bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protective heterologous T cell immunity in COVID-19 induced by MMR and Tdap vaccine antigens
Authors: Mysore Vijayashree , Cullere Xavier , Settles Matthew L. , Ji Xinge , Kattan Michael W. , Desjardins Michaël , Durbin-Johnson Blythe , Gilboa Tal , Baden Lindsey R. , Walt David R. , Lichtman Andrew , Jehi Lara , Mayadas Tanya N. 
Published: May 2021

ABSTRACTT cells are critical for control of viral infection and effective vaccination. We investigated whether prior Measles-Mumps-Rubella (MMR) or Tetanus-Diphtheria-pertussis (Tdap) vaccination elicit cross-reactive T cells that mitigate COVID-19. Using co-cultures of antigen presenting cells (APC) loaded with antigens and autologous T cells, we found a high correlation between responses to SARS-CoV-2 (Spike-S1 and Nucleocapsid) and MMR and Tdap vaccine proteins in both SARS-CoV-2 infected individuals and individuals immunized with mRNA-based SARS-CoV-2 vaccines. The overlapping T cell population contained effector memory T cells (TEMRA) previously implicated in anti-viral immunity and their activation required APC-derived IL-15. TCR- and scRNA-sequencing detected cross-reactive clones with TEMRA features among the cells recognizing SARS-CoV-2, MMR and Tdap epitopes. A propensity-weighted analysis of 73,582 COVID-19 patients revealed that severe disease outcomes (hospitalization and transfer to intensive care unit or death) were reduced in MMR or Tdap vaccinated individuals by 38-32% and 23-20% respectively. In summary, SARS-CoV-2 re-activates memory T cells generated by Tdap and MMR vaccines, which may reduce disease severity.
Fabrication and Evaluation of Mechanical and Tribological Properties of ultra-high-molecular-weight polyethylene-based Nanocomposites Reinforced with Hydroxyapatite, Zirconia and Multi-walled Carbon Nanotubes
Authors: Nikbakht Alireza , Javadpour Jafar , Naimi-Jamal M. Reza , Rezaie Hamidreza 
Published: May 2021

AbstractThe unique properties of ultra-high-molecular-weight polyethylene (UHMWPE) have made composites based on this polymer the gold standard choice for articulating surfaces used in arthroplasty. However, wear debris released by prosthesis is still a major concern of the implants. In this study, we address the urgent need to revisit the current methodologies used in designing these biomaterials by fabricating UHMWPE-based nanocomposite with Hydroxyapatite (HA), Multi-walled Carbon Nanotubes (MWCNTs), and Zirconia as additives. We investigated how different combinations of these additives impact the nanocomposites’ hardness, plasticity index (PI), and friction coefficient. Our results show a constant increase in hardness by increasing Zirconia. The MTT assay test and Scanning Electron Microscopy (SEM) demonstrated an increase in cell attachment and cell viability. Examining various additives’ amounts, we can further explore the possibility of reaching an optimum proportion of the ingredients. Compared with other UHMWPE-based nanocomposites (UHMWPE-HA-MWCNT’s), the fabricated nanocomposite shows an improvement in tribological properties.
Minian an Open-source Miniscope Analysis Pipeline
Authors: Dong Zhe , Mau William , Feng Yu , Pennington Zachary T. , Chen Lingxuan , Zaki Yosif , Rajan Kanaka , Shuman Tristan , Aharoni Daniel , Cai Denise J. 
Published: May 2021

AbstractMiniature microscopes have gained considerable traction forin vivocalcium imaging in freely behaving animals. However, extracting calcium signals from raw videos is a computationally complex problem and remains a bottleneck for many researchers utilizing single-photonin vivocalcium imaging. Despite the existence of many powerful analysis packages designed to detect and extract calcium dynamics, most have either key parameters that are hard-coded or insufficient step-by-step guidance and validations to help the users choose the best parameters. This makes it difficult to know whether the output is reliable and meets the assumptions necessary for proper analysis. Moreover, large memory demand is often a constraint for setting up these pipelines since it limits the choice of hardware to specialized computers. Given these difficulties, there is a need for a low memory demand, user-friendly tool offering interactive visualizations of how altering parameters at each step of the analysis affects data output. Our open-source analysis pipeline, Minian (Miniscope Analysis), facilitates the transparency and accessibility of single-photon calcium imaging analysis, permitting users with little computational experience to extract the location of cells and their corresponding calcium traces and deconvolved neural activities. Minian contains interactive visualization tools for every step of the analysis, as well as detailed documentation and tips on parameter exploration. Furthermore, Minian has relatively small memory demands and can be run on a laptop, making it available to labs that do not have access to specialized computational hardware. Minian has been validated to reliably and robustly extract calcium events across different brain regions and from different cell types. In practice, Minian provides an open-source calcium imaging analysis pipeline with user-friendly interactive visualizations to explore parameters and validate results.
Global Gene Expression Divergence in Spontaneous Mutation Accumulation Lines ofCaenorhabditis elegansunder Varying Efficiency of Selection
Authors: Deiss Thaddeus C. , Konrad Anke , Bergthorsson Ulfar , Katju Vaishali 
Published: May 2021

