bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fatal case of traumatic brain injury with severe coagulopathy due to Rhabdophis tigrinus (yamakagashi) bites: a case report
Authors: Ueno Daisuke , Yasukazu Shiino , Takahashi Jiro , Miyamoto Satomi , Inoue Takahiro 
Published: December 2021

AbstractBackgroundYamakagashi venom is a prothrombin activator, leading to disseminated intravascular coagulation. We report a fatal case of severe coagulopathy from head trauma assumed to be caused by a yamakagashi bite.Case presentationAn 80-year-old man fell and developed systemic tonic–clonic convulsions. Head computed tomography revealed brain contusion and acute subdural hematoma. Physical examination revealed two bite marks with persistent bleeding on the right lower leg. The patient stated that he had been bitten by some creature 3 days prior, but the bite was left untreated. Laboratory tests showed fibrinogen levels below the detection limit. Although eighteen units of fresh frozen plasma were administered for coagulopathy, fibrinogen levels did not improve. He died about 18 h after a head injury.ConclusionIn this case of a yamakagashi bite with active bleeding due to trauma, early administration of yamakagashi antivenom should be considered to control coagulopathy.
pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science
Authors: Guerra João Victor da Silva , Ribeiro-Filho Helder Veras , Jara Gabriel Ernesto , Bortot Leandro Oliveira , Pereira José Geraldo de Carvalho , Lopes-de-Oliveira Paulo Sérgio 
Published: December 2021

Abstract
Background
Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from the increasing availability of biostructural data due to advances in structural determination and computational methods. In this scenario, data-intensive cavity analysis demands efficient scripting routines built on easily manipulated data structures. To fulfill this need, we developed pyKVFinder, a Python package to detect and characterize cavities in biomolecular structures for data science and automated pipelines.

Results
pyKVFinder efficiently detects cavities in biomolecular structures and computes their volume, area, depth and hydropathy, storing these cavity properties in NumPy arrays. Benefited from Python ecosystem interoperability and data structures, pyKVFinder can be integrated with third-party scientific packages and libraries for mathematical calculations, machine learning and 3D visualization in automated workflows. As proof of pyKVFinder’s capabilities, we successfully identified and compared ADRP substrate-binding site of SARS-CoV-2 and a set of homologous proteins with pyKVFinder, showing its integrability with data science packages such as matplotlib, NGL Viewer, SciPy and Jupyter notebook.

Conclusions
We introduce an efficient, highly versatile and easily integrable software for detecting and characterizing biomolecular cavities in data science applications and automated protocols. pyKVFinder facilitates biostructural data analysis with scripting routines in the Python ecosystem and can be building blocks for data science and drug design applications.
LDexpress: an online tool for integrating population-specific linkage disequilibrium patterns with tissue-specific expression data
Authors: Lin Shu-Hong , Thakur Rohit , Machiela Mitchell J. 
Published: December 2021

AbstractGenome-wide association studies have identified thousands of genetic susceptibility loci associated with cancer as well as other traits and diseases. Mapping germline variation in identified genetic susceptibility regions to alterations in nearby gene expression nominates candidate genes potentially related to disease risk for further functional investigation. We developed LDexpress as an online resource that integrates population-specific linkage disequilibrium data from the 1000 Genomes (1000G) project and tissue-specific expression data from the Genotype-Tissue Expression project to better study regional germline variation impacting gene expression. LDexpress is a publicly available web tool designed to be easy to use, flexible to conduct a wide range of variant queries, and quick to efficiently investigate dozens of query variants across multiple tissue types. We demonstrate the utility of LDexpress using example genomic queries and anticipate this tool will accelerate understanding of disease etiology by uncovering associations of regional germline variation to nearby gene expression.
A systematic review and meta-analysis of host genetic factors associated with influenza severity
Authors: Van Goethem Nina , Danwang Célestin , Bossuyt Nathalie , Van Oyen Herman , Roosens Nancy H. C. , Robert Annie 
Published: December 2021

Abstract
Background
The severity of influenza disease can range from mild symptoms to severe respiratory failure and can partly be explained by host genetic factors that predisposes the host to severe influenza. Here, we aimed to summarize the current state of evidence that host genetic variants play a role in the susceptibility to severe influenza infection by conducting a systematic review and performing a meta-analysis for all markers with at least three or more data entries.

