bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of cepharanthine against a SARS-CoV-2-related coronavirus
Authors: Li Shasha , Liu Wenli , Chen Yangzhen , Wang Liqin , An Wenlin , An Xiaoping , Song Lihua , Tong Yigang , Fan Huahao , Lu Chenyang 
Published: November 2020

Abstract
Antiviral therapies targeting the pandemic coronavirus disease 2019 (COVID-19) are urgently required. We studied an already-approved botanical drug cepharanthine (CEP) in a cell culture model of GX_P2V, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related virus. RNA-sequencing results showed the virus perturbed the expression of multiple genes including those associated with cellular stress responses such as endoplasmic reticulum (ER) stress and heat shock factor 1 (HSF1)-mediated heat shock response, of which heat shock response-related genes and pathways were at the core. CEP was potent to reverse most dysregulated genes and pathways in infected cells including ER stress/unfolded protein response and HSF1-mediated heat shock response. Additionally, single-cell transcriptomes also confirmed that genes of cellular stress responses and autophagy pathways were enriched in several peripheral blood mononuclear cells populations from COVID-19 patients. In summary, this study uncovered the transcriptome of a SARS-CoV-2-related coronavirus infection model and anti-viral activities of CEP, providing evidence for CEP as a promising therapeutic option for SARS-CoV-2 infection.
Complete populations of virtual patients forin silicoclinical trials
Authors: Sinisi S , Alimguzhin V , Mancini T , Tronci E , Leeners B 
Published: November 2020

AbstractMotivationModel-based approaches to safety and efficacy assessment of pharmacological drugs, treatment strategies or medical devices (In Silico Clinical Trial, ISCT) aim to decrease time and cost for the needed experimentations, reduce animal and human testing, and enable precision medicine. Unfortunately, in presence of non-identifiable models (e.g. reaction networks), parameter estimation is not enough to generate complete populations of Virtual Patients (VPs), i.e. populations guaranteed to show the entire spectrum of model behaviours (phenotypes), thus ensuring representativeness of the trial.ResultsWe present methods and software based on global search driven by statistical model checking that, starting from a (non-identifiable) quantitative model of the human physiology (plus drugs PK/PD) and suitable biological and medical knowledge elicited from experts, compute a population of VPs whose behaviours are representative of the whole spectrum of phenotypes entailed by the model (completeness) and pairwise distinguishable according to user-provided criteria. This enables full granularity control on the size of the population to employ in an ISCT, guaranteeing representativeness while avoiding over-representation of behaviours. We proved the effectiveness of our algorithm on a non-identifiable ODE-based model of the female Hypothalamic-Pituitary-Gonadal axis, by generating a population of 4 830 264 VPs stratified into 7 levels (at different granularity of behaviours), and assessed its representativeness against 86 retrospective health records from Pfizer, Hannover Medical School and University Hospital of Lausanne. The datasets are respectively covered by our VPs within Average Normalized Mean Absolute Error of 15%, 20% and 35% (90% of the latter dataset is covered within 20% error).Availability and implementation. Our open-source software is available at https://bitbucket.org/mclab/vipgeneratorSupplementary informationSupplementary data are available at Bioinformatics online.
Osteotomies for avascular necrosis of the femoral head
Authors: Quaranta Marco , Miranda Luca , Oliva Francesco , Aletto Cristian , Maffulli Nicola 
Published: November 2020

AbstractBackgroundIn osteonecrosis of the femoral head (ONFH), blood supply is insufficient for the metabolic requirements of the bone. The initial management is conservative, and, in case of failure, surgery is indicated. Osteotomies aim to change the spatial position of the necrotic portion of the femoral head. This systematic review evaluates the effectiveness and safety of osteotomies for ONFH.Source of dataThe systematic review, organized, conducted and reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines, was performed on PubMed and Google Scholar. We analysed outcomes in term of Harris Hip Score, leg shortening, secondary collapse and blood loss. We also verified the percentage of patients who required total hip replacement (THR) after osteotomy for ONFH.Areas of agreementA total of 16 articles were selected, including 775 patients and 852 osteotomies [curved varus osteotomy in 369 (43.3%) patients; transtrochanteric rotational osteotomy in 435 (51.05%) patients; half wedge osteotomy in 48 (5.6%) patients]. There was an overall THR conversion rate of 31.5% (268 hips on 852 osteotomies).Areas of controversyThere were no prospective randomized trials, and the outcome measures employed were often heterogeneous.Growing pointsApproximately one-third of the osteotomies performed in cases of ONFH are converted to THR over a period of ~7 years. In older patients, primary THR should be considered, especially as the conversion to THR after osteotomy is technically demanding.Areas timely for developing researchRandomized clinical studies should be conducted in order to define the parameters of the patient that can direct towards the most suitable osteotomic technique.
The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding
Authors: Gonda Itay , Faigenboim Adi , Adler Chen , Milavski Renana , Karp Merrie-Jean , Shachter Alona , Ronen Gil , Baruch Kobi , Chaimovitsh David , Dudai Nativ 
Published: November 2020

