bluuebunny/crossref_metadata_2025_split huggingface dataset:
Land use change and livestock revolution as contributors to Coronavirus emergence risk
Authors: Rulli Maria Cristina , D'Odorico Paolo , Galli Nikolas , Hayman David 
Published: September 2020

Abstract
The recorded number of epidemics from emerging diseases is increasing at alarming rates, posing new threats on human societies. Despite the consensus on the existence of a nexus between emerging diseases and human pressure on the environment, the link to global and regional trends in food demand and agricultural production remains poorly understood. The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) is no difference. SARS-related coronaviruses are mostly discovered in Asian horseshoe bat species. It is unclear to what extent the transmission to humans is facilitated by ongoing land use and animal husbandry trends underlying recent shifts in the food system. Forest fragmentation, human encroachment into wildlife habitats as a result of expanding urbanization, cropland, and concentrated animal farming are hypothesized to favor the emergence of zoonotic diseases. In the regions of the world populated by Asian horseshoe bats (>28.5 million km2), we analyze comprehensive high-resolution (30m-1000m) datasets on forest cover, cropland distribution, livestock density, human population, human settlements, bat species’ distribution, and land-use changes to explain why China was and remains at risk for SARS-coronavirus outbreaks. We show that in China areas populated by horseshoe bats exhibit statistically significant higher forest fragmentation and concentrations of livestock (e.g. poultry and pigs) and humans than other countries. Moreover, regions of China populated by horseshoe bats are hotspots of forest fragmentation, livestock density, and human settlements. These results are consistent with the notion that population growth and increasing meat consumption associated with urbanization and economic growth have expanded the footprint of agriculture, leading to human encroachment in wildlife habitat and increased livestock density in areas adjacent to fragmented forest patches. These results indicate that conditions in China put it at high risk for SARS-related coronavirus transmission to humans because land use patterns reduce the distance between wildlife reservoir species and humans.
A comparative study between local bone graft with or without cages in unilateral posterior lumbar interbody fusion (PLIF): a retrospective study
Authors: He Tao Jiang , Feng Jun-fei , Chen Qian , Yang Yang , Zhou Qing-song , Liu Kai-xin 
Published: September 2020

Abstract
Objective

A retrospective study of the clinical and radiological results between local bone graft with a cage and without cage in patients treated with unilateral fixation and posterior lumbar interbody fusion surgery.
Methods

A total of 52 patients who underwent PLIF in our institution were evaluated from January 2015 to January 2018. 30 of these patients received PLIF with local bone graft combined with using one cage, and 22 patients received PLIF with local bone graft without using cage. The clinical data and perioperative complications of the two groups were recorded. X-ray were taken before, after operation and at the end of follow-up to calculate the height of intervertebral disc and the fusion rate. SUK's criteria were used to evaluate the quality of spinal fusion at the follow-up time. The results between the cage and non- cage group were compared.
Results

There was no statistical difference in baseline data between the two groups, and The mean follow-up time was 18.43 months in cage group and 17.50 months in non- cage group (P = 0.553). In additions, the significant difference was not found in the comparison of perioperative evaluation data between the two groups, such as operation time (P = 0.299), blood loss (P = 0.342) and incidence of complications (P = 1.000). Furthermore, the significant difference of VAS score cannot be found in preoperation (Pleg=0.731, Plowback=0.786), postoperation (Pleg=0.534, Plowback=0.725) and the final follow-up (Pleg=0.654, Plowback=0.362) between the two groups. The same results were also obtained in the comparison of ODI index (Ppre=0.682, Pfinal=0.712) and intervertebral height (Ppost=0.363, Pfinal=0.094). The final fusion rates were 96.7% (cage group) and 86.4% (non- cage group) respectively, and there was no statistical difference (P = 0.553).
Conclusion

