bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional dynamics following freezing stress reveal selection for mechanisms of freeze tolerance at the poleward range margin in the cold water intertidal barnacleSemibalanus balanoides
Authors: Marshall Katie E. , Dowle Eddy J. , Petrunina Alexandra , Kolbasov Gregory , Chan Benny K. K. 
Published: October 2018

AbstractThe ability to survive freezing has repeatedly evolved across multiple phyla. This suggests that the mechanisms of freeze tolerance must be readily evolvable from basal physiological traits. While several biochemical correlates to freeze tolerance have been described, the mechanism that confers freeze tolerance is still not well understood. To understand both the basic biochemical mechanisms of freeze tolerance as well as their role in local adaptation at the poleward range edge, we conducted a transcriptomic study on two populations (one from the poleward range margin in the White Sea, Russia, and one from the central coast of British Columbia, Canada) of the cold water acorn barnacleSemibalanus balanoideson a time series following a freezing event. We found that the British Columbia population (at the equatorward range margin) was significantly less freeze tolerant than the White Sea population (at the poleward range margin). After assembling and annotating ade novotranscriptome forS. balanoides, we found that the patterns of differential transcript expression following freezing were almost entirely non-overlapping between the two populations, with the White Sea population expressing a series of heat shock proteins in response to freezing stress as well as several aquaporins, while the British Columbia population expressed a series of proteases instead, indicating severe protein damage. We found strong evidence of purifying selection on the significantly upregulated transcripts in the White Sea population, suggesting local adaptation to freezing threat. Taken together, this shows the importance of freeze tolerance to population survival at the poleward range margin, and highlights the central roles of aquaporins and heat shock proteins to the trait of freeze tolerance across taxa.
Look4TRs: A de-novo tool for detecting simple tandem repeats using self-supervised hidden Markov models
Authors: Velasco Alfredo , James Benjamin T. , Wells Vincent D. , Girgis Hani Z. 
Published: October 2018

ABSTRACTSimple tandem repeats, microsatellites in particular, have regulatory functions, links to several diseases, and applications in biotechnology. Sequences of thousands of species will be available soon. There is immediate need for an accurate tool for detecting microsatellites in the new genomes. The current available tools have limitations. As a remedy, we proposed Look4TRs, which is the first application of self-supervised hidden Markov models to discovering microsatellites. It adapts itself to the input genomes, balancing high sensitivity and low false positive rate. It auto-calibrates itself, freeing the user from adjusting the parameters manually, leading to consistent results across different studies. We evaluated Look4TRs on eight genomes. Based on F-measure, which combines sensitivity and false positive rate, Look4TRs outperformed TRF and MISA — the most widely-used tools — by 106% and 82%. Look4TRs outperformed the second best tool, MsDetector or Tantan, by 11%. Look4TRs represents technical advances in the annotation of microsatellites.
A simulation-based approach to improve decoded neurofeedback performance
Authors: Oblak Ethan , Sulzer James , Lewis-Peacock Jarrod 
Published: October 2018

AbstractThe neural correlates of specific brain functions such as visual orientation tuning and individual finger movements can be revealed using multivoxel pattern analysis (MVPA) of fMRI data. Neurofeedback based on these distributed patterns of brain activity presents a unique ability for precise neuromodulation. Recent applications of this technique, known as decoded neurofeedback, have manipulated fear conditioning, visual perception, confidence judgements and facial preference. However, there has yet to be an empirical justification of the timing and data processing parameters of these experiments. Suboptimal parameter settings could impact the efficacy of neurofeedback learning and contribute to the ‘non-responder’ effect. The goal of this study was to investigate how design parameters of decoded neurofeedback experiments affect decoding accuracy and neurofeedback performance. Subjects participated in three fMRI sessions: two ‘finger localizer’ sessions to identify the fMRI patterns associated with each of the four fingers of the right hand, and one ‘finger finding’ neurofeedback session to assess neurofeedback performance. Using only the localizer data, we show that real-time decoding can be degraded by poor experiment timing or ROI selection. To set key parameters for the neurofeedback session, we used offline simulations of decoded neurofeedback using data from the localizer sessions to predict neurofeedback performance. We show that these predictions align with real neurofeedback performance at the group level and can also explain individual differences in neurofeedback success. Overall, this work demonstrates the usefulness of offline simulation to improve the success of real-time decoded neurofeedback experiments.
Influence of nutritional tyrosine on cognition and functional connectivity in healthy old humans
Authors: Hensel Christian , Becker Maxi , Düzel Sandra , Demuth Ilja , Norman Kristina , Steinhagen-Thiessen Elisabeth , Gallinat Jürgen , Lindenberger Ulman , Kühn Simone 
Published: October 2018

