bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and characteristics of coronary artery fistulas among 20 259 patients undergoing invasive coronary angiography
Authors: Yan Wei , He Ziling , Luo Yong , Huang Weiyi , Zhu Bo , Zhong Yi , Wang Xuefeng 
Published: January 2024

Background
Coronary artery fistula (CAF) is a rare coronary anomaly. This study aimed to investigate the prevalence, clinical features, and imaging characteristics of CAF among patients undergoing coronary angiography (CAG).

Method
This was a retrospective study including 20 259 consecutive patients (12 458 were male) who underwent CAG at our institution from September 2018 to March 2023. Electronic angiography records were reviewed, and a total of 86 (0.42%) CAF patients were enrolled and analyzed.

Result
Of the 86 CAF patients, 42 (49%) were male. Thus, the prevalence of CAF for males and females was 0.34% and 0.56%, respectively. Arrhythmia, left ventricular (LV) hypertrophy, LV dilation, and LV systolic dysfunction were observed in 38, 25, 10 and 5 cases, respectively. Among the 86 CAF patients, a total of 117 CAFs were detected. 61 (71%) patients had a single CAF, and the remaining 25 (29%) patients had multiple CAFs. Of the 117 CAFs, the most common origins and terminations were the left anterior descending artery (n = 50) and the pulmonary artery (n = 73), respectively. The CAF diameters were greatly varied, ranging from unmeasurable to 7.8 mm, and 22 (18%) CAFs were larger than 3 mm.

Conclusion
In the present study, the prevalence of CAF was 0.42% with a female predilection. Arrhythmia, LV remodeling and dysfunction were common. Seventy-one percent of patients had a single CAF. The left anterior descending artery and the pulmonary artery were the most common origin and termination of CAFs, respectively. Most CAFs were small, and 18% of CAFs were larger than 3 mm.
The existence of a bidirectional link between ischemic heart disease and fibromyalgia
Authors: Mansour Mahmoud , Ehrenberg Scott , Mahroum Naim , Tsur Avishai M. , Fisher Lior , Amital Howard 
Published: January 2024

Study objectives
Fibromyalgia (FM) is one of the most common causes of chronic widespread musculoskeletal pain, but also sleep disturbances, cognitive and psychological disorders. It has been suggested that FM may have a correlation with cardiovascular events. In this study, we aimed to assess the association between FM and ischemic heart disease (IHD).

Methods
A population-based cross-sectional study was conducted utilizing data retrieved from the largest medical records database in Israel, Clalit Health Services. Patients were defined as having FM or IHD when there were at least two such documented diagnoses in their medical records. The occurrence of IHD was compared between FM and age- and sex-frequency-matched healthy controls. A logistic regression model was used to estimate this association following an adjustment for conventional cardiovascular risk factors and depression.

Results
An overall population of 18 598 FM patients and 36 985 age- and gender-matched controls were included in the study. The proportion of IHD amongst FM patients was increased in comparison to controls (9.2% and 6.2%, respectively; P < 0.001). Furthermore, FM demonstrated an independent association with IHD on multivariate analysis (odds ratio [OR], 1.43; 95% confidence intervals [CI], 1.33–1.54; P < 0.0001). Finally, IHD was also found to be independently associated with the diagnosis of FM (OR, 1.40; CI, 1.31–1.51; P < 0.0001).

Conclusion
Our data suggest a bidirectional link between FM and IHD even after the adjustment for conventional cardiovascular risk factors. These findings should be considered when treating patients with either FM or IHD, and their routine interactional screening may be of clinical importance.
Evidence Map of Clinical Practice Guideline Recommendations on Stroke Rehabilitation
Authors: Wei Lili , Shang Wenru , Nan Yaxing , Liu Yuming , Yang Jingyu , Yang Kehu 
Published: January 2024

