bluuebunny/crossref_metadata_2025_split huggingface dataset:
SeqRepo: A system for managing local collections of biological sequences
Authors: Hart Reece K. , Prlić Andreas 
Published: December 2020

Motivation
Access to biological sequence data, such as genome, transcript, or protein sequence, is at the core of many bioinformatics analysis workflows. The National Center for Biotechnology Information (NCBI), Ensembl, and other sequence database maintainers provide methods to access sequences through network connections. For many users, the convenience and currency of remotely managed data are compelling, and the network latency is non-consequential. However, for high-throughput and clinical applications, local sequence collections are essential for performance, stability, privacy, and reproducibility.

Results
Here we describe SeqRepo, a novel system for building a local, high-performance, non-redundant collection of biological sequences. SeqRepo enables clients to use primary database identifiers and several digests to identify sequences and sequence alises. SeqRepo provides a native Python interface and a REST interface, which can run locally and enables access from other programming languages. SeqRepo also provides an alternative REST interface based on the GA4GH refget protocol.
SeqRepo provides fast random access to sequence slices. We provide results that demonstrate that a local SeqRepo sequence collection yields significant performance benefits of up to 1300-fold over remote sequence collections. In our use case for a variant validation and normalization pipeline, SeqRepo improved throughput 50-fold relative to use with remote sequences. SeqRepo may be used with any species or sequence type. Regular snapshots of Human sequence collections are available.
It is often convenient or necessary to use a computed digest as a sequence identifier. For example, a digest-based identifier may be used to refer to proprietary reference genomes or segments of a graph genome, for which conventional identifiers will not be available. Here we also introduce a convention for the application of the SHA-512 hashing algorithm with Base64 encoding to generate URL-safe identifiers. This convention, sha512t24u, combines a fast digest mechanism with a space-efficient representation that can be used for any object. Our report includes an analysis of timing and collision probabilities for sha512t24u. SeqRepo enables clients to use sha512t24u as identifiers, thereby seamlessly integrating public and private sequence sets.

Availability
SeqRepo is released under the Apache License 2.0 and is available on github and PyPi. Docker images and database snapshots are also available. See https://github.com/biocommons/biocommons.seqrepo.
Manual ability in hand surgery patients: Validation of the ABILHAND scale in four diagnostic groups
Authors: El Khoury Ghady , Barbier Olivier , Libouton Xavier , Thonnard Jean-Louis , Lefèvre Philippe , Penta Massimo 
Published: December 2020

Background
Patients treated in hand surgery (HS) belong to different demographic groups and have varying impairments related to different pathologies. HS outcomes are measured to assess treatment results, complication risks and intervention reliability. A one-dimensional and linear measure would allow for unbiased comparisons of manual ability between patients and different treatment effects.

Objective
To adapt the ABILHAND questionnaire through Rasch analysis for specific use in HS patients and to examine its validity.

Methods
A preliminary 90-item questionnaire was presented to 216 patients representing the diagnoses most frequently encountered in HS, including distal radius fracture (n = 74), basal thumb arthritis (n = 66), carpal tunnel syndrome (n = 53), and heavy wrist surgery (n = 23). Patients were assessed during the early recovery and in the late follow-up period (0–3 months, 3–6 months and >6 months), leading to a total of 305 assessments. They rated their perceived difficulty with queried activities as impossible, difficult, or easy. Responses were analyzed using the RUMM2030 software. Items were refined based on item-patient targeting, fit statistics, differential item functioning, local independence and item redundancy. Patients also completed the QuickDASH, 12-item Short Form Survey (SF-12) and a numerical pain scale.

Results
The rating scale Rasch model was used to select 23 mostly bimanual items on a 3-level scale, which constitute a unidimensional, linear measure of manual ability with good reliability across all included diagnostic groups (Person-Separation Index = 0.90). The resulting scale was found to be invariant across demographic and clinical subgroups and over time. ABILHAND-HS patient measures correlated significantly (p<0.001) with the QuickDASH (r = -0.77), SF-12 Physical Component Summary (r = 0.56), SF-12 Mental Component Summary (r = 0.31), and pain scale (r = -0.49).

