bluuebunny/crossref_metadata_2025_split huggingface dataset:
A scalable method to improve gray matter segmentation at ultra high field MRI
Authors: Gulban Omer Faruk , Schneider Marian , Marquardt Ingo , Haast Roy A.M. , De Martino Federico 
Published: January 2018

AbstractHigh-resolution (functional) magnetic resonance imaging (MRI) at ultra high magnetic fields (7 Tesla and above) enables researchers to study how anatomical and functional properties change within the cortical ribbon, along surfaces and across cortical depths. These studies require an accurate delineation of the gray matter ribbon, which often suffers from inclusion of blood vessels, dura mater and other non-brain tissue. Residual segmentation errors are commonly corrected by browsing the data slice-by-slice and manually changing labels. This task becomes increasingly laborious and prone to error at higher resolutions since both work and error scale with the number of voxels. Here we show that many mislabeled, non-brain voxels can be corrected more efficiently and semi-automatically by representing three-dimensional anatomical images using two-dimensional histograms. We propose both a uni-modal (based on first spatial derivative) and multi-modal (based on compositional data analysis) approach to this representation and quantify the benefits in 7 Tesla MRI data of nine volunteers. We present an openly accessible Python implementation of these approaches and demonstrate that editing cortical segmentations using two-dimensional histogram representations as an additional post-processing step aids existing algorithms and yields improved gray matter borders. By making our data and corresponding expert (ground truth) segmentations openly available, we facilitate future efforts to develop and test segmentation algorithms on this challenging type of data.
Extrapolating Weak Selection in Evolutionary Games
Authors: Zhuoqun Wang Nanjing U. , Rick Durrett Duke 
Published: January 2018

AbstractThis work is inspired by a 2013 paper from Arne Traulsen’s lab at the Max Plank Institute for Evolutionary Biology [10]. They studied the small mutation limit of evolutionary games. It has been shown that for 2×2 games the ranking of the strategies does not change as strength of selection is increased [11]. The point of the 2013 paper is that when there are three or more strategies the ordering can change as selection is increased. Wu et al [10] did numerical computations for fixed N. Here, we will instead let the strength of selection β = c/N and let N → ∞ to obtain formulas for the invadability probabilities ϕij that determine the rankings. These formulas, which are integrals on [0, 1], are intractable calculus problems but can be easily evaluated numerically. Here, we concentrate on simple formulas for the ranking order when c is small or c is large.
A thermodynamic atlas of carbon redox chemical space
Authors: Jinich Adrian , Sanchez-Lengeling Benjamin , Ren Haniu , Goldford Joshua E. , Noor Elad , Sanders Jacob N. , Segrè Daniel , Aspuru-Guzik Alán 
Published: January 2018

AbstractRedox biochemistry plays a key role in the transduction of chemical energy in living systems. However, the compounds observed in metabolic redox reactions are a minuscule fraction of chemical space. It is not clear whether compounds that ended up being selected as metabolites display specific properties that distinguish them from non-biological compounds. Here we introduce a systematic approach for comparing the chemical space of all possible redox states of linear-chain carbon molecules to the corresponding metabolites that appear in biology. Using cheminformatics and quantum chemistry, we analyze the physicochemical and thermodynamic properties of the biological and non-biological compounds. We find that, among all compounds, aldose sugars have the highest possible number of redox connections to other molecules. Metabolites are enriched in carboxylic acid functional groups and depleted of carbonyls, and have higher solubility than non-biological compounds. Upon constructing the energy landscape for the full chemical space as a function of pH and electron donor potential, we find that over a large range of conditions metabolites tend to have lower Gibbs energies than non-biological molecules. Finally, we generate Pourbaix phase diagrams that serve as a thermodynamic atlas to indicate which compounds are local and global energy minima in redox chemical space across a set of pH values and electron donor potentials. Our work yields insight into the physicochemical principles governing redox metabolism, and suggests that thermodynamic stability in aqueous environments may have played an important role in early metabolic processes.
Subgoal- and Goal-Related Prediction Errors in Medial Prefrontal Cortex
Authors: Ribas Fernandes José J. F. , Shahnazian Danesh , Holroyd Clay B. , Botvinick Matthew M. 
Published: January 2018