Abstract
Sweet basil, Ocimum basilicum L., is a well-known culinary herb grown worldwide, but its uses go beyond the kitchen to traditional medicine, cosmetics and gardening. To date, the lack of an available reference genome has limited the utilization of advanced molecular breeding methods. We present a draft version of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil. Genome sequencing showed basil to be a tetraploid organism with a genome size of 2.13 Gbp, assembled in 12,212 scaffolds, with &gt; 90% of the assembly being composed of 107 scaffolds. About 76% of the genome is composed of repetitive elements, with the majority being long-terminal repeats. We constructed and annotated 62,067 protein-coding genes and determined their expression in different plant tissues. We analysed the currently known phenylpropanoid volatiles biosynthesis genes. We demonstrated the necessity of the reference genome for a comprehensive understanding of this important pathway in the context of tetraploidy and gene redundancy. A complete reference genome is essential to overcome this redundancy and to avoid off-targeting when designing a CRISPR: Cas9-based genome editing research. This work bears promise for developing fast and accurate breeding tools to provide better cultivars for farmers and improved products for consumers.
Inactivation of the core cheVAWY chemotaxis genes disrupts chemotactic motility and organised biofilm formation in Campylobacter jejuni
Authors: Reuter Mark , Ultee Eveline , Toseafa Yasmin , Tan Andrew , van Vliet Arnoud H M 
Published: November 2020

ABSTRACT
Flagellar motility plays a central role in the bacterial foodborne pathogen Campylobacter jejuni, as flagellar motility is required for reaching the intestinal epithelium and subsequent colonisation or disease. Flagellar proteins also contribute strongly to biofilm formation during transmission. Chemotaxis is the process directing flagellar motility in response to attractant and repellent stimuli, but its role in biofilm formation of C. jejuni is not well understood. Here we show that inactivation of the core chemotaxis genes cheVAWY in C. jejuni strain NCTC 11168 affects both chemotactic motility and biofilm formation. Inactivation of any of the core chemotaxis genes (cheA, cheY, cheV or cheW) impaired chemotactic motility but did not affect flagellar assembly or growth. The ∆cheY mutant swam in clockwise loops, while complementation restored normal motility. Inactivation of the core chemotaxis genes interfered with the ability to form a discrete biofilm at the air-media interface, and the ∆cheY mutant displayed reduced dispersal/shedding of bacteria into the planktonic fraction. This suggests that while the chemotaxis system is not required for biofilm formation per se, it is necessary for organized biofilm formation. Hence interference with the Campylobacter chemotaxis system at any level disrupts optimal chemotactic motility and transmission modes such as biofilm formation.
Fractional ridge regression: a fast, interpretable reparameterization of ridge regression
Authors: Rokem Ariel , Kay Kendrick 
Published: November 2020

Abstract

Background
Ridge regression is a regularization technique that penalizes the L2-norm of the coefficients in linear regression. One of the challenges of using ridge regression is the need to set a hyperparameter (α) that controls the amount of regularization. Cross-validation is typically used to select the best α from a set of candidates. However, efficient and appropriate selection of α can be challenging. This becomes prohibitive when large amounts of data are analyzed. Because the selected α depends on the scale of the data and correlations across predictors, it is also not straightforwardly interpretable.

Results
The present work addresses these challenges through a novel approach to ridge regression. We propose to reparameterize ridge regression in terms of the ratio γ between the L2-norms of the regularized and unregularized coefficients. We provide an algorithm that efficiently implements this approach, called fractional ridge regression, as well as open-source software implementations in Python and matlab (https://github.com/nrdg/fracridge). We show that the proposed method is fast and scalable for large-scale data problems. In brain imaging data, we demonstrate that this approach delivers results that are straightforward to interpret and compare across models and datasets.

Conclusion
Fractional ridge regression has several benefits: the solutions obtained for different γ are guaranteed to vary, guarding against wasted calculations; and automatically span the relevant range of regularization, avoiding the need for arduous manual exploration. These properties make fractional ridge regression particularly suitable for analysis of large complex datasets.
Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology
Authors: Weißbecker Christina , Schnabel Beatrix , Heintz-Buschart Anna 
Published: November 2020

AbstractBackgroundAmplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.ResultsWe present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.ConclusionsBy use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.
Pulse recruitment and recovery of Cayman Islands Nassau Grouper (Epinephelus striatus) spawning aggregations revealed by in situ length-frequency data
Authors: Stock Brian C , Heppell Scott A , Waterhouse Lynn , Dove India C , Pattengill-Semmens Christy V , McCoy Croy M , Bush Phillippe G , Ebanks-Petrie Gina , Semmens Brice X 
Published: November 2020

