bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative Analysis of Phenomic, Genomic, and Transcriptomic to Identify Potential Functional Genes of Yaks in Plain and Plateau
Authors: Wang Jiabo , Guan Jiuqiang , Yixi Kangzhu , Shu Tao , Chai Zhixin , Wang Jikun , Wang Hui , Wu Zhijuan , Cai Xin , Zhong Jincheng , Luo Xiaolin 
Published: November 2020

AbstractBackgroundThe yak is an important source of livelihood for the people living in the Qinghai-Tibet Plateau. Most genetics detection studies have focused on the comparison between different tissues of different breeds, both living in the Plateau and in the plains. The genetic background and complex regulatory relationship have frequently puzzled researchers. In this study, we divided a population of 10 yaks into two subgroups, namely Plateau (living in the Plateau) and Plain (living in the plains). Phenomic, genomic, and transcriptomic analyses were used to reveal the molecular genetic type in the body weight, slaughter, and beef quality of yaks.ResultsWe found a significant difference (P <0.01) between the third (60 days), fourth (90 days), fifth (120 days), and sixth (150 days) weights of Plateau and plain subpopulations. The difference in body weight was due to differences in kidney weight, meat weight, fur weight, and head weight. However, the beef quality was not significantly different. We identified 540 Differentially Expressed Genes (DEGs). Using weighted gene co-expression network analysis (WGCNA), we have constructed a co-express network, and the modules were strongly related to traits. In the genome-wide association studies (GWAS), we detected significant 156, 52, 33, 15, and 3 signals in the meat weight, head weight, fur weight, liver weight, and the last body weight traits. Based on the epigenome-wide association studies (eWAS) results, we created a link relationship between the DEGs expression level and genotype.ConclusionIn summary, our study demonstrated the effectiveness and representative of multidimensional data from a finite number of yak populations. The study highlights the underlying way, as well as a related network, to yield new information on genome genetics and pathogen-host interactions of both the living Plateau and plain yak populations.
CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing ofCoxiella burnetiigenomic sequences
Authors: Fasemore Akinyemi. M. , Helbich Andrea , Walter Mathias. C. , Dandekar Thomas , Vergnaud Gilles , Förstner Konrad U. , Frangoulidis Dimitrios 
Published: November 2020

ABSTRACTQ (query) fever is an infectious zoonotic disease caused by the Gram-negative bacteriaCoxiella burnetii. Although the disease has been studied since decades, it still represents a threat due to sporadic outbreaks across farms in Europe. The absence of a central platform forCoxiellatyping data management in an important epidemiological gap which is relevant in the case of an outbreak. To fill this gap, we have designed and implemented an online, open-source, and, web-based platform called CoxBase (https://coxbase.q-gaps.de). This platform includes a database that holds genotyping information of more than 400Coxiellaisolates alongside metadata that annotates them. We have also implemented features forin silicogenotyping of completely or minimally assembledCoxiellasequences using five different typing methods, querying existing isolates, visualization of isolate’s geodata via aggregation on a world map and submission of new isolates. We tested ourin silicotyping method on 50Coxiellagenomes downloaded from the RefSeq database and we successfully genotyped all except for cases where the sequence quality was poor. We identified new spacer sequences using our implementation of the MSTin silicotyping method, and established adaA gene phenotypes for all 50 genomes as well as their plasmid types.
Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS Cov2 infection
Authors: Nanda Piyush , Ghosh Amit 
Published: November 2020

AbstractThe COVID-19 pandemic is posing an unprecedented threat to the whole world. In this regard, it is absolutely imperative to understand the mechanism of metabolic reprogramming of host human cells by SARS Cov2. A better understanding of the metabolic alterations would aid in design of better therapeutics to deal with COVID-19 pandemic. We developed an integrated genome-scale metabolic model of normal human bronchial epithelial cells (NHBE) infected with SARS Cov2 using gene-expression and macromolecular make-up of the virus. The reconstructed model predicts growth rates of the virus in high agreement with the experimental measured values. Furthermore, we report a method for conducting genome-scale differential flux analysis (GS-DFA) in context-specific metabolic models. We apply the method to the context-specific model and identify severely affected metabolic modules predominantly comprising of lipid metabolism. We conduct an integrated analysis of the flux-altered reactions, host-virus protein-protein interaction network and phospho-proteomics data to understand the mechanism of flux alteration in host cells. We show that several enzymes driving the altered reactions inferred by our method to be directly interacting with viral proteins and also undergoing differential phosphorylation under diseased state. In case of SARS Cov2 infection, lipid metabolism particularly fatty acid oxidation and beta-oxidation cycle along with arachidonic acid metabolism are predicted to be most affected which confirms with clinical metabolomics studies. GS-DFA can be applied to existing repertoire of high-throughput proteomic or transcriptomic data in diseased condition to understand metabolic deregulation at the level of flux.
The Company Canids Confront: Spatiotemporal Partitioning at Local Scales Facilitates Carnivore Coexistence at the Landscape Level
Authors: Devarajan Kadambari , Vanak Abi Tamim 
Published: November 2020

