “readiness potentials” (RPs). With spontaneous acts involving no preplanning, the main negative RP shift begins at about—550 ms. Such RPs were used to indicate the minimum onset times for the cerebral activity that precedes a fully endogenous voluntary act. The time of conscious intention to act was obtained from the subject's recall of the spatial clock position of a revolving spot at the time of his initial awareness of intending or wanting to move (W). W occurred at about—200 ms. Control experiments, in which a skin stimulus was timed (S), helped evaluate each subject's error in reporting the clock times for awareness of any perceived event.For spontaneous voluntary acts, RP onset preceded the uncorrected Ws by about 350 ms and the Ws corrected for S by about 400 ms. The direction of this difference was consistent and significant throughout, regardless of which of several measures of RP onset or W were used. It was concluded that cerebral initiation of a spontaneous voluntary act begins unconsciously. However, it was found that the final decision to act could still be consciously controlled during the 150 ms or so remaining after the specific conscious intention appears. Subjects can in fact “veto” motor performance during a 100–200-ms period before a prearranged time to act.The role of conscious will would be not to initiate a specific voluntary act but rather to select and control volitional outcome. It is proposed that conscious will can function in a permissive fashion, either to permit or to prevent the motor implementation of the intention to act that arises unconsciously. Alternatively, there may be the need for a conscious activation or triggering, without which the final motor output would not follow the unconscious cerebral initiating and preparatory processes.
Adaptability of innate motor patterns and motor control mechanisms
Authors: Berkinblit M. B. , Feldman A. G. , Fukson O. I. 
Published: February 2010

AbstractThe following factors underlying behavioral plasticity are discussed: (1) reflex adaptability and its role in the voluntary control of movement, (2) degrees of freedom and motor equivalence, and (3) the problem of the discrete organization of motor behavior. Our discussion concerns a variety of innate motor patterns, with emphasis on the wiping reflex in the frog.It is proposed that central regulation of stretch reflex thresholds governs voluntary control over muscle force and length. This suggestion is an integral part of the equilibrium-point hypothesis, two versions of which are compared.Kinematic analysis of the wiping reflex in the spinal frog has shown that each stimulated skin site is associated with a group of different but equally effective trajectories directed to the target site. Such phenomena reflect the principle of motor equivalence -the capacity of the neuronal structures responsible for movement to select one or another of a set of possible trajectories leading to the goal. Redundancy of degrees of freedom at the neuronal level as well as at the mechanical level of the body's joints makes motor equivalence possible. This sort of equivalence accommodates the overall flexibility of motor behavior.An integrated behavioral act or a single movement consists of dynamic components. We distinguish six components for the wiping reflex, each associated with a certain functional goal, specific body positions, and motor-equivalent movement patterns. The nervous system can combine the available components in various ways in forming integrated behavioral sequences. The significance of command neuronal organization is discussed with respect to (1) the combinatory strategy of the nervous system and (2) the relation between continuous and discrete forms of motor control. We conclude that voluntary movements are effected by the central nervous system with the help of the mechanisms that underlie the variability and modifiability of innate motor patterns.
Spontaneous tool use and sensorimotor intelligence inCebuscompared with other monkeys and apes
Authors: Chevalier-Skolnikoff Suzanne 
Published: February 2010

AbstractSpontaneous tool use and sensorimotor intelligence in Cebus were observed to determine whether tool use is discovered fortuitously and learned by trial-and-error or, rather, whether advanced sensorimotor abilities (experimentation and insight) are critical in its ontogeny and evolution.
Surface organization of aqueous MgCl
2
and application to atmospheric marine aerosol chemistry
Authors: Casillas-Ituarte Nadia N. , Callahan Karen M. , Tang Cheng Y. , Chen Xiangke , Roeselová Martina , Tobias Douglas J. , Allen Heather C. 
Published: February 2010

Inorganic salts in marine aerosols play an active role in atmospheric chemistry, particularly in coastal urban regions. The study of the interactions of these ions with water molecules at the aqueous surface helps to elucidate the role of inorganic cations and anions in atmospheric processes. We present surface vibrational sum frequency generation (SFG) spectroscopic and molecular dynamics (MD) studies of aqueous MgCl
2
surfaces as models of marine aerosol. Spectroscopy results reveal that the disturbance of the hydrogen bonding environment of the air/aqueous interface is dependent on the MgCl
2
concentration. At low concentrations (< 1 M) minor changes are observed. At concentrations above 1 M the hydrogen bonding environment is highly perturbed. The 2.1 M intermediate concentration solution shows the largest SFG response relative to the other solutions including concentrations as high as 4.7 M. The enhancement of SFG signal observed for the 2.1 M solution is attributed to a larger SFG-active interfacial region and more strongly oriented water molecules relative to other concentrations. MD simulations reveal concentration dependent compression of stratified layers of ions and water orientation differences at higher concentrations. SFG and MD studies of the dangling OH of the surface water reveal that the topmost water layer is affected structurally at high concentrations (> 3.1 M). Finally, the MgCl
2
concentration effect on a fatty acid coated aqueous surface was investigated and SFG spectra reveal that deprotonation of the carboxylic acid of atmospherically relevant palmitic acid (PA) is accompanied by binding of the Mg
2+
to the PA headgroup.
Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus
Authors: Bush William S. , Dudek Scott M. , Ritchie Marylyn D. 
Published: February 2010