Abstract
The purpose of this study was to provide an evidence map for explaining research trends and gaps. Four databases and clinical practice guidelines-related Websites were searched up to March 2022. Basic information, methodological quality, reporting quality of clinical practice guidelines, and similar stroke recommendations were extracted. The methodological and reporting quality of stroke clinical practice guidelines were evaluated using the Appraisal of Guidelines Research and Evaluation (second version) instrument and the Reporting Items for Practice Guidelines in Healthcare checklist. The bubble plot format of the evidence map helped visualize the overall quality. Data management and analysis were performed using Excel 2013 and SPSS 22.0 software. A total of 12 clinical practice guidelines, published between 1997 and 2020, were included for in-depth analysis. The identified clinical practice guidelines had a mixed quality and scored poorly in the developmental rigor and applicability domains by Appraisal of Guidelines Research and Evaluation (second version). According to the Reporting Items for Practice Guidelines in Healthcare checklist, field four (clarity of expression) showed the highest (79.2%), and field three (rigor of formulation) secured the lowest (28%) reporting rates. The stroke rehabilitation recommendations primarily focused on organizational management, timing and intensity, rehabilitation and nutritional management of dysphagia, return to work, communication, speech, and language function. This would promote improvement in developing trustworthy clinical practice guidelines for stroke rehabilitation.
Prescription Trends of Opioid and Nonopioid Controlled Prescription Adjunctive Analgesics Before and After Cervical Spinal Surgery
Authors: Shermon Suzanna , Kim Chong 
Published: January 2024

Objective
Cervical spine surgery may be needed in those with refractory pain or neurologic deficits to improve outcomes in patients with cervical spine disease. However, consensus varies in the literature on the effect of surgery on opioid use. The objectives of this study were to analyze prescription rates of multiple controlled substances before and after cervical spine surgery and distinguish factors that may have contributed to opioid use after surgery.

Design
This is a retrospective cohort study analyzing prescription trends of various controlled substances in 632 patients who underwent cervical spine surgery from 2019 to 2021.

Results
Opioids have the largest rise in prescriptions at 3- and 6-mo time points after cervical spine surgery. A significant association (P < 0.001) was found between opioid use 1 yr before and 1 yr after cervical spine surgery. Exposure to opioids before surgery (odds ratio = 2.77, 95% confidence interval = 1.43–5.51, P = 0.003) and higher morphine milligram equivalent dose (odds ratio = 1.02, 95% confidence interval =1.01–1.04, P = 0.012) were found to be associated with opioid use after surgery. Significantly more females were prescribed controlled substances (P = 0002).

Conclusions
Higher morphine milligram equivalent dose and opioid exposure before surgery are important factors in predicting postsurgical opioid use.
Inadequacies in Undergraduate Musculoskeletal Education - A Survey of Nationally Accredited Allopathic Medical Programs in Canada
Authors: Peeler Jason , Mann Steve , Orchard Taylor , Yu Jaime 
Published: January 2024

Abstract

Objective
To document the current state of MSK medicine education across nationally accredited undergraduate medical programs.

Design
A cross-sectional survey design was used to gather curricular data on three MSK themes: 1) anatomy education; 2) preclinical education; and 3) clerkship education.

Results
The survey had a 100% response rate with all 14 english language medical schools in Canada responding. The mean time spent teaching MSK anatomy was 29.8 hours (SD ± 13.7, range 12 – 60), with all but one program using some form of cadaveric-based instruction. MSK preclinical curricula averaged 58.0 hours (SD ± 53.4, range 6 - 204), with didactic lectures, case-based learning, and small group tutorials being the most common modes of instruction. Curricular content varied greatly, with only 25% of “core or must-know” MSK topics being covered in detail by all programs. MSK training in clerkship was required by only 50% of programs, most commonly being two-weeks in duration.

Conclusion
Results document the large variability and curricular inadequacies that exist in MSK education across nationally accredited allopathic programs and highlight the need for the identification and implementation of more consistent MSK curricular content and educational standards by all nationally accredited medical programs.
Non-canonical induction of autophagy increases adeno-associated virus type 2 (AAV2) transduction efficiency
Authors: Sutter Sereina O. , Jetzer Sarah , Lkharrazi Anouk , Pedersen Sofia , Schraner Elisabeth M. , Vogt Bernd , Büning Hildegard , Fraefel Cornel 
Published: January 2024