Conclusion
ABILHAND-HS is a robust person-centered measure of manual ability in HS patients.
Cesarean delivery and early childhood diseases in Bangladesh: An analysis of Demographic and Health Survey (BDHS) and Multiple Indicator Cluster Survey (MICS)
Authors: Hasan Mohammad Nayeem , Chowdhury Muhammad Abdul Baker , Jahan Jenifar , Jahan Sumyea , Ahmed Nasar U. , Uddin Md Jamal 
Published: December 2020

Introduction
The rate of cesarean delivery (C-section) has been increasing worldwide, including Bangladesh, and it has a negative impact on the mother and child's health. Our aim was to examine the association between C-section and childhood diseases and to identify the key factors associated with childhood diseases.

Methods
We used four nationally representative data sets from multiple indicator cluster survey (MICS, 2012 and 2019) and Bangladesh Demographic and Health Survey (BDHS, 2011and 2014) and analyzed 25,270 mother-child pairs. We used the frequency of common childhood diseases (fever, short or rapid breaths, cough, blood in stools, and diarrhea) as our outcome variable and C-section as exposure variable. We included mother’s age, place of residence, division, mother’s education, wealth index, child age, child sex, and child size at birth as confounding variables. Negative binomial regression model was used to analyze the data.

Results
In the BDHS data, the prevalence of C-section increased from 17.95% in 2011 to 23.33% in 2014. Also, in MICS, the prevalence almost doubled over an eight-year period (17.74% in 2012 to 35.41% in 2019). We did not observe any significant effect of C-section on childhood diseases in both surveys. Only in 2014 BDHS, we found that C-section increases the risk of childhood disease by 5% [Risk Ratio (RR): 1.05, 95% CI: 0.95, 1.17, p = 0.33]. However, the risk of childhood disease differed significantly in all survey years by division, child's age, and child’s size at birth after adjusting for important confounding variables. For example, children living in Chittagong division had a higher risk [(2011 BDHS RR: 1.22, 95% CI: 1.08, 1.38) and (2019 MICS RR: 1.21, 95% CI: 1.08, 1.35)] of having disease compared to Dhaka division. Maternal age, education, and wealth status showed significant differences with the outcome in some survey years.

Conclusion
Our study shows that C-section in Bangladesh continued to increase over time, and we did not find significant association between C-section and early childhood diseases. High C-section rate has a greater impact on maternal and child health as well as the burden on the health care system. We recommend raising public awareness of the negative impact of unnecessary C-section in Bangladesh.
Explaining the increment in coronary heart disease mortality in Mexico between 2000 and 2012
Authors: Arroyo-Quiroz Carmen , O’Flaherty Martin , Guzman-Castillo Maria , Capewell Simon , Chuquiure-Valenzuela Eduardo , Jerjes-Sanchez Carlos , Barrientos-Gutierrez Tonatiuh 
Published: December 2020

Background
Mexico is still in the growing phase of the epidemic of coronary heart disease (CHD), with mortality increasing by 48% since 1980. However, no studies have analyzed the drivers of these trends. We aimed to model CHD deaths between 2000 and 2012 in Mexico and to quantify the proportion of the mortality change attributable to advances in medical treatments and to changes in population-wide cardiovascular risk factors.

Methods
We performed a retrospective analysis using the previously validated IMPACT model to explain observed changes in CHD mortality in Mexican adults. The model integrates nationwide data at two-time points (2000 and 2012) to quantify the effects on CHD mortality attributable to changes in risk factors and therapeutic trends.

Results
From 2000 to 2012, CHD mortality rates increased by 33.8% in men and by 22.8% in women. The IMPACT model explained 71% of the CHD mortality increase. Most of the mortality increases could be attributed to increases in population risk factors, such as diabetes (43%), physical inactivity (28%) and total cholesterol (24%). Improvements in medical and surgical treatments together prevented or postponed 40.3% of deaths; 10% was attributable to improvements in secondary prevention treatments following MI, while 5.3% to community heart failure treatments.

Conclusions
CHD mortality in Mexico is increasing due to adverse trends in major risk factors and suboptimal use of CHD treatments. Population-level interventions to reduce CHD risk factors are urgently needed, along with increased access and equitable distribution of therapies.
Health outcomes in a national sample of American Indian and Alaska Native adults: Differences between multiple-race and single-race subgroups
Authors: Running Bear Ursula , Asdigian Nancy L. , Beals Janette , Manson Spero M. , Kaufman Carol E. 
Published: December 2020

Objectives
To determine differences among multi-race (MR) American Indian and Alaska Natives (AIAN), single race (SR) AIANs, and SR-Whites on multiple health outcomes. We tested the following hypotheses: MR-AIANs will have worse health outcomes than SR-AIANs; SR-AIANs will have worse health outcomes than SR-Whites; MR-AIANs will have worse health outcomes than SR-Whites.

