bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics of blood glucose distribution in a health examination population in Sichuan (2009–2017)
Authors: Ding Fei , Nie Xin , Liao Jing , He Yong , Li Guixing 
Published: November 2020

Abstract
The prevalence of diabetes mellitus and impaired fasting glucose is rapidly increasing in the recent years. Hyperglycemia associated atherosclerosis and other complications are posing a serious threat to human health. The present study aimed to analyze the blood glucose distribution characteristics within a large size of health examination population of Sichuan province, China.
This was a retrospective study conducted in 878,019 subjects (483,914 males and 394,105 females) aged more than 18 years old from the Health Examination Center at West China Hospital, Sichuan University during 2009 to 2017. The blood glucose levels were compared in different age groups and different years.
The blood glucose levels were significantly increased in recent years. The percentage of cases with high glucose levels was significantly higher in males than that in females since 2009 to 2017. Moreover, the blood glucose levels and the percentage of high glucose levels in aged population were significantly higher than those in younger population every year.
The health examination population showed increased percentage of blood glucose levels, and so regular physical examination and glucose control are highly important in aged population.
Venous Thromboembolism in Hospitalized COVID-19 Patients
Authors: Sridharan Gurusaravanan Kutti , Vegunta Radhakrishna , Rokkam Venkata Ram Pradeep , Meyyur Aravamudan Veeraraghavan , Vegunta Rathnamitreyee , Khan Shahab R. , Ponnada Suresh , Boregowda Umesha , Prudhvi Kalyan , Chamarthi Gajapathiraju , Mohan Babu P. 
Published: November 2020

Background:
Venous thromboembolism (VTE) is increasingly reported in seriously ill patients with COVID-19 infection. Incidence of VTE has been reported before and results varied widely in study cohorts.

Area of uncertainty:
Incidence of major VTE (segmental pulmonary embolism and above and proximal deep vein thrombosis) which is a contributor to mortality and morbidity is not known. Also, data is unclear on the optimal anticoagulation regimen to prevent VTE.

Data sources:
Multiple databases including PubMed were searched until May 12, 2020, to include studies reporting VTE in hospitalized COVID-19 adult patients. MOOSE guidelines were followed in selection, and 11 studies were included. We conducted a systematic review and meta-analysis to quantitatively assess the VTE burden in hospitalized COVID-19 patients and potential benefits of therapeutic dosing of anticoagulation compared with prophylaxis dosing for VTE prevention.

Therapeutic advances:
Many societies and experts recommend routine prophylactic anticoagulation with heparin for VTE prevention in hospitalized COVID-19 patients. In this meta-analysis, the pooled rate of major VTE was 12.5% in hospitalized patients and 17.2% in intensive care unit patients. When therapeutic anticoagulation dosing was compared with prophylactic anticoagulation, the pooled odds ratio of VTE was 0.33 (95% confidence interval 0.14–0.75; P = 0.008, I2 = 0%) suggesting statistical significance with therapeutic dosing of anticoagulation for primary prevention of VTE in all hospitalized patients. However, this should be interpreted with caution as the bleeding events and safety profile could not be ascertained because of lack of adequate information. We recommend applying this finding to hospitalized COVID 19 patients only after carefully weighing individual bleeding risks and benefits.

Conclusion:
Major VTE events, especially pulmonary embolism, seem to be high in COVID-19 patients admitted to the intensive care unit. Therapeutic anticoagulation dosing seems to significantly benefit the odds of preventing any VTE when compared with prophylactic dosing in all hospitalized patients.
Gut Microbiome
Authors: Jain Vandana , Alexander Emma C. , Burford Charlotte , Verma Anita , Dhawan Anil 
Published: November 2020

ABSTRACTBiliary atresia (BA) is a fibro‐obliterative condition of the biliary tree, presenting in infancy. The bilioenteric conduit formed at Kasai portoenterostomy (KPE), achieves restoration of bile flow in approximately 60% of infants. Even if the operation is successful, cirrhosis and its associated complications are, however, common. BA remains the leading cause for liver transplantation (LT) in children. Antibiotic, choleretic, and steroid therapy post‐KPE have not convincingly reduced LT rates. Advances in molecular technology have enabled characterisation of the encoded genes of the gut microbiota (gut microbiome). The gut microbiome plays an important role in host metabolism, nutrition, and immune function, with alterations in its diversity and/or composition, known as dysbiosis, being described in disease states, including liver disease. Liver‐gut microbiome exploration in adulthood largely focuses on nonalcoholic liver disease, cirrhosis (mainly alcohol‐ or viral‐based aetiology) and cholestatic liver diseases (eg, primary sclerosing cholangitis), with microbial signatures correlating to disease severity. Investigation of the gut microbiota in BA had been limited to culture‐based methodology, but molecular studies are emerging, and although in their infancy, highlight a potential pathogenic role for Enterobacteriaceae and Streptococcus, and a potential beneficial role for Bifidobacteria. Bacterial translocation, and the production of gut microbiome‐derived metabolites, are key host‐microbiome‐mechanistic pathways in liver disease pathogenesis. Microbiome‐targeted therapeutics for liver disease are in development, with faecal microbiota transplantation showing promise in cirrhosis. Could the gut microbiome be a novel modifiable risk factor in BA, reducing the need for LT?
A Mixed Methods Study of Senior Medical Student Help Calling in an Individual, Acute Care Simulation Experience
Authors: Young Timothy P. , Estes Molly , Shank Thomas , Smith Dustin D. , Kuntz Heather M. 
Published: November 2020