AbstractCanids are the most widely distributed carnivores in the world. The increasing impacts of commensal carnivores such as free-ranging dogs on wildlife communities has resulted in an urgent need to understand putative interactions within carnivore guilds. It is thus imperative to understand the processes driving canid assemblages in different landscapes and at multiple spatial and temporal scales, in order to conserve and manage wildlife communities. Here, we demonstrate the complex interactions and spatiotemporal dynamics underlying the coexistence of co-occurring carnivores in a landscape modified by the invasive,Prosopis juliflora. We investigated spatial, temporal, and habitat partitioning within a guild of four co-occurring canids in the arid northwest of India. The results indicate complex associations between the study species, where co-occurrence at the local spatial scale between species corresponds with temporal partitioning. Our study offers evidence that avoidance at the local scale and coexistence at the landscape scale are maintained in co-occurring intra-guild carnivores that are of similar body size through both facultative and behavioral character displacement such as temporal partitioning. It has also resulted in essential baseline information on the occurrence and distribution patterns of multiple canids in a human-dominated and understudied landscape threatened by global change. Understanding these biotic and abiotic drivers that impact carnivore guilds is crucial for the conservation and management of communities at the landscape scale.
CSF1R-dependent macrophages control postnatal somatic growth and organ maturation
Authors: Keshvari Sahar , Caruso Melanie , Teakle Ngari , Batoon Lena , Sehgal Anuj , Patkar Omkar L. , Ferrari-Cestari Michelle , Snell Cameron E. , Chen Chen , Stevenson Alex , Davis Felicity M. , Bush Stephen J. , Pridans Clare , Summers Kim M. , Pettit Allison R. , Irvine Katharine M. , Hume David A. 
Published: November 2020

AbstractHomozygous mutation of theCsf1rlocus (Csf1rko) in mice, rats and humans leads to multiple postnatal developmental abnormalities. To enable analysis of the mechanisms underlying the phenotypic impacts ofCsf1rmutation, we bred a ratCsf1rkoallele to the inbred dark agouti (DA) genetic background and to aCsf1r-mApple reporter transgene. TheCsf1rkoled to almost complete loss of embryonic macrophages and ablation of most adult tissue macrophage populations. We extended previous analysis of theCsf1rkophenotype to early postnatal development to reveal impacts on musculoskeletal development and proliferation and morphogenesis in multiple organs. Expression profiling of 3-week old wild-type (WT) andCsf1rkolivers identified 2760 differentially expressed genes associated with the loss of macrophages, severe hypoplasia, delayed hepatocyte maturation, disrupted lipid metabolism and the IGF1/IGF binding protein system. OlderCsf1rkorats developed severe hepatic steatosis. Consistent with the developmental delay in the liverCsf1rkorats had greatly-reduced circulating IGF1. Transfer of WT bone marrow (BM) cells at weaning without conditioning repopulated resident macrophages in all organs, including microglia in the brain and reversed the mutant phenotypes enabling long term survival and fertility. WT BM transfer restored osteoclasts, eliminated osteopetrosis, restored bone marrow cellularity and architecture and reversed granulocytosis and B cell deficiency.Csf1rkorats had an elevated circulating CSF1 concentration which was rapidly reduced to WT levels following BMT. However, CD43hinon-classical monocytes, absent in theCsf1rko, were not rescued and bone marrow progenitors remained unresponsive to CSF1. The results demonstrate that theCsf1rkophenotype is autonomous to BM-derived cells and indicate that BM contains a progenitor of tissue macrophages distinct from hematopoietic stem cells. The model provides a unique system in which to define the pathways of development of resident tissue macrophages and their local and systemic roles in growth and organ maturation.
Experimental evaluation of thermodynamic speed limit in living cells via information geometry
Authors: Ashida Keita , Aoki Kazuhiro , Ito Sosuke 
Published: November 2020