Local bone graft has the same advantages as a cage in unilateral PLIF. Comparing with local bone graft using cage, we believe that the local bone graft is a more ideal way in unilateral PLIF, and decrease operation cost.
Validation of a method evaluating T cell metabolic potential in compliance with ICH Q2 (R1)
Authors: Letondal Patricia , Marton Chrystel , Godet Yann , Galaine Jeanne 
Published: September 2020

Abstract
Background
Metabolic cell features are able to give reliable information on cell functional state. Thus, metabolic potential assessment of T cells in malignancy setting represents a promising area, especially in adoptive cell therapy procedures. Easy to set up and convenient Seahorse technology have recently been proposed by Agilent Technologies and it could be used to monitor T cells metabolic potential. However, this method demonstrates an inter-assay variability and lacks practices standardization.
Results
We aimed to overcome these shortcomings thanks to a lymphoblastic derived JURKAT cell line seeding in each experiment to standardize the Seahorse process. We used an adapted XF Cell MitoStress Kit protocol, consisting in the evaluation of basal, stressed and maximal glycolysis and oxidative phosphorylation related parameters, through sequential addition of oligomycin and FCCP to a glucose containing medium. Data were acquired and analyzed through Agilent Seahorse XFe96 analyzer. Indeed, we validated this method in the light of ICH Q2 (R1) guidelines. We were able to confirm the specificity and accuracy of the method. We also demonstrated the precision, linearity and range of the method in our experimental conditions.
Conclusion
The validation of the method consisting in a JURKAT cell line experimental incorporation as internal control contributes to improve the Seahorse technology’s robustness. These results lay the groundwork for the implementation of this technology to optimize T cell based cellular therapy products production process and monitoring.
Analysis of Circulating Protein Aggregates Reveals Pathological Hallmarks of Amyotrophic Lateral Sclerosis
Authors: Adiutori Rocco , Puentes Fabiola , Bremang Michael , Lombardi Vittoria , Zubiri Irene , Leoni Emanuela , Aarum Johan , Sheer Denise , McArthur Simon , Pike Ian , Malaspina Andrea 
Published: September 2020

Abstract
Background: plasma proteins composition reflects the inflammatory and metabolic state of an organism and can be predictive of system-level and organ-specific pathologies. Circulating protein aggregates (CPA) are enriched with heavy chain neurofilaments (NfH), axonal proteins involved in brain protein aggregates (BPA) formation and recently identified as biomarkers of the fatal neuromuscular disorder amyotrophic lateral sclerosis (ALS). Methods: here we use mass spectrometry and brain-enhanced TMTcalibrator™-based proteomics to evaluate the composition and the brain-derived protein component of CPA extracted from ALS and healthy controls (HC) plasma samples using high-performance ultracentrifugation. We also test CPA and BPA proteins aggregation propensity and the resistance to proteases digestion by trypsin, chymotrypsin, calpain and enterokinase of NFH within aggregates. Finally, we study CPA biological effects on neuronal and endothelial cell lines. Results: electron microscopy confirms the presence in CPA of electron-dense macromolecular particles appearing as either large globular or as small filamentous formations. CPA from ALS are enriched with proteasome system proteins while HC CPA show a prominent expression of proteins involved in metabolism. CPA enterokinase digestion in ALS generates 171 and 31 KDa NfH fragments not seen in HC samples. Compared to the whole human proteome, proteins within CPA and BPA show distinct chemical features of aggregation propensity, which appear dependent on the tissue or fluid of origin and not on the healthy or pathological source of plasma. The use of a TMTcalibrator™ proteomics workflow reveals 4973 brain-derived low-abundance proteins in CPA, including products of translation of 24 ALS risk genes. 285 (5.7%) are regulated in ALS (p < 0.05) and belong to biochemical pathways previously linked to ALS pathogenesis and aggregates formation. CPA from both ALS and HC have a higher effect on hCMEC/D3 endothelial and PC12 neuronal cells viability than immunoglobulins extracted from the same plasma samples. Compared to HC, CPA from ALS plasma samples exert a higher toxic effect on both cell lines at lower concentrations.Conclusions: this study demonstrates that CPA are significantly enriched with brain proteins which are representative of ALS pathology and a potential source of biomarkers and therapeutic targets for this incurable disorder.
Mechanisms and Candidate Genes for Seed and Fruit Set in Grapevine
Authors: Costantini Laura , Moreno-Sanz Paula , Nwafor Chinedu Charles , Lorenzi Silvia , Marrano Annarita , Cristofolini Fabiana , Gottardini Elena , Raimondi Stefano , Ruffa Paola , Gribaudo Ivana , Schneider Anna , Grando Maria Stella 
Published: September 2020