Introduction
The ability to appropriately seek help is a key skill for medical students transitioning to residency. We designed a simulation activity for senior medical students and became interested in studying help calling behaviors and attitudes.

Methods
We collected quantitative data regarding help calling for 2 simulation cases and qualitative data using a survey. We undertook a structured thematic analysis based on grounded theory methodology. We identified and compared groups who did and did not call for help.

Results
One hundred thirty-four students participated and 122 (91%) completed an evaluation. More students called for help without prompting in the second case (34/134, 25% in first case; 110/134, 82% in second case, P < 0.001). Most students did not call for help in the first case but called in the second case (81, 60%). Our qualitative analysis identified 5 themes: (1) students seek to avoid shame and burdening their team, (2) prior institutional simulation and testing experience may imprint help calling behaviors, (3) students view help calling primarily through an individual lens, (4) students overestimate the complexity of the help calling process, and (5) the simulation environment and intentional experimentation make it difficult to observe natural behavior. When compared with help callers, more non–help callers had phrases coded as “perception of expectations” (37% vs. 10%, P = 0.03).

Conclusions
Learners participating in simulation exercises designed to promote help-calling behaviors face training-based barriers related to shame and the desire for autonomy and simulation-based challenges related to assessment.
“Talk-Through Walk-Through”—A Simulation Approach Adapted During Preparation for COVID-19
Authors: Lee Matthew , Chen Stephanie , Tosif Shervin , Graham Jonathon 
Published: November 2020

Summary Statement
Talk-through walk-through is a simulation format that enables the rapid development and improvement of complex systems for patient care. This approach was adapted from task analysis literature and used to develop and test processes for the safe management of COVID-19 patients. Talk-through walk-through is a 2-part process that is paired with a simulated clinical scenario. The talk-through focuses on identifying and solving major process issues and establishing a shared mental model. The walk-through tests these proposed solutions and identifies previously unanticipated system and process challenges. The talk-through walk-through approach enables process development and testing in a single session, making it particularly valuable for patient care systems that involve multiple locations and healthcare disciplines, and where the availability of these disciplines and time are scarce.
Early epidemiological analysis of the 2019-nCoV outbreak based on a crowdsourced data
Authors: Sun Kaiyuan , Chen Jenny , Viboud Cécile 
Published: November 2020

AbstractAs the outbreak of novel 2019 coronavirus (2019-nCoV) progresses within China and beyond, there is a need for rapidly available epidemiological data to guide situational awareness and intervention strategies. Here we present an effort to compile epidemiological information on 2019-nCoV from media news reports and a physician community website (dxy.cn) between Jan 20, 2020 and Jan 30, 2020, as the outbreak entered its 7thweek. We compiled a line list of patients reported in China and internationally and daily case counts by Chinese province. We describe the demographics, hospitalization and reporting delays for 288 patients, over time and geographically. We find a decrease in case detection lags in provinces outside of Wuhan and internationally, compared to Wuhan, and after Jan 18, 2020, as outbreak awareness increased. The rapid progression of reported cases in different provinces of China is consistent with local transmission beyond Wuhan. The age profile of cases points at a deficit among children under 15 years of age, possibly related to prior immunity with related coronavirus or behavioral differences. Overall, our datasets, which have been publicly available since Jan 21, 2020, align with official reports from Chinese authorities published more than a week later. Availability of publicly available datasets in the early stages of an outbreak is important to encourage disease modeling efforts by independent academic modeling teams and provide robust evidence to guide interventions.
Using Community Science to Reveal the Global Chemogeography of River Metabolomes
Authors: Garayburu-Caruso Vanessa A. , Danczak Robert E. , Stegen James C. , Renteria Lupita , Mccall Marcy , Goldman Amy E. , Chu Rosalie K. , Toyoda Jason , Resch Charles T. , Torgeson Joshua M. , Wells Jacqueline , Fansler Sarah , Kumar Swatantar , Graham Emily B. 
Published: November 2020