AbstractTyrosine is precursor for monoamine neurotransmitters such as dopamine (DA), which is one of the key neurotransmitters in the frontostriatal network and of crucial relevance for mental disorders. Recent research reported that high dose tyrosine application resulted in increased brain DA synthesis, which is consistent with the observation of positive associations between daily tyrosine intake and cognitive test performance. In the present study, we investigated the associations between working memory (WM) dependent tasks and self-reported nutritional tyrosine intake within a large group of healthy elderly humans (286 subjects) by additionally including brain functional data. We observed a negative correlation between tyrosine intake and resting-state functional connectivity (rsFC) between the striatum (putamen) and the prefrontal cortex. That is to say, we found higher rsFC in individuals consuming less tyrosine per day. At the same time, this increased rsFC or hyperconnectivity was associated with lower WM performance. These findings suggest that lower or insufficient supply of tyrosine might result in dysfunctional connectivity between striatal and frontal regions leading to lower WM capacity in healthy elderly humans.
LEM domain proteins control the efficiency of adaptation through copy number variation
Authors: Colombi Paolo , King Diane E. , Williams Jessica F. , Lusk C. Patrick , King Megan C. 
Published: October 2018

AbstractWhile loss of genome integrity is at the basis of numerous pathologies, including cancer, genome plasticity is necessary to adapt to a changing environment and thus is essential for long-term organismal success. Here we present data supporting a targeted mechanism that promotes adaptation to environmental stress by driving site-specific genome instability tied to transcriptional induction and the formation of RNA-DNA hybrids. Using anin vitroevolution assay we observe that the inner nuclear membrane LEM domain proteins Heh1 and Heh2 play antagonistic roles in inhibiting or promoting adaptation through copy number expansion, respectively, which is also reflected in their genetic interaction networks with genes responsible for transcription-dependent genome instability. Taken together, our data suggest the existence of a LEM domain protein-mediated mechanism by which an immediate transcriptional response to a changing environment drives targeted genome instability to promote increased variation on which selection can act to support long-term adaptation.
Translational control of cardiac fibrosis
Authors: Chothani Sonia , Schafer Sebastian , Adami Eleonora , Viswanathan Sivakumar , Widjaja Anissa A , Langley Sarah R , Tan Jessie , Pua Chee Jian , D’Agostino Giuseppe , van Heesch Sebastiaan , Witte Franziska , Felkin Leanne E , Christodoulou Eleni G. , Dong Jinrui , Blachut Susanne , Patone Giannino , Barton Paul JR , Hubner Norbert , Cook Stuart A , Rackham Owen JL 
Published: October 2018

AbstractBackgroundFibrosis is a common pathology in many cardiac disorders and is driven by the activation of resident fibroblasts. The global post-transcriptional mechanisms underlying fibroblast-to-myofibroblast conversion in the heart have not been explored.MethodsGenome-wide changes of RNA transcription and translation during human cardiac fibroblast activation were monitored with RNA sequencing and ribosome profiling. We then used miRNA-and RNA-binding protein-based analyses to identify translational regulators of fibrogenic genes. To reveal post-transcriptional mechanisms in the human fibrotic heart, we then integrated our findings with cardiac ribosome occupancy levels of 30 dilated cardiomyopathy patients.ResultsWe generated nucleotide-resolution translatome data during the TGFβ1-driven cellular transition of human cardiac fibroblasts to myofibroblasts. This identified dynamic changes of RNA transcription and translation at several time points during the fibrotic response, revealing transient and early-responder genes. Remarkably, about one-third of all changes in gene expression in activated fibroblasts are subject to translational regulation and dynamic variation in ribosome occupancy affects protein abundance independent of RNA levels. Targets of RNA-binding proteins were strongly enriched in post-transcriptionally regulated genes, suggesting genes such as MBNL2 can act as translational activators or repressors. Ribosome occupancy in the hearts of patients with dilated cardiomyopathy suggested an extensive post-transcriptional regulatory network underlying cardiac fibrosis. Key network hubs include RNA-binding proteins such as PUM2 and QKI that work in concert to regulate the translation of target transcripts in human diseased hearts.ConclusionsWe reveal widespread translational effects of TGFβ1 and define novel post-transcriptional events that control the fibroblast-to-myofibroblast transition. Regulatory networks that affect ribosome occupancy in fibroblasts are paralleled in human heart disease. Our findings show the central importance of translational control in fibrosis and highlight novel pathogenic mechanisms in heart failure.
Characterisation of a type II functionally-deficient variant of alpha-1-antitrypsin discovered in the general population
Authors: Laffranchi Mattia , Elliston Emma L. K. , Gangemi Fabrizio , Berardelli Romina , Lomas David A. , Irving James A. , Fra Annamaria 
Published: October 2018