Methods
Behavioral Risk Factor Surveillance System data were used to examine general health, risk behaviors, access to health care, and diagnosed chronic health conditions. Those identifying as SR-White, SR-AIAN, and MR-AIAN were included in multinomial logistic regression models.

Results
Compared to SR-AIANs, MR-AIANs had more activity limitations, a greater likelihood of experiencing cost as a barrier to health care and were more likely to be at increased risk and diagnosed with more chronic health conditions. Both SR and MR-AIANs have worse health than SR-Whites; MR-AIANs appear to be at increased risk for poor health.

Conclusions
The current study examined access to health care and nine chronic health conditions, neither of which have been considered in prior work. MR AIANs are at increased risk compared to SR groups. These observations beg for further inquire into the mechanisms underlying these differences including stress related to identify, access to care, and discrimination. Findings support the continued need to address health disparities among AIANs regardless of SR or MR identification.
Genotypes of Mycobacterium tuberculosis isolates circulating in Shaanxi Province, China
Authors: Li Yan , Pang Yu , Zhang Tianhua , Xian Xiaoping , Yang Jian , Wang Rui , Wang Panting , Zhang Meng , Chen Wei 
Published: December 2020

Objectives
The prevalence of drug-resistant TB in Shaanxi Province is higher than other areas. This study was aimed to investigate the genetic diversity and epidemiology of Mycobacterium tuberculosis clinical strains in Shaanxi Province, China.

Methods
From January to December 2016, a total of 298 Mycobacterium tuberculosis clinical isolates from smear-positive pulmonary tuberculosis patients were genotyped by Mcspoligotyping and 15-locus VNTR.

Results
We found that the Beijing family strains was the most prominent family(81.54%, 243/298). Other family strains included T family(9.06%, 27/298), U family(0.67%, 2/298), LAM9 family(0.34%, 1/298) and Manu family(0.34%, 1/298). The rates of multidrug-resistant (MDR) M.Tuberculosis, age, type of case and education between Beijing and non-Beijing family strains were not statistically different, while the distribution in the three different regions among these was statistically significant.
VNTR results showed that strains were classified into 280 genotypes, and 33 (11.07%) strains could be grouped into 14 clusters. 11 of the 15-VNTR loci were highly or moderately discriminative according to the Hunter-Gaston discriminatory index.

Conclusions
We concluded that the Beijing family genotype was the most prevalent genotype and 15-locus VNTR typing might be suitable for genotyping of M. tuberculosis in Shaanxi Province. There was less association between Beijing family genotypes and drug resistance in our study area.
Neurotoxicity of different amyloid beta subspecies in mice and their interaction with isoflurane anaesthesia
Authors: Borgstedt Laura , Blobner Manfred , Musiol Maximilian , Bratke Sebastian , Syryca Finn , Rammes Gerhard , Jungwirth Bettina , Schmid Sebastian 
Published: December 2020

BackgroundThe aim of this study was to assess different amyloid beta subspecies’ effects on behaviour and cognition in mice and their interaction with isoflurane anaesthesia.MethodsAfter governmental approval, cannulas were implanted in the lateral cerebral ventricle. After 14 days the mice were randomly intracerebroventricularly injected with Aβ 1–40 (Aβ40), Aβ 1–42 (Aβ42), 3NTyr10-Aβ (Aβ nitro), AβpE3-42 (Aβ pyro), or phosphate buffered saline. Four days after the injection, 30 mice (6 animals per subgroup) underwent general anaesthesia with isoflurane. A “sham” anaesthetic procedure was performed in another 30 mice (6 animals per subgroup, 10 subgroups in total). During the next eight consecutive days a blinded assessor evaluated behavioural and cognitive performance using the modified hole-board test. Following the testing we investigated 2 brains per subgroup for insoluble amyloid deposits using methoxy staining. We used western blotting in 4 brains per subgroup for analysis of tumour-necrosis factor alpha, caspase 3, glutamate receptors NR2B, and mGlu5. Data were analysed using general linear modelling and analysis of variance.ResultsAβ pyro improved overall cognitive performance (p = 0.038). This cognitive improvement was reversed by isoflurane anaesthesia (p = 0.007), presumably mediated by decreased exploratory behaviour (p = 0.022 and p = 0.037). Injection of Aβ42 was associated with increased anxiety (p = 0.079). Explorative analysis on a limited number of brains did not reveal insoluble amyloid deposits or differences in the expression of tumour-necrosis factor alpha, NR2B, mGlu5, or caspase 3.ConclusionsTesting cognitive performance after intracerebroventricular injection of different amyloid beta subspecies revealed that Aβ pyro might be less harmful, which was reversed by isoflurane anaesthesia. There is minor evidence for Aβ42-mediated neurotoxicity. Preliminary molecular analysis of biomarkers did not clarify pathophysiological mechanisms.
Sensitivity and specificity of rapid hepatitis C antibody assays in freshly collected whole blood, plasma and serum samples: A multicentre prospective study
Authors: Vetter Beatrice N. , Ongarello Stefano , Tyshkovskiy Alexander , Alkhazashvili Maia , Chitadze Nazibrola , Choun Kimcheng , Sokkab An , De Weggheleire Anja , Vanroye Fien , Reipold Elena Ivanova 
Published: December 2020