Abstract
Fish spawning aggregations (FSAs) are vulnerable to overexploitation, yet quantitative assessments of FSA populations are rare. We document an approach for how to conduct such an assessment, evaluating the response of Critically Endangered Nassau Grouper (Epinephelus striatus) to protections in the Cayman Islands. We assessed pre-protection status on all islands using length data from fishery catch. We then used 17 years of noninvasive length-frequency data, collected via diver-operated laser calipers, to estimate recruitment and spawning biomass of Nassau Grouper on Little Cayman following protection. Bimodal length distributions in 2017–2019 indicated a large recruitment pulse (4–8× average) derived from spawning in 2011. Biomass recovered to 90–106% of the pre-exploitation level after 16 years, largely driven by the strong 2011 year class. Length distributions were also bimodal in 2017–2019 on nearby Cayman Brac, implying a synchronous recruitment pulse occurred on both islands. Our results demonstrate that: (i) in situ length data can be used to monitor protected FSAs; (ii) spatiotemporal FSA closures can be effective, but success takes time if population recovery depends upon sporadic recruitment; and (iii) FSA fishery management targets may need to be higher than commonly recommended (i.e. spawning potential ratio &gt;0.6 instead of 0.4).
COVID-19 is having a destructive impact on health-care workers’ mental well-being
Authors: Vanhaecht Kris , Seys Deborah , Bruyneel Luk , Cox Bianca , Kaesemans Gorik , Cloet Margot , Van Den Broeck Kris , Cools Olivia , De Witte Andy , Lowet Koen , Hellings Johan , Bilsen Johan , Lemmens Gilbert , Claes Stephan 
Published: November 2020

Abstract

Background
The coronavirus disease 2019 (COVID-19) may aggravate workplace conditions that impact health-care workers’ mental health. However, it can also place other stresses on workers outside of their work. This study determines the effect of COVID-19 on symptoms of negative and positive mental health and the workforce’s experience with various sources of support. Effect modification by demographic variables was also studied.

Methods
A cross-sectional survey study, conducted between 2 April and 4 May 2020 (two waves), led to a convenience sample of 4509 health-care workers in Flanders (Belgium), including paramedics (40.6%), nurses (33.4%), doctors (13.4%) and management staff (12.2%). About three in four were employed in university and acute hospitals (29.6%), primary care practices (25.7%), residential care centers (21.3%) or care sites for disabled and mental health care. In each of the two waves, participants were asked how frequently (on a scale of 0–10) they experienced positive and negative mental health symptoms during normal circumstances and during last week, referred to as before and during COVID-19, respectively. These symptoms were stress, hypervigilance, fatigue, difficulty sleeping, unable to relax, fear, irregular lifestyle, flashback, difficulty concentrating, feeling unhappy and dejected, failing to recognize their own emotional response, doubting knowledge and skills and feeling uncomfortable within the team. Associations between COVID-19 and mental health symptoms were estimated by cumulative logit models and reported as odds ratios. The needed support was our secondary outcome and was reported as the degree to which health-care workers relied on sources of support and how they experienced them.

Results
All symptoms were significantly more pronounced during versus before COVID-19. For hypervigilance, there was a 12-fold odds (odds ratio 12.24, 95% confidence interval 11.11–13.49) during versus before COVID-19. Positive professional symptoms such as the feeling that one can make a difference were less frequently experienced. The association between COVID-19 and mental health was generally strongest for the age group 30–49 years, females, nurses and residential care centers. Health-care workers reported to rely on support from relatives and peers. A considerable proportion, respectively, 18 and 27%, reported the need for professional guidance from psychologists and more support from their leadership.

Conclusions
The toll of the crisis has been heavy on health-care workers. Those who carry leadership positions at an organizational or system level should take this opportunity to develop targeted strategies to mitigate key stressors of health-care workers’ mental well-being.
245 Equine research programs: Where are they going?
Authors: Nielsen Brian D 
Published: November 2020

