bluuebunny/crossref_metadata_2025_split huggingface dataset:
webMCP-counter: a web interface for transcriptomics-based quantification of immune and stromal cells in heterogeneous human or murine samples
Authors: Meylan Maxime , Becht Etienne , Sautès-Fridman Catherine , de Reyniès Aurélien , Fridman Wolf H. , Petitprez Florent 
Published: December 2020

AbstractSummaryWe previously reported MCP-counter and mMCP-counter, methods that allow precise estimation of the immune and stromal composition of human and murine samples from bulk transcriptomic data, but they were only distributed as R packages. Here, we report webMCP-counter, a user-friendly web interface to allow all users to use these methods, regardless of their proficiency in the R programming language.Availability and ImplementationFreely available fromhttp://134.157.229.105:3838/webMCP/. Website developed with the R package shiny. Source code available from GitHub:https://github.com/FPetitprez/webMCP-counter.
Global analysis of multi-mutants to improve protein function
Authors: Johansson Kristoffer E. , Lindorff-Larsen Kresten , Winther Jakob R. 
Published: December 2020

AbstractThe identification of amino acid substitutions that both enhance the stability and function of a protein is a key challenge in protein engineering. Technological advances have enabled assaying thousands of protein variants in a single high-throughput experiment, and more recent studies use such data in protein engineering. We present a Global Multi-Mutant Analysis (GMMA) that exploits the presence of multiply-substituted variants to identify individual amino acid substitutions that are beneficial for the stability and function across a large library of protein variants. We have applied GMMA to >54,000 variants of green fluorescent protein (GFP), each with known fluorescence output, and each carrying 1–15 amino acid substitutions. The GMMA method achieves a good fit to the data while being analytically transparent. The six top-ranking substitutions are demonstrated to progressively enhance GFP and in general, our analysis recovers nearly all the substitutions previously reported to be beneficial for GFP folding and function, only using a single experiment as input.Significance StatementProtein engineering is carried out to improve proteins for practical applications by changing one or more amino acid residues in a protein. We present a method termed global multi-mutant analysis (GMMA) that helps solve two problems in protein engineering. First, because many proteins are already highly optimized, it can be difficult to identify individual variants that further improve function. Second, while it is possible to combine variants with small individual effects, such approaches may be hampered by non-additivity. GMMA identifies combinable effects of single substitutions from a large set of variants each carrying multiple substitutions. We demonstrate the approach on a set of 54,000 variants of green fluorescent protein and identify many enhancing single-substitutions from a single experiment.
Epithelial-stromal cell interactions and ECM mechanics drive the formation of airway-mimetic tubular morphology in lung organoids
Authors: Guney Tankut G. , Herranz Alfonso Muinelo , Mumby Sharon , Dunlop Iain E. , Adcock Ian M. 
Published: December 2020

AbstractThe complex cellular organisation of the human airway tract where interaction between epithelial and stromal lineages and the extracellular matrix (ECM) make it a difficult organ to studyin vitro. Currentin vitrolung models focus on modelling the lung epithelium such as air-liquid interface (ALI) cultures and bronchospheres, do not model the complex morphology and the cell-ECM interaction seenin vivo. Models that include stromal populations often separate them via a semipermeable barrier, which precludes the effect of cell-cell interaction or do not include the ECM or the effect of ECM mechanics such as viscoelasticity and stiffness. Here we investigated the effect of stromal cells on basal epithelial cell-derived bronchosphere structure and function through a triple culture of bronchial epithelial, lung fibroblast and airway smooth muscle cells. Epithelial-stromal cross talk enabled formation of epithelial cell-driven branching tubules consisting of luminal epithelial cells surrounded by stromal cells termed bronchotubules. Addition of agarose to the Matrigel scaffold (Agrigel) created a mechanically tunable ECM, where viscoelasticity and stiffness could be altered to enable long term tubule survival. Bronchotubule models enable the investigation of how epithelial-stromal cell and cell-ECM communication drive tissue patterning, repair and development of disease.Significance StatementCurrent models of airways diseases such as asthma and COPD do not reflect the physical characteristics of the diseased airway which may impact upon our understanding of disease pathophysiology. We have utilised the physical properties of agarose to modify the 3D stiffness of Matrigel to resemble the human airway. Using a primary airway epithelial cell-derived organoid model we demonstrate that a combined Matrigel/agrigel matrix allows sustained 3D organoid structure and the creation of tubules that can contract in response to a clinically relevant bronchoconstrictor. A complex 3D organoid composed of functioning epithelial cells, smooth muscle cells and fibroblasts may provide opportunities for refined drug discovery programmes.Graphical AbstractMixture of healthy lung basal epithelial cells and healthy lung fibroblast cultured in matrigel result in tubules that fail in 4 days.Addition of healthy airway smooth muscle allows for a contractile phenotype.Triple culture of cells in a stiffer scaffold agrigel allows maintenance of tubular organoids for a minimum of 20 days.
A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium
Authors: Pabst Martin , Grouzdev Denis , Lawson Christopher E. , Kleikamp Hugo B.C. , de Ram Carol , Louwen Rogier , Lin Yuemei , Lücker Sebastian , van Loosdrecht Mark C.M. , Laureni Michele 
Published: December 2020

