bluuebunny/crossref_metadata_2025_split huggingface dataset:
CopyMix: Mixture Model Based Single-Cell Clustering and Copy Number Profiling using Variational Inference
Authors: Safinianaini Negar , P. E. de Souza Camila , Roth Andrew , Koptagel Hazal , Toosi Hosein , Lagergren Jens 
Published: January 2020

AbstractInvestigating tumor heterogeneity using single-cell sequencing technologies is imperative to understand how tumors evolve since each cell subpopulation harbors a unique set of genomic features that yields a unique phenotype, which is bound to have clinical relevance. Clustering of cells based on copy number data obtained from single-cell DNA sequencing provides an opportunity to identify different tumor cell subpopulations. Accordingly, computational methods have emerged for single-cell copy number profiling and clustering; however, these two tasks have been handled sequentially by applying various ad-hoc pre- and post-processing steps; hence, a procedure vulnerable to introducing clustering artifacts. Moreover, clonal copy number profiling has been missing except for one method, CONET, which unfortunately computes it by a post-processing tool. Finally, a common copy number profiling tool, HMMcopy, requires parameter tuning. We avoid the clustering artifact issues and provide clonal copy number profiles without the labor of parameter tuning in our method, CopyMix, a Variational Inference for a novel mixture model, by jointly inferring cell clusters and their underlying copy number profile. We evaluate CopyMix using simulated data and published biological data from ovarian cancer. The results reveal high clustering performance and low errors in copy number profiling. These favorable results indicate a considerable potential to obtain clinical impact by using CopyMix in studies of cancer tumor heterogeneity.
Pdap1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification
Authors: Delgado-Benito Verónica , Berruezo-Llacuna Maria , Altwasser Robert , Winkler Wiebke , Balasubramanian Sandhya , Sundaravinayagam Devakumar , Graf Robin , Rahjouei Ali , Driesner Madlen , Keller Lisa , Janz Martin , Akalin Altuna , Virgilio Michela Di 
Published: January 2020

AbstractThe establishment of protective humoral immunity is dependent on the ability of mature B cells to undergo antibody gene diversification while adjusting to the physiological stressors induced by activation with the antigen. Mature B cells diversify their antibody genes by class switch recombination (CSR) and somatic hypermutation (SHM), which are both dependent on efficient induction of activation-induced cytidine deaminase (AID). Here, we identified PDGFA-associated protein 1 (Pdap1) as an essential regulator of cellular homeostasis in mature B cells. Pdap1 deficiency leads to sustained expression of the integrated stress response (ISR) effector activating transcription factor 4 (Atf4) and induction of the ISR transcriptional program, increased cell death, and defective AID expression. As a consequence, loss of Pdap1 reduces germinal center B cell formation and impairs CSR and SHM. Thus, Pdap1 protects mature B cells against chronic ISR activation and ensures efficient antibody diversification by promoting their survival and optimal function.
Transferability, development of Single Sequence Repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopumMart.) in Benin
Authors: Kpaténon Mariano Joly , Salako Valère Kolawolé , Santoni Sylvain , Zekraoui Leila , Latreille Muriel , Tollon-Cordet Christine , Mariac Cédric , Jaligot Estelle , Beulé Thierry , Adéoti Kifouli 
Published: January 2020

AbstractIn Sub-Saharan Africa, the fan palmBorassus aethiopumMart. is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource.The present work is a first attempt at characterizing the genetic diversity of this palm species as well as its spatial structuration in Benin, West Africa. During a first phase we implemented a microsatellite markers-based approach relying on the reported transferability of primers developed in other palm species and found that, in disagreement with previously published results, only 22.5% of the 80 markers tested enabled amplification of African fan palm DNA and polymorphism detection was insufficient. During a second phase, we therefore generated aB. aethiopum-specific genomic dataset through high-throughput sequencing and used it for thede novodetection of potential microsatellite markers. Among these, 11 enabled polymorphism detection and were further used for analyzing genetic diversity in nineB. aethiopumpopulations.Our results show that genetic diversity of Beninese fan palm populations is low, with an overall average expected heterozygosity (He) of 0.354. Moreover, the positive values of the fixation index (F) in populations from both the Central (Soudano-Guinean) and the Southern (Guinean) regions suggest limited gene flows. Our analysis show that sampledB. aethiopumpopulations are clustered into two groups, one spanning populations from both the Southern and most of the Central region, and the other including the Central population of Savè (which also has the highest He) and populations from the North.In light of our results, we discuss the use of inter-species transfer vs.de novodevelopment of microsatellite markers in genetic diversity analyses targeting under-studied species. We also suggest future applications for the molecular resources generated through the present study.
Improving Heart disease risk through quality-focused diet logging: pre-post study of a diet quality tracking app
Authors: VanDam Courtland , Kwon Bum Chul , Chiuve Stephanie , Choi Hyung-Wook , Entler Paul , Tan Pang-Ning , Huh-Yoo Jina 
Published: January 2020

