bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biophysical modeling of neural plasticity induced by transcranial magnetic stimulation
Authors: Wilson Marcus T. , Fulcher Ben D. , Fung Park K. , Robinson Peter A. , Fornito Alex , Rogasch Nigel C. 
Published: August 2017

AbstractTranscranial magnetic stimulation (TMS) is a widely used noninvasive brain stimulation method capable of inducing plastic reorganisation of cortical circuits in humans. Changes in neural activity following TMS are often attributed to synaptic plasticity (e.g long-term potentiation and depression; LTP/LTD). However, the precise way in which synaptic processes such as LTP/LTD modulate the activity of large populations of neurons, as stimulated en masse by TMS, are unclear. The recent development of biophysically-informed models, which capture the physiological properties of TMS-induced plasticity using mathematics, provide an excellent framework for reconciling synaptic and macroscopic plasticity. In this article, we overview the TMS paradigms used to induce plasticity, and their limitations. We then describe the development of biophysically-based numerical models of the mechanisms underlying LTP/LTD on population-level neuronal activity, and the application of these models to TMS plasticity paradigms, including theta burst and paired associative stimulation. Finally, we outline how modeling can complement experiment to improve mechanistic understandings and optimize outcomes of TMS-induced plasticity.AbbreviationsTMStranscranial magnetic stimulationLTPlong-term potentiationLTDlong-term depressionrTMSrepetitive TMSTBStheta burst stimulationPASpaired-associative stimulationMEPmotor-evoked potentialcTBScontinuous TBSiTBSintermittent TBSNMDAn-methyl-d-aspartateCaDPcalcium dependent plasticityEEGelectroencephalographyMRImagnetic resonance imagingSTDPspike timing dependent plasticityBCMBienenstock-Cooper-MunroGABAgamma-aminobutyric-acidISIinter-stimulus interval
Spontaneous activity synchronizes whisker-related sensorimotor networks prior to their maturation in the developing rat cortex
Authors: McVea David A. , Murphy Timothy H. , Mohajerani Majid H. 
Published: August 2017

AbstractA prominent feature of the cortical systems controlling the whiskers in the adult rodent is tight coupling between sensory and motor systems. Stimulation of the whiskers evokes activation of discrete motor regions of cortex shortly after activation of the sensory cortex. To explore the factors that direct the development of sensorimotor functional connectivity, we recorded spontaneous and whisker-evoked cortical activity using voltage-sensitive imaging over a large (7X7 mm) craniotomy in postnatal rats (day 5-12) under anesthesia. We found that spontaneous bursts of activity in the barrel cortex were correlated predominantly with activity in motor (anterio-medial) cortex, at ages before whisker stimulation evoked activation in this area. Intracortical microstimulation and anatomical tracing experiments confirmed there were no functional or anatomical intracortical sensorimotor connections. We interpret these results as evidence that the spontaneous patterns of activity in the cortex synchronize functionally related regions of the brain prior to their maturation.Author ContributionsD.A.M, T.H.M., and M.H.M. designed the study. D.A.M, and M.H.M performed the experiments and analyzed the data and wrote the manuscript, which all authors commented on and edited. T.H.M. and M.H.M. supervised the study.
Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model
Authors: Clayton Jonathan B. , Al-Ghalith Gabriel A. , Long Ha Thang , Tuan Bui Van , Cabana Francis , Huang Hu , Vangay Pajau , Ward Tonya , Minh Vo Van , Tam Nguyen Ai , Dat Nguyen Tat , Travis Dominic A. , Murtaugh Michael P. , Covert Herbert , Glander Kenneth E. , Nadler Tilo , Toddes Barbara , Sha John C.M. , Singer Randall S. , Knights Dan , Johnson Timothy J. 
Published: August 2017

ABSTRACTRed-shanked doucs (Pygathrix nemaeus) are endangered, foregut-fermenting colobine primates which are difficult to maintain in captivity. There are critical gaps in our understanding of their natural dietary habits including consumption of leaves, unripe fruit, flowers, seeds, and other plant parts. There is also a lack of understanding of enteric adaptations, including their unique microflora. To address these knowledge gaps, we used the douc as a model to study relationships between gastrointestinal microbial community structure, diet, and health. We analyzed published fecal samples as well as detailed dietary history from doucs with four distinct lifestyles (wild, semi-wild, semi-captive, and captive) and determined gastrointestinal bacterial microbiome composition using 16S rRNA sequencing. A clear gradient of microbiome composition was revealed along an axis of natural lifestyle disruption, including significant associations with diet, health, biodiversity, and microbial function. We identified potential microbial biomarkers of douc dysbiosis, includingBacteroidesandPrevotella. Our results suggest a gradient-like shift in captivity causes an attendant shift to severe gut dysbiosis, thereby resulting in gastrointestinal issues.
Thiol-linked alkylation for the metabolic sequencing of RNA
Authors: Herzog Veronika A. , Reichholf Brian , Neumann Tobias , Rescheneder Philipp , Bhat Pooja , Burkard Thomas R. , Wlotzka Wiebke , von Haeseler Arndt , Zuber Johannes , Ameres Stefan L. 
Published: August 2017

