bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)
Authors: Escalante Marco A. , Perrier Charles , García-De León Francisco J. , Ruiz-Luna Arturo , Ortega-Abboud Enrique , Manel Stéphanie 
Published: December 2018

AbstractHow environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization withO. mykissand of riverscape and climatic variables on the genetic variation amongO. chrysogasterpopulations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272O. chrysogasterandO. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six forO. chrysogaterand one for aquacultureO. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests thatO. chrysogatermay require conservation planning given i) exotic introgression fromO. mykisslocally threateningO. chrysogatergenetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.
Comparative RNAi Screens in Isogenic Human Stem Cells RevealSMARCA4as a Differential Regulator
Authors: Güneş Ceren , Paszkowski-Rogacz Maciej , Rahmig Susann , Khattak Shahryar , Wermke Martin , Dahl Andreas , Bornhäuser Martin , Waskow Claudia , Buchholz Frank 
Published: December 2018

SUMMARYLarge-scale RNAi screens are a powerful approach to identify functions of genes in a cell-type specific manner. For model organisms, genetically identical (isogenic) cells from different cell-types are readily available, making comparative studies meaningful. For humans, however, screening isogenic cells is not straightforward. Here, we show that RNAi screens are possible in genetically identical human stem cells, employing induced pluripotent stem cell as intermediates. The screens revealedSMARCA4(SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4) as a stemness regulator, while balancing differentiation distinctively for each cell type.SMARCA4knockdown in hematopoietic stem progenitor cells (HSPC) caused impaired self-renewalin-vitroandin-vivowith skewed myeloid differentiation; whereas in neural stem cells (NSC), it impaired selfrenewal while biasing differentiation towards neural lineage, through combinatorial SWI/SNF subunit assembly. Our findings pose a powerful approach for deciphering human stem cell biology and attribute distinct roles toSMARCA4in stem cell maintenance.
Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism
Authors: Kapoor Manav , Wang Jen-Chyong , Farris Sean P. , Liu Yunlong , McClintick Jeanette , Gupta Ishaan , Meyers Jacquelyn L. , Bertelsen Sarah , Chao Michael , Nurnberger John , Tischfield Jay , Harari Oscar , Zeran Li , Hesselbrock Victor , Bauer Lance , Raj Towfique , Porjesz Bernice , Agrawal Arpana , Foroud Tatiana , Edenberg Howard J. , Mayfield R. Dayne , Goate Alison 
Published: December 2018

ABSTRACTAlcohol exposure triggers changes in gene expression and biological pathways in human brain. We explored alterations in gene expression in the Pre-Frontal Cortex (PFC) of 65 alcoholics and 73 controls of European descent, and identified 129 genes that showed altered expression (FDR < 0.05) in subjects with alcohol dependence. Differentially expressed genes were enriched for pathways related to interferon signaling and Growth Arrest and DNA Damage-inducible 45 (GADD45) signaling. A coexpression module (thistle2) identified by weighted gene co-expression network analysis (WGCNA) was significantly correlated with alcohol dependence, alcohol consumption, and AUDIT scores. Genes in the thistle2 module were enriched with genes related to calcium signaling pathways and showed significant downregulation of these pathways, as well as enrichment for biological processes related to nicotine response and opioid signaling. A second module (brown4) showed significant upregulation of pathways related to immune signaling. Expression quantitative trait loci (eQTLs) for genes in the brown4 module were also enriched for genetic associations with alcohol dependence and alcohol consumption in large genome-wide studies included in the Psychiatric Genetic Consortium and the UK Biobank’s alcohol consumption dataset. By leveraging multi-omics data, this transcriptome analysis has identified genes and biological pathways that could provide insight for identifying therapeutic targets for alcohol dependence.
Structural Modeling of γ-Secretase Aβn Complex Formation and Substrate Processing
Authors: Hitzenberger M. , Zacharias M. 
Published: December 2018