AbstractDiet-tracking mobile apps have been effective in behavior change. At the same time, quantity-focused diet tracking (e.g., calorie counting) can be time-consuming and tedious, leading to unsustained adoption. Diet Quality—focusing on high-quality dietary patterns rather than quantifying diet into calories—has shown effectiveness in improving heart disease risk. Healthy Heart Score (HHS) predicts 20-year cardiovascular risks based on quality-focused food category consumptions, rather than detailed serving sizes. No studies have examined how mobile health apps focusing on diet quality can bring promising results on health outcomes and ease of adoption. We designed a mobile app to support the HHS informed quality-focused dietary approach by enabling users to log simplified diet quality and view its real-time impact on future heart disease risks. Users were asked to log food categories that are the main predictors of HHS. We measured the app’s feasibility and efficacy on improving individuals’ clinical and behavioral factors affecting future heart disease risks and app use. We recruited 38 overweight or obese participants at high heart disease risk, who used the app for 5 weeks and measured weight, blood sugar, and blood pressure, HHS, and Diet Score (DS) measuring diet quality at baseline and the fifth week of the intervention. The majority used the application every week (84%) and significantly improved DS and HHS at the fifth week (p<0.05), although only 10 participants (31%) checked their risk scores more than once. Other outcomes did not show significant changes. Our study showed logging simplified diet quality significantly improved dietary behavior. The participants were not interested in seeing HHS, and the participants perceived logging diet categories irrelevant to improving HHS as important. We discuss the complexities of addressing health risks, quantity vs. quality-based health monitoring, and incorporating secondary behavior change goals that matter to users when designing mobile health.
Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms
Authors: Pabis Anna , Rawle Robert J. , Kasson Peter M. 
Published: January 2020

AbstractEnveloped viruses enter cells via a process of membrane fusion between the viral envelope and a cellular membrane. For influenza virus, mutational data have shown that the membrane-inserted portions of the hemagglutinin protein play a critical role in achieving fusion. In contrast to the relatively well-understood ectodomain, a predictive mechanistic understanding of the intramembrane mechanisms by which influenza hemagglutinin drives fusion has been elusive. We have used molecular dynamics simulations of fusion between a full-length hemagglutinin proteoliposome and a lipid bilayer to analyze these mechanisms. In our simulations, hemagglutinin first acts within the membrane to increase lipid tail protrusion and promote stalk formation and then acts to engage the distal leaflets of each membrane and promote stalk widening, curvature, and eventual fusion. These two sequential mechanisms, one occurring prior to stalk formation and one after, are consistent with experimental measurements we report of single-virus fusion kinetics to liposomes of different sizes. The resulting model also helps explain and integrate prior mutational and biophysical data, particularly the mutational sensitivity of the fusion peptide N-terminus and the length sensitivity of the transmembrane domain. We hypothesize that entry by other enveloped viruses may also utilize sequential processes of acyl tail exposure followed by membrane curvature and distal leaflet engagement.
Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes
Authors: Rut Wioletta , Żmudziński Mikołaj , Snipas Scott J. , Bekes Miklos , Huang Tony T. , Drag Marcin 
Published: January 2020

AbstractDeubiquitinating enzymes (DUBs) are responsible for removing ubiquitin (Ub) from its protein conjugates. DUBs have been implicated as attractive therapeutic targets in the treatment of viral diseases, neurodegenerative disorders and cancer. The lack of selective chemical tools for the exploration of these enzymes significantly impairs the determination of their roles in both normal and pathological states. Commercially available fluorogenic substrates are based on the C-terminal Ub motif or contain Ub coupled to a fluorophore (Z-LRGG-AMC, Ub-AMC); therefore, these substrates suffer from lack of selectivity. By using a hybrid combinatorial substrate library (HyCoSuL) and a defined P2 library containing a wide variety of nonproteinogenic amino acids, we established a full substrate specificity profile for two DUBs—MERS PLpro and human UCH-L3. Based on these results, we designed and synthesized Ub-based substrates and activity-based probes (ABPs) containing selected unnatural amino acids located in the C-terminal Ub motif. Biochemical analysis and cell-based experiments confirmed the activity and selectivity of engineered Ub-based substrates and probes. Using this approach, we propose that for any protease that recognizes Ub and Ub-like substrates, a highly active and selective unnatural substrate or probe can be engineered.
Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets
Authors: Erbe Rossin , Kessler Michael D. , Favorov Alexander V. , Easwaran Hariharan , Gaykalova Daria A. , Fertig Elana J. 
Published: January 2020