ABSTRACTTo ascertain the effect of relaxation of selection on global gene expression,Caenorhabditis elegansmutation accumulation (MA) lines were propagated under varying degrees of efficiency of selection determined by their different population sizes (N= 1, 10 and 100). Both the mutational variance (Vm), and the residual variance (Vr) were greatest in MA lines with the lowest efficiency of natural selection. The results suggest that gene expression is under strong balancing selection. Furthermore, mutations resulting in increased transcriptional noise or sensitivity to microenvironmental variation accumulate most under extreme genetic drift. In contrast, theVm/Vrratio was lowest in theN=1 lines. Chromatin domains associated with broad gene silencing and active transcription exhibited the greatest and the smallest increase in transcriptional variation, respectively. Furthermore, the preponderance of overexpressed genes was especially pronounced in mitochondrial respiration, stress response, and immune system pathways, especially in low fitnessN= 1 lines.
High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0
Authors: Gibbs Claudia Skok , Jackson Christopher A , Saldi Giuseppe-Antonio , Tjärnberg Andreas , Shah Aashna , Watters Aaron , De Veaux Nicholas , Tchourine Konstantine , Yi Ren , Hamamsy Tymor , Castro Dayanne M , Carriero Nicholas , Gorissen Bram L , Gresham David , Miraldi Emily R , Bonneau Richard 
Published: May 2021

AbstractMotivationGene regulatory networks define regulatory relationships between transcription factors and target genes within a biological system, and reconstructing them is essential for understanding cellular growth and function. Methods for inferring and reconstructing networks from genomics data have evolved rapidly over the last decade in response to advances in sequencing technology and machine learning. The scale of data collection has increased dramatically; the largest genome-wide gene expression datasets have grown from thousands of measurements to millions of single cells, and new technologies are on the horizon to increase to tens of millions of cells and above.ResultsIn this work, we present the Inferelator 3.0, which has been significantly updated to integrate data from distinct cell types to learn context-specific regulatory networks and aggregate them into a shared regulatory network, while retaining the functionality of the previous versions. The Inferelator is able to integrate the largest single-cell datasets and learn cell-type specific gene regulatory networks. Compared to other network inference methods, the Inferelator learns new and informativeSaccharomyces cerevisiaenetworks from single-cell gene expression data, measured by recovery of a known gold standard. We demonstrate its scaling capabilities by learning networks for multiple distinct neuronal and glial cell types in the developingMus musculusbrain at E18 from a large (1.3 million) single-cell gene expression dataset with paired single-cell chromatin accessibility data.AvailabilityThe inferelator software is available on GitHub (https://github.com/flatironinstitute/inferelator) under the MIT license and has been released as python packages with associated documentation (https://inferelator.readthedocs.io/).
Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes
Authors: Tiley George P. , Crowl Andrew A. , Manos Paul S. , Sessa Emily B. , Solís-Lemus Claudia , Yoder Anne D. , Burleigh J. Gordon 
Published: May 2021

AbstractAccurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared to haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North AmericanDryopterisfern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared to using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical non-identifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.
Time to fixation in changing environments
Authors: Kaushik Sachin , Jain Kavita 
Published: May 2021

AbstractAlthough a large number of experimental and theoretical studies have been carried out in a constant environment, as natural environments vary in time, it is important to ask if and how these results are affected by a changing environment. Here, we study the properties of the conditional fixation time of a mutant in a finite, randomly mating diploid population which is evolving in a periodically changing environment. In a static environment, as the conditional mean fixation time of a co-dominant beneficial mutant is equal to that of a deleterious mutant with the same magnitude of selection coefficient, similar patterns for beneficial and deleterious sweeps may result. We find that this symmetry breaks even when the environment is changing slowly. Furthermore, for intermediate dominance, the conditional mean fixation time of a beneficial mutant in a slowly changing environment depends weakly on the dominance coefficient and is close to the corresponding results in the static environment; however, the fixation time for a deleterious mutant under moderate selection with a slowly varying selection coefficient differs substantially from that in the constant environment when the mutant is recessive. Our results thus suggest that the variability patterns and levels for beneficial sweeps are mildly affected by temporally varying environment but changing environment is likely to strongly impact those due to recessive deleterious sweeps.
From corporate social responsibility activities to financial performance: role of innovation and competitive advantage
Authors: Zahid Mahnoor , Naeem Hina , Aftab Iqra , Mughal Sajawal Ali 
Published: May 2021