Abstract
Background: Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like cluster compactness, bunch and berry size, berry skin to pulp ratio or seedlessness. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with contrasting seed content in two germplasm collections. Results: We identified eight variant pairs that seemingly differ only in seed-related characteristics while showing identical genotype when tested with the GrapeReSeq_Illumina_20K_SNP_chip and several microsatellites. We performed multi-year observations on fruit and seed set deriving from different pollination treatments, with special emphasis on the pair composed by Sangiovese and its seedless variant locally named Corinto Nero. The pollen of Corinto Nero failed to germinate in vitro and gave poor berry set when used to pollinate other varieties. Most berries from both open- and cross-pollinated Corinto Nero inflorescences did not contain seeds. The genetic analysis of seedlings derived from occasional Corinto Nero normal seeds revealed that the few Corinto Nero functional gametes are mostly unreduced. A number of genes potentially involved in sporogenesis and gametogenesis showed contrasting expression between Corinto Nero and Sangiovese and five missense single nucleotide polymorphisms were identified from transcriptomic data. The above findings suggest that the seedless phenotype of Corinto Nero is driven by pollen and/or embryo sac defects, and both events likely arise from meiotic anomalies. Finally, three genotypes, including Sangiovese and Corinto Nero, were unexpectedly found to develop fruits without pollen contribution and occasionally showed normal-like seeds. Conclusions: Our collective results suggest that parthenocarpy and stenospermocarpy are not restricted to Black Corinth (alias Korinthiaki) and Sultanina-derived cultivars. The single nucleotide polymorphisms identified between Sangiovese and its parthenocarpic variant Corinto Nero are suitable for testing as traceability markers for propagated material and as functional candidates for the seedless phenotype.
The Protective Role of Intracellular Glutathione in Saccharomyces Cerevisiae During Lignocellulosic Ethanol Fermentation&nbsp;
Authors: Raghavendran Vijayendran , Marx Christian , Olsson Lisbeth , Bettiga Maurizio 
Published: September 2020

Abstract
To enhance the competitiveness of industrial lignocellulose ethanol production, robust enzymes and cell factories are vital. Lignocellulose derived streams contain a cocktail of inhibitors that drain the cell of its redox power and ATP, leading to a decrease in overall ethanol productivity. Many studies have attempted to address this issue, and we have shown that increasing the glutathione (GSH) content in yeasts confers tolerance towards lignocellulose inhibitors, subsequently increasing the ethanol titres. However, GSH levels in yeast are limited by feedback inhibition of GSH biosynthesis. Multidomain and dual functional enzymes exist in several bacterial genera and they catalyse the GSH biosynthesis in a single step without the feedback inhibition. To test if even higher intracellular glutathione levels could be achieved and if this might lead to increased tolerance, we overexpressed the genes from two bacterial genera and assessed the recombinants in simultaneous saccharification and fermentation (SSF) with steam pretreated spruce hydrolysate containing 10% solids. Although overexpressing the heterologous genes led to a six-fold increase in maximum glutathione content (18 µmol·gdrycellmass-1) compared to the control strain, this only led to a three-fold increase in final ethanol titres (8.5 g·L-1). As our work does not conclusively indicate the cause-effect of increased GSH levels towards ethanol titres, we cautiously conclude that there is a limit to cellular fitness that could be accomplished via increased levels of glutathione.
Combined Mode of Courses on Dental Virtual Clerkship During COVID-19 Pandemic for Final-year Undergraduates in Wuhan
Authors: Li Shue , Zhao Jiajia , Wu Yuelin , Yu Ran , Zhou Xin , Huang Xiaofei , Yu Shaoling , Chen Lili 
Published: September 2020

