bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic and feature-specific (anticipatory) prediction-related neural activity in the human auditory system
Authors: Demarchi Gianpaolo , Sanchez Gaëtan , Weisz Nathan 
Published: February 2018

AbstractPrior experience shapes sensory perception by enabling the formation of expectations with regards to the occurrence of upcoming sensory events. Especially in the visual modality, an increasing number of studies show that prediction-related neural signals carry feature-specific information about the stimulus. This is less established in the auditory modality, in particular without bottom-up signals driving neural activity. We studied whether auditory predictions are sharply tuned to even carry tonotopic specific information. For this purpose, we conducted a Magnetoencephalography (MEG) experiment in which participants passively listened to sound sequences that varied in their regularity (i.e. entropy). Sound presentations were temporally predictable (3 Hz rate), but were occasionally omitted. Training classifiers on the random (high entropy) sound sequence and applying them to all conditions in a time-generalized manner, allowed us to assess whether and how carrier frequency specific information in the MEG signal is modulated according to the entropy level. We show that especially in an ordered (most predictable) sensory context neural activity during the anticipatory and omission periods contains carrier-frequency specific information. Overall our results illustrate in the human auditory system that prediction-related neural activity can be tuned in a tonotopically specific manner.
De novoassembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data
Authors: Ameur Adam , Che Huiwen , Martin Marcel , Bunikis Ignas , Dahlberg Johan , Höijer Ida , Häggqvist Susana , Vezzi Francesco , Nordlund Jessica , Olason Pall , Feuk Lars , Gyllensten Ulf 
Published: February 2018

AbstractWe have performedde novoassembly of two Swedish genomes using long-read sequencing and optical mapping, resulting in total assembly sizes of nearly 3 Gb and hybrid scaffold N50 values of over 45 Mb. A further analysis revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have elevated GC-content and are primarily located in centromeric or telomeric regions. A BLAST search showed that 31% of the NS are different from any sequences deposited in nucleotide databases. The remaining NS correspond to human (62%) or primate (6%) nucleotide entries, while 1% of hits show the highest similarity to other species, including mouse and a few different classes of parasitic worms. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are missing from GRCh38 also at chromosomes 14, 17 and 21. Inclusion of these novel sequences into the GRCh38 reference radically improves the alignment and variant calling of whole-genome sequencing data at several genomic loci. Through a re-analysis of 200 samples from a Swedish population-scale sequencing project, we obtained over 75,000 putative novel SNVs per individual when using a custom version of GRCh38 extended with 17.3 Mb of NS. In addition, about 10,000 false positive SNV calls per individual were removed from the GRCh38 autosomes and sex chromosomes in the re-analysis, with some of them located in protein coding regions.
PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling
Authors: Letort Gaelle , Montagud Arnau , Stoll Gautier , Heiland Randy , Barillot Emmanuel , Macklin Paul , Zinovyev Andrei , Calzone Laurence 
Published: February 2018

AbstractDue to the complexity of biological systems, their heterogeneity, and the internal regulation of each cell and its surrounding, mathematical models that take into account cell signalling, cell population behaviour and the extracellular environment are particularly helpful to understand such complex systems. However, very few of these tools, freely available and computationally efficient, are currently available. To fill this gap, we present here our open-source software, PhysiBoSS, which is built on two available software packages that focus on different scales: intracellular signalling using continuous-time markovian Boolean modelling (MaBoSS) and multicellular behaviour using agent-based modelling (PhysiCell).The multi-scale feature of PhysiBoSS - its agent-based structure and the possibility to integrate any Boolean network to it - provide a flexible and computationally efficient framework to study heterogeneous cell population growth in diverse experimental set-ups. This tool allows one to explore the effect of environmental and genetic alterations of individual cells at the population level, bridging the critical gap from genotype to phenotype. PhysiBoSS thus becomes very useful when studying population response to treatment, mutations effects, cell modes of invasion or isomorphic morphogenesis events.To illustrate potential use of PhysiBoSS, we studied heterogeneous cell fate decisions in response to TNF treatment in a 2-D cell population and in a tumour cell 3-D spheroid. We explored the effect of different treatment regimes and the behaviour and selection of several resistant mutants. We highlighted the importance of spatial information on the population dynamics by considering the effect of competition for resources like oxygen. PhysiBoSS is freely available on GitHub (https://github.com/gletort/PhysiBoSS), and is distributed open source under the BSD 3-clause license. It is compatible with most Unix systems, and a Docker package (https://hub.docker.com/r/gletort/physiboss/) is provided to ease its deployment in other systems.
Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT
Authors: Kinmonth-Schultz Hannah A. , MacEwen Melissa J. , Seaton Daniel D. , Millar Andrew J. , Imaizumi Takato , Kim Soo-Hyung 
Published: February 2018