AbstractA longstanding view of the organization of human and animal behavior holds that behavior is hierarchically organized, meaning that it can be understood as directed towards achieving superordinate goals through subordinate goals, or subgoals. For example, the superordinate goal of making coffee can be broken down as accomplishing a series of subgoals, namely boiling water, grinding coffee, pouring cream, etc.Learning and behavioral adaptation depend on prediction-error signals, which have been observed in ventral striatum (VS) and medial prefrontal cortex (mPFC). In past work, we have shown that prediction error signals (PEs) can be linked not only to superordinate goals, but also to subgoals.Here we present two functional magnetic resonance imagining experiments that replicate and extend these findings. In the first experiment, we replicated the finding that mPFC signals subgoal-related PEs, independently of goal PEs. Together with our past work, this experiment reveals that BOLD responses to PEs in mPFC are unsigned. In the second experiment, we showed that when a task involves both goal and subgoal PEs, mPFC shows only goal-related PEs, suggesting that context or attention can strongly impact hierarchical PE coding. Furthermore, we observed a dissociation between the coding of PEs in mPFC and VS. These experiments suggest that the mPFC selectively attends to information at different levels of hierarchy depending on the task context.
IsoCon: Deciphering highly similar multigene family transcripts from Iso-Seq data
Authors: Sahlin Kristoffer , Tomaszkiewicz Marta , Makova Kateryna D. , Medvedev Paul 
Published: January 2018

AbstractA significant portion of genes in vertebrate genomes belongs to multigene families, with each family containing several gene copies whose presence/absence can be highly variable across individuals. For example, each Y chromosome ampliconic gene family harbors several nearly identical (up to 99.99%) gene copies. Existing de novo techniques for assaying the sequences of such highly-similar gene families fall short of reconstructing end to end transcripts with nucleotide-level precision or assigning them to their respective gene copies. We present IsoCon, a novel approach that combines experimental and computational techniques that leverage the power of long PacBio Iso-Seq reads to determine the full-length transcripts of highly similar multicopy gene families. IsoCon uses a cautiously iterative process to correct errors, followed by a statistical framework that allows it to distinguish errors from true variants with high precision. IsoCon outperforms existing methods for transcriptome analysis of Y ampliconic gene families in both simulated and real human data and is able to detect rare transcripts that differ by as little as one base pair from much more abundant transcripts. IsoCon has allowed us to detect an unprecedented number of novel isoforms, as well as to derive estimates on the number of gene copies in human Y ampliconic gene families.
Flexible information coding in frontoparietal cortex across the functional stages of cognitive processing
Authors: Vromen Joyce M. G. , Becker Stefanie I. , Baumann Oliver , Mattingley Jason B. , Remington Roger W. 
Published: January 2018

AbstractNeural activity in frontoparietal cortex shows overlap across cognitive domains and has been proposed to reflect flexible information processing according to current task demands (Dosenbach et al., 2007; Duncan, 2001). However, a strong assertion of flexibility requires investigating activity across stages of cognitive processing. The current study assessed neural activity in Multiple Demand (MD) regions across the stages of processing that form the core of long-standing cognitive models (Welford, 1952). Specifically, many complex tasks share a comparable structure of subsequent operations: target selection, stimulus-response (SR) mapping, and response execution. We independently manipulated the difficulty of target selection and SR mapping in identical stimulus displays and assessed changes in frontoparietal activity with increased demands in either stage. The results confirmed flexibility in MD regions, with enhanced information representation during difficult target selection as well as SR mapping. Additionally, anterior insula (AI) and anterior cingulate cortex (ACC) showed preferential representation of SR stage information, whereas the medial frontal gyrus (MFG) and inferior parietal sulcus (IPS) showed preferential representation of target selection-stage information. Together these results suggest that MD regions dynamically alter the information they represent with changing task demands. This is the first study to demonstrate that MD regions support flexible goal-directed cognition across multiple processing stages. At the same time we show a preference for the representation of information from a specific processing stage in a subset of MD regions.Significance StatementGoal-directed cognition in complex tasks is critical to key life outcomes including longevity and academic performance. Nevertheless, the mechanisms underlying cognition in complex tasks are not well understood. Distinct neural networks are critical to the navigation of specific cognitive domains (e.g. attention), but frontoparietal activity shows cross-domain and -task overlap and supports flexible representation of goal-critical information. This study links flexible frontoparietal processing to longstanding models of meta-cognition that propose a unifying structure of operations underlying most tasks: target selection, SR mapping, and response execution. Our results demonstrate that flexible information representation in frontoparietal cortex is not limited to the SR mapping stage, but applies across the functional stages of cognitive processing, thus maximizing neural efficiency and supporting flexible cognition.
Cigarette smoking and personality: Investigating causality using Mendelian randomization
Authors: Sallis Hannah M , Smith George Davey , Munafò Marcus R 
Published: January 2018