AbstractWhile single-cell ATAC-seq analysis methods allow for robust clustering of cell types, the question of how to integrate multiple scATAC-seq data sets and/or sequencing modalities is still open. We present an analysis framework that enables such integration by applying the CoGAPS Matrix Factorization algorithm and the projectR transfer learning program to identify common regulatory patterns across scATAC-seq data sets. Using publicly available scATAC-seq data, we find patterns that accurately characterize cell types both within and across data sets. Furthermore, we demonstrate that these patterns are both consistent with current biological understanding and reflective of novel regulatory biology.
Excess crossovers impede faithful meiotic chromosome segregation inC. elegans
Authors: Hollis Jeremy A. , Glover Marissa L. , Schlientz Aleesa , Cahoon Cori K. , Bowerman Bruce , Wignall Sarah M. , Libuda Diana E. 
Published: January 2020

AbstractDuring meiosis, at least one crossover must form between each pair of homologous chromosomes to ensure their proper partitioning. However, most organisms limit the number of crossovers by a phenomenon called crossover interference; why this occurs is not well understood. Here we investigate the functional consequences of extra crossovers inCaenorhabditis elegans. Using a fusion chromosome that exhibits a high frequency of supernumerary crossovers, we find that essential chromosomal structures are mispatterned, subjecting chromosomes to improper spindle forces and leading to congression and segregation defects. Moreover, we uncover mechanisms that counteract these errors; anaphase I chromosome bridges were often able to resolve in a LEM-3 nuclease dependent manner, and tethers between homologs that persisted were frequently resolved during Meiosis II by a second mechanism. This study thus provides evidence that excess crossovers impact chromosome patterning and segregation, and also sheds light on how these errors are corrected.
Effect of micro-arc oxidation coating on stress corrosion behavior of AA7050
Authors: Song R.G. , Hua T.S. , Zong Y. , Cai S.W. 
Published: January 2020

Purpose
This paper aims to study the effect of Micro-arc oxidation (MAO) coating on stress corrosion and electrochemical behavior of aluminum alloy.

Design/methodology/approach
The stress corrosion cracking behavior of 7050 aluminum alloy (AA7050) after MAO treatment was investigated in 3.5 Wt.% NaCl solution using the constant load ring. Electrochemical impedance spectroscopy (EIS) was used to evaluate the change of corrosion resistance of MAO specimens in 3.5  Wt.% NaCl solution, and appropriate equivalent circuits were established.

Findings
The results demonstrated that the MAO coating can improve the corrosion resistance of the AA7050 and avoid the reduction of mechanical properties caused by corrosion. In the initial stage of corrosion, the corrosion resistance of coated specimen decreased at first and then increased. In the middle and final stage of corrosion, the corrosion resistance of coated specimen decreased at first and then stabilized.

Originality/value
The long-term corrosion behavior of MAO specimens under stress was studied by constant load experiment and EIS. It has guiding significance for the application of MAO technology on aluminum alloy.
Simulation of bipolar charge transport in graphene on h-BN
Authors: Coco Marco , Nastasi Giovanni 
Published: January 2020

Purpose
The purpose of this paper is to simulate charge transport in monolayer graphene on a substrate made of hexagonal boron nitride (h-BN). This choice is motivated by the fact that h-BN is one of the most promising substrates on account of the reduced degradation of the velocity due to the remote impurities.

Design/methodology/approach
The semiclassical Boltzmann equations for electrons in the monolayer graphene are numerically solved by an approach based on a discontinuous Galerkin (DG) method. Both the conduction and valence bands are included, and the inter-band scatterings are taken into account as well.

Findings
The importance of the inter-band scatterings is accurately evaluated for several values of the Fermi energy, addressing the issue related to the validity of neglecting the generation-recombination terms. It is found out that the inclusion of the inter-band scatterings produces sizable variations in the average values, like the current density, at zero Fermi energy, whereas, as expected, the effect of the inter-band scattering becomes negligible by increasing the absolute value of the Fermi energy.

Research limitations/implications
The correct evaluation of the influence of the inter-band scatterings on the electronic performances is deeply important not only from a theoretical point of view but also for the applications. In particular, it will be shown that the time necessary to reach the steady state is greatly affected by the inter-band scatterings, with not negligible consequences on the switching on/off processes of realistic devices. As a limitation of the present work, the proposed approach refers to the spatially homogeneous case. For the simulation of electron devices, non-homogenous numerical solutions are required. This last case will be tackled in a forthcoming paper.