Abstract
Those in the equine community have a strong desire for knowledge in the quest to provide the best care for their horses. Unfortunately, they often seek out advice through on-line sources and are quick to take anecdotal evidence or testimonials as fact. While those in the scientific community would encourage decisions to be made based upon quality research, often there are insufficient data available to answer questions posed by the industry. One of the reasons for this is limited resources. In the past it was common to have departmental-funded assistantships for graduate students. However, those assistantships have disappeared in many departments and now students are often supported through grants. Likewise, there is additional pressure by administrators for federal funding though “horse research” is often considered less important to such funding agencies as horses are viewed as recreational animals as opposed to being a food-producing animals. Hence, much funded equine research would fall under the category of product-testing. While somewhat limited in scope, such research may provide the opportunity to answer other research questions if projects are appropriately planned. However, such “side-projects” are only useful if adequate subject numbers and controls are in place. Reduced animal availability and increased costs of utilizing horses in research may necessitate using other animal models for horses to answer fundamental questions and, if appropriately designed, may allow projects to be competitive for federal funding. Especially as it pertains to junior faculty, collaborative research utilizing colleagues with specialized skills can be important in terms of promoting competitive and fundamental research proposals. While limited resources may increase the appeal for low-cost studies, there is still a need for well-designed studies that answer questions critical to the horse industry and doing quality research is important to enhance the reputation of equine research.
95 Evaluation of variation attributable to lab and technician for measurements of beef carcass traits made using ultrasound
Authors: Schmidt Bradie M , MacNeil Michael , Gonda Michael 
Published: November 2020

Abstract
Carcass data that is collected using ultrasound contributes to national genetic evaluation of beef cattle. Cattle are scanned by many technicians and the resulting images are processed by three laboratories providing data to breed associations. The Ultrasound Guidelines Council certifies technicians and laboratories as being proficient. However, there has been no comprehensive evaluation of non-genetic sources of variation that affect the data. The objective of this study was to partition the variance of ultrasound carcass measurements to animal genetic effects, ultrasound scanning technician and image interpretation laboratory. Ultrasound carcass data for longissimus muscle area, percent intramuscular fat, and subcutaneous fat depth were provided by the American Angus Association (n=65,971), American Hereford Association (n=43,380), and American Simmental Association (n=48,298). For each breed variance components were estimated for additive genetic effects of each animal, technician, contemporary group nested within technician and residual. Genetic correlations were estimated treating measurements from the different interpretation laboratories as separate traits. Across all three breeds, additive genetic effects explained between 15 and 30%, 11 and 25%, and 6 and 13% of the phenotypic variance for IMF, SQF, and LMA, respectively. Similarly, technician explained 12-27%, 4-28%, and 4-26% of the phenotypic variance; contemporary groups within technician accounted for 25-45%, 20-54%, and 43-73% of phenotypic variance. Among the image interpretation laboratories, the ratio of greatest to least residual variance was 3.96, 1.62, and 1.50 for IMF, SQF, and LMA, respectively. Genetic correlations between labs ranged from 0.79 to 0.95 for IMF, 0.64 to 0.94 for SQF and 0.78 to 0.98 for LMA. These results suggest the potential for the residual variances to be heterogeneous, particularly for IMF, depending on the image interpretation laboratory.
217 Young Scholar Presentation: The use of diverse cattle breeds to understand marbling development and growth
Authors: Jaborek Jerad , Fluharty Francis L , Relling Alejandro E 
Published: November 2020

Abstract
Wagyu cattle have been genetically selected to have superior marbling deposition compared with many other cattle breeds, including Angus. It was hypothesized that greater marbling deposition by Wagyu influenced cattle may be due to an additional wave of adipogenic gene expression compared with Angus cattle. The present study compared the expression of lipid metabolism genes within the longissimus muscle (LM) of Wagyu and Angus sired cattle at similar harvest endpoints: days on feed and age, or body weight (613 kg). Angus sired steers were sired by an Angus bull selected for marbling (T1), while Wagyu sired steers were sired by either a Wagyu bull selected for growth (T2 & T4) or marbling (T3 & T5), at the respective age or body weight endpoints. Cattle were weaned at 7 months of age, entered the feedlot 54 d later, and consumed the same growing (119 d) and finishing ration. Muscle biopsies were collected from the LM posterior to the 13th rib at approximately 7, 9, 11, 14, and 17 months of age (harvest) for T1, T2, and T3 cattle. Muscle biopsies for T4 and T5 cattle were collected when their body weight was similar to T1 cattle at the time of biopsy, approximately 241, 276, 400, 531, and 613 kg (harvest). The high marbling sired Wagyu steers (T3 &T5) had greater marbling scores and percent LM lipid compared with high growth Wagyu (T2 & T4) and Angus sired steers. Gene expression results from high marbling sired Wagyu steers (T3 &T5) demonstrated additional peaks of PPARδ mRNA expression, greater and earlier PPARγ mRNA expression, and greater or additional peaks of GPAM1, LPIN1, and HSL mRNA expression compared with high growth Wagyu (T2 & T4) and Angus sired steers.
117 Consumer perceptions of beef and beef production
Authors: Husted Rick 
Published: November 2020

Abstract
Consumers love beef but are often uncertain about how beef is raised. In this session we’ll learn more about consumer perceptions, where we are strong and areas where the industry could improve. Focus will be given to consumer attitudes related to beef production and how misconceptions are driving the need for more and more education in this area. Time will also be spent looking at beef’s competition, including focus on meat substitutes and how consumers few these products.