AbstractRiver corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabolism. However, there have been no studies on the global chemogeography of surface water and sediment metabolomes using ultrahigh-resolution techniques. Here, we describe a community science effort from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to characterize global metabolomes in surface water and sediment that span multiple stream orders and biomes. We describe the distribution of key aspects of metabolomes including elemental groups, chemical classes, indices, and inferred biochemical transformations. We show that metabolomes significantly differ across surface water and sediment and that surface water metabolomes are more rich and variable. We also use inferred biochemical transformations to identify core metabolic processes shared among surface water and sediment. Finally, we observe significant spatial variation in sediment metabolites between rivers in the eastern and western portions of the contiguous United States. Our work not only provides a basis for understanding global patterns in river corridor biogeochemical cycles but also demonstrates that community science endeavors can enable global research projects that are unfeasible with traditional research models.
The evolution of latitudinal ranges in reef-associated fishes: heritability, limits, and inverse Rapoport’s rule
Authors: Pie Marcio R. , Divieso Raquel , Caron Fernanda S. , Siqueira Alexandre C. , Barneche Diego R. , Luiz Osmar J. 
Published: November 2020

ABSTRACTAimVariation in the size and position of geographical ranges is a key variable that underlies most biogeographical patterns. However, relatively little is known in terms of general principles driving their evolution, particularly in the marine realm. In this study we explore several fundamental properties regarding the evolution of reef fish latitudinal ranges, namely the degree of similarity in range size between ancestor and descendant lineages (i.e. phylogenetic signal); the evolution of range limits; and the latitudinal distribution of range sizes, particularly with respect to Rapoport’s rule.LocationGlobal.TaxonReef-associated fishes.MethodsWe integrate data on the latitudinal distribution and evolutionary history of 5,071 reef fish species with phylogenetic comparative methods to assess the level of phylogenetic signal in latitudinal range size, low- and high-latitude limits, and range midpoints, and to estimate rates of evolution of those traits. Finally, we test whether latitudinal ranges become smaller near the equator, as predicted by Rapoport’s rule, using phylogenetic generalized least squares.ResultsThere were varying levels of phylogenetic signal in latitudinal range size, low- and high-latitude limits, and range midpoints. Despite these differences, latitudinal midpoints were consistently shown to have the highest phylogenetic signal among all measured geographic features. Interestingly, the position of high-latitude limits in general evolved at substantially faster rates than their low-latitude counterparts. Finally, we confirm for the first time the existence of an inverse Rapoport’s rule in reef-associated fishes using phylogenetic comparative methods. Indeed, mean latitudinal range size of tropical species is nearly twice the size of their temperate counterparts (2067±1431 km vs. 1168±725 km, respectively).Main conclusionsWe uncovered several congruent patterns in phylogenetic signal and rates of evolution of latitudinal ranges, despite vastly disparate biogeographical distributions and ecological differences between the studied fish lineages. Such broad congruence across different taxa and oceans, as well as with previous data from terrestrial environments, suggests that the observed patterns might represent general principles governing geographical range evolution.
COVID-19’s U.S. Temperature Response Profile
Authors: Carson Richard T. , Carson Samuel L. , Dye Thayne Keegan , Mayfield Samuel A. , Moyer Daniel C. , A. (Alex) Yu Chu 
Published: November 2020

AbstractWe estimate the U.S. temperature response curve for COVID-19 and show transmission is highly sensitive to temperature variation despite summer outbreaks widely assumed to show otherwise. By largely replacing the daily death counts states initially reported with counts based on death certificate date, we build a week-ahead statistical forecasting model that explains most of the daily variation (R2 = 0.97) and isolates COVID-19’s temperature response profile (p < 0.001). These counts normalized at 31°C (U.S. mid-summer average) scale up to nearly 160% at 5°C. Positive cases are more temperature sensitive, scaling up to almost 400% between 31°C and 5°C. Dynamic feedback amplifies these effects, suggesting that cooling temperatures are likely to the substantially increase COVID-19 transmission.Article Summary LineCOVID-19’s temperature response profile is reliably estimated using re-assembled state-reported data and suggests the onset of cold weather will amplify its spread.
Fast and accurate estimation of species-specific diversification rates using data augmentation
Authors: Maliet Odile , Morlon Hélène 
Published: November 2020

1AbstractDiversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model (ClaDS), which allows inferring subtle rate variations across lineages. Here we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.
Spatial structure impacts adaptive therapy by shaping intra-tumoral competition
Authors: Strobl Maximilian A. R. , Gallaher Jill , West Jeffrey , Robertson-Tessi Mark , Maini Philip K. , Anderson Alexander R. A. 
Published: November 2020

