bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lack of selectivity for syntax relative to word meanings throughout the language network
Authors: Fedorenko Evelina , Blank Idan , Siegelman Matthew , Mineroff Zachary 
Published: November 2018

AbstractTo understand what you are reading now, your mind retrieves the meanings of words and constructions from a linguistic knowledge store (lexico-semantic processing) and identifies the relationships among them to construct a complex meaning (syntactic or combinatorial processing). Do these two sets of processes rely on distinct, specialized mechanisms or, rather, share a common pool of resources? Linguistic theorizing, empirical evidence from language acquisition and processing, and computational modeling have jointly painted a picture whereby lexico-semantic and syntactic processing are deeply inter-connected and perhaps not separable. In contrast, many current proposals of the neural architecture of language continue to endorse a view whereby certain brain regions selectively support syntactic/combinatorial processing, although the locus of such “syntactic hub”, and its nature, vary across proposals. Here, we searched for selectivity for syntactic over lexico-semantic processing using a powerful individual-subjects fMRI approach across three sentence comprehension paradigms that have been used in prior work to argue for such selectivity: responses to lexico-semanticvs.morpho-syntactic violations (Experiment 1); recovery from neural suppression across pairs of sentences differing in only lexical itemsvs.only syntactic structure (Experiment 2); and same/different meaning judgments on such sentence pairs (Experiment 3). Across experiments, both lexico-semantic and syntactic conditions elicited robust responses throughout the left fronto-temporal language network. Critically, however, no regions were more strongly engaged by syntactic than lexico-semantic processing, although some regions showed the opposite pattern. Thus, contra many current proposals of the neural architecture of language, syntactic/combinatorial processing is not separable from lexico-semantic processing at the level of brain regions—or even voxel subsets—within the language network, in line with strong integration between these two processes that has been consistently observed in behavioral and computational language research. The results further suggest that the language network may be generally more strongly concerned with meaning than syntactic form, in line with the primary function of language—to share meanings across minds.
Hidden patterns of codon usage bias across kingdoms
Authors: Deng Yun , de Lima Hedayioglu Fabio , Kalfon Jeremie , Chu Dominique , von der Haar Tobias 
Published: November 2018

AbstractThe genetic code is necessarily degenerate with 64 possible nucleotide triplets being translated into 20 amino acids. 18 out of the 20 amino acids are encoded by multiple synonymous codons. While synonymous codons are clearly equivalent in terms of the information they carry, it is now well established that they are used in a biased fashion. There is currently no consensus as to the origin of this bias. Drawing on ideas from stochastic thermodynamics we derive from first principles a mathematical model describing the statistics of codon usage bias. We show that the model accurately describes the distribution of codon usage bias of genomes in the fungal and bacterial kingdoms. Based on it, we derive a new computational measure of codon usage bias — the distancecapturing two aspects of codon usage bias: (i) Differences in the genome-wide frequency of codons and (ii) apparent non-random distributions of codons across mRNAs. By means of large scale computational analysis of over 900 species across 2 kingdoms of life, we demonstrate that our measure provides novel biological insights. Specifically, we show that while codon usage bias is clearly based on heritable traits and closely related species show similar degrees of bias, there is considerable variation in the magnitude ofwithin taxonomic classes suggesting that the contribution of sequence-level selection to codon bias varies substantially within relatively confined taxonomic groups. Interestingly, commonly used model organisms are near the median for values offor their taxonomic class, suggesting that they may not be good representative models for species with more extreme, which comprise organisms of medical an agricultural interest. We also demonstrate that amino acid specific patterns of codon usage are themselves quite variable between branches of the tree of life, and that some of this variability correlates with organismal tRNA content.
Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq
Authors: Bayega Anthony , Oikonomopoulos Spyros , Zorbas Eleftherios , Wang Yu Chang , Gregoriou Maria-Eleni , Tsoumani Konstantina T , Mathiopoulos Kostas D , Ragoussis Jiannis 
Published: November 2018