AbstractThe intra-membrane aspartyl protease γ-secretase (GSEC) cleaves single-span transmembrane helices including the C-terminal fragment of the amyloid precursor protein (APP). This substrate is initially cleaved at the ɛ-site followed by successive processing (trimming) events mostly in steps of three amino acids. GSEC is responsible for the formation of N-terminal APP amyloid-β (A β) peptides of different length (e.g. Aβ42) that can form aggregates involved in Alzheimer’s disease pathogenesis. The molecular mechanism of GSEC-APP substrate recognition is key for understanding how different peptide products are formed and could help in designing APP-selective modulators. Based on the known structure of apo GSEC and the APP-C99 fragment we have generated putative structural models of the initial binding in three different possible modes using extensive Molecular Dynamics (MD) simulations. The binding mode with the substrate helix located in a cleft between the transmembrane helices 2 and 3 of the presenilin subunit was identified as a most likely binding mode. Based on this arrangement the processing steps were investigated using restraint MD simulations to pull the scissile bond (for each processing step) into a transition like (cleavable) state. This allowed us to analyze in detail the motions and energetic contributions of participating residues. The structural model agrees qualitatively well with the influence of many mutations in GSEC and C99. It also explains the effects of inhibitors, cross-linking as well as spectroscopic data on GSEC substrate binding and can serve as working model for the future planning of structural and biochemical studies.
Moments reconstruction and local dynamic range compression of high order Superresolution Optical Fluctuation Imaging
Authors: Yi Xiyu , Son Sungho , Ando Ryoko , Miyawaki Atsushi , Weiss Shimon 
Published: December 2018

Abstract:Super-resolution Optical Fluctuation Imaging (SOFI) offers a simple and affordable alternative to other super-resolution (SR) imaging techniques. The theoretical resolution enhancement of SOFI scales linearly with the cumulants’ order, while imaging conditions are less phototoxic to living samples as compared to other SR methods. High order SOFI could, therefore, be a method of choice for dynamic live cell imaging. However, due to cusp-artifacts and to dynamic range expansion of pixel intensities, this promise has not been materialized as of yet. Here we investigated and compared high order moments vs. high order cumulants SOFI reconstructions. We demonstrate that even-order moments reconstructions are intrinsically free of cusp artifacts, allowing for a subsequent deconvolution operation to be performed, hence enhancing the resolution even further. High order moments reconstructions performance was examined for various (simulated) conditions and applied to (experimental) imaging of QD labeled microtubules in fixed cells, and actin stress fiber dynamics in live cells.
Small RNA bidirectional crosstalk during the interaction between wheat andZymoseptoria tritici
Authors: Ma Xin , Bologna Nicolas , Palma-Guerrero Javier 
Published: December 2018

AbstractCross-kingdom RNAi has been shown to play important roles during plant pathogen interactions. But this cross-kingdom RNAi was still unexplored in the wheat-Zymoseptoria triticipathosystem. Here we performed a detailed analysis of the sRNA bidirectional crosstalk between wheat andZ.tritici. Using a combination of sRNA-seq and mRNA-seq we were able to identify known and novel sRNAs and study their expression and their action on putative targets in both wheat andZ.tritici. We predicted the target genes of all the sRNAs in either wheat orZ.triticitranscriptome and used degradome analysis to validate the cleavage of these gene transcripts. We could not find any clear evidence of a cross-kingdom RNAi in this pathosystem. We also found that the fungal sRNA enrichment was lowerin plantathan duringin vitrogrowth, probably due to the lower expression of the only Dicer gene of the fungus during plant infection. However, we found a downregulation of specific wheat sRNAs during the fungal infection, leading to a boost expression of wheat defense related genes, which may be enhancing the plant defense ability against the pathogen. Additionally, the fungal infection also induced sRNAs regulating the expression of specific wheat genes, including auxin related genes, as an immune response. These results confirm the role of sRNAs in the regulation of wheat defenses duringZ.triticiinfection. Our findings contribute to improve our understanding of the interactions between wheat andZ.tritici.
The impact of learning on perceptual decisions and its implication for speed-accuracy tradeoffs
Authors: Mendonça André G. , Drugowitsch Jan , Inês Vicente M. , DeWitt Eric , Pouget Alexandre , Mainen Zachary F. 
Published: December 2018

SUMMARYIn standard models of perceptual decision-making, noisy sensory evidence is considered to be the primary source of choice errors and the accumulation of evidence needed to overcome this noise gives rise to speed-accuracy tradeoffs. Here, we investigated how the history of recent choices and their outcomes interacts with these processes using a combination of theory and experiment. We found that the speed and accuracy of performance of rats on olfactory decision tasks could be best explained by a Bayesian model that combines reinforcement-based learning with accumulation of uncertain sensory evidence. This model predicted the specific pattern of trial history effects that were found in the data. The results suggest that learning is a critical factor contributing to speed-accuracy tradeoffs in decision-making and that task history effects are not simply biases but rather the signatures of an optimal learning strategy.
Benchmarking supplier external risk factors in electronic equipment industry supply chains
Authors: Lockamy III Archie 
Published: December 2018

Purpose
The global electronic equipment industry has evolved into one of the most innovative technology-based business sectors to transpire in the last three decades. Much of its success has been attributed to effective supply chain management. The purpose of this paper is to provide an examination of external risk factors associated with the industry’s key suppliers through the creation of Bayesian networks which can be used to benchmark external risks among these suppliers.