Abstract
Summary: Often in human genetic analysis, multiple tables of single nucleotide polymorphism (SNP) statistics are shown alongside a Haploview style correlation plot. Readers are then asked to make inferences that incorporate knowledge across these multiple sets of results. To better facilitate a collective understanding of all available data, we developed a Ruby-based web application, LD-Plus, to generate figures that simultaneously display physical location of SNPs, binary SNP attributes (such as coding/non-coding or presence on genotyping platforms), common haplotypes and their frequencies and continuously scaled values (such as Fst, minor allele frequency, genotyping efficiency or P-values), all in the context of the D′ and r2 linkage disequilibrium structures. Combining these results into one comprehensive figure reduces dereferencing between figures and tables, and can provide unique insights into genetic features that are not clearly seen when results are partitioned across multiple figures and tables.
Availability: LD-Plus is freely available for non-commercial research institutions. For full details see http://chgr.mc.vanderbilt.edu/ritchielab/ldplus.
Contact: ritchie@chgr.mc.vanderbilt.edu
Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase
Authors: Cammer Stephen , Carter Charles W. 
Published: February 2010

Abstract
Motivation: Similarities in core residue packing provide evidence for divergence or convergence not reported using other methods.
Results: We apply a new method for rapid structure comparison based on Simplicial Neighborhood Analysis of Protein Packing (SNAPP) to the diverse structural classification of proteins (SCOP) α/β-class of protein folds. The procedure identifies inter-residue packing motifs shared by protein pairs from different folds. A threshold of 0.67 Å RMSD for all atoms of corresponding residues ensures inclusion of only highly significant similarities comparable with those observed for identical catalytic residues in homologues. Many tertiary packing motifs are shared among the three classical Rossmannoid folds, as well as thousands of other motifs that occur in at least two distinct folds. Merging of neighboring packing motifs facilitated recognition of larger, recurrent substructures or cores. The anti-codon-binding domain of an archeal aminoacyl-tRNA synthetase (aaRS) was discovered to possess a packed core in which eight identical amino acid residues are within 0.55 Å RMSD of the comparable structure in the FixJ receiver, a member of the Rossmannoid family that also includes the CheY signaling protein and flavodoxin-like proteins. Further investigation identified close variants of this core in five other Rossmannoid folds, including a functionally relevant core in Class Ia aminoacyl-tRNA synthetases. Although it is possible that the two essentially identical cores in the ProRS anti-codon-binding domain and the FixJ receiver converged to the same structure, the consensus core obtained from the structural and sequence alignments suggests that all the implicated protein folds descended from a simpler ancestral protein in which this core provided nucleotide binding and proto-allosteric functions.
Availability: Programs are available at http://staff.vbi.vt.edu/cammer/snapp/download/
Implementation: Programs were written in Perl and c and run under Linux.
Contact: cammer@vbi.vt.edu
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors
Authors: Goya Rodrigo , Sun Mark G.F. , Morin Ryan D. , Leung Gillian , Ha Gavin , Wiegand Kimberley C. , Senz Janine , Crisan Anamaria , Marra Marco A. , Hirst Martin , Huntsman David , Murphy Kevin P. , Aparicio Sam , Shah Sohrab P. 
Published: February 2010

Abstract
Motivation: Next-generation sequencing (NGS) has enabled whole genome and transcriptome single nucleotide variant (SNV) discovery in cancer. NGS produces millions of short sequence reads that, once aligned to a reference genome sequence, can be interpreted for the presence of SNVs. Although tools exist for SNV discovery from NGS data, none are specifically suited to work with data from tumors, where altered ploidy and tumor cellularity impact the statistical expectations of SNV discovery.
Results: We developed three implementations of a probabilistic Binomial mixture model, called SNVMix, designed to infer SNVs from NGS data from tumors to address this problem. The first models allelic counts as observations and infers SNVs and model parameters using an expectation maximization (EM) algorithm and is therefore capable of adjusting to deviation of allelic frequencies inherent in genomically unstable tumor genomes. The second models nucleotide and mapping qualities of the reads by probabilistically weighting the contribution of a read/nucleotide to the inference of a SNV based on the confidence we have in the base call and the read alignment. The third combines filtering out low-quality data in addition to probabilistic weighting of the qualities. We quantitatively evaluated these approaches on 16 ovarian cancer RNASeq datasets with matched genotyping arrays and a human breast cancer genome sequenced to &gt;40× (haploid) coverage with ground truth data and show systematically that the SNVMix models outperform competing approaches.
Availability: Software and data are available at http://compbio.bccrc.ca
Contact: sshah@bccrc.ca
Supplemantary information: Supplementary data are available at Bioinformatics online.
Identifying biologically relevant differences between metagenomic communities
Authors: Parks Donovan H. , Beiko Robert G. 
Published: February 2010

AbstractMotivation: Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis.Results: We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of ‘Candidatus Accumulibacter phosphatis’ in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport.Availability: Python source code and binaries are freely available from our website at http://kiwi.cs.dal.ca/Software/STAMPContact: beiko@cs.dal.caSupplementary information: Supplementary data are available at Bioinformatics online.