AbstractThe olive fruit fly or olive fly (Bactrocera oleae) is the most important pest of cultivated olive trees. Like all insects the olive fly undergoes complete metamorphosis. However, the transcription dynamics that occur during early embryonic development have not been explored, while detailed transcriptomic analysis in the absence of a fully annotated genome is challenging. We collected olive fly embryos at hourly intervals for the first 6 hours of development and performed full-length cDNA-Seq using a purpose designed SMARTer cDNA synthesis protocol followed by sequencing on the MinION (Oxford Nanopore Technologies). We generated 31 million total reads across the timepoints (median yield 4.2 million per timepoint). The reads showed 98 % alignment rate to the olive fly genome and 91 % alignment rate to the NBCI predicted B. oleae gene models. Over 50 % of the expressed genes had at least one read covering its entire length validating our full-length RNA-Seq procedure. Expression of 68 % of the predicted B. oleae genes was detected in the first six hours of development. We generated a de novo transcriptome assembly of the olive fly and identified 3553 novel genes and a total of 79,810 transcripts; a fourfold increase in transcriptome diversity compared to the NCBI predicted transcriptome. On a global scale, the first six hours of embryo development were characterized by dramatic transcriptome changes with the total number of transcripts per embryo dropping to half from the first hour to the second hour of embryo development. Clustering of genes based on temporal co-expression followed by gene-set enrichment analysiss of genes expressed in the first six hours of embryo development showed that genes involved in transcription and translation, macro-molecule biosynthesis, and neurodevelopment were highly enriched. These data provide the first insight into the transcriptome landscape of the developing olive fly embryo. The data also reveal transcript signatures of sex development. Overall, full-length sequencing of the cDNA molecules permitted a detailed characterization of the isoform complexity and the transcriptional dynamics of the first embryonic stages of the B. oleae.
Landscape of RNA editing reveals new insights into the dynamic gene regulation of spermatogenesis based on integrated RNA-Seq
Authors: Wang Xiaodan , Zhu Zhenshuo , Wu Xiaolong , Li Hao , Li Tongtong , Li Qun , Zhang Peng , Li Leijie , Che Dongxue , Xiao Xia , Hua Jinlian , Liao Mingzhi 
Published: November 2018

ABSTRACTSpermatogenesis is an important physiological process associated with male infertility. But whether there are RNA editings (REs) and what’s the role of REs during the process are still unclear. In this study, we integrated published RNA-Seq datasets and established a landscape of REs during the development of mouse spermatogenesis. 7530 editing sites among all types of male germ cells were found, which enrich on some regions of chromosome, including chromosome 17 and both ends of chromosome Y. Totally, REs occur in 2012 genes during spermatogenesis, more than half of which harbor at two different sites of the same gene at least. We also found REs mainly occur in introns, coding regions (CDSs) and intergenic regions. Moreover, about half of the REs in CDSs can cause amino acids changes. Finally, based on our adult male Kunming mice, we verified that there is a non-synonymous A-to-I RNA editing site inCog3during spermatogenesis, which is conserved not only between species but also across tissues. In short, based on the power of integrating RNA-Seq datasets, we provided the landscape of REs and found their dynamic changes during mouse spermatogenesis. This research strategy is general for other types of sequencing datasets and biological problems.
Entropic forces drive cellular contact guidance
Authors: Buskermolen A.B.C. , Suresh H. , Shishvan S.S. , Vigliotti A. , DeSimone A. , Kurniawan N.A. , Bouten C.V.C. , Deshpande V.S. 
Published: November 2018

AbstractContact guidance—the widely-known phenomenon of cell alignment induced by anisotropic environmental features—is an essential step in the organization of adherent cells, but the mechanisms by which cells achieve this orientational ordering remain unclear. Here we seeded myofibroblasts on substrates micropatterned with stripes of fibronectin and observed that contact guidance emerges at stripe widths much greater than the cell size. To understand the origins of this surprising observation, we combined morphometric analysis of cells and their subcellular components with a novel statistical framework for modelling non-thermal fluctuations of living cells. This modelling framework is shown to predict not only the trends but also the statistical variability of a wide range of biological observables including cell (and nucleus) shapes, sizes and orientations, as well as stress-fibre arrangements within the cells with remarkable fidelity. By comparing observations and theory, we identified two regimes of contact guidance: (i) guidance on stripe widths smaller than the cell size (w ≤ 160 μm), which is accompanied by biochemical changes within the cells, including increasing stress-fibre polarisation and cell elongation, and (ii) entropic guidance on larger stripe widths, which is governed by fluctuations in the cell morphology. Overall, our findings suggest an entropy-mediated mechanism for contact guidance associated with the tendency of cells to maximise their morphological entropy through shape fluctuations.
Structures of TOG1 and TOG2 From the Human Microtubule Dynamics Regulator CLASP1
Authors: Leano Jonathan B. , Slep Kevin C. 
Published: November 2018