Results
A total of 34 primary human genetic association studies were identified that investigated a total of 20 different genes. The only significant pooled ORs were retrieved for the rs12252 polymorphism: an overall OR of 1.52 (95% CI [1.06–2.17]) for the rs12252-C allele compared to the rs12252-T allele. A stratified analysis by ethnicity revealed opposite effects in different populations.

Conclusion
With exception for the rs12252 polymorphism, we could not identify specific genetic polymorphisms to be associated with severe influenza infection in a pooled meta-analysis. This advocates for the use of large, hypothesis-free, genome-wide association studies that account for the polygenic nature and the interactions with other host, pathogen and environmental factors.
Endoluminal vacuum therapy in the management of an esophago-pleural fistula as a complication of Boerhaave syndrome in a patient with eosinophilic esophagitis
Authors: Tuñon Carlos , De Lucas Juan , Cubilla Jan , Andrade Rafael , Aguirre Miguel , Zúñiga Cisneros Julio 
Published: December 2021

Abstract
Background
Boerhaave syndrome is an uncommon condition that represents about 15% of all esophageal perforation. A subset of these patients has eosinophilic esophagitis, a chronic inflammatory disease of the esophagus, that carries a risk of perforation of about 2%. Esophageal perforations can rarely result in the development of an esophago-pleural fistula. Treatment of esophago-pleural fistula represent a challenge due to lack of high quality evidence and scarce reported experience. Endoluminal vacuum-assisted therapy could have a role in the management by using the same principle applied in external wounds which provide wound drainage and tissue granulation.

Case presentation
We report a unique case of a 24-year-old man with eosinophilic esophagitis complicated with an esophageal rupture who developed an esophago-pleural fistula and was successfully managed with a non-surgical approach using endoluminal vacuum-assisted therapy. To our knowledge this could be the first experience reported in a patient with eosinophilic esophagitis.

Conclusion
Endoluminal vacuum-assisted therapy might be an effective and novel strategy in patients with eosinophilic esophagitis and esophago-pleural fistula as a consequence of Boerhaave syndrome. Appropriately designed studies are required.
Association of HSD17B13 rs72613567: TA allelic variant with liver disease: review and meta-analysis
Authors: Tang Shan , Zhang Jing , Mei Ting-Ting , Zhang Wen-Yan , Zheng Su-Jun , Yu Hai-Bin 
Published: December 2021

AbstractBackgroundTo assess the association of HSD17B13 rs72613567:TA allelic variant with liver disease, we performed the current review and meta-analysis.MethodsSeven studies were identified by a search of CNKI,CBM,MEDLINE, PubMed, EMBASE, and CENTRAL databases from inception to November 2021. Odds ratios (ORs) with 95% confidence interval (CI) were calculated using random effects model or fixed effects model based on the between-study heterogeneity. The Stata 14.0 software was employed for data analysis.ResultsStatistical analysis showed that the HSD17B13 rs72613567:TA allelic variant can decrease the risk of hepatocellular carcinoma(HCC) in nonalcoholic fatty liver disease (NAFLD) patients, alcoholic fatty liver disease (ALD) patients and viral hepatitis patients (TA vs T OR = 0.766, 95% CI = 0.682–0.860, P = 0.000; TATA + TAT vs TT OR = 0.755, 95% CI = 0.645–0.885, P = 0.001) or healthy controls(TA vs T OR = 0.649, 95% CI = 0.431–0.977, P = 0.038). Besides, the HSD17B13 rs72613567:TA allelic variant can also provide protection from nonalcoholic fatty liver disease (NAFLD) not only in entire population (TA vs T OR = 0.669, 95% CI = 0.524–0.856, P = 0.001) but also in healthy people (TA vs T OR = 0.600, 95% CI = 0.464–0.777, P = 0.000). No significant publication bias found in this airticle.ConclusionThe present findings suggest HSD17B13 rs72613567:TA allelic variant can reduce the risk of HCC and NAFLD in the entire population studied.
Association of FIB-4 index and clinical outcomes in critically ill patients with acute kidney injury: a cohort study
Authors: Shi Yi-Yi , Zheng Rui , Cai Jie-Jie , Fang Zheng-Dong , Chen Wen-Jing , Pan Jing-Ye , Qian Song-Zan 
Published: December 2021