Design/methodology/approach
The study sample consists of the suppliers to seven of the leading global electronic equipment companies. Bayesian networks are used as a methodology for examining the supplier external risk profiles of the study sample.

Findings
The results of this study show that Bayesian networks can be effectively used to assist managers in making decisions regarding current and prospective suppliers with respect to their potential impact on supply chains as illustrated through their corresponding external risk profiles.

Research limitations/implications
A limitation to the use of Bayesian networks for modeling external risk profiles is the proper identification of risk events and risk categories that can impact a supply chain.

Practical implications
The methodology used in this study can be adopted by managers to assist them in making decisions regarding current or prospective suppliers vis-à-vis their corresponding external risk profiles.

Originality/value
As part of a comprehensive supplier risk management program, companies along with their suppliers can develop specific strategies and tactics to minimize the effects of supply chain external risk events.
Digital preservation practices in university libraries
Authors: Anyaoku Ebele N. , Echedom Anthonia U. Nwabueze , Baro Ebikabowei Emmanuel 
Published: December 2018

Purpose
The purpose of the study is to investigate the digital preservation practices in institutional repositories (IRs) in Africa.

Design/methodology/approach
Data were collected from the IRs developed in university libraries in Africa, and it was done in two phases. The phases are website investigation to identify the university libraries in Africa that have developed IR and online questionnaire.

Findings
Results from the study showed that the majority of IRs in Africa used DSpace software to manage their digital contents, and more than half of the IRs engage in information migration. The study also revealed that the majority of the responding institutions provide long-term digital preservation in their IR. Interestingly, the majority of the IRs has developed digital preservation policy to guide the implementation of digital preservation for IR contents. Finally, the majority of the respondents indicated that they do not have long-term funding and lack the necessary technical staff with required skills to handle and manage the IR.

Research limitations/implications
Because of language barriers, data were collected from only universities in English speaking countries in Africa.

Practical implications
The findings of this study will make librarians in universities in Africa and other developing countries understand the key issues relating to digital preservation and longevity.

Originality/value
The findings of this study will inform information professionals, librarians in developing countries that are planning to create IRs and provide long-term digital preservation of electronic resources in their institution.
Exaptation in management: beyond technological innovations
Authors: De Sordi José Osvaldo , Nelson Reed Elliot , Meireles Manuel , Hashimoto Marcos , Rigato Carlos 
Published: December 2018

PurposeAlthough exaptation is recognized as a means of creation capable of generating significant economic implications for organizations, this mechanism has not been explored in depth in the field of management, where it remains restricted to innovation and product research and development. With this limitation in mind, this study aims to explore and discuss exaptation along with other entities that are more greatly concerned with the interests of and direct contact with practitioners and academics in the field of management, such as processes, data, tacit knowledge and skills.Design/methodology/approachFor the purposes of this study, a comprehensive review of the literature on exaptation was conducted, and 46 entrepreneurs from companies of different sizes and segments were interviewed.FindingsThe results of the review of the literature and interviews with entrepreneurs helped to identify and describe 13 cases of exaptation associated with nine different kinds of organizational entities. For four of these entities, which are closely associated with management, the restrictions of the business environment regarding the exaptation of these entities are discussed, together with the more favorable organizational structures for their occurrence.Practical implicationsThis paper discusses the exaptation to the four types of entity closely linked with management: tacit knowledge, data, process and skill. For each one of these entities the following is discussed: the organizational characteristics that hinder the exaptation of the entity in question and the managerial actions that could alter these characteristics and facilitate the occurrence of the exaptation mechanism with the entity in question.Originality/valueThis process led to the development of an algorithm for analyzing the exaptation mechanism and the adaptation of the attributes associated with the agent-artifact[entity]-context tripartite to describe and analyze exaptation event, including another attribute: the type of entity.
Dynamic capabilities
Authors: Sunder M. Vijaya , L.S. Ganesh , Marathe Rahul R. 
Published: December 2018

PurposeThe growth, diversity and applications of research into dynamic capabilities (DCs) have resulted in the whole literature on DCs becoming a complex and disconnected body of knowledge. This has led to criticisms of the subject of DCs as being vague, tautological and without practical value. Hence, the purpose of this paper is to synthesize the diverse scholarly literature about DCs and develop a more integrated understanding to minimize the reported apparent vagueness.Design/methodology/approachIn this paper, the authors review various relevant themes on DCs using a selection of 133 articles published in 22 recognized, top-tier management journals during the period between 1990 and 2016, with an aim to build a structured and integrated theory. For this, morphological analysis (MA), a systems-thinking technique, is applied.FindingsMA is applied to develop a multi-dimensional conceptual framework comprising five dimensions and 26 variants that enable a structured representation of the conceptual foundations of DCs. Further, the authors identify 81 individual DCs noted by various scholars; elucidate assumptions and antecedents relevant to the DCs approach; structure the key characteristics; and expound the input factors, impacting factors, desired outcomes and assessment yardsticks.Research limitations/implicationsThis would be a useful resource for researchers working in the area of DCs to explore opportunities for future research.Practical implicationsThe MA framework helps managers to look at DCs more holistically, and hence would help them in developing, managing and retaining DCs in organizations.Originality/valueThis study is the original work contributed by the authors and has no specific organizational reference. This research implies new directions to look beyond individual DCs in firms toward a more integrated theory building.
When to use and how to report the results of PLS-SEM
Authors: Hair Joseph F. , Risher Jeffrey J. , Sarstedt Marko , Ringle Christian M. 
Published: December 2018

PurposeThe purpose of this paper is to provide a comprehensive, yet concise, overview of the considerations and metrics required for partial least squares structural equation modeling (PLS-SEM) analysis and result reporting. Preliminary considerations are summarized first, including reasons for choosing PLS-SEM, recommended sample size in selected contexts, distributional assumptions, use of secondary data, statistical power and the need for goodness-of-fit testing. Next, the metrics as well as the rules of thumb that should be applied to assess the PLS-SEM results are covered. Besides presenting established PLS-SEM evaluation criteria, the overview includes the following new guidelines: PLSpredict (i.e., a novel approach for assessing a model’s out-of-sample prediction), metrics for model comparisons, and several complementary methods for checking the results’ robustness.Design/methodology/approachThis paper provides an overview of previously and recently proposed metrics as well as rules of thumb for evaluating the research results based on the application of PLS-SEM.FindingsMost of the previously applied metrics for evaluating PLS-SEM results are still relevant. Nevertheless, scholars need to be knowledgeable about recently proposed metrics (e.g. model comparison criteria) and methods (e.g. endogeneity assessment, latent class analysis and PLSpredict), and when and how to apply them to extend their analyses.Research limitations/implicationsMethodological developments associated with PLS-SEM are rapidly emerging. The metrics reported in this paper are useful for current applications, but must always be up to date with the latest developments in the PLS-SEM method.Originality/valueIn light of more recent research and methodological developments in the PLS-SEM domain, guidelines for the method’s use need to be continuously extended and updated. This paper is the most current and comprehensive summary of the PLS-SEM method and the metrics applied to assess its solutions.
Vibration simulation for a cantilever beam including a slant vertical crack
Authors: Song Xiaohua , Shao Yiming 
Published: December 2018

Purpose
Modelling methods can be helpful for understanding vibrations of beam structures including cracks, as well as for early detection of crack. This study aims to provide an analytical modelling approach for a cantilever beam considering a slant vertical crack along its height. However, previous uniform crack methods cannot be used for describing this case. The results from the analytical, finite element (FE) and experimental methods are compared to verify the vibration problem.

Design/methodology/approach
A massless rotational spring model is adopted to describe the crack. An extended method based on the calculation method for a uniform vertical edge crack is proposed to obtain the stiffness of the slant case. The beam is divided into a series of independent thin slices along the beam height. An Euler–Bernoulli beam model is applied to formulate each slice. The crack in each slice is considered as a uniform one. The transfer matrix method in the literature is used to obtain the beam vibration frequencies and mode shapes. Influences of crack location and sizes on the natural frequencies for the cantilever beam, as well as the mode shapes, are analysed. An established FE model and test results in the listed references are used to validate the developed method.

Findings
The numerical results show that the rotational stiffness at the cracked section and the natural frequencies of the beam decrease by increasing the crack sizes; the natural frequencies for the beam are greatly influenced by the crack sizes and location; the first natural frequency decreases with the distance from the beam fixed end to the crack location; the value of the first natural frequency reaches a minimum value when the crack is at the beam fixed end; the value of the second natural frequency is a minimum value when the crack is at the beam middle; and the value of the third natural frequency is a minimum value when the crack is at the beam free end. Saltation is observed in some mode shapes at the crack location, especially for larger crack depths; but, the mode shapes of the beam are slightly influenced by the vertical crack.

Originality/value
This study gives a useful analytical modelling method for free vibration analysis for the cantilever beam with a vertical crack, which can overcome the disadvantages of the previous uniform crack methods.