Background
This study evaluated performance of two hepatitis C virus (HCV) rapid diagnostic tests (RDTs) performed by intended users in resource-limited settings.

Methods
Testing was conducted at three facilities in two countries (Georgia, Cambodia) using matched fingerstick whole blood, plasma and serum samples. Investigational RDTs were compared with a composite reference standard (CRS) comprised of three laboratory tests, and a reference RDT.

Results
In matched samples from 489 HCV positive and 967 HCV negative participants, specificity with both investigational RDTs was high using either reference method (≥98.4% in all sample types). Sensitivity was lower in whole blood versus plasma and serum for both RDTs compared with the CRS (86.5–91.4% vs 97.5–98.0% and 97.3–97.1%) and reference RDT (93.6–97.8% vs 100% and 99.4%). Sensitivity improved when considering only samples with detectable HCV viral load.

Conclusion
Sensitivity was highest in serum and plasma versus whole blood. The World Health Organization prequalification criterion (≥98%) was narrowly missed by both RDTs in serum, and one in plasma, possibly due to the intended user factor. Performance in whole blood was considered adequate, given potential roles of HCV infection history, improved sensitivity with detectable viral load and performance similarities to the reference RDT.
“It’s because I think too much”: Perspectives and experiences of adults with hypertension engaged in HIV care in northern Tanzania
Authors: Manavalan Preeti , Minja Linda , Wanda Lisa , Hertz Julian T. , Thielman Nathan M. , Okeke Nwora Lance , Mmbaga Blandina T. , Watt Melissa H. 
Published: December 2020

BackgroundHypertension, a leading risk for cardiovascular mortality, is an important co-morbidity among people living with HIV (PLHIV). In Tanzania, hypertension prevalence among PLHIV approaches 20 to 30%. However, most patients are unaware of their diagnosis and are not receiving treatment. Understanding the barriers to hypertension care is a critical first step in developing interventions to improve cardiovascular outcomes among PLHIV in Tanzania and similar settings.MethodsBetween September 1stand November 26th, 2018 thirteen semi structured in-depth interviews were conducted with hypertensive patients engaged in HIV care in two HIV clinics located in government health facilities in northern Tanzania. Interviews were audio-recorded, translated into English, transcribed and thematically coded using NVivo. Data analysis was conducted using applied thematic analysis.ResultsParticipants had a median age of 54 (IQR 41–65) years. Of the 13 participants, eight stated they had used antihypertensive medication previously, but only one participant described current use of antihypertensive therapy. All participants were currently using antiretroviral therapy. The data revealed a range of themes including limited hypertension knowledge. Universally, all participants believed that “thinking too much”, i.e. stress, was the major contributor to hypertension and that by “reducing thoughts”, one may control hypertension. Additional emerging themes included a perceived overlap between hypertension and HIV, delays in hypertension diagnosis and linkage to care, challenges with provider communication and counseling, reluctance towards antihypertensive medication, lack of integration of hypertension and HIV care, and additional structural barriers to hypertension care.ConclusionsParticipants described multiple, intersecting challenges related to hypertension management. Barriers specific to PLHIV included siloed care, HIV-related stigma, and burden from multiple medical conditions. Multifaceted strategies that seek to address structural barriers, hypertension education, psychosocial stressors and stigma, and that are integrated within HIV care are urgently needed to improve cardiovascular outcomes among PLHIV in sub-Saharan Africa.
Skill retention with ultrasound curricula
Authors: Matthews Lawrence , Contino Krysta , Nussbaum Charlotte , Hunter Krystal , Schorr Christa , Puri Nitin 
Published: December 2020