The enormous chemical diversity and strain variability of prokaryotic protein glycosylation makes a large-scale exploration exceptionally challenging. Therefore, despite the universal relevance of protein glycosylation across all domains of life, the understanding of their biological significance and the evolutionary forces shaping oligosaccharide structures remains highly limited.Here, we report on a newly established mass binning glycoproteomics approach that establishes the chemical identity of the carbohydrate components and performs untargeted exploration of prokaryotic oligosaccharides from large-scale proteomics data directly. We demonstrate our approach by exploring an enrichment culture of the globally relevant anaerobic ammonium-oxidizing bacteriumCa.Kuenenia stuttgartiensis. By doing so we resolved a remarkable array of oligosaccharides, produced by two entirely unrelated glycosylation machineries targeting the same surface-layer protein (SLP) simultaneously. More intriguingly, the investigated strain also accomplished modulation of highly specialized sugars, supposedly in response to its energy metabolism—the anaerobic oxidation of ammonium —which depends on the acquisition of substrates of opposite charge. Ultimately, we provide a systematic approach for the compositional exploration of prokaryotic protein glycosylation, and reveal for the first time a remarkable balance between maximising cellular protection through a complex array of oligosaccharides and adhering to the requirements of the ‘metabolic lifestyle’.
Induced Arp2/3 complex depletion increases FMNL2/3 formin expression and filopodia formation
Authors: Dimchev Vanessa , Lahmann Ines , Koestler Stefan A. , Kage Frieda , Dimchev Georgi , Steffen Anika , Stradal Theresia E.B. , Vauti Franz , Arnold Hans-Henning , Rottner Klemens 
Published: December 2020

AbstractThe Arp2/3 complex generates branched actin filament networks operating in cell edge protrusion and vesicle trafficking. Here we employ a novel, conditional knockout mouse model permitting tissue- or cell-type specific deletion of the murineActr3gene (encoding Arp3). A functional Actr3 gene appeared essential for fibroblast viability and growth. Thus, we developed cell lines for exploring the consequences of acute, tamoxifen-inducedActr3deletion causing near-complete loss of Arp/3 complex function as well as abolished lamellipodia formation and membrane ruffling, as expected. However, Arp3-depleted cells displayed enhanced rather than reduced cell spreading, employing numerous filopodia, and showed little defects in individual cell migration. Reduction of collective cell migration as observed for instance in wound healing assays likely derived from defects in maintaining directionality during migration, while the principal ability to chemotax was only moderately affected. Analyses of actin turnover at the cell periphery revealed reduced actin turnover rates in Arp2/3-deficient cells, clearly deviating from previous sequestration approaches. Most surprisingly, induced removal of Arp2/3 complexes reproducibly increased FMNL formin expression, which correlated with the explosive induction of filopodia formation. Our results thus highlight both direct and indirect effects of acute Arp2/3 complex removal on actin cytoskeleton regulation.
HEd-INNOSERV: perceived service innovation scale for the higher education sector
Authors: Manohar Sridhar , Mittal Amit , Tandon Urvashi 
Published: December 2020

PurposeThe study aims to emphasize the need for an exclusive theory, approach and measurement scale for service innovation. In the past three decades, the importance of services and service-related industry has grown tremendously. Well-established scales used for research in manufacturing cannot be directly adopted and measured in the service industry. This article follows the synthesis approach by including both technological and non-technological typologies for measuring service innovation. This is followed by reporting the effect of service innovation on outcome performances. The context of the study is the higher education sector.Design/methodology/approachAn integrated research design was used to collect data from students in various parts of south India. In total, two focus group discussions and three in-depth interviews were conducted for item generation. Confirmatory factor analysis was performed for the reliability and validity of the scale. The study developed the HEd-INNOSERV scale consisting of seven dimensions comprising 34 items.FindingsThe study developed the HEd-INNOSERV scale consisting of seven dimensions comprising 34 items. The empirical results demonstrate that the scale is reliable, valid and generalizable across higher education institutions (HEIs). The scope for future research is to develop a generalized scale that can measure across the entire service sector.Research limitations/implicationsThe scale shall help researchers in testing the conceptual models earlier developed in the service innovation domain. Similarly, HEIs could measure their stakeholders' perceptions of their innovation activity. Further, the result indicates that innovation enhances the reputation of the institution, which ultimately results in positive word of mouth.Practical implicationsCommercialization of the scale by developing an appropriate algorithm would help institutions in measuring their innovation-led initiatives continually and establish quality and standards. The scale can be used complementarily with other measures adopted from regulatory and rating agencies.Originality/valueThe HEd-INNOSERV scale shall help in optimizing the existing business processes of HEIs by helping them consciously introduce appropriate technological and non-technological innovations.
The relationship between mentor support experiences and STEM graduate student career optimism
Authors: Olson Kristine J. , Huffman Ann Hergatt , Litson Kaylee 
Published: December 2020