Abstract
Background
The relationship between fibrosis-4 (FIB-4) index and clinical outcomes in patients with acute kidney injury (AKI) is unclear. We aimed to investigate the association between FIB-4 index and all-cause mortality in critically ill patients with AKI.

Methods
We used data from the Multiparameter Intelligent Monitoring in Intensive Care III (MIMIC-III) database (v1.4). The FIB-4 score was calculated using the existing formulas. logistic regression model, and Cox proportional hazards model were used to assessed the relationship between the FIB-4 index and in-hospital,28-day and 90-day mortality, respectively.

Results
A total of 3592 patients with AKI included in the data analysis. 395 (10.99%) patients died during hospitalization and 458 (12.74%) patients died in 28-day. During the 90-day follow-up, 893 (22.54%) patients were dead. An elevated FIB-4 value was significantly associated with increased in-hospital mortality when used as a continuous variable (odds ratio [OR] 1.183, 95% confidence interval [CI] 1.072–1.305, P = 0.002) and as a quartile variable (OR of Q2 to Q4 1.216–1.744, with Q1 as reference). FIB-4 was positively associated with 28-day mortality of AKI patients with hazard ratio (HR) of 1.097 (95% CI 1.008, 1.194) and 1.098 (95% 1.032, 1.167) for 90-day mortality, respectively.

Conclusion
This study demonstrated the FIB-4 index is associated with clinical outcomes in critically ill patients with acute kidney injury.
Reactivation of BCG vaccination scars after vaccination with mRNA-Covid-vaccines: two case reports
Authors: Mohamed Libin , Madsen Anne Marie Rosendahl , Schaltz-Buchholzer Frederik , Ostenfeld Anne , Netea Mihai G. , Benn Christine Stabell , Kofoed Poul-Erik 
Published: December 2021

Abstract
Background
From May 2020 to January 2021, we enrolled 1233 health care workers (HCW) from Danish Hospitals in a randomized trial evaluating whether Bacille Calmette-Guérin (BCG) provides protection against COVID-19. Participants were randomized 1:1 to BCG vs saline and followed for 6 months. From December 2020, Covid-19 vaccines were offered to the HCW. In most cases, BCG vaccination results in a characteristic scar. Reactivation of the BCG scar has been described in children during viral infections and following influenza vaccination, but is mostly associated to Kawasaki’s disease, a disease entity with pathogenesis likely similar to the child Covid-19 complication MIS-C: Multi-System Inflammatory Syndrome. Reactivation of scars after neonatal BCG vaccination has recently been described in four women after Covid-19 mRNA vaccination. Two of our trial participants experienced reactivation of their novel BCG scars after receiving mRNA Covid-19 vaccination 6 to 8 months post-BCG.

Case presentations
Two female HCW participants that had been randomly allocated to BCG in the BCG-DENMARK-COVID trial, spontaneously reported itching and secretion at the BCG scar site after having received mRNA Covid-19 vaccination (Moderna and Pfizer-BioNTech) 6 to 8 months following inclusion and BCG vaccination. One participant, who had a larger BCG skin reaction, noticed re-appearing symptoms after both the first and the second COVID-vaccine dose, while the other participant only noted symptoms after the second dose. Both had been BCG vaccinated during childhood, and no reactivation was noted in the older scars. No treatment was needed or provided.