Background
Implementation of a point of care ultrasound curricula is valuable, but optimal integration for internal medicine residency is unclear. The purpose of this study was to evaluate if a structured ultrasound curriculum vs. structured ultrasound curriculum plus supervised thoracic ultrasounds would improve internal medicine residents’ skill and retention 6 and 12 months from baseline.

Methods
We conducted a randomized controlled study evaluating internal medical residents’ skill retention of thoracic ultrasound using a structured curriculum (control, n = 14) vs. structured curriculum plus 20 supervised bedside thoracic ultrasounds (intervention, n = 14). We used a stratified randomization based on program year. All subjects attended a half-day course that included 5 lectures and hands-on sessions at baseline. Assessments included written and practical exams at baseline, immediately post-course and at 6 and 12 months. Scores are reported as a percentage for the number of correct responses/number of questions (range 0–100%). The Mann Whitney U and the Friedman tests were used for analyses.

Results
Twenty-eight residents were enrolled. Two subjects withdrew prior to the 6-month exams. Written exam scores for all subjects improved, baseline median (IQR) 60 (46.47 to 66.67) post-course 80 (65 to 86.67), 6-month 80 (66.67 to 86.67) and 12-month 86.67 (80 to 88.34), p = <0.001. All subjects practical exam scores median (IQR) significantly improved, baseline 18.18 (7.95 to 32.95), post-course 59.09 (45.45 to 70.45), 6 month 71.74 (60.87 to 82.61) and 12-month 76.09 (65.22 to 88.05), p = <0.001. Comparing the control group to the intervention group, there were statistically significant higher scores, median (IQR), in the intervention group on the practical exam at 6 months 63.05 (48.92 to 69.57) vs. 82.61(72.83 to89.13), p = <0.001.

Conclusion
In this cohort, internal medicine residents participating in a structured thoracic ultrasound course plus 20-supervised ultrasounds achieved higher practical exam scores long-term compared to controls.
Inflammatory patterns in fixed airflow obstruction are dependent on the presence of asthma
Authors: Mogensen Ida , Jacinto Tiago , Alving Kjell , Fonseca João A. , Janson Christer , Malinovschi Andrei 
Published: December 2020

Rationale
Fixed airflow obstruction (FAO) can complicate asthma. Inflammation is a proposed underlying mechanism.

Objective
Our aim in this cross-sectional investigation was to evaluate the blood leucocyte pattern and level of exhaled nitric oxide in asthmatics and non-asthmatics with or without FAO.

Methods
A total of 11,579 individuals aged ≥20 years from the US National Health and Nutrition Examination Survey were included. They were grouped as: controls without asthma and FAO (n = 9,935), asthmatics without FAO (n = 674), asthmatics with FAO (n = 180) and non-asthmatics with FAO (n = 790). FAO was defined as post-bronchodilator FEV1/FVC < lower limit of normal. Exhaled nitric oxide ≥ 25ppb, blood eosinophil levels ≥300 cells/μL, and blood neutrophil levels ≥5100 cells/μL were defined as elevated. Stratified analyses for smoking and smoking history were performed.

Results
Elevated blood eosinophil levels were more common in all groups compared to the controls, with the highest prevalence in the group with asthma and fixed airflow obstruction (p<0.01). In a multiple logistic regression model adjusted for potential confounders including smoking, the asthma groups had significantly higher odds ratios for elevated B-Eos levels compared to the control group (odds ratio 1.4, (confidence interval: 1.1–1.7) for the asthma group without fixed airflow obstruction and 2.5 (1.4–4.2) for the asthma group with fixed airflow obstruction). The group with fixed airflow obstruction without asthma had higher odds ratio for elevated blood neutrophil levels compared to the controls: 1.4 (1.1–1.8). Smoking and a history of smoking were associated to elevated B-Neu levels.

Conclusion
Fixed airflow obstruction in asthma was associated with elevated blood eosinophil levels, whereas fixed airflow obstruction without asthma was associated with elevated blood neutrophil levels.