AbstractGene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady-state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), an orthogonal chemistry-based epitranscriptomics-sequencing technology that uncovers 4-thiouridine (s4U)-incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM-seq enables rapid access to RNA polymerase II-dependent gene expression dynamics in the context of total RNA. When applied to mouse embryonic stem cells, SLAM-seq provides global and transcript-specific insights into pluripotency-associated gene expression. We validated the method by showing that the RNA-polymerase II-dependent transcriptional output scales with Oct4/Sox2/Nanog-defined enhancer activity; and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs andN6-methyladenosine. SLAM-seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective, and scalable manner.One Sentence Summary:Chemical nucleotide-analog derivatization provides global insights into transcriptional and post-transcriptional gene regulation
Stronger effects of heterozygosity on survival in harsher environments
Authors: Vincenzi S , Jesensek D , Garza JC , Crivelli AJ 
Published: August 2017

AbstractA stronger correlation between heterozygosity and fitness or its components (e.g., life-history traits such as survival, growth, morphology) is expected in harsher environments, but few studies have investigated whether the effects of heterozygosity on life-history traits vary with environmental conditions in natural populations. Here, the hypothesis that the effects of heterozygosity vary with environmental conditions was tested using six populations of marble troutSalmo marmoratusfrom Western Slovenia as a model system. Specifically, the tested hypotheses were: stronger effects of heterozygosity on survival in populations characterized by low average survival, no effects of heterozygosity on probability of surviving flash floods owing to their largely non-selective effects across traits, and stronger effects of heterozygosity on survival for fish born after floods than fish born before. A significant effect of heterozygosity on survival was found in populations characterized by low average survival. There were no effects of heterozygosity on probability of surviving flash floods, but in one population a positive correlation between heterozygosity and survival for fish born after the extreme events was found, probably because crowding in a small section of the stream caused more intense competition for resources.
A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture
Authors: Gassler Johanna , Brandão Hugo B. , Imakaev Maxim , Flyamer Ilya M. , Ladstätter Sabrina , Bickmore Wendy A. , Peters Jan-Michael , Mirny Leonid A. , Tachibana-Konwalski Kikuë 
Published: August 2017

SUMMARYFertilization triggers assembly of higher-order chromatin structure from a naïve genome to generate a totipotent embryo. Chromatin loops and domains are detected in mouse zygotes by single-nucleus Hi-C (snHi-C) but not bulk Hi-C. We resolve this discrepancy by investigating whether a mechanism of cohesin-dependent loop extrusion generates zygotic chromatin conformations. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that depend on Scc1-cohesin and are regulated in size by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting loop extrusion dynamics and epigenetic reprogramming. Polymer simulations based on snHi-C are consistent with a model where cohesin locally compacts chromatin and thus restricts inter-chromosomal interactions by active loop extrusion, whose processivity is controlled by Wapl. Our simulations and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onwards.HighlightsZygotic genomes are organized into cohesin-dependent chromatin loops and TADsLoop extrusion leads to different loop strengths in maternal and paternal genomesCohesin restricts inter-chromosomal interactions by altering chromosome surface areaLoop extrusion organizes chromatin at multiple genomic scales
The many hands of science
Authors: Sundling Pär 
Published: August 2017

Purpose
The purpose of this paper is to identify the research contributions of authors and subauthors in order to outline how authorship, as opposed to acknowledgment, is awarded in the lab-based life sciences.

Design/methodology/approach
The work tasks described in author contribution statements and acknowledgments sections of research articles published in Nature Chemical Biology were classified according to a three-layered taxonomy: core layer; middle layer; outer layer.

Findings
Most authors are core or middle layer contributors, i.e. they perform at least one core or middle layer task. In contrast, most subauthors are outer layer contributors. While authors tend to be involved in several tasks, subauthors tend to make single contributions. The small but significant share of authors performing only outer layer tasks suggests a disconnect in author attribution between traditional author guidelines and scientific practice. A level of arbitrariness in whether a contributor is awarded authorship or subauthorship status is reported. However, this does not implicate first or last authorships.

Research limitations/implications
Data from one journal only are used. Transferability is limited to research in high impact journals in the lab-based life sciences.