PurposeUsing social cognitive career theory in tandem with gender role theory, the current research examines how instrumental and socioemotional mentor support experiences are linked to mentee career optimism among a sample of STEM graduate students. More specifically, this study examines how self-efficacy and school satisfaction mediate the relationship dependent on the gender of the student as well as the gender of the mentor.Design/methodology/approachA total of N = 828 (n = 408 women, n = 420 men) graduate students enrolled in one of 119 public STEM graduate programs in the USA participated in an online survey.FindingsResults suggest that student gender did not moderate the proposed mediation model. However, the instrumental support experiences → self-efficacy → career optimism mediation relationship was moderated by mentor gender with female mentors strengthening the relationship between mentor support experiences and optimism. Finally, same-gender mentor–student dyads experience consistency of school satisfaction regardless of instrumental mentor support experiences compared to the heterogeneous gender mentor–student dyads where school satisfaction is positively associated with mentor instrumental support.Originality/valueThis study expands Lent et al.'s (2015) social cognitive career model by providing an analysis of independent parallel mediation paths to examine the direct link between mentor support experiences and career optimism through self-efficacy and school satisfaction. Based on the findings, graduate programs should emphasize the importance of mentor support experiences and help graduate faculty explore how they can best provide mentor experiences to their mentees.
Presenting a proposed framework for evaluating university websites
Authors: Gharibe Niazi Monireh , Karbala Aghaei Kamran Masumeh , Ghaebi Amir 
Published: December 2020

PurposeThis study aims to design a proposed framework for evaluating university websites.Design/methodology/approachThis study is an exploratory mixed research. It was an applied research in terms of objective and used the Delphi technique and systematic review and meta-analysis approaches. Data collection tools were done through library studies, Delphi checklist and observation. The statistical population of the research comprised 17 experts who are designers of university websites and 20 Iranian university websites selected from the Webometrics website. The statistical data were analyzed using fuzzy methods, descriptive and inferential statistical methods and the SWARA weighting method. Also, the statistical analysis software SPSS 20 and Excel 2016, TOPSIS engineering software and MAXQDA were used.FindingsFindings indicated that the dimensions of the designed proposed framework in order of their weights are credibility (0.130), reliability (0.125), usability (0.120), website design (0.110), functionality (0.104), content (0.100), page design (0.0922), efficiency (0.082), Webometrics (0.070) and systematic evaluation (0.067). Mebrate’s (2010) framework had the highest overlap (mean = 74.65), and Webometrics (mean = 18.5) had the least overlap and dependency (mean = 19) with the proposed framework. In the evaluation of the 20 university websites of Iran selected from the Webometrics site, the University of Tehran was ranked first with a score of 82.7 and Shiraz University was ranked last with a score of 75.Originality/valueThis study provides a comprehensive proposed framework for evaluating university websites that eliminates the shortcomings of all models, frameworks and methods of university website evaluation that focused only on one or more dimensions of university websites.
National social capital, perceived entrepreneurial ability and entrepreneurial intentions
Authors: Amini Sedeh Amirmahmood , Abootorabi Hooman , Zhang Jing 
Published: December 2020

PurposeGrounded in theory of planned behavior, this study explores how national social capital, as an important but untested element of institutional environment, influences the effect of perceived entrepreneurial ability on entrepreneurial intentions.Design/methodology/approachUsing data of more than 95,000 individuals in 33 countries from Adult Population Survey (APS) conducted by Global Entrepreneurship Monitor (GEM), combined with data collected by World Values Survey (WVS), this study employs hierarchical linear modeling (HLM) to assess the moderation effect of national social capital on the relationship between perceived entrepreneurial ability of individuals nested within different countries and entrepreneurial intentions.FindingsThe results reveal that national social capital enhances the positive impact of perceived entrepreneurial ability on the intent of individuals to start a new business. Notably, this study finds all three components of national social capital – generalized trust, breadth of formal organizational memberships and civic engagement– strengthen the influence of perceived entrepreneurial ability on entrepreneurial intentions.Originality/valueAs the main contribution, this research illustrates the combined effects of social environment (i.e. national social capital) and individuals' evaluations regarding their ability to start a business (i.e. perceived entrepreneurial ability) on entrepreneurial intentions. This study highlights that national social capital complements perceived entrepreneurial ability by helping identify favorable start-up conditions and increasing the tendency of people to act on those conditions.
Dynamics of a medium value consumer apparel supply chain key parameters
Authors: Kumar Vimal , Verma Pratima , Jha Ajay , Lai Kuei-Kuei , Do Manh-Hoang 
Published: December 2020