AbstractWe assessed temperature influence on flowering by incorporating temperature-responsive flowering mechanisms across developmental age into an existing model. Temperature influences both the leaf production rate and expression of FLOWERING LOCUS T (FT), a photoperiodic flowering regulator, in leaves. The Arabidopsis Framework Model incorporated temperature influence on leaf growth but ignored the consequences of leaf growth on and direct temperature influence of FT expression. We measured FT production in differently aged leaves and modified the model, adding the mechanistic temperature influence on FT transcription, and linking FT to leaf growth. Our simulations suggest that in long days, the developmental timing (leaf number) at which the reproductive transition occurs is influenced by day length and temperature through FT, while temperature influences the rate of leaf production and the time (in days) the transition occurs. Further, we demonstrated that FT is mainly produced in the first 10 leaves in the Columbia ecotype, and that FT accumulation alone cannot explain flowering in conditions in which flowering is delayed. Our simulations supported our hypotheses that: 1) temperature regulation of FT, accumulated with leaf growth, is a component of thermal time, and 2) incorporating mechanistic temperature regulation of FT can improve model predictions in fluctuating temperatures.
DNAscan: a fast, computationally and memory efficient bioinformatics pipeline for the analysis of DNA next-generation-sequencing data
Authors: Iacoangeli A , Al Khleifat A , Sproviero W , Shatunov A , Jones AR , Dobson R , Newhouse SJ , Al-Chalabi A 
Published: February 2018

AbstractThe generation of DNA Next Generation Sequencing (NGS) data is a commonly applied approach for studying the genetic basis of biological processes, including diseases, and underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. A huge number of bioinformatics tools exist and it is therefore challenging to design an analysis pipeline; NGS analysis is computationally intensive, requiring expensive infrastructure which can be problematic given that many medical and research centres do not have adequate high performance computing facilities and the use of cloud computing facilities is not always possible due to privacy and ownership issues. We have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. We achieved this by exploiting state-of-the-art bioinformatics tools. DNAscan can analyse raw, 40x whole genome NGS data in 8 hours, using as little as 8 threads and 16 Gbs of RAM, while guaranteeing a high performance. DNAscan can look for SNVs, small indels, SVs, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases including ClinVar, Exac and dbSNP, and a local deployment of the gene.iobio platform is available for an on-the-fly result visualisation.
Investigation of Electrical Stimulation Effect on Intracellular Calcium Dynamics Using Locally Uniform Mesh Refinement
Authors: Oftadeh Mohammad Omid 
Published: February 2018

AbstractModeling-based methods are conventionally exploited to simulate and predict the dynamics of a system in various fields of engineering. However, due to the intricacy of biological systems, these methods were rarely utilized in bioengineering until recently. By developing advanced computers with the ability to cope with enormous calculations and extending our knowledge about biological systems, modeling-based approaches have been adopted to manipulate biological systems. While utilizing the models to investigate the behavior of a system has some advantages including lower cost and time consumption, such methods were used for tissue engineering scarcely. Exploiting modeling-based methods to tissue engineering field requires developing and utilizing efficient computational methods to model gene regulation and signaling networks, which determine cell response to environmental changes and cellular fate.In the present work, a novel spatio-temporal method was proposed, predicated on locally uniform mesh refinement. A benchmark comparison was performed with the previously used method and the results indicated the better performance of the incipiently adopted method. Besides, the model was utilized to investigate the effect of a popular differentiating stimulator, namely electrical stimulation, on mesenchymal stem cells as a type of stem cells widely used in tissue engineering. The results of the simulations demonstrated the puissance of such computational models in analyzing and predicting the effect of biochemical and biophysical perturbations on the cells and hence, their potential utility in tissue engineering.
Generation of functional human adipose tissue in mice from primed progenitor cells
Authors: Rojas-Rodriguez Raziel , Lujan-Hernandez Jorge , Min So Yun , DeSouza Tiffany , Teebagy Patrick , Desai Anand , Tessier Heather , Slamin Robert , Siegel-Reamer Leah , Berg Cara , Baez Angel , Lalikos Janice , Corvera Silvia 
Published: February 2018