AbstractTubulin-binding TOG domains are found arrayed in a number of proteins that regulate microtubule dynamics. While much is known about the structure and function of TOG domains in the XMAP215 microtubule polymerase family, less in known about the TOG domain array found in the CLASP family. The CLASP TOG array promotes microtubule pause, potentiates rescue, and limits catastrophe. How distinct the TOG domains of CLASP are from one another, from XMAP215 TOG domains, and whether they are positionally conserved across CLASP family members is poorly understood. We present the x-ray crystal structures of human CLASP1 TOG1 and TOG2. The structures of CLASP1 TOG1 and TOG2 are distinct from each other, from CLASP TOG3, and are positionally conserved across species. While studies have failed to detect CLASP TOG1 tubulin-binding activity, TOG1 is structurally similar to the free-tubulin binding TOG domains of XMAP215. In contrast, though CLASP TOG2 and TOG3 have tubulin binding activity, they are structurally distinct from the free-tubulin binding TOG domains of XMAP215. CLASP TOG2 has a convex architecture, predicted to engage a hyper-curved tubulin state. CLASP TOG3 has unique structural elements in the C-terminal half of its α-solenoid domain that modeling studies implicate in binding to laterally-associated tubulin subunits in the microtubule lattice in a mode similar to, yet distinct from XMAP215 TOG4. These findings highlight the structural diversity of TOG domains within the CLASP TOG array and provide a molecular foundation for understanding CLASP-dependent effects on microtubule dynamics.
The influence of managers’ social networking information on job applicants
Authors: Ballweg Christopher A. , Ross William H. , Secchi Davide , Uting Chad 
Published: November 2018

PurposeThe purpose of this paper is to investigate the prevalence and influence of social network website (SNW) content about alcohol use and abuse on job applicant reactions to their prospective immediate supervisor and toward applying for the job.Design/methodology/approachIn Study 1, raters coded photographs and photo captions found on 1,048 personal SNWs of US managers or business owners. Approximately 22 percent of managers’ personal SNWs contained references to alcohol, providing a base rate large enough to warrant further research. In Study 2, laboratory experiment participants saw a fictitious company’s website including a professional managerial profile. A 3 × 3 factorial design then varied whether the prospective manager’s comments on his personal SNW emphasized professional activities, social drinking, or alcohol abuse; also, the manager’s friends’ comments emphasized work activities, social drinking, or alcohol abuse. A control group did not see a personal SNW.FindingsAlcohol abuse information on personal SNWs – whether posted by the manager or by the manager’s friends – negatively affected attitudes toward the manager. Alcohol abuse information posted by the manager (but not by the manager’s friends) decreased the willingness of participants to apply for the position. These findings were consistent with the Brunswick Lens Model and the warranting hypothesis.Originality/valueThis is the first study to investigate managerial SNW content and it effects upon prospective job seekers’ attitudes.
Self-efficacy’s role in success of quality training programmes
Authors: Loomba Arvinder P.S. , Karsten Rex 
Published: November 2018

PurposeThe purpose of this paper is to explore why some firms succeed while others flounder or fail to implement quality improvement programmes. It synthesises self-efficacy literature to propose a model of self-efficacy’s role in affecting implementation success of quality improvement programmes in organisations.Design/methodology/approachA review of scholarly articles on the topics of self-efficacy and quality initiatives brings to light self-efficacy’s role in successful quality programme implementation. When considered in the context of organisation barriers, it can lead to organisational success.FindingsIt is determined that quality training programmes play an important role in affecting existing efficacies and leading to “quality self-efficacy” in employees. The proposed model and related propositions suggest that right approaches of implementing quality training among certain types of employees and/or organisations can promote teamwork to achieve performance success.Research limitations/implicationsMoving forward, the proposed model should be empirically tested to improve our understanding of quality self-efficacy construct and its role in aiding organisational success. Furthermore, it would offer guidelines for the implementation of quality programmes in the most optimal way.Practical implicationsIn applying theories on self-efficacy, motivation, empowerment, and quality training, the authors posit that existing efficacy and quality self-efficacy are crucial for quality implementation efforts to overcome organisational barriers and lead to effective teamwork and performance success.Social implicationsThe authors postulate that deciding factors for organisational success originate from employees themselves as existing efficacies. Even though employees can foster quality self-efficacy through the implementation of quality improvement initiatives, existing self-efficacy, and organisation barriers will be moderating forces on eventual effectiveness of quality self-efficacy, teamwork, and organisational performance.Originality/valueThe model and related propositions, linking self- and collective efficacies to quality training, teamwork, and quality performance, offered in this paper will prove useful for organisational decision-makers in selecting quality programmes for implementation in organisation to achieve performance success.
Objective institutionalized barriers and subjective performance factors of new migrant entrepreneurs
Authors: Hagos Sirak , Izak Michal , Scott Jonathan M. 
Published: November 2018

Purpose
The purpose of this paper is to explain how the “objective” institutionalized barriers (of which social, human and financial capital are decisive factors) and the subjective performance of new migrant entrepreneurs jointly affect their business attitudes and observed behavior.