AbstractLung disease in alpha-1-antitrypsin deficiency (AATD) results from dysregulated proteolytic activity, mainly by neutrophil elastase (HNE), in the lung parenchyma. This is the result of a substantial reduction of circulating alpha-1-antitrypsin (AAT) and the presence in the plasma of inactive polymers of AAT. Moreover, some AAT mutants have reduced intrinsic activity toward HNE, as demonstrated for the common Z mutant, as well as for other rarer variants. Here we report the identification and characterisation of the novel AAT reactive centre loop variant Gly349Arg (p.G373R) present in the ExAC database. This AAT variant is secreted at normal levels in cellular models of AATD but shows a severe reduction in anti-HNE activity. Biochemical and molecular dynamics studies suggest it exhibits unfavourable RCL presentation to cognate proteases and compromised insertion of the RCL into β-sheet A. Identification of a fully dysfunctional AAT mutant that does not show a secretory defect underlines the importance of accurate genotyping of patients with pulmonary AATD manifestations regardless of the presence of normal levels of AAT in the circulation. This subtype of disease is reminiscent of dysfunctional phenotypes in antithrombin and C1-inibitor deficiencies so, accordingly, we classify this variant as the first pure functionally-deficient (type II) AATD mutant.
Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus inDrosophila melanogaster
Authors: Jorgensen Victoria , Chen Jingxun , Wende Helen Vander , Harris Devon , Wong-Deyrup Siu Wah , Chen Yuzhang , Rangan Prashanth , Brar Gloria Ann , Sawyer Eric M. , Chan Leon , Ünal Elçin 
Published: October 2018

AbstractNeighboring sequences of a gene can influence its expression. In the phenomenon known as transcriptional interference, transcription at one region in the genome can repress transcription at a nearby region incis. Transcriptional interference occurs at a number of eukaryotic loci, including the alcohol dehydrogenase (Adh) gene inDrosophila melanogaster. Adhis regulated by two promoters, which are distinct in their developmental timing of activation. It has been shown using transgene insertion that when the promoter distal from theAdhstart codon is deleted, transcription from the proximal promoter becomes de-regulated. As a result, theAdhproximal promoter, which is normally active only during the early larval stages, becomes abnormally activated in adults. Whether this type of regulation occurs in the endogenousAdhcontext, however, remains unclear. Here, we employed the CRISPR/Cas9 system to edit the endogenousAdhlocus and found that removal of the distal promoter does also result in the untimely expression of the proximal promoter-driven mRNA isoform in adults, albeit at lower levels than previously reported. Importantly, we show that transcription from the distal promoter is sufficient to repress proximal transcription in larvae and that the degree of this repression depends on the degree of distal promoter activity. Finally, repression of the endogenousAdhproximal promoter is associated with the enrichment of histone 3 lysine 36 trimethylation (H3K36me3), a chromatin mark necessary for transcription-coupled gene repression in yeast. We conclude that the endogenousAdhlocus is developmentally regulated by transcriptional interference in a tunable manner.
Corporate governance and innovation: a theoretical review
Authors: Asensio-López Diego , Cabeza-García Laura , González-Álvarez Nuria 
Published: October 2018

PurposeThe purpose of this paper is to present a review of the literature on two lines of research, corporate governance and innovation, explaining how different internal corporate governance mechanisms may be determinants of business innovation.Design/methodology/approachIt explores the theoretical background and the empirical evidence regarding the influence of both ownership structure and the board of directors on company innovation. Then, conclusions are drawn and possible future research lines are presented.FindingsNo consensus was observed regarding the relation between corporate governance and innovation, with both positive and negative arguments being found, and with empirical evidence not always pointing in the same direction. Thus, new studies trying to clarify this relationship are needed.Originality/valueOver recent years, interest has grown in the influence of governance mechanisms on innovation decisions taken by the management. Innovation efforts and results depend on factors that are influenced by corporate governance, such as ownership structure or the functioning of the board of directors. Thus, the paper shows an updated state of the art in this field proposing future lines for empirical research.
Implementing connectivism by semantic technologies for self-directed learning
Authors: Vas Réka , Weber Christian , Gkoumas Dimitris 
Published: October 2018

Purpose
Connectivism has been proposed to explain the impact of new technologies on learning. According to this approach, learning may occur even outside the individual within an organization or a system. Learning objectives are not defined in advance and learning requires the ability to form connections and use networks to find the required knowledge. The connections by which individuals can learn are more important than what they currently know. The purpose of this paper is to investigate if a measure, rating the importance of concepts, can be derived from a network representation of the learning domain and if highly connected concepts – with high importance value – can describe whether information is explored in such ways as assumed by connectivism.

Design/methodology/approach
The authors empirically examined if the proposed measure can provide insight on the role of connections in learning and explain the reasons behind passing certain parts of a test using a linear regression model.