AbstarctAdipose tissue is used extensively in reconstructive and regenerative therapies, but transplanted fat often undergoes inflammation and cell death, requiring further revision surgery. We report that functional human adipose tissue can be generated from mesenchymal progenitor cells in-vivo, providing an alternative approach to its therapeutic use. We leveraged previous findings that progenitor cells within the vasculature of human adipose tissue robustly proliferate in 3-dimensional culture under proangiogenic conditions. Implantation of these progenitor cells into immunocompromised mice results in differentiation towards non-adipocyte fates, incapable of generating a distinct tissue structure. However, priming of these progenitor cells in-vitro towards adipogenic differentiation results in formation of functional adipose tissue in-vivo. Mechanistically, priming induces the expression of genes encoding specific extracellular matrix and remodeling proteins, and induces extensive vascularization by host blood vessels. In comparison, grafts from adipose tissue obtained by liposuction undergo poor vascularization, adipocyte death, cyst formation, calcification and inefficient adiponectin secretion. Thus, primed mesenchymal adipose tissue progenitors reveal mechanisms of human adipose tissue development, and have potential to improve outcomes in reconstructive and regenerative medicine.
Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium difficile Patients With and Without IBD
Authors: Hirten Robert P , Grinspan Ari , Fu Shih-Chen , Luo Yuying , Suarez-Farinas Mayte , Rowland John , Contijoch Eduardo J. , Mogno Ilaria , Yang Nancy , Luong Tramy , Labrias Philippe R. , Peter Inga , Cho Judy H. , Sands Bruce E. , Colombel Jean Frederic , Faith Jeremiah J. , Clemente Jose C. 
Published: February 2018

AbstractBackground & AimsRecurrent and refractory Clostridium difficile infections (CDI) are effectively treated with fecal microbiota transplant (FMT). Uncertainty exists regarding the effectiveness of FMT for CDI with underlying inflammatory bowel disease (IBD), its effects on disease activity and its effectiveness transferring the donor microbiome to patients with and without IBD. This study aims to determine FMTs effectiveness in subjects with and without IBD, its impact on IBD activity, the level of microbiome engraftment, and predictors of CDI recurrence.MethodsSubjects with and without IBD who underwent FMT for recurrent or refractory CDI between 2013 and 2016 at The Mount Sinai Hospital were followed for up to 6 months. The primary outcome was CDI recurrence 6 months after FMT. Secondary outcomes were (1) CDI recurrence 2 months after FMT; (2) Frequency of IBD flare after FMT; (3) Microbiome engraftment after FMT; (4) Predictors of CDI recurrence.ResultsOverall, 134 patients, 46 with IBD, were treated with FMT. There was no difference in recurrence in patients with and without IBD at 2 months (22.5% vs 17.9%; p=0.63) and 6 months (38.7% vs 36.5%; p>0.99). Proton pump inhibitor use, severe CDI, and comorbid conditions were predictors of recurrence. The pre-FMT microbiome was not predictive of CDI recurrence. Subjects with active disease requiring medication escalation had reduced engraftment. There was no difference in engraftment based on IBD endoscopic severity at FMT.ConclusionsIBD did not affect CDI recurrence rates 6 months after FMT. Pre-FMT microbiome was not predictive of recurrence, and microbial engraftment was dependent on IBD treatment escalation but not on underlying disease severity.
The dyslexia susceptibility KIAA0319 gene shows a highly specific expression pattern during zebrafish development supporting a role beyond neuronal migration
Authors: Gostic Monika , Martinelli Angela , Tucker Carl , Yang Zhengyi , Gasparoli Federico , Ewart Jade-Yi , Dholakia Kishan , Sillar Keith , Tello Javier , Paracchini Silvia 
Published: February 2018

AbstractDyslexia is a common neurodevelopmental disorder that affects reading abilities and is predicted to be caused by a significant genetic component. Very few genetic susceptibility factors have been identified so far and amongst those,KIAA0319is a key candidate.KIAA0319is highly expressed during brain development but its function remains poorly understood. Initial RNA-interference studies in rats suggested a role in neuronal migration whereas subsequent work with double knock-out mouse models for bothKiaa0319and its paralogueKiaa0319-likereported effects in the auditory system but not in neuronal migration. To further understand the role ofKIAA0319during neurodevelopment, we carried out an expression study of the zebrafish orthologue at different embryonic stages. We report particularly high gene expression during the first few hours of development. At later stages, expression becomes localised in well-defined structures such as the eyes, the telencephalon and the notochord, supporting a role forkiaa0319that is not restricted to brain development. Surprisingly,kiaa0319-like, which generally shows a similar expression pattern, was not expressed in the notochord suggesting a role specific tokiaa0319in this structure. This study contributes to our understanding ofKIAA0319function during embryonic development which might involve additional roles in the visual system and in the notochord. Such a specific spatiotemporal expression pattern is likely to be under the controlled of tightly regulated sequences. Therefore, these data provide a framework to interpret the effects of the dyslexia-associated genetic variants that reside inKIAA0319non-coding regulatory regions.
Sustainability of microenterprises: an empirical analysis
Authors: Chatterjee Susmita , DuttaGupta Sangita , Upadhyay Parijat 
Published: February 2018