Originality/value
The growth in scientific collaboration underlines the importance of gaining a deeper understanding of the distinction between authorship and subauthorship in terms of the types of research contributions that they de facto represent. By utilizing hitherto unexplored data sources this study addresses a gap in the literature, and gives an important insight into the reward system of science.
A resource- and impact-based micro-level conceptualization of collaborative academic work
Authors: Perez Vico Eugenia , Hallonsten Olof 
Published: August 2017

Purpose
The purpose of this paper is to develop new conceptual tools for analyzing how contemporary collaborative academic work is organized on micro-level, and its social and economic impact, in broad terms. Thus it makes a contribution towards a better view on how contemporary academics organize their professional activities in light of profound changes to the framework conditions of academic work, and a better view on the productivity and potentially very wide societal impact of academia.

Design/methodology/approach
Based on previous research, the arguments are developed conceptually. The paper builds both on previous empirical findings and strong traditions in organization theory (resource dependence theory) and innovation studies.

Findings
The paper achieves a synthesized conceptual view on impact of academia, strongly related to how individual academics organize their professional activities today, given the recent profound structural changes to the academic system. The paper launches resource dependence as a key concept for understanding contemporary academic work in a collaborative context, and sequences of impact as a key tool for conceptualizing the very varied role of academia in society.

Research limitations/implications
While building strongly on previous research, the paper is conceptual in nature and thus its value lies chiefly in assisting future studies.

Practical implications
The contribution can assist in policymaking by promoting the achievement of more accurate and better balanced models and appraisal schemes.

Originality/value
The paper has theoretical originality and its synthesized argument about organizing and impact is of high value for current scholarly debate on these topics.
Analysis of interaction among the barriers to 5S implementation using interpretive structural modeling approach
Authors: Attri Rajesh , Singh Bhupender , Mehra Sunil 
Published: August 2017

Purpose
The purpose of this paper is to ascertain and analyze the interactions among different barriers of 5S implementation in manufacturing organizations.

Design/methodology/approach
In this paper, 15 barriers affecting the implementation of 5S in manufacturing organizations have been identified from literature analysis and discussion with academic and industrial experts. Afterwards, identified barriers were validated by using nation-wide questionnaire-based survey. Then, interpretive structural modeling (ISM) approach has been utilized to find out the interaction among the identified barriers in order to develop hierarchy-based model.

Findings
The research identifies several key barriers which have high driving power and weak dependence power. In this concern, these barriers entail extreme care and handling for successful implementation of 5S. Financial constraints, lack of top management commitment, and no proper vision and mission are found to be the key barriers.

Research limitations/implications
The developed ISM model is based on experts’ opinion. This developed hierarchy-based model requires further validation by using structural equation modeling approach or by performing detailed case studies.

Originality/value
In this paper, ISM-based structural model has been recommended for Indian manufacturing organizations, which is a novel exertion in the area of 5S implementation.
Russian railways on the Eurasian market: issue of sustainability
Authors: Panova Yulia , Korovyakovsky Eugene , Semerkin Anton , Henttu Ville , Li Weidong , Hilmola Olli-Pekka 
Published: August 2017

Purpose
This research examines factors that determine the improvement of the Russian supply chain sustainability. The strategic business model incorporates ecological, social and economic aspects.

Design/methodology/approach
Considering Trans-Siberian Railway as a typical case, the study selected several cases or the parts of the primary rail connection with the affiliation of important neighbouring countries. The study uses quantitative analyses of a variety of size parameters (e.g. volumes of traffic, logistics costs, delivery distance and air pollutants).

Findings
The empirical findings stress that supply chains should favour in the future railway (or intermodal) connections for piggyback and containerised cargo. Herein lays the reason for the examination of all traditional factors affecting the modal choice and their complementation by the parameters to measure sustainability throughout the supply chains. The inclusion of the green practices positively affected the environmental, social and economic performance of the new approach.

Research limitations/implications
This research focuses on the delivery of cargo in containers and semi-trailers within wagons through the overland corridors. Despite the restrictive empirical findings within the national transport system, some elements can be representative of the international supply chains, provided that intermodal services are the most appropriate for the transportation over long distances.

Practical implications
Clients, media and regulatory bodies stress the consideration of environmental aspects at all stages of a global supply chain. Therefore, their adoption into strategic imperatives of local supply chains becomes inevitable.

Originality/value
An assessment of supply chains for longer distance transportation in Russia has not taken sustainability into account within cost analyses.
Product innovation capability, export scope and export experience
Authors: Arslanagic-Kalajdzic Maja , Balboni Bernardo , Kadic-Maglajlic Selma , Bortoluzzi Guido 
Published: August 2017

Purpose
By applying the logic of the resource-based view and process-based internationalisation theory, this study aims to provide a better understanding of the effects of product innovation capability on the export scope of firms based in developing countries and the role of export experience as a facilitating mechanism.