Abstract
BackgroundOnline teaching is being widely adopted to achieve medical teaching objectives during the COVID-19 pandemic. To explore the dental virtual clerkship so as to continue the education of final-year dental undergraduate interns, combined mode of courses including small private online course, problem-based learning, online dental practice broadcasting and dental practice based on relatives’ or friends’ oral health management were applied for clerkship education for final-year interns.MethodsCombined courses of virtual clerkship was conducted from March to May, 2020 for final-year interns, while online preclerkship curriculum teaching was conducted for non-final-year students. Using the online students’ engagement scale (OSE), Biggs’ revised two-factor version of the study process questionnaire (R-SPQ-2F), student engagement and study process were evaluated for both. Teaching efficacy were evaluated via teachers' sense of efficacy scale (TSES) as well. ResultsStudents’ engagement was higher in final-year students, especially the emotion and participation categories (P<0.01). In the emotion category, 80.95% identified with putting forth effort on lecture and applying knowledge to life. Study approaches on deep motive and strategy were dominated in final-year interns (P<0.01). Teacher’ sense of efficacy also reflected the positive influence on student virtual clerkship. There was no significant difference among three categories including the sense of student engagement, instructional strategies and classroom management (P>0.05).ConclusionThis combined mode of courses on dental virtual clerkship could be potentially applied during the pandemic or be supplementary for traditional by-chair clerkship after the pandemic.
PrEP in Primary Care; Health Care Worker Adaptations to PrEP Delivery in Eswatini
Authors: Barnighausen Kate , Dalglish Sarah , Matse Sindy , Hughey Allison , Hettema Anita , Kahn Kathleen , Barnighausen Till , Geldsetzer Pascal , McMahon Shannon 
Published: September 2020

Abstract
BackgroundImplementation evidence for pre-exposure prophylaxis (PrEP) for the general population in primary-care clinics in Southern Africa is limited. Perspective from those providing PrEP in ‘real world’ settings is needed to better inform future programming, policy, and scale up. MethodsFrom September 2017 to January 2019 we conducted 54 semi-structured in-depth interviews with purposively selected healthcare workers (HCWs) from six public sector, nurse-led, primary-care clinics in Eswatini. Data from observational notes, daily debriefing sessions and interview transcripts were analyzed using Nvivo 12 following the tenets of Grounded Theory. We present our results within six domains of a modified Consolidated Framework for Implementation (CFIR). ResultsHCWs said that they adapted implementation guidelines in order to inform more people of PrEP. HCWs said that clinic and community based PrEP education and promotion was essential for demand creation, uptake and continued PrEP use. Clinic modifications included conducting PrEP risk assessments during existing TB screening services, and targeting PrEP counselling for pregnant women and clients with sexually transmitted infections. HCWs described streamlining the PrEP initiation process by fast-tracking at-risk clients for initiation and pill collection. HCW said they emphasised PrEP as being for ‘everyone’ to avoid stigma. ConclusionsIntegration of PrEP delivery into existing screening and treatment services may help reach those most vulnerable to HIV infection, avoid time-consuming referrals, and prevent loss of clients between different components of the care continuum. PrEP education and promotion should be both clinic and community based to ensure potential clients have enough information before reaching the clinic, prevent PrEP-associated stigma and assist in family and partner understanding of PrEP use. HCWs providing PrEP in public-sector clinics have first-hand knowledge of implementation in ‘real world’ settings in a field where policy and program implementation is largely undefined. Integrating their feedback into future programming and policy may support effective PrEP delivery in Eswatini and other high prevalence settings in Southern Africa.
Prognostic value and underlying mechanism of autophagy-related genes in bladder cancer
Authors: Zhang Keying , Wang Jingwei , Xu Chao , Zhang Jingliang , Liu Shaojie , Zhou Xiang , Zhao Xiaolong , Peng Shiyuan , Jiang Yao , Yang Fa , Qin Jun , Meng Ping , Shi Changhong , Zhang Rui , Yang An-Gang , Han Donghui , Wen Weihong , Qin Weijun 
Published: September 2020