PurposeThe purpose of this paper is to investigate the facilitators and impediments of business sustainability of the microenterprises. The study also proposes a framework of social sustainability through women microentrepreneurs in India.Design/methodology/approachIn order to fulfill the objectives, primary data have been collected and analyzed by employing binary logit model. Additionally, in-depth interviews and focus group interviews were conducted to get more precise insight on the issue.FindingsThe study finds out the factors determining sustainability of microenterprises. The economic, political, demographic factors along with family contribution are found to be important factors in determining sustainability and success of microenterprises. The study also show that microenterprises emerging from self-help groups (SHGs) are adding value to the society by overall women empowerment.Research limitations/implicationsThe study will pave the way for further research about the sustainability factors of microenterprises in emerging economies.Practical implicationsThe finding of this paper will give directions to policy makers as well as to stakeholders as small businesses are becoming way of life in all developing countries.Originality/valueThis study contributes to the literature by identifying how microentrepreneurs emerging from SHGs are achieving societal goals of poverty eradication. It determines the indicators of business sustainability for small businesses run by women. Empirical and in-depth study explores the issues those have policy implications.
Work disengagement among SME workers: evidence from India
Authors: Rastogi Ashish , Pati Surya Prakash , Dixit Jitendra Kumar , Kumar Pankaj 
Published: February 2018

PurposeThe purpose of this paper is to examine the two alternative theoretical explanations of disengagement at work. Following the job demands-resources (JD-R) perspective, the relationship between job complexity and disengagement is tested. In accordance with the process model of burnout, the association between exhaustion and disengagement is examined. The paper also examines conservation of resources (COR) as an integrative framework as far as the moderating role of resilience in both these relationships is concerned.Design/methodology/approachSurvey-based quantitative methodology was followed. A total of 138 employees of an agro-processing unit in North India were surveyed, and 119 usable responses were obtained. Besides the constructs of interest, the questionnaire also sought responses on the relevant demographic variables.FindingsBoth job complexity and exhaustion predicted disengagement at work. However, contrary to a negatively hypothesized relationship between job complexity and disengagement, a positive association was found. Resilience was found to be negatively moderating exhaustion-disengagement relationship. No influence of resilience was found on the complexity-disengagement association.Research limitations/implicationsThe findings could be specific to the sample and to India. Caution should be exercised while generalizing. Future researchers should validate the findings across contexts.Practical implicationsThe results suggest that complexity may not necessarily be perceived as a resource. Hence organizations must invest in training and skill development programs for their workers. Further, managers should assess resilience as an important component while selecting workers.Originality/valueContrary findingsvis-à-visjob complexity and disengagement could have implications for the JD-R perspective. Further, this research integrates alternative explanations of disengagement employing the COR framework.
Quantifying the contribution of competencies toward performance
Authors: Poovathingal James Sebastian , Kumar Deepti V. 
Published: February 2018

Purpose
Performance management (PM) is an important tool to enhance productivity. However, its Achilles heel is its lack of future orientation. The main reason for this is that PM systems fail to empirically link competencies to results. The purpose of this paper is to address this gap.

Design/methodology/approach
This study uses literature review and deductive logic to evolve the concept of “Contribution of Competencies (CC)” and proof tests it quantitatively.

Findings
The impact of a level of competency on the results of a job can be determined by CC. The gap between expected and actual CC can predict future performance, determine the training needs with precision and measure individual efficacy and human capital adequacy of a department/an organization.

Research limitations/implications
This is single organization research for proof of concept. Multi-organizational research using empirical study linking CC with demonstrated performance can make the concept of CC more robust.

Practical implications
CC helps to: prioritize training for competencies that would impact performance with surgical precision, fix responsibility for failure to perform on individual/organizational factors, compare individual employees across functions, determine interdepartmental/inter-firm human capital efficacy, and evaluate human capital of a firm.

Originality/value
Empirical expression of the nature of relationship between competency levels and results through CC and its byproducts, individual efficacy ratio, and human capital adequacy ratio are original contributions.