Purpose
The purpose of this study is to scrutinize the effect of corporate social responsibility activities (CSRA) of the firm on its financial performance (FP) and analyze the mediating role of innovation and competitive advantage (CA) in the relationship between CSRA and FP in the manufacturing sector of an emerging country, i.e. Pakistan.

Design/methodology/approach
Data has been collected through an electronic structured questionnaire from 300 middle-level and top-level managers by surveying different manufacturing firms of Gujranwala, Pakistan. The study’s hypotheses have been checked by analyzing the reliability and validity of data and applying confirmatory factor analysis and structural equation modeling through statistical package for the social sciences and analysis of moment structures.

Findings
Outcomes of this study supported the hypothesized model. It has been found that the CSRA plays a significant positive role in determining the FP of the firm. Furthermore, the CA and innovation have been proved as significant mediators between CSRA and FP.

Originality/value
The first time examining the intermediation of innovation and CA in the relationship between CSRA and FP is the primary input of this study to the literature. Practically, this study’s findings will help strategy makers of manufacturing firms in emerging countries develop better strategies for implementing CSRA, enhancing innovation, seeking CA and improving FP.
Numerical modeling for the effects of gravel permeability coefficient based on DEM and CFD method
Authors: Zhang Anan , Yang Jie , Ma Chunhui , Cheng Lin , Hu Liangcai 
Published: May 2021

PurposeThe purpose of this paper is to form a numerical simulation method for permeability coefficient that can consider the characteristics of gravel gradation and further explore the effects of indoor test factors and gradation characteristics on the permeability coefficient of gravel.Design/methodology/approachThe random point method is used to establish the polyhedral gravel particle model, the discrete element method (DEM) is used to construct the gravel permeability test sample with gradation characteristics and the finite element method is used to calculate the permeability coefficient to form a DEM-computational fluid dynamics combined method to simulate the gravel seepage characteristics. Then, verified by the indoor test results. Based on this method, the influence of sample size, treatment method of oversize particles and the content of fine particles on the permeability coefficient of gravel is studied.FindingsFor the gravel containing large particles, the larger size permeameter should be used as far as possible. When the permeameter size is limited, the equal weight substitution method is recommended for the treatment method of oversized particles. Compared with the porosity, the pore connectivity has a higher correlation with the permeability coefficient of the sample.Research limitations/implicationsInsufficient consideration of the movement of gravel particles in the seepage process is also an issue for further study.Originality/valueThe simulation method described in this paper is helpful for qualitative analysis, quantitative expression of pore size and makes up for the defect that the seepage characteristics in pores cannot be observed in laboratory tests.
Personality and eating behavior in a food festival: understanding visitors’ loyalty from the perspective of food-related personality traits
Authors: Hsu Li-Chun 
Published: May 2021

Purpose
This study aims to investigate the effects of visitors’ dietary habits on their acceptance of local food from the perspective of positive (e.g. local food involvement) and negative (e.g. food neophobia) food-related personality traits.

Design/methodology/approach
A survey was conducted on visitors to the Slow Food Festival in Taitung, Taiwan. A total of 327 valid questionnaire responses were collected and structural equation modeling was used to conduct path analyzes.

Findings
The analysis results supported all hypotheses. Food neophobia plays a key factor in moderating roles.

Originality/value
This study contributes to the literature by integrating positive and negative perspectives of food-related personality traits. In addition, this study proposes that food neophobia plays a moderating role in food choice and behavioral decisions.
RHCC intervention: strengthening the delivery and coverage of sexual and reproductive health care during floods in Bangladesh
Authors: Ray-Bennett Nibedita Shankar , Corsel Denise Marsha Jeanor , Goswami Nimisha , Bhuiyan Maqbul Hossain 
Published: May 2021

Purpose
The quality and availability of sexual and reproductive health care are key determinants to reducing maternal mortalities and morbidities in disaster settings; yet, these services are often lacking in developing countries. Reducing maternal mortality and morbidity is currently the main targets of the UN’s Sustainable Development Goal (SDG) 3. The purpose of this study was to develop an intervention package called RHCC (Reproductive Health Kit 8; Capacity building; Community awareness), and to implement and evaluate it in three primary health-care (PHC) facilities in Belkuchi, Bangladesh, in order to improve the quality and availability of post-abortion care (PAC) during the 2017 floods.