Abstract
Background
Bladder cancer (BLCA) is the most common malignancy whose early diagnosis can ensure better prognosis. However, the predictive accuracy of commonly used predictors, including patients’ general condition, histological grade and pathological stage, is insufficient to identify the patients who need invasive treatment. Autophagy is regarded as a vital factor in maintaining mitochondrial function and energy homeostasis in cancer cells. Whether autophagy-related genes (ARGs) can predict the prognosis of BLCA patients deserves to be investigated.
Methods
Based on BLCA data retrieved from the Cancer Genome Atlas (TCGA) and ARGs list obtained from the Human Autophagy Database (HADb) website, we identified prognosis-related differentially expressed ARGs (PDEARGs) through Wilcox text and constructed a PDEARGs-based prognostic model through multivariate Cox regression analysis. The predictive accuracy, independent forecasting capability, and the correlation between present model and clinical variables or tumor microenvironment (TME) were evaluated through R software. Enrichment analysis of PDEARGs was performed to explore the underlying mechanism, and a systematic prognostic signature with nomogram was constructed by integrating clinical variables and aforementioned PDEARGs-based model.
Results
We identified several PDEARGs and constructed a PDEARGs-based prognostic model, which could precisely predict the prognosis of BLCA patients. Then, we found that the risk score generated by PDEARGs-based model could effectively reflect deteriorated clinical variables and tumor-promoting microenvironment. Additionally, several immune-related gene ontology (GO) terms were significantly enriched by PDEARGs, which might provide insights for present model and propose potential therapeutic targets for BLCA patients. Finally, a systematic prognostic signature with promoted clinical utility and predictive accuracy was constructed to assist clinician decision.
Conclusion
PDEARGs are valuable prognostic predictor and potential therapeutic targets for BLCA patients.
Characterization and analysis of some chilling-response WRKY transcription factors in tomato
Authors: Wang Yixuan , Zhuang Kunyang , Meng Qingwei , Meng Chen 
Published: September 2020

Abstract
WRKY transcription factors play various important roles in biotic and abiotic stress. In present study, a total of 81 WRKYs in tomato (Solanum lycopersicum) was identified and their gene structure, phylogeny and sub-location were analyzed. Here, we further analyzed their expression and potential roles under chilling stress. Nevertheless, the predicted chloroplast-located WRKYs are failed to be detected in the chloroplast. Then, 27 SlWRKYs with high chilling-induced mRNA levels (more than 3 fold to the control) are selected from these WRKYs. Promoter analysis showed that some cold stress-related cis-acting elements (CBFs binding site) existed in many promoter regions of these chilling response WRKYs (WRKY2, WRKY50, WRKY59 etc.), implying that these WRKY transcription factors may participate in CBFs mediated pathway under chilling stress. The interaction proteins of WRKYs are essential to affect the DNA binding and transcription regulatory activities of WRKYs, thus controlling its downstream genes expression. Therefore, we predicted and analyzed the protein-protein interactions of those chilling related WRKY transcription factors and then speculated the complex regulatory and functional network of WRKY transcription factors under chilling stress. A better understanding of SlWRKYs would be helpful for providing a theoretical basis for further illustrating the regulatory mechanism of SlWRKYs under chilling stress.