AbstractBackgroundDespite the well-documented association between smoking and personality traits such as neuroticism and extraversion, little is known about the potential causal nature of these findings. If it were possible to unpick the association between personality and smoking, it may be possible to develop more targeted smoking cessation programmes that could lead to both improved uptake and efficacy.MethodsRecent genome-wide association studies (GWAS) have identified variants robustly associated with both smoking phenotypes and personality traits. Here we use publicly available GWAS summary statistics in addition to data from UK Biobank to investigate the link between smoking and personality. We first estimated genetic overlap between traits using LD score regression and then applied both one- and two-sample Mendelian randomization methods to unpick the nature of this relationship.ResultsWe found clear evidence of a modest genetic correlation between smoking behaviours and both neuroticism and extraversion, suggesting shared genetic aetiology. We found some evidence to suggest an association between neuroticism and increased smoking initiation. We also found some evidence that personality traits appear to be causally linked to certain smoking phenotypes: higher neuroticism and heavier cigarette consumption, and higher extraversion and increased odds of smoking initiation. The latter finding could lead to more targeted smoking prevention programmes.ConclusionThe association between neuroticism and cigarette consumption lends support to the self-medication hypothesis, while the association between extraversion and smoking initiation could lead to more targeted smoking prevention programmes.
Count does not recover major events of gene flux in real biological data
Authors: Kapust Nils , Nelson-Sathi Shijulal , Schönfeld Barbara , Hazkani-Covo Einat , Bryant David , Lockhart Peter J. , Röttger Mayo , Xavier Joana C. , Martin William F. 
Published: January 2018

AbstractIn prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional birth-and-death phylogenetic models to investigate prokaryote genome evolution to claim that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here we test the ability of Count, a birth-and-death based program, to recover known events of mass acquisition and differential loss using plastid genomes and eukaryotic protein families that were acquired from plastids. Count showed a strong bias towards reconstructed histories having gene acquisitions distributed uniformly across the tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, Count recovered gradual and continuous lateral gene transfer among lineages, even when massive gains followed by gradual differential loss is the true evolutionary process that generated the gene distribution data.
Orbitofrontal and Thalamic Influences on Striatal Involvement in Human Reversal Learning
Authors: Bell Tiffany , Langdon Angela , Lindner Michael , Lloyd William , Christakou Anastasia 
Published: January 2018

ABSTRACTCognitive flexibility is crucial for adaptation and is disrupted in neuropsychiatric disorders and psychopathology. Human studies of flexibility using reversal learning tasks typically contrast error trials before and after reversal, which provides little information about the mechanisms that support learning and expressing a new response. However, animal studies suggest a specific role in this latter process for the connections between the dorsal striatum and the centromedian parafascicular (CM-Pf) thalamus, a system which may recruit the striatal cholinergic interneurons, but which is not well understood in humans. This study investigated the role of this system in human probabilistic reversal learning, specifically with respect to learning a new response strategy, contrasting its function to that of the better understood orbitoftontal-striatal systems. Using psychophysiological interaction (PPI) analysis of functional magnetic resonance imaging (fMRI) data we show that connectivity between the striatum and both the lateral orbitofrontal cortex (lOFC) and CM-Pf pathways increased during reversal, but not initial learning. However, while the strength of lOFC-striatal connectivity was associated with the speed of the reversal, the strength of CM-Pf-striatal connectivity was associated specifically with the quality of the reversal (reduced regressive errors). These findings expand our understanding of flexibility mechanisms in the human brain, bridging the gap with animal studies of this system.
Women directors’ propensity towards risk in technology firms
Authors: Mukarram Syed Shafqat , Ajmal Tahira , Saeed Abubakr 
Published: January 2018

PurposeThis study aims to investigate the impact of the presence of women directors on firm’s risk-taking behavior in industries where innovation is pivotal and how this impact varies across ownership structure.Design/methodology/approachA sample of 71 listed technology firms on the National Stock Exchange of India for the period of 2008 to 2013 was used. Generalized method of moment estimation technique was used for data analysis.FindingsResults reveal a positive impact of the presence of women directors on technology firms’ risk-taking behavior measured in terms of R&D spending, which is in contrast to the traditional notion that women are risk-averse. Further, results also reveal that family ownership negatively affects the impact of the presence of women directors on risk taking in technology firms.Practical implicationsThe findings of the study suggest that females are risk takers in the context of R&D-intensive technology firms, thus providing new insight for policymakers to formulate more effective board gender diversity policies.Originality/valueBased on the integration of agency and behavioral theories, it is suggested that female executives may be risk-averse or risk-takers depending on contextual factors such as innovation and ownership, which drive the impact of the presence of women directors on firms’ risk-taking behavior.
Cultural heritage in sustainable development
Authors: Chalhoub Michel Soto 
Published: January 2018