Originality/value
As observed in Majorana et al. (2019), the use of a Direct Simulation Monte Carlo (DSMC) approach, which properly describes the inter-band scatterings, is computationally very expensive because the valence band is highly populated and a huge number of particles is needed. Even by simulating holes instead of electrons does not overcome the problem because there is a certain degree of ambiguity in the generation and recombination terms of electron-hole pairs. The DG approach, used in this paper, does not suffer from the previous drawbacks and requires a reasonable computing effort.
Logics behind evading overnight taxes: a configurational analysis
Authors: Beritelli Pietro , Reinhold Stephan , Laesser Christian 
Published: January 2020

Purpose
Overnight taxes are controversial. They affect tourists’ consumption behavior and hotels’ profits. This potentially generates undesirable industry practices such as underreporting overnights to evade overnight taxes. The aim of the paper is to understand the conditions and outcomes of underreporting. This is important because underreporting affects destinations’ tax income, which in turn may have further effects on tourism or other public services.

Design/methodology/approach
This study uses qualitative comparative analysis to identify what specific combinations of conditions motivate managers of hospitality businesses to evade overnight taxes.

Findings
While potential economic gain seems to be the obvious answer, this study finds that different configurations of causal conditions account for non-compliance. Four different configurations combining six conditions explain the logics behind hotel overnight tax evasion behavior. The conditions refer to both utilitarian affordances and the individual tax morale of hospitality managers. Certain utilitarian conditions in combination can overrule moral objections to non-compliance.

Originality/value
The study provides a nuanced understanding of overnight tax evasion motives and suggests how to connect work on tourism taxes with destination governance issues and destination management organization funding.
Effects of African local food consumption experiences on post-tasting behavior
Authors: Kim Seongseop (Sam) , Badu-Baiden Frank , Oh Munhyang (Moon) , Kim Jungkeun 
Published: January 2020

Purpose
The purpose of this paper is to investigate the effects of experiences with local food in Ghana on satisfaction, favorability and behavioral intention.

Design/methodology/approach
Unlike previous studies that have used multiple regression analysis or structural equation modeling, this study adopts impact-range performance analysis (IRPA) and impact asymmetry analysis (IAA). A total of 336 questionnaires were used in the data analyses.

Findings
Factor analysis generates five domains of experience of consuming local food. Socialization and boasting and experience with various menus and quality of food contribute most to explaining the three dependent variables.

Originality/value
This study has significant value because it extends the study of local food consumption experience to the understudied area of African food tourism, particularly Ghanaian food and tourists to Ghana.
Multiple identities of a festival
Authors: Masiello Barbara , Bonetti Enrico , Izzo Francesco 
Published: January 2020

Purpose
This paper aims to understand how festival brand personality is built and managed in the social media environment by explaining the intended (by the organizers) festival brand personality and how this concept is communicated and perceived by social media users.

Design/methodology/approach
A multi-method research design was used. Initially, a qualitative analysis based on the free-listing psychological meaning approach was adopted. Then, a content analysis of 23,717 Facebook posts and tweets was performed through NVivo11. Finally, the resulting data were examined through a non-parametric statistical analysis.

Findings
The results show an “internal brand personality gap” (between the intended and communicated brand personality) and an “external brand personality gap” (between the communicated and perceived brand personality). The findings also highlight the existence of an “ultimate brand personality on social media,” which represents a collective and dynamic construct that is co-created by the organization and its customers through interaction and the key role of the customers’ experiences.

Research limitations/implications
The findings contribute to a theory of event brand personality and its management on social media by showing a case with multiple identities.

Practical implications
Implications for the organizers of festivals and non-sport events are discussed to reduce internal and external gaps and better understand the “fit/unfit problem” when dealing with brand personality on social media.

Originality/value
This paper contributes to a research area that is in its infancy because it is one of the first attempts to analyze festival brand personality and its relationship with social media.
Contexts and gender – looking back and thinking forward
Authors: Welter Friederike 
Published: January 2020

Purpose
This paper aims to illustrate the main contributions of the context-gender discussion in entrepreneurship research and its main developments over time to identify promising future research avenues.

Design/methodology/approach
This paper builds on the author’s extensive knowledge of the context-gender debate and on several recent overviews and reviews of the debate. It is written as essay, introducing its main themes through a personal reflection and complemented by a selective review of research on gendered contexts and women’s entrepreneurship.

Findings
The context-gender discussion has moved forward. The first wave of context-gender studies contextualized gender, considering the impact of contexts on women’s entrepreneurship. Nowadays, studies are conducted on how contexts are gendered and how they are constructed in gendered ways through, for example, words, images, cognitions, as well as how women entrepreneurs can impact on and enact their contexts.

Originality/value
This paper contributes novel insights into contextualizing gender and gendering contexts. It is unique in suggesting that a perspective on gendering contexts will allow to explore the diversity of entrepreneurship and further develop theories related to contexts and gender.