Conclusions
The reactivation of the BCG scar after receiving mRNA vaccine might have been caused by cross-reactivity between BCG and SARS-CoV-2. In both cases, the symptoms were bothersome, but self-limiting and left no sequelae. The risk of reactivation at the scar site is thus not a reason to avoid vaccination with either vaccine.
Optimised electronic patient records to improve clinical monitoring of HIV-positive patients in rural South Africa (MONART trial): study protocol for a cluster-randomised trial
Authors: Iwuji Collins , Osler Meg , Mazibuko Lusanda , Hounsome Natalia , Ngwenya Nothando , Chimukuche Rujeko Samanthia , Khoza Thandeka , Gareta Dickman , Sunpath Henry , Boulle Andrew , Herbst Kobus 
Published: December 2021

AbstractBackgroundThere is poor viral load monitoring (VLM) and inadequate management of virological failure in HIV-positive individuals on antiretroviral therapy in rural KwaZulu-Natal, South Africa. This could be contributing to increasing HIV drug resistance in the setting. This study aims to investigate the clinical and process impediments in VLM within the health system and to evaluate a quality improvement package (QIP) to address the identified gaps. The QIP comprises (i) a designated viral load champion responsible for administrative management and triaging of viral load results (ii) technological enhancement of the routine clinic-based Three Interlinked Electronic Register (TIER.Net) to facilitate daily automatic import of viral load results from the National Health Service Laboratory to TIER.Net (iii) development of a dashboard system to support VLM.Methods/designThe study will evaluate the effectiveness of the QIP compared to current care for improving VLM and virological suppression using an effectiveness implementation hybrid type 3 design. This will use a cluster-randomised design with the primary healthcare clinics as the unit of randomisation with ten clinics randomised in a 1:1 ratio to either the intervention or control arm. We will enrol 150 HIV-positive individuals who had been on ART for ≥ 12 months from each of the ten clinics (750 in 5 intervention clinics vs. 750 in 5 control clinics) and follow them up for a period of 12 months. The primary outcome is the proportion of all patients who have a viral load (VL) measurement and are virally suppressed (composite outcome) after 12 months of follow up. Secondary outcomes during follow up include proportion of all patients with at least one documented VL in TIER.Net, proportion with VL ≥ 50 copies/mL, proportion with VL ≥ 1000 copies/mL (virological failure) and subsequent switch to second-line ART.DiscussionWe aim to provide evidence that a staff-centred quality improvement package, designated viral load monitoring champion, and augmentation of TIER.Net with a dashboard system will improve viral load monitoring and lead to improved virological suppression.Trial registration:This trial is registered on ClinicalTrials.gov on 8 Oct 2021. Identifier: NCT05071573;https://clinicaltrials.gov/ct2/show/NCT05071573?term=NCT05071573&draw=2&rank=1
Empyema caused by Streptococcus constellatus: a case report and literature review
Authors: Xia Jingyan , Xia Lexin , Zhou Hui , Lin Xiuhui , Xu Feng 
Published: December 2021

Abstract
Background
Streptococcus constellatus is a member of Streptococcus anginosus group (SAG) that tends to cause pyogenic infections in various sites. However, Streptococcus constellatus is easily ignored by routine clinical laboratory tests for its prolonged anaerobic culture environment.

Case presentation
A 71-year-old man was admitted to our hospital due to productive cough, fever, chest pain and shortness of breath for 3 weeks. Chest computed tomography showed patchy opacities and right-sided pleural effusion, so a chest tube was inserted and purulent and hemorrhagic fluid was aspirated. The routine etiological examinations of the pleural effusion were all negative, and next-generation sequencing (NGS) detected Streptococcus constellatus. Intravenous piperacillin-tazobactam 4.5 g every 8 h was used accordingly. The patient recovered and subsequent chest computed tomography confirmed the improvement.