AbstractChemical reactions are responsible for information processing in living cells, and thermodynamic trade-off relations can explain their accuracy and speed. Its experimental test in living cells had not existed despite its importance because it is hard to justify sample size sufficiency. This paper reports the first experimental test of the thermodynamic trade-off relation, namely the thermodynamic speed limit, in living systems at the single-cell level where the sample size is relatively small. Due to the information-geometric approach, we can demonstrate the thermodynamic speed limit for the extracellular signal-regulated kinase phosphorylation using time-series fluorescence imaging data. Our approach quantifies the intrinsic speed of cell proliferation and can potentially apply other signal transduction pathways to detect their information processing speed.One-Sentence SummaryExperimental measurement of information thermodynamic speed by fluorescence imaging in living cells
Syphilis self-testing to expand test uptake among men who have sex with men: a theoretically informed mixed methods study in Zimbabwe
Authors: Sri-Pathmanathan Clarisse , Nhamo Definate , Mamvuto Takudzwa , Chapwanya Gwendoline , Terris-Prestholt Fern , Mahaka Imelda , Marks Michael , Tucker Joseph D. 
Published: November 2020

ABSTRACTObjectivesSelf-testing for STIs such as HIV and syphilis may empower sexual minorities and expand uptake of STI testing. While much is known about HIV self-testing (HIVST), less is known about syphilis self-testing, particularly in low-income settings. The objective of this study is to determine context-specific facilitators and barriers for self-testing and to assess the usability of syphilis self-testing in Zimbabwe among men who have sex with men (MSM).MethodsThis mixed methods study was conducted in Harare as part of a larger syphilis self-testing trial. The study included in-depth interviews (phase one) followed by usability testing and a second interview (phase two). In-depth interviews were conducted with MSM and key informants prior to syphilis self-testing. The same MSM then used the syphilis self-test, quantitatively assessed its usability and participated in a second in-depth interview. Phase one data was analysed using a thematic approach, guided by an adapted Social Ecological Model conceptual framework. Phase two interviews were analysed using Rapid Assessment Procedure qualitative methodology, and usability was assessed using a pre-established index, adapted from existing HIVST evaluation scales.ResultsTwenty MSM and 10 key informants were recruited for phase one in-depth interviews and 16 of these MSM participated in phase two by completing a syphilis self-test kit. Facilitating factors for self-testing included the potential for increased privacy, convenience, autonomy and avoidance of social and healthcare provider stigma. Barriers included the fear to test and uncertainty about linkage to care and treatment. Data from the usability index suggested high usability (89.6% on a 0-100 scale) among the men who received the self-test.ConclusionsMSM in Zimbabwe were willing to use syphilis self-test kits and many of the barriers and facilitators were similar to those observed for HIVST. Syphilis self-testing may increase syphilis test uptake among sexual minorities in Zimbabwe and other low- and middle-income countries.Key messages-Syphilis self-testing is an empowering, innovative tool that can be used to expand uptake of STI testing among sexual minorities in Zimbabwe.-Facilitators and barriers for syphilis self-testing are similar to those observed for HIV self-testing in Zimbabwe and other low- and middle-income countries.-Participants reported high self-test usability and found that self-testing provided increased privacy, convenience and autonomy in comparison to facility-based testing.
An efficient local search for large-scale set-union knapsack problem
Authors: Zhou Yupeng , Zhao Mengyu , Fan Mingjie , Wang Yiyuan , Wang Jianan 
Published: November 2020

PurposeThe set-union knapsack problem is one of the most significant generalizations of the Non-deterministic Polynomial (NP)-hard 0-1 knapsack problem in combinatorial optimization, which has rich application scenarios. Although some researchers performed effective algorithms on normal-sized instances, the authors found these methods deteriorated rapidly as the scale became larger. Therefore, the authors design an efficient yet effective algorithm to solve this large-scale optimization problem, making it applicable to real-world cases under the era of big data.Design/methodology/approachThe authors develop three targeted strategies and adjust them into the adaptive tabu search framework. Specifically, the dynamic item scoring tries to select proper items into the knapsack dynamically to enhance the intensification, while the age-guided perturbation places more emphasis on the diversification of the algorithm. The lightweight neighborhood updating simplifies the neighborhood operators to reduce the algorithm complexity distinctly as well as maintains potential solutions. The authors conduct comparative experiments against currently best solvers to show the performance of the proposed algorithm.FindingsStatistical experiments show that the proposed algorithm can find 18 out of 24 better solutions than other algorithms. For the remaining six instances on which the competitor also achieves the same solutions, ours performs more stably due to its narrow gap between best and mean value. Besides, the convergence time is also verified efficiency against other algorithms.Originality/valueThe authors present the first implementation of heuristic algorithm for solving large-scale set-union knapsack problem and achieve the best results. Also, the authors provide the benchmarks on the website for the first time.
Enhancing student engagement through heterogeneous pedagogical approaches: action research in a university level course in Saudi Arabia
Authors: Asif Muhammad , Thomas George , Awan Muhammad Usman , Muhammad Din Asfa 
Published: November 2020