Design/methodology/approach
Using survey data obtained from three developing countries, two main research hypotheses were empirically tested: a quadratic relationship exists between product innovation capability and export scope and export experience has a moderating effect in this relationship.

Findings
Product innovation capability and export scope have a U-shaped relationship, and export experience exerts a moderating effect. The greater the export experience is, the more the relationship between product innovation and export scope changes, taking on a more inverted U-shaped form.

Practical implications
Firms based in developing countries need to catch-up on innovation capabilities before being able to succeed in international markets. Managers must be aware that initial investments in product innovation could not pay off immediately and that significant additional efforts might be needed to obtain noteworthy results in terms of international expansion.

Originality/value
This study is among the first to focus on the curvilinear relationship between product innovation capability and export scope for firms based in developing countries while accounting for the moderating role of firms’ export experience.
The role of innovation in building competitive advantages: an empirical investigation
Authors: Chatzoglou Prodromos , Chatzoudes Dimitrios 
Published: August 2017

PurposeNowadays, innovation appears as one of the main driving forces of organisational success. Despite the above fact, its impact on the propensity of an organisation to develop and sustain a competitive advantage has not yet received sufficient empirical investigation. The purpose of this paper is to enhance the existing empirical literature by focusing on the antecedents of innovation and its impact on competitive advantage. It proposes a newly developed conceptual framework that adopts a three-step approach, highlighting areas that have rarely been simultaneously examined before.Design/methodology/approachThe examination of the proposed conceptual framework was performed with the use of a newly developed structured questionnaire that was distributed to a group of Greek manufacturing companies. The questionnaire has been successfully completed by chief executive officers (CEOs) from 189 different companies. CEOs were used as key respondents due to their knowledge and experience. The reliability and the validity of the questionnaire were thoroughly examined. Empirical data were analysed using the structural equation modelling technique. The study is empirical (based on primary data), explanatory (examines cause and effect relationships), deductive (tests research hypotheses) and quantitative (includes the analysis of quantitative data collected with the use of a structured questionnaire).FindingsResults indicate that knowledge management, intellectual capital, organisational capabilities and organisational culture have significant direct and indirect effects on innovation, underlining the importance of their simultaneous enhancement. Finally, the positive effect of innovation on the creation of competitive advantages is empirically validated, bridging the gap in the relevant literature and offering avenues for additional future research.Originality/valueThe causal relationship between innovation and competitive advantage, despite its significant theoretical support, has not been empirically validated. The present paper aspires to bridge this gap, investigating the impact of innovation on the development of competitive advantages. Moreover, the present study adopts a multidimensional approach that has never been explored in the existing innovation literature, making the examination of the proposed conceptual framework an interesting research topic.
Pragmatic pilot cluster randomised control trial of a school-based peer-led anti-smoking intervention for 13-14 year olds in Malaysia
Authors: Melson Elniee , Bridle Christopher , Markham Wolfgang 
Published: August 2017

Purpose
The purpose of this paper is to report the process evaluation of a pilot randomised control trial of an anti-smoking intervention for Malaysian 13-14-year olds, conducted in 2011/2012. It was hypothesised that trained peer supporters would promote non-smoking among classmates through informal conversations.

Design/methodology/approach
Smoking-related baseline and follow-up questionnaires were administered, seven months apart, to Form 1 students (n=2,118) attending eight schools across two districts in Sabah (Kota Kinabalu; Keningau). Concealed stratified randomisation assigned two schools per district to the control and intervention arms. Control schools received usual care. Intervention schools received usual care and the peer supporter intervention. Peer supporters completed smoking-related knowledge and attitudes questionnaires before and after peer supporter training and peer supporter training evaluation questionnaires. They also discussed the peer supporter training and role in focus groups immediately following training (n=4) and three months later (n=3), and additionally, recorded post-training anti-smoking activity in diaries.

Findings
The pilot trial found that student recruitment was high (baseline students matched at follow-up n=1,681 (79 per cent of class-registered students). More boys (n=38) than girls (n=35) attended peer supporter training. Post-training, most peer supporters had improved smoking-related knowledge (n=55; 75 per cent) and attitudes (n=57; 78 per cent) and returned diaries (n=49; 67 per cent). Some focus group boys reported they were reluctant peer supporters and/or found resisting smoking difficult.

Practical implications
Future trials would benefit from outlined modifications to peer supporter selection, recruitment and training and additionally, assessments of context and intervention acceptability and reach.

Originality/value
Trials of complex public health interventions are scarce in economically developing countries.