Abstract(1) Background: Adaptive therapy aims to tackle cancer drug resistance by leveraging intra-tumoral competition between drug-sensitive and resistant cells. Motivated by promising results in prostate cancer there is growing interest in extending this approach to other cancers. Here we present a theoretical study of intra-tumoral competition during adaptive therapy, to identify under which circumstances it will be superior to aggressive treatment; (2) Methods: We use a 2-D, on-lattice, agent-based tumour model to examine the impact of different microenvironmental factors on the comparison between continuous drug administration and adaptive therapy. (3) Results: We show that the degree of crowding, the initial resistance fraction, the presence of resistance costs, and the rate of tumour cell turnover are key determinants of the benefit of adaptive therapy, and we study in detail how these factors alter competition between cells. We find that intra-specific competition between resistant cells plays an unexpectedly important role in the ability to control resistance. To conclude we show how differences in resistance cost and turnover change the tumour’s spatial organisation and may explain differences in cycling speed observed in a cohort of 67 prostate cancer patients undergoing intermittent androgen deprivation therapy; (4) Conclusion: Our work provides insights into how adaptive therapy leverages inter- and intra-specific competition to control resistance, and shows that the tumour’s spatial architecture will likely be an important factor in determining the quantitative benefit of adaptive therapy in patients.
Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants
Authors: Miller Danny E. , Sulovari Arvis , Wang Tianyun , Loucks Hailey , Hoekzema Kendra , Munson Katherine M. , Lewis Alexandra P. , Fuerte Edith P. Almanza , Paschal Catherine R. , Thies Jenny , Bennett James T. , Glass Ian , Dipple Katrina M. , Patterson Karynne , Bonkowski Emily S. , Nelson Zoe , Squire Audrey , Sikes Megan , Beckman Erika , Bennett Robin L. , Earl Dawn , Lee Winston , Allikmets Rando , Perlman Seth J. , Chow Penny , Hing Anne V. , Adam Margaret P. , Sun Angela , Lam Christina , Chang Irene ,   University of Washington Center for Mendelian Genomics, Cherry Tim , Chong Jessica X. , Bamshad Michael J. , Nickerson Deborah A. , Mefford Heather C. , Doherty Dan , Eichler Evan E. 
Published: November 2020

ABSTRACTBACKGROUNDDespite widespread availability of clinical genetic testing, many individuals with suspected genetic conditions do not have a precise diagnosis. This limits their opportunity to take advantage of state-of-the-art treatments. In such instances, testing sometimes reveals difficult-to-evaluate complex structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in specific genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted.METHODSTargeted long-read sequencing (T-LRS) was performed on 33 individuals using Read Until on the Oxford Nanopore platform. This method allowed us to computationally target up to 100 Mbp of sequence per experiment, resulting in an average of 20x coverage of target regions, a 500% increase over background. We analyzed patient DNA for pathogenic substitutions, structural variants, and methylation differences using a single data source.RESULTSThe effectiveness of T-LRS was validated by detecting all genomic aberrations, including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences, previously identified by prior clinical testing. In 6/7 individuals who had complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, which led, in one case, to a change in clinical management. In nine individuals with suspected Mendelian conditions who lacked a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in five and variants of uncertain significance in two others.CONCLUSIONST-LRS can accurately predict pathogenic copy number variants and triplet repeat expansions, resolve complex rearrangements, and identify single-nucleotide variants not detected by other technologies, including short-read sequencing. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority candidate genes and regions or to further evaluate complex clinical testing results. The application of T-LRS will likely increase the diagnostic rate of rare disorders.
Protein Structural Alignments From Sequence
Authors: Morton James T. , Strauss Charlie E. M. , Blackwell Robert , Berenberg Daniel , Gligorijevic Vladimir , Bonneau Richard 
Published: November 2020

AbstractComputing sequence similarity is a fundamental task in biology, with alignment forming the basis for the annotation of genes and genomes and providing the core data structures for evolutionary analysis. Standard approaches are a mainstay of modern molecular biology and rely on variations of edit distance to obtain explicit alignments between pairs of biological sequences. However, sequence alignment algorithms struggle with remote homology tasks and cannot identify similarities between many pairs of proteins with similar structures and likely homology. Recent work suggests that using machine learning language models can improve remote homology detection. To this end, we introduce DeepBLAST, that obtains explicit alignments from residue embeddings learned from a protein language model integrated into an end-to-end differentiable alignment framework. This approach can be accelerated on the GPU architectures and outperforms conventional sequence alignment techniques in terms of both speed and accuracy when identifying structurally similar proteins.