PurposePreservation of historic structures meets ecological criteria of sustainable development. In Mount Lebanon, the traditional house is a cultural asset built of native stone one-meter thick double-wythe walls. Today, lack of public policies is causing those environmental assets to approach extinction. The paper aims to discuss this issue.Design/methodology/approachThe methodology uses multivariate regression on 128 data points. A mathematical model is developed and empirically tested on public attitudes toward restoration. Independent variables represent the need for protectionist policies, X1; contribution of restoration to environmental sustainability, X2; contribution to culture, X3; and financial benefits, X4.FindingsIt is found that stone houses transfer heat significantly slower than modern construction. There is a statistically significant and positive correlation with X1, X2, and X3, but negative with X4, most likely due to favoring return on investment of multistory buildings over the attractiveness of stone houses.Research limitations/implicationsAs future research implications, the undergirding of urban planning policies need to be revisited. Current policies neither protect heritage, nor offer legal means to restore heritage houses.Practical implicationsPractical implications include revisions to building laws in Mount Lebanon, as they marginalize old stone structures. Environmental valuation techniques, use value and existence value, are recommended.Social implicationsSocial awareness needs to be built about valuation techniques to account for complex assets that cannot be approximated through short-term real estate market price. Social rather than financial cost-benefit analysis must be performed to quantify environmental assets.Originality/valueThis research illustrates a pilot restoration project with critical issues faced by heritage stone houses. These assets are underrepresented in building laws which warrants social and environmental activism.
Identifying vulnerability to violence: the role of psychopathy and gender
Authors: Ritchie Mary B. , Blais Julie , Forth Adelle E. , Book Angela S. 
Published: January 2018

Purpose
Recent research has suggested that a heightened sensitivity to nonverbal cues may give individuals with psychopathic traits an advantage when selecting potential victims. The purpose of this paper is to examine the effect of gender on the association between psychopathy and perceptions of vulnerability to violent victimization.

Design/methodology/approach
A sample of 291 undergraduate students viewed a series of eight videos depicting individual female targets walking down a hallway from behind. Participants rated each target’s vulnerability to violent victimization and provided a justification for each rating. In addition to these ratings, participants completed the Self-Report Psychopathy Scale.

Findings
A series of hierarchical linear regressions revealed gender differences in the association between psychopathy and accuracy. Among male observers, total psychopathy scores, Factor 2 psychopathy scores, and scores on the antisocial behavior facet were positively associated with accuracy in perceiving vulnerability to violent victimization. Conversely, no associations were identified between psychopathy (total, Factors, and facets) and accuracy among female observers. This suggests that the adept ability to accurately perceive nonverbal cues signalling vulnerability is specific to males exhibiting psychopathic traits.

Originality/value
The results of the current study highlight the importance of distinguishing male and female psychopathy in research and practice. Moreover, with an understanding of individual differences in the ability to accurately perceive nonverbal cues associated with vulnerability, we may begin to develop intervention strategies aimed at reducing future incidences of victimization.
Justice in technology policy
Authors: Yeganehfar Masomeh , Zarei Atefe , Isfandyari-Mogghadam Ali Reza , Famil-Rouhani AliAkbar 
Published: January 2018

Purpose
The purpose of this paper is to provide a systematic literature review of available research evidence on marginal participation of women in ICT-related jobs (ICT – information and communication technology). In this study, it has been attempted to identify gaps in these literature studies according to the Global Index of Gender dimensions and briefly has been explained guidelines for policymakers to improve the participation of women in this area.

Design/methodology/approach
The authors follow from the method of (Tranfield et al., 2003) for conducting a systematic literature review (a systematic review means that the research has specific and systematic steps). Then key words were searched and appropriate resources with this study were evaluated. Accidentally, 55 articles in the period 2000 to 2014 were investigated, and articles were reviewed according to the Global Index of Gender dimensions.

Findings
A review of previous studies indicated that despite considerable attention given to open access to information and women’s skills, role of women in ICT has been underestimated. Results indicated that to keep pace with today’s information society, we would have to reinforce knowledge and abilities of women and provide them employment grounds in jobs that require new skills in ICT. To reinforce participation of women in the jobs, we need to invest in education and design policies to increase the number of women in educational courses related to ICTs. Also, we need to promote equal educational opportunities. Libraries are suitable platforms to create bold employment of women in jobs related to ICTs. Because it seems that majority of professionals are women in these places. In current information communities, we have to raise the level of individual development for reaching total development. Thus, women’s progress at professional jobs is needed to remove barriers of creativity and entrepreneurship for women. Also, development of strategies for providing contribution of women in ICT jobs should not be neglected.

Originality/value
This study is the first comprehensive study on the systematic review of the literature in the field of Gender Gap to show marginal participation of women in the ICT-related jobs.