Design/methodology/approach
The paper’s analysis of individualized performance factors (dependent on how “objective” institutionalized barriers are subjectively construed) – in line with the theory of planned behavior – enables a response to recent calls to embrace complexity and pluralism in entrepreneurship through applying social constructivist lenses. Semi-structured interviews were conducted with 32 Eritrean entrepreneurs, and the empirical data were subjected to grounded theory analytical procedures and interpretative phenomenological analysis theoretical coding.

Findings
Six core beliefs mitigated entrepreneurial attitudes independently from the objectivized institutionalized barriers: know-how needs to be acquired formally; available sources of financing are internal, and scarce; market expertise is in the books, rather than in the market; blending in the host country’s culture is uncalled for, and the resulting difficulty of operating in the “foreign” market is a price worth paying; risk is to be avoided at all cost; and strong intra-communal bonds need not entail support for their business activity, rendering external contacts hardly necessary or trustworthy.

Originality/value
The paper concludes with recommendations potentially informing policies and targeted interventions by highlighting that any policy intervention or an attempt at structural change of conditions in which new migrant entrepreneurship unfolds should consider entrepreneurs as “performing” individuals, as well as representatives of wider cultural, economic and social dynamics relating to these “objective” institutionalized barriers.
Foreign aid, workers’ remittances and economic growth in Jordan
Authors: Husein Jamal G. 
Published: November 2018

PurposeThe purpose of this paper is to investigate the long-run impact of foreign aid and workers’ remittances on Jordanian economic growth using time series data for the period 1970–2014. Following the most recent literature, the author also assess whether economic policy enhances economic growth and whether aid effectiveness is conditional on levels of economic policy.Design/methodology/approachThe author employs unit root tests that allow for endogenously determined structural breaks (Perron, 1997) and properly utilize the autoregressive distributed lag (ARDL) or bounds testing approach to cointegration by applying both theF- and thet-test statistics (Pesaranet al., 2001). The analysis is applied to 12 different models that incorporates the various types and sources of foreign aid.FindingsEmpirical results suggest that aid and its various components, and workers’ remittances have had a positive and significant long-run impact on economic growth. Empirical results also show: no evidence supporting the hypothesis that aid is only or more effective in spurring economic growth during periods of “good” macroeconomic policy, i.e., when Jordan has undertaken World Bank Structural Adjustment Programs (SAPs); no robust evidence supporting the World Bank’s claim thatSAPs are growth enhancing. Moreover, the author found strong empirical evidence suggesting that exports and human capital are also major determinants of long-run growth in Jordan.Research limitations/implicationsAlthough Jordan and the region at large have experienced periods of major political instability that may have had a varying impact on the economy, lack of a reliable and lengthy time series measure that accounts for political instability is not available to include in the study.Practical implicationsUsing cointegration analysis, our empirical evidence reveals that foreign aid, labor remittances, exports and human capital have had a robust positive long-run impact on economic growth. Hence, the Jordanian government should promote policies that encourage donor countries and agencies to further extend aid to Jordan. Moreover, policies that promote exports and facilitate labor mobility to neighboring countries should also be encouraged and promoted.Originality/valueDespite receiving a significant amount of foreign aid and labor remittances in the last 50 years, the author found no time series study that tested the long-run impact of these external financing sources on growth in Jordan. This study fills that gap and extends the analysis to test whether macroeconomic policy is growth enhancing and whether aid (and several of its components) are only effective or more effective in promoting growth during periods of “good” macroeconomic policy, i.e., when Jordan has undertaken a World BankSAP.
Nanotribological characteristics of laser surface melted Stellite 12+Mo hardfacing
Authors: Dilawary Shaikh Asad Ali , Motallebzadeh Amir , Afzal Muhammad , Atar Erdem , Cimenoglu Huseyin 
Published: November 2018

Purpose
The purpose of the study is to examine the sliding wear performance of plasma transfer arc (PTA) deposited and laser surface melted (LSM) Mo modified Stellite 12 hardfacings under high contact stresses (i.e. >20 GPa).

Design/methodology/approach
For this purpose, after structural characterization, sliding wear tests have been conducted using sphero-conical diamond indenter as the counterface with different normal loads. The wear tracks formed on the hardfacings were examined by atomic force microscopy and scanning electron microscopy.

Findings
Both hardfacings showed severe wear (at high contact stress levels ranging from 24 to 41 GPa), which progressed by plastic deformation, although the wear resistance of LSMed hardfacings was better than the PTA hardfacings by a factor of two due to its near surface microstructure characterized as carbide-rich zone.

Originality/value
Sliding wear characterization of a promising 10 Wt.% Mo modified version of commercial Stellite 12 hardfacings (as reported previously by authors) was done in as PTA and LSMed states using nanomechanical test system. To the best of authors’ knowledge, no report is available in the open literature on such hardfacings under these testing conditions.