PurposePrevious studies have mainly discussed the impact of student engagement on different facets of academic performance. Research on the approaches to promote student engagement in a classroom setting (i.e., micro-level practices) is relatively sparse. This paper provides a framework for enhancing student engagement in a university undergraduate classroom setting.Design/methodology/approachThis study builds on action research. At the core of this approach is making interventions through a set of pedagogical approaches, derived from the literature. The impact of these interventions was measured, followed by reflections on the outcomes and developing a future improvement strategy.FindingsStudent engagement can be enhanced by using heterogeneous pedagogical approaches that positively influence student performance. Further, the use of mixed pedagogical approaches helps students and teachers acquire meta-cognitive knowledge (i.e., knowledge of their learning preferences) and sets the direction for learning.Research limitations/implicationsThe key contribution of this study is providing a student engagement framework applicable in a sophomore-level classroom setting. The framework discusses a set of techniques, their theoretical underpinnings, the course of their execution and the challenges faced in this process. The framework can be used to guide enhancing student engagement.Originality/valueContrary to the macro-level measures, research on micro-level measures for promoting student engagement approaches is scarce. This study discusses not only different strategies but also details the dynamic course of their deployment. The study, therefore, is unique in its contribution.
Country-of-origin as a dynamic concept: an analysis of Chinese consumer electronics brands in Germany
Authors: Polfuß Jonas , Sönmez Dilara 
Published: November 2020

Purpose
Using consumer electronics brands as examples, this paper aims to present country-of-origin (COO) as a dynamic concept, by analyzing changes in the representation and perception of the “Made in China” label in Germany.

Design/methodology/approach
Building on previous COO research, the study formulates four research questions, which are answered with a comprehensive brand analysis using website, media, and consumer data. Information were collected from 11 Chinese brand websites, 10,681 German media articles and a sample of 490 German consumers. The authors statistically evaluated the survey data and examined the website and media data by means of a qualitative content analysis.

Findings
The results of the study show how Chinese brands currently present their COO in Germany and how the perception of “Made in China,” by German media and consumers, has changed to varying degrees. These changes pose marketing challenges for the increasingly prevalent Chinese brands in Germany, which need to be addressed by companies using strategic PR and marketing activities.

Research limitations/implications
This study suggests that COO images should be understood as a dynamic construct, and the multifaceted brand perceptions, including media reports, should be given greater consideration.

Practical implications
International marketers will find information on current country product recognition, and recommendations for the analysis and strategic communication of (Chinese) brands abroad.

Originality/value
This study contributes to COO research by examining the recent status of “Made in China” labels in Germany, focusing on China not as a manufacturing location, but as the home country for branded products. A media analysis is incorporated to add a novel dimension to the examination of brand identity-image gaps.
Embedding sustainability dimensions in university collections management: a “scientific journey” into a natural history museum
Authors: Magliacani Michela , Sorrentino Daniela 
Published: November 2020

PurposeThe purpose of this research aims at extending the knowledge on whether and how universities include sustainability dimensions in managing their collections. Precisely, the study focusses on the creation of a university museum (UM), as an embryonic stage of life during which management concerns both strategic and operational issues.Design/methodology/approachSustainability is envisioned as a multifaceted concept, composed of the economic, cultural, environmental and social dimensions. Resorting to an acknowledged theoretical model for sustainable development in museum management, a qualitative interpretative study is carried out, gathering data from multiple sources. The empirical setting is the University of Pavia, which has recently created a new Museum of Natural History (Kosmos).FindingsResults highlight how sustainability dimensions intertwin in UM creation. Moreover, the economic dimension emerges as a basement for the others. Value for the community, expressed in economic terms, must be ensured in UMs creation as well as throughout its entire life, in order to support cultural, environmental and social sustainability.Research limitations/implicationsFocussing on the embryonic stage of UMs life allowed to consider how sustainability is embedded in relevant strategic and operational decisions. Nevertheless, scholars are encouraged to replicate the study in other stages of UMs' life, in a way to provide insights on its dynamics.Practical implicationsUniversity collections managers can benefit from this research by acknowledging the role played by the economic dimension of sustainability. Notwithstanding their mission, universities should pay attention to extracting economic value from the management of their collections, as a means to ensure innovative and sustainable management on the cultural, environmental and social respects. Furthermore, this research suggests how a higher education system is able to create a new museum by relying on interdisciplinary competencies, which support sustainability since the embryonic stage.Originality/valueThis research contributes to the cultural heritage management literature by proposing an updated version of the sustainable development model for museums, which highlights the different relevance of the sustainability dimensions with particular regard to the UM creation and management.