PurposeThis research presents a study on the supply chain process of an Indian apparel industry considering various parameters involved. The study aims to identify the main parameters to improve the supply chain process and develop a comprehensive structural relationship to rank them to streamline the apparel supply chain process and business environment.Design/methodology/approachThe team of five experts from this apparel industry was made to give scores to multiple parameters. The TOPSIS (Technique for Order of Preference by Similarity to Ideal Solution) technique is used to develop the model for eleven key parameters and then rank them.FindingsBased on the data analysis the planning, customer and warehouse storage have emerged as top three key parameters while the non-replenishment approach, push and pull strategy and manufacturing of the product are identified as the bottom three parameters from a hierarchy level. These parameters have been ranked based on their contributing attributes in this apparel supply chain process.Research limitations/implicationsThe study provides an overall ranking of parameters and the implications are in the direction of helping the industry to improve its supply chain performances rather than focus only on productivity. Further, the key parameters are identified as critical inputs and show that the firms are being more proactive and well prepared comprised of the industry.Originality/valueThe study indicates that the key parameters are identified by this apparel brand to improve its supply chain process. The key supply chain process involves planning, manufacturing, distribution, end customer and returns logistics of the goods, etc. So, this research also provides the focused parameters on the supply chain performance received by end customer from the supplier and rank them for effectiveness and improve their overall organizational performance. It also provides a critical observation of their supply chain process improvement which includes different brand uses, strategies and approaches.
An integrative literature review exploring the impact of alcohol workplace policies
Authors: Alfred Lolita , Limmer Mark , Cartwright Susan 
Published: December 2020

PurposeAlcohol workplace policies (AWPs) can help organizations to manage and support employees with alcohol-related problems. Over the last two decades, there has been a slow but steady rise of research on AWPs with some indication that these can contribute to reducing employee excessive consumption. However, there does not appear to be any empirical literature reviews to consolidate and evaluate what this body of evidence says regarding the impact of these policies. The following review seeks to address this gap.Design/methodology/approachFive electronic databases were searched for papers published between January 1996 and January 2020. To capture additional relevant papers (including those from non-peer reviewed sources), the search was extended to Google Scholar, professional and human resource management websites, trade publications and the website of one United Kingdom (UK)-based alcohol charity. Inclusion and exclusion criteria were used to systematically screen the paper titles, abstracts and full-text records. 14 papers were deemed eligible and therefore included in the integrative review. After extracting data, all 14 papers were appraised for quality and then analysed using the narrative synthesis guide by Popay et al. (2006).FindingsFive themes were identified, namely, Associations between Policy and Consumption Levels/Patterns, Deterrence, Policy and Programme Type, Knowledge and Understanding and Enforcement and Discipline. These themes encapsulated what the included papers concluded about the impact and associated benefits or challenges of AWPs.Research limitations/implicationsThis review identifies that despite the benefits of AWPs, up to 40% of workplaces do not have these policies in place. Future research needs to explicitly explore the reasons for this.Practical implicationsThis review highlights that AWPs can benefit employees and workplaces. Therefore, organizations are encouraged to develop and implement AWPs to support health improvement and prevention of alcohol problems in the workplace.Originality/valueThis review provides a current synthesis of literature published over the last two decades regarding the impact of AWPs on employees and workplaces.
Social entrepreneurship competency: an approach by discipline and gender
Authors: Vázquez-Parra José Carlos , García-González Abel , Ramírez-Montoya María Soledad 
Published: December 2020

PurposeThe purpose of this study is to analyze how university men and women in different disciplines of study in Mexico perceive social entrepreneurship competencies, using a multifactorial analysis to find possible areas of opportunity to reduce the gender gap in social-entrepreneurship-project proposals.Design/methodology/approachThis is a quantitative study with a validated questionnaire that records the perception levels of five social entrepreneurship subcompetencies. The survey, which includes 28 indicators, was applied to 140 university students from different disciplines. Hypothesis testing was applied to identify significant differences between men and women in each subcompetency by disciplinary area.FindingsIn the global sample, significant differences by gender were observed only in the social value subcompetency. In the disciplinary analysis, significant differences were found in architecture and design, business, and engineering and science.Research limitations/implicationsThe questionnaire only gathered data about the students' perceptions. To the extent that perception is triangulated with other instruments, it is possible to increase knowledge regarding how to train in social entrepreneurship.Practical implicationsThe results can be useful for university training and increasing the envisioning and formulating of government projects by young people who create new businesses.Originality/valueThis research contributes to the literature on the role of gender-specific perceptions of social entrepreneurship in Mexico.