Conclusions
We reported a case of empyema secondary to Streptococcus constellatus infection, which was identified by NGS, instead of bacterial culture. This case highlights the utility of NGS in detecting pathogens negative in traditional bacterial tests.
Risk factors for Lyme disease stage and manifestation using electronic health records
Authors: Moon Katherine A. , Pollak Jonathan S. , Poulsen Melissa N. , Heaney Christopher D. , Hirsch Annemarie G. , Schwartz Brian S. 
Published: December 2021

Abstract
Background
Little is known about risk factors for early (e.g., erythema migrans) and disseminated Lyme disease manifestations, such as arthritis, neurological complications, and carditis. No study has used both diagnoses and free text to classify Lyme disease by disease stage and manifestation.

Methods
We identified Lyme disease cases in 2012–2016 in the electronic health record (EHR) of a large, integrated health system in Pennsylvania. We developed a rule-based text-matching algorithm using regular expressions to extract clinical data from free text. Lyme disease cases were then classified by stage and manifestation using data from both diagnoses and free text. Among cases classified by stage, we evaluated individual, community, and health care variables as predictors of disseminated stage (vs. early) disease using Poisson regression models with robust errors. Final models adjusted for sociodemographic factors, receipt of Medical Assistance (i.e., Medicaid, a proxy for low socioeconomic status), primary care contact, setting of diagnosis, season of diagnosis, and urban/rural status.

Results
Among 7310 cases of Lyme disease, we classified 62% by stage. Overall, 23% were classified using both diagnoses and text, 26% were classified using diagnoses only, and 13% were classified using text only. Among the staged diagnoses (n = 4530), 30% were disseminated stage (762 arthritis, 426 neurological manifestations, 76 carditis, 95 secondary erythema migrans, and 76 other manifestations). In adjusted models, we found that persons on Medical Assistance at least 50% of time under observation, compared to never users, had a higher risk (risk ratio [95% confidence interval]) of disseminated Lyme disease (1.20 [1.05, 1.37]). Primary care contact (0.59 [0.54, 0.64]) and diagnosis in the urgent care (0.22 [0.17, 0.29]), compared to the outpatient setting, were associated with lower risk of disseminated Lyme disease.

Conclusions
The associations between insurance payor, primary care status, and diagnostic setting with disseminated Lyme disease suggest that lower socioeconomic status and less health care access could be linked with disseminated stage Lyme disease. Intervening on these factors could reduce the individual and health care burden of disseminated Lyme disease. Our findings demonstrate the value of both diagnostic and narrative text data to identify Lyme disease manifestations in the EHR.
Ureaplasma parvum meningitis following atypical choroid plexus papilloma resection in an adult patient: a case report and literature review
Authors: Xing Na , Zhao Zhenxiang , Li Qingjing , Dong Yalan , Li Jianfeng , Zhang Shuping 
Published: December 2021

Abstract
Background
While Ureaplasma parvum has previously been linked to the incidence of chorioamnionitis, abortion, premature birth, and perinatal complications, there have only been rare reports of invasive infections of the central nervous system (CNS) in adults. Owing to its atypical presentation and the fact that it will yield sterile cultures using conventional techniques, diagnosing U. parvum meningitis can be challenging.

Case presentation
We describe a case of U. parvum meningitis detected in an adult patient following surgical brain tumor ablation. After operation, the patient experienced epilepsy, meningeal irritation, and fever with unconsciousness. Cerebrospinal fluid (CSF) analysis showed leukocytosis (484 * 106 /L), elevated protein levels (1.92 g/L), and decreased glucose concentrations (0.02 mmol/L). Evidence suggested that the patient was suffering from bacterial meningitis. However, no bacterial pathogens in either CSF or blood were detected by routine culture or serology. The symptoms did not improve with empirical antibiotics. Therefore, we performed metagenomic next-generation sequencing (mNGS) to identify the etiology of the meningitis. Ureaplasma parvum was detected by mNGS in CSF samples. To the best of our knowledge, this case is the first reported instance of U. parvum meningitis in an adult patient in Asian. After diagnosis, the patient underwent successful moxifloxacin treatment and recovered without complications.

Conclusions
As mNGS strategies can enable the simultaneous detection of a diverse array of microbes in a single analysis, they may represent a valuable means of diagnosing the pathogens responsible for CNS infections and other clinical conditions with atypical presentations.