Findings
The results are twofold. First, an implementation of the information exploration principle of connectivism has been introduced, applying semantic technologies and the importance measure. Second, although no significant effects could be isolated, trends in performance improvement concerning highly important concepts were identified.

Originality/value
However, connectivism has been known since 2005, it is still lacking for successful implementations. The presented approach of a concept importance measure is a promising starting point by providing means of connected learning, enabling individuals to effectively improve their personal abilities to better fit job demand.
What constitutes successful African enterprises? A survey of performance variations in 210 African food processors
Authors: Hansen Michael Wendelboe , Ishengoma Esther K. , Upadhyaya Radha 
Published: October 2018

PurposeTo understand African small and medium-sized enterprise (SME) performance and its antecedents is essential, both from a strategic management and an industrial development perspective. While a substantial literature on African SMEs has emerged in recent years, studies of their performance specifically are few and inconclusive. The purpose of this paper is to address this lacuna in the literature by examining variations in performance of 210 East African SMEs.Design/methodology/approachThe paper employs OLS and logistic regression and Classify k-means test to analyze performance variations in a unique data set of 210 food processing enterprises in Tanzania, Kenya and Zambia.FindingsThree generic types of African SMEs are identified based on performance: laggards, followers and gazelles. The gazelles are typically medium-sized, skill-intensive companies selling relatively differentiated products in niche markets. The laggards are typically small, capital-intensive companies involved in grain milling that adopt a cost differentiation strategy. A key driver of variation in performance is found to be the quality of the external business environment (in particular the quality of intermediary markets), and also capability factors such as the strength of management. Strategy factors such as differentiation and political strategies explain performance variations.Practical implicationsAmong the policy implications are that African industrial policy should focus on improving the functioning of intermediary markets, e.g. by reducing the transaction costs of inter-firm collaboration. Moreover, rather than focusing industrial policy on SMEsper se, policymakers should focus on those types of enterprises that are capable of generating high performance, e.g. skill-intensive enterprises with strong managerial capabilities, engaged in differentiation strategies.Originality/valueThe paper integrates the extant literature on African SME performance, develops an analytical framework for studying it and presents novel empirical insights based on one of the most detailed surveys of SME performance in the continent to date. The findings have important and tangible implications for literature, as well as for industrial policy.
Industry structure, macroeconomic fundamentals and return on equity
Authors: Ndlovu Chiedza , Alagidede Paul 
Published: October 2018

PurposeThe purpose of this paper is to examine the impact of industry structure and macroeconomic indicators on return on equity (ROE) of listed financial services firms.Design/methodology/approachHerfindahl–Hirschman Index concentration scales were used to categorise industries into competitive, moderate and concentrated segments, while Arbitrage Pricing Model principles were used to capture the effect of macroeconomic fundamentals on ROE. Generalised method of moments estimator was used to model random effects which were supported by the Hausman test.FindingsFindings suggest that the influence of macroeconomic fundamentals on ROE deteriorates as one moves from competitive to concentrated industries. ROE is volatile in concentrated markets and less volatile in competitive markets. Concentrated markets generally enjoy monopoly profits. Gross domestic product and interest rates have a positive impact on ROE, while inflation, unemployment and exchange rates have a negative effect.Originality/valueThis study highlights the need to apply appropriate business strategies and policies depending on the structure of the industry. Competitive advantage strategies may assist in sustaining profits of firms in competitive markets. Regulators need to be proactive and stress test the impact of a policy on industry performance before implementation because competitive and concentrated markets react differently to external shocks. Risk tolerant investors may invest in volatile markets such as Russia and South Africa, while risk-averse investors may prefer to invest in less volatile markets such as India and China.
The non-economic consequences of disclosure in Islamic banks
Authors: El-Halaby Sherif , Hussainey Khaled , Abou-El-Sood Heba 
Published: October 2018

PurposeThe purpose of this paper is to examine the effect of sharia, social and financial disclosure on stakeholders’ loyalty towards Islamic banks (IBs). The paper also aims to examine the extent to which trust and satisfaction mediate this effect.Design/methodology/approachIt uses data collected from 600 respondents to survey questionnaires disseminated to stakeholders from 15 countries dealing with IBs. Structural equation modelling is adopted with a partial least square approach.FindingsThe results indicate that there is a significant impact of disclosure on stakeholders’ trust, satisfaction, and loyalty. The results also indicate that there is a partial mediating effect of trust and satisfaction in the relationship between disclosure and loyalty. This paper is one of the first studies examining the effect of disclosure on stakeholders’ loyalty. The authors provide novel findings, which have theoretical and practical implications for disclosure in IBs and their relationship with stakeholders.Originality/valueThe analysis offers a novel contribution to the Islamic banking literature by offering the first evidence on the impact of disclosure on stakeholders’ trust, satisfaction, and loyalty.