ABSTRACTAdeno-associated virus (AAV) serotypes infect a wide range of cell types, making this member of the parvovirus family a versatile tool in gene therapy. Infection as well as transduction is set in motion by means of specific receptors in conjunction with trafficking pathways, particularly endocytosis, a main cell entry pathway of non-enveloped viruses. Here, we report that efficacy of transduction is enhanced upon treating cells with hyperosmotic sucrose, a known blocker of clathrin-mediated endocytosis, through the non-canonical induction of autophagy. This mechanism of autophagy induction, however, is different from the previously reported AAV2-mediated induction of autophagy, which relies on a canonical, phosphoinositide 3-kinase class III (PI3K-III) complex-dependent pathway and appears to be dependent on the virus intrinsic secreted phospholipase A2 (sPLA2) domain, particularly its catalytic center activity.IMPORTANCEAdeno-associated virus (AAV) vectors are among the most frequently applied virus-based delivery vehicles for gene therapy. Lack of pathogenicity for humans, availability of a huge number of AAV serotypes differing in their cellular tropism, and the mainly episomal persistence of AAV vector genomes are clear advantages of these biological nanoparticles. By exploring non-pharmacological inducers of autophagy, we provide evidence for a potent and easy to apply strategy to significantly improve the efficacy of recombinant AAV-based gene delivery in hepatic and structural cells. Besides, our data also demonstrate the importance of autophagy for AAV2 infection and vector-mediated transduction in non-hepatic cells.
Machine Learning Uncovers the Transcriptional Regulatory Network for the Production HostStreptomyces albidoflavus
Authors: Jönsson Mathias , Sigrist Renata , Gren Tetiana , Petrov Mykhaylo Semenov , Marcussen Nils , Svetlova Anna , Charusanti Pep , Gockel Peter , Palsson Bernhard O. , Yang Lei , Özdemir Emre 
Published: January 2024

AbstractStreptomyces albidoflavusis a popular and genetically tractable platform strain used for natural product discovery and production via the expression of heterologous biosynthetic gene clusters (BGCs). However, its transcriptional regulatory network (TRN) and its impact on secondary metabolism is poorly understood. Here we characterized its TRN by applying an independent component analysis to a compendium of 218 high quality RNA-seq transcriptomes from both in-house and public sources spanning 88 unique growth conditions. We obtained 78 independently modulated sets of genes (iModulons) that quantitatively describe the TRN and its activity state across diverse conditions. Through analyses of condition-dependent TRN activity states, we (i) describe how the TRN adapts to different growth conditions, (ii) conduct a cross-species iModulon comparison, uncovering shared features and unique characteristics of the TRN across lineages, (iii) detail the transcriptional activation of several endogenous BGCs, including surugamide, minimycin and paulomycin, and (iv) infer potential functions of 40% of the uncharacterized genes in theS. albidoflavusgenome. Our findings provide a comprehensive and quantitative understanding of the TRN ofS. albidoflavus, providing a knowledge base for further exploration and experimental validation.Graphical Abstract
WITHDRAWN: Environmentally-informed functional characterization of a plastid diatom metabolic bridge of mitochondrial origin
Authors: Dorrell Richard G. , Zhang Youjun , Liang Yue , Gueguen Nolwenn , Nonoyama Tomomi , Croteau Dany , Penot Mathias , Adiba Sandrine , Bailleul Benjamin , Gros Valérie , Pierella Karlusich Juan José , Zweig Nathanaël , Fernie Alisdair R. , Jouhet Juliette , Maréchal Eric , Bowler Chris 
Published: January 2024

Withdrawal statementThe authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2022/507166. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: 10.1101/2022.09.08.507166
MATES: A Deep Learning-Based Model for Locus-specific Quantification of Transposable Elements in Single Cell
Authors: Wang Ruohan , Zheng Yumin , Zhang Zijian , Song Kailu , Wu Erxi , Zhu Xiaopeng , Wu Tao P. , Ding Jun 
Published: January 2024

AbstractTransposable elements (TEs) are crucial for genetic diversity and gene regulation. Current single-cell quantification methods often align multi-mapping reads to either ‘best-mapped’ or ‘random-mapped’ locations and categorize them at subfamily levels, overlooking the biological necessity for accurate, locus-specific TE quantification. Moreover, these existing methods are primarily designed for and focused on transcriptomics data, which restricts their adaptability to single-cell data of other modalities. To address these challenges, here we introduce MATES, a deep-learning approach that accurately allocates multi-mapping reads to specific loci of TEs, utilizing context from adjