bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
Authors: Qin Qian , Fan Jingyu , Zheng Rongbin , Wan Changxin , Mei Shenglin , Wu Qiu , Sun Hanfei , Zhang Jing , Brown Myles , Meyer Clifford A. , Shirley Liu X. 
Published: November 2019

AbstractWe developed Lisa (http://lisa.cistrome.org) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses compendia of public histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Then using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes, and outperformed alternative methods in identifying the perturbed TRs.
The substrate-dependent stereoselectivity of the multicopper oxidase (MCO)-catalyzed oxidative coupling in the biosynthesis of the bisnaphthopyrone viriditoxin
Authors: Hu Jinyu , Flematti Gavin R. , Chooi Yit-Heng 
Published: November 2019

AbstractVdtB, the multiple-copper oxidase (MCO) from the bisnaphthopyrone (M)-viriditoxin biosynthetic pathway inPaecilomyces variotii, was shown to catalyze regioselective 6,6′-coupling of semi-viriditoxin (1). The stereoselectivity of the oxidative coupling reaction for the production of the atropisomer (M)-viriditoxin, however, was controlled by VdtD, a non-catalytic dirigent protein from the pathway. In this work, VdtB either alone or together with VdtD were investigated for its stereoselective control upon coupling of other monomeric naphthopyrone derivatives from the pathway with different minor structural variations in terms of presence/absence ofO-methylation at C7-position and C3-C4Δ2double bond on the pyrone ring, and the different side-chain modifications. We showed that VdtB could favour eitherM- orP-form coupling in a substrate-dependent manner. For some substrates, VdtB could catalyze oxidative coupling in an enantiomerically selective manner. The efficiency of the VdtD in exerting stereoselective control of the oxidative coupling reaction also varies between substrates. The results point to a model whereby VdtB and VdtD form a VdtB-ligand-VdtD complex in which the stereochemical outcome of the coupling reaction depends on how the substrate interacts with both proteins, based on the substrate structure. Our findings contributed to a more comprehensive understanding of dirigent protein-mediated MCO-catalyzed stereoselective oxidative coupling reactions in fungi.
FastFeatGen: Faster parallel feature extraction from genome sequences and efficient prediction of DNA N6-methyladenine sites
Authors: Rahman Md. Khaledur 
Published: November 2019

AbstractN6-methyladenine is widely found in both prokaryotes and eukaryotes. It is responsible for many biological processes including prokaryotic defense system and human diseases. So, it is important to know its correct location in genome which may play a significant role in different biological functions. Few computational tools exist to serve this purpose but they are computationally expensive and still there is scope to improve accuracy. An informative feature extraction pipeline from genome sequences is the heart of these tools as well as for many other bioinformatics tools. But it becomes reasonably expensive for sequential approaches when the size of data is large. Hence, a scalable parallel approach is highly desirable. In this paper, we have developed a new tool, called FastFeatGen, emphasizing both developing a parallel feature extraction technique and improving accuracy using machine learning methods. We have implemented our feature extraction approach using shared memory parallelism which achieves around 10× speed over the sequential one. Then we have employed an exploratory feature selection technique which helps to find more relevant features that can be fed to machine learning methods. We have employed Extra-Tree Classifier (ETC) in FastFeatGen and performed experiments on rice and mouse genomes. Our experimental results achieve accuracy of 85.57% and 96.64%, respectively, which are better or competitive to current state-of-the-art methods. Our shared memory based tool can also serve queries much faster than sequential technique. All source codes and datasets are available at https://github.com/khaled-rahman/FastFeatGen.
Decentralized multi-site VBM analysis during adolescence shows structural changes linked to age, body mass index, and smoking: A COINSTAC analysis
Authors: Gazula Harshvardhan , Holla Bharath , Zhang Zuo , Xu Jiayuan , Verner Eric , Kelly Ross , Schumann Gunter , Calhoun Vince D. 
Published: November 2019

AbstractIn the recent past, there has been an upward trend in developing frameworks that enable neuroimaging researchers to address challenging questions by leveraging data across multiple sites all over the world. One such framework, Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC), provides a platform to analyze neuroimaging data stored locally across multiple organizations without the need for pooling the data at any point during the analysis. In this paper, we perform a decentralized voxel-based morphometry analysis of structural magnetic resonance imaging data across two different sites to understand the structural changes in the brain as linked to age, body mass index and smoking. Results produced by the decentralized analysis are contrasted with similar findings in literature. This work showcases the potential benefits of performing multi-voxel and multivariate analyses of large-scale neuroimaging data located at multiple sites.
UFMylation of MRE11 is essential for maintenance of telomere length and hematopoietic stem cell survival
Authors: Lee Lara , Perez Oliva Ana Belen , Churikov Dmitri , Martinez-Balsalobre Elena , Peter Joshua , Rahmouni Dalicya , Audoly Gilles , Azzoni Violette , Audebert Stephane , Camoin Luc , Mulero Victoriano , Cayuela Maria L. , Geli Vincent , Kulathu Yogesh , Lachaud Christophe 
Published: November 2019

AbstractGenetic studies using knockout mouse models provide strong evidence for the essential role of the ubiquitin-like protein UFM1 for hematopoiesis, especially erythroid development, yet its biological roles in this process are largely unknown. Here we have identified a UFL1-dependent UFMylation of the MRE11 nuclease on the K281 and K282 residues. We show that Hela cells lacking the specific UFM1 E3 ligase display severe telomere shortening. We further demonstrate either by deleting UFM1 or by mutating MRE11 UFMylation sites that preventing MRE11 UFMylation impacts its interaction with the telomere protein TRF2. However, the MRE11 function in double-strand-break repair remains intact. We validate these resultsin vivoby showing that Zebrafish knockouts for the genesufl1andufm1have shorter telomeres in hematopoietic cells. Here we present UFMylation has a new mechanisms of regulation for telomere length maintenance with a role in hematopoiesis.Key pointsModification of MRE11 by UFM1 regulates telomere maintenance and cell death in HSCsScientific categoryUFMylation, telomere maintenance, hematopoietic stem cell survival.
Hepatocytic Prominin-1 protects against liver fibrosis by stabilizing the SMAD7 protein
Authors: Lee Hyun , Yu Dong-Min , Um Min Jee , Yoon Seo Yeon , Kim Ki-Tae , Kwon Young Jae , Lee Sungsoo , Bahn Myeong-Seok , Koo Seung-Hoi , Jung Ki Hoon , Lee Jae-Seon , Ko Young-Gyu 
Published: November 2019

AbstractBackground and AimsProminin-1 (PROM1) is known to be upregulated in hepatocytic progenitor cells (HPCs) and cholangiocytes of fibrotic livers. To understand the function of upregulated PROM1 during liver fibrosis, we analyzed liver fibrosis from global and liver-specific Prom1 knockout mice and investigated the molecular mechanism of how Prom1 protects the liver against liver fibrosis.MethodsWe analyzed PROM1 expression from human liver with mild and severe liver fibrosis (n=4-9). Liver fibrosis was induced by carbon tetrachloride (CCl4) treatment and bile duct ligation (BDL) from wild type and global and liver-specific knockout mice (n=3-13). The severity of liver fibrosis was determined by qRT-PCR, immunostaining and immunoblotting for fibrotic markers such as αSMA, collagen. TGFβ signaling was also analyzed from fibrotic liver and primary hepatocytes of wild type and global and liver-specific knockout mice (n=3-5). Molecular interaction between PROM1 and SMAD7 was determined by endogenous and exogenous co-immunoprecipitation.ResultsPROM1 was found in the plasma membranes of both healthy and fibrotic hepatocytes and cholangiocytes. Global Prom1 knockout aggravated BDL- and CCl4-induced liver fibrosis.Prom1-/-hepatocytes showed increased TGFβ signaling due to reduced SMAD7 protein expression compared to that in wild-type hepatocytes. PROM1 prevented SMURF2-induced SMAD7 ubiquitination and degradation by interfering with the molecular association of SMAD7 with SMURF2. We also demonstrated that liver-specific Prom 1 knockout aggravated BDL-induced liver fibrosis due to reduced levels of SMAD7.ConclusionHepatocytic PROM1 stabilizes SMAD7, preventing TGFβ signaling. Thus, PROM1 is necessary for the negative regulation of TGFβ signaling during liver fibrosis.
Quantitative Analysis of 1300-nm Three-photon Calcium Imaging in the Mouse Brain
Authors: Wang Tianyu , Wu Chunyan , Ouzounov Dimitre G. , Gu Wenchao , Xia Fei , Kim Minsu , Yang Xusan , Warden Melissa R. , Xu Chris 
Published: November 2019

Abstract1300-nm three-photon calcium imaging has emerged as a useful technique to allow calcium imaging in deep brain regions. Application to large-scale neural activity imaging entails a careful balance between recording fidelity and tissue heating. We calculated and experimentally verified the excitation pulse energy to achieve the minimum photon count required for the detection of calcium transients in GCaMP6s-expressing neurons for 920-nm two-photon and 1320-nm three-photon excitation, respectively. Brain tissue heating by continuous three-photon imaging was simulated with Monte Carlo method and experimentally validated with immunohistochemistry. We observed increased immunoreactivity with 150 mW excitation power at 1.0- and 1.2-mm imaging depths. Based on the data, we explained how three-photon excitation achieves better calcium imaging fidelity than two-photon excitation in the deep brain and quantified the imaging depth where three-photon microscopy should be applied. Our analysis presents a translatable model for the optimization of three-photon calcium imaging based on experimentally tractable parameters.
Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1
Authors: Gaullier Guillaume , Roberts Genevieve , Muthurajan Uma M. , Bowerman Samuel , Rudolph Johannes , Mahadevan Jyothi , Jha Asmita , Rae Purushka S. , Luger Karolin 
Published: November 2019

AbstractPoly(ADP-ribose) Polymerase 2 (PARP2) is one of three DNA-dependent PARPs involved in the detection of DNA damage. Upon binding to DNA double-strand breaks, PARP2 uses nicotinamide adenine dinucleotide to synthesize poly(ADP-ribose) (PAR) onto itself and other proteins, including histones. PAR chains in turn promote the DNA damage response by recruiting downstream repair factors. These early steps of DNA damage signaling are relevant for understanding how genome integrity is maintained and how their failure leads to genome instability or cancer. There is no structural information on DNA double-strand break detection in the context of chromatin. Here we present a cryo-EM structure of two nucleosomes bridged by human PARP2 and confirm that PARP2 bridges DNA ends in the context of nucleosomes bearing short linker DNA. We demonstrate that the conformation of PARP2 bound to damaged chromatin provides a binding platform for the regulatory protein Histone PARylation Factor 1 (HPF1), and that the resulting HPF1•PARP2•nucleosome complex is enzymatically active. Our results contribute to a structural view of the early steps of the DNA damage response in chromatin.
Gender and wine consumption: sociodemographic profiles
Authors: Rodríguez-Donate María Carolina , Romero-Rodríguez Margarita Esther , Cano-Fernández Víctor Javier , Guirao-Pérez Ginés 
Published: November 2019

Purpose
The globalization of wine markets together with a prolonged decline in wine consumption, especially in traditional wine-producing countries such as Spain, make it more relevant than ever to study population segments such as female wine consumers. Such segments could contribute to increasing consumption. The purpose of this paper is to investigate the distinctive features of wine consumption according to gender, identifying sociodemographic profiles of female wine consumers and non-consumers in Tenerife (Canary Islands). The Canarian archipelago is one of the Spanish regions with a long tradition in wine production.

Design/methodology/approach
This study uses data from a survey carried out on a representative sample of 1,028 Tenerife residents. Independent tests and correspondence analyses were performed. Moreover, an ordered mixed logit model was estimated.

Findings
Gender is a determining factor when analysing the frequency of wine consumption. The profiles of female consumers and female non-consumers differ substantially. Considering unobserved heterogeneity in the estimated model also allows us to verify the variability of the effects on the probability of women with the same sociodemographic characteristics having the same consumption pattern.

Research limitations/implications
Non-sociodemographic variables could be considered in this paper.

Practical implications
Marketing strategies should not consider women as a homogenous group.

Originality/value
This study examines in depth the sociodemographic factors that influence the frequency of wine consumption according to gender. It is relevant given the scarcity of studies that analyse these factors. Likewise, unobserved heterogeneity in consumer decisions is taken into account, an aspect that has not been sufficiently considered in wine consumption literature so far.
Effect of information on consumer preferences and willingness-to-pay for sparkling mock wines
Authors: Naspetti Simona , Alberti Francesca , Mozzon Massimo , Zingaretti Sara , Zanoli Raffaele 
Published: November 2019

Purpose
The purpose of this paper is to explore the role of information about alcohol content, organic labelling and packaging on consumer preferences and willingness-to-pay (WTP) of non-alcoholic sparkling mock wines.

Design/methodology/approach
In a two-step study, the consumer’s expectations and overall liking of two novel brands of mock wines were investigated by focus groups followed by a common hedonic test combined with a choice experiment aimed at measuring consumer WTP. A total of 240 consumers were assigned to two tasting groups of equal size: all were presented at least one brand of mock wine, while drinkers also tasted a familiar brand of low-alcohol sweet sparkling wine. A paper-and-pencil choice experiment followed the tasting sessions.

Findings
The results demonstrate that participants in blind or manipulated “informed” conditions are not able to discriminate among mock wines and wine, whereas significant differences in preferences for brands under investigation appeared when labels and other information were disclosed. In effect, drinkers and non-drinkers did not differ in hedonic scores of mock wines. While younger participants exhibited the highest scores in blind liking, the overall expected liking is significantly higher for non-drinkers and women if compared, respectively, to drinkers and men. WTP for mock wines is influenced by taste, glass bottle packaging and the organic label, while mock-wine colour is not relevant.

Research limitations/implications
Although limited in sample size and representativeness, this study has brought some new insights into the consumption of non-alcoholic mock wines. In this study, a significant influence of blind sensory liking on WTP is demonstrated. This result has theoretical implications: while the effect of product information on WTP is well established, the relationship between hedonic scores and WTP – while theoretically consistent – is not so clear-cut in the literature. Further research is needed to confirm/disconfirm these findings.

Practical implications
Sparkling no-alcohol mock wines, despite their sweetness, appear not different in taste to medium-to-low APV (7.5 per cent) sweet wines.

Originality/value
The paper suggests that marketing of mock (no-alcohol) wines needs careful branding to elicit significant hedonic effects, while interacting sensory (blind liking) scores with price information in choice models may help to represent taste heterogeneity in WTP estimates in a better way.
Pure donation or hybrid donation crowdfunding
Authors: Zhao Liang , Sun Zhe 
Published: November 2019

PurposeDespite the growing research exploring the possibility and feasibility of financing socially oriented projects through crowdfunding, relatively little research examines which crowdfunding model is better to serve such purpose. The purpose of this paper is to offer novel insights to mitigate this research gap.Design/methodology/approachA unique data set collected from the largest Chinese crowdfunding platform is used to test the hypotheses. To solve the perceived self-selection problem, the propensity score matching method is adopted in this paper. Based on this approach, the results of similar prosocial campaigns in two different models (pure donation and hybrid donation) are compared.FindingsThe empirical results show that the hybrid donation model is negatively associated with the status of success and the extent of success of prosocial campaigns. Specifically, compared to the pure donation model, hybrid donation model leads to a lower probability of success, fewer contributors, a lower funding amount and a lower completion ratio.Originality/valueThe paper contributes to a relatively understudied theme in crowdfunding, namely, donations. It does so by introducing the concepts of pure vs hybrid donation models and investigates the model selection problem in financing social projects through crowdfunding based on cognitive evaluation theory.
CRM campaigns with choice for enhanced business process performance
Authors: Christofi Michael , Thrassou Alkis , Chebbi Hela , Ahmed Zafar U. , Grandhi Balakrishna , Iaia Lea 
Published: November 2019

Purpose
A substantial body of research evidence has now accumulated in the cause-related marketing (CRM) literature. Yet, research on positive word of mouth (WOM) in the CRM domain is scarce. Based on this, the purpose of this paper is to present a framework that enhances positive WOM persuasion in a CRM context.

Design/methodology/approach
Specifically, the authors explore collectivism as a contextual dimension for positive WOM persuasion in a CRM setting and discusses three novel constructs for effectively designing such campaigns, namely, cause proximity, choice of donation type and choice variety of donation types in a single offering frame. Based on conceptual logic and drawing on literature from a variety of disciplines, this framework should provide deeper insight into achieving positive WOM persuasion with CRM strategy and implementation.

Findings
Additionally, the analysis leads to specific research questions regarding the associations between these contrasts and positive WOM persuasion in a CRM context.

Originality/value
Finally, the managerial and theoretical contributions are discussed, as well as directions for further research.
To invest or to harvest?
Authors: Rossi Matteo , Festa Giuseppe , Fiano Fabio , Giacobbe Rosa 
Published: November 2019

PurposeRecently, corporate venture capital (CVC) has been gaining increasing attention worldwide as a special form of venturing through which non-financial corporations invest in target companies, usually technological firms, as start-ups. These investments mostly aim not at financial goals but constitute a strategic way for the corporation to obtain access to new technologies and innovations through financing entrepreneurial initiatives. The purpose of this paper is to analyze the connections between the core business of the parent company and its venturing investments, investigating, in particular, its “ambidexterity,” i.e., the ability of the CVC company to invest in ventures close to its core activities, exploiting internal resources and exploring new markets.Design/methodology/approachStemming from the results of previous studies, this research has applied a discriminating analysis methodology to the 18 most active CVC companies in the world, all of which have technology innovation as the core business of the corporation, in the 2015/2017 period.FindingsAn evident correlation between the Financing Round (as the independent variable) and the Entrepreneurial Intensity (as the dependent variable) influences the CVCs investment policies and their behavior with respect to their ambidexterity. This link could also influence the strategic orientation of the CVC policy, forcing the company to appropriately govern and manage the starting nature and/or the variable nature of the CVC (ambidextrous, hybrid, dis-ambidextrous or random).Research limitations/implicationsThe current research has used only secondary data to explore the behavior of only 18 CVCs in a relatively short period. Thus, it would be advisable to extend the number of observations, to enlarge the period under investigation, and to retrieve field data to obtain more detailed and reliable results.Originality/valueThe main objective/contribution of this study is to understand if there is a correlation between the Financing Round (as the independent variable) and the Entrepreneurial Intensity (as the dependent variable) for the 18 most active CVCs in the world, according to CB Insights, in 2015–2017, adopting and further confirming the model by Rossiet al.(2019). The statistical investigation, based on the conclusions of that linear regression model, has highlighted a total or large correlation between these two variables for the current research perimeter, which includes CVC companies with technology as the core business of the corporation.
Organizational lifecycle and strategic management accounting
Authors: Pasch Timur 
Published: November 2019

PurposeThis study aims to examine the relationship between organizational lifecycle stages, the adoption of strategic management accounting (SMA) practices and the performance consequences of SMA adoption.Design/methodology/approachThe analysis is based on survey data from 377 firms operating in German speaking countries.FindingsThe author finds that the firms’ adoption rates of SMA increase from the birth to the revival lifecycle stages and drop at the decline stage. Firms that deviate from the optimal SMA profile have lower performance compared to the firms that do not deviate. The negative performance effect, however, is only significant for firms that have too little SMA practices and is not significant for firms that adopt too much SMA practices.Research limitations/implicationsThese results suggest that firms that fail to implement a sufficient level of SMA suitable for their development stage will not develop as fast as their competitors. This study is subject to general limitations of survey research, particularly with respect to the operationalization of the variables, the number of contextual variables in the empirical model and sample coverage.Practical implicationsThe implication for managerial practice is that greater efforts should be directed toward eliminating underfit than overfit regarding the implementation of management control systems.Originality/valueThis is the first analysis of the adoption of SMA at different life cycle stages and the consequences of misfitted adoption.