Design/methodology/approach
This research used both quantitative and qualitative methods to develop, implement and assess the RHCC in three flood-prone PHC facilities in Belkuchi.

Findings
The RHCC was implemented during the floods of 2017. The findings pre- and post-intervention suggest it led to an increase in skilled management among health workers, an increase in the quality of care for clients and the availability of PAC at three PHC facilities during floods.

Originality/value
Due to its geographic location, Bangladesh is exposed to recurrent floods and cyclones. Evidence-based integrated intervention packages, such as the RHCC, can improve the quality and availability of reproductive health care during disasters at PHC level and, in doing so, can promote the UN’s agenda on “disaster resilient health system” to achieve the SDG 3, and the WHO’s campaign on universal health coverage.
Management of the COVID-19 epidemic in a French immigration detention center
Authors: Soussy Nicolas , Dufayet Laurène , Ravault Etienne , Viron Sophie , Gorgiard Charlotte , Fournier Lionel 
Published: May 2021

Purpose
The purpose of this paper is to give an overview of management of the COVID-19 epidemic in a French immigration detention center.

Design/methodology/approach
During containment in France because of COVID-19, the judicial authorities had to deal with the risk of contamination within immigration detention centers (IDC). In the Paris IDC, which can usually receive up to 240 individuals, measures have been taken to limit the risk of contamination by releasing individuals without prior judicial conviction and testing the others by a nasal swab.

Findings
The test was done for all the present individuals (48), except two who refused. Eight tests (17.4%) were positive and only one was symptomatic. Individuals testing positive for COVID-19 were transferred into COVID-centers specially created during this health crisis.

Originality/value
Management of the COVID-19 epidemic in this French IDC illustrates the necessity of good cooperation between judicial authorities and medical teams in charge of those centers and the difficulty of balancing public health actions with state security.
Mining and exploring electronic word-of-mouth from Twitter: case of the Java Jazz Festival
Authors: Saragih Harriman Samuel 
Published: May 2021

Purpose
This paper aims to explore textual patterns in ten years of electronic word-of-mouth communications amongst social media (SM) users of the Java Jazz Festival.

Design/methodology/approach
This study uses a data-scraping technique to gather user-generated content from Twitter. Word-cloud and word-frequency analysis, along with descriptive coding and pattern matching, are used to categorise the initial findings. Trends and differences in terms of the number of tweets over a ten-year period were examined using analysis of variance and seasonality analysis.

Findings
From more than 1.3 million Twitter tweets between 2008 and 2018, this study identified six initial themes. Quantitative analysis revealed that the number of tweets differed significantly in the four quarters of the ten-year period.

Research limitations/implications
The results of this study contrast with the claim that digital media communication generally occurs before a festival begins and are least during the festival. Nevertheless, this study supports the notion that SM interaction results in positive consequences, drives conversations amongst users and increases engagement.

Practical implications
This study offers five practical implications for music festival organisers and related entities.

Originality/value
To the best of the author’s knowledge, this study is the first to provide a systematic and practical data mining and interpretation approach from Twitter within a ten-year period in the Asia Pacific context, through the case of the Java Jazz Festival.
Reforming state budgeting in the vortex of policy conditionality, political instability and technical support flux
Authors: Cohen Sandra , Karatzimas Sotirios 
Published: May 2021

Purpose
Greece had to undertake several reforms under intense policy conditionality pressures – stemming from the three financial support programs agreed between the Greek Government and the Troika – and political instability. Within this context, this study aims to analyze the role of politicians and technical assistance staff in the administrative reform of the Greek state budget.

Design/methodology/approach
The study adopts the approach of an extreme country-case study which is analyzed through a theoretical framework with insights from the resource dependency theory and the concept of policy conditionality. The theoretical framework is supported by documents of the International Monetary Fund and the European Commission, including the technical Memoranda of Understanding (MoUs) and their progress reports and is informed by the outcome of interviews with General Accounting Office executives.

Findings
While the budget reform eventually met the MoU requirements, the frequent changes at the government level, the constant renegotiations with the Troika that initiated changes to the plan and the instability of the technical assistance teams formed to support the reform contributed to important implementation delays.

Originality/value
The study contributes to the research agenda on accounting reforms during periods of financial crises by providing evidence on the role of politicians’ level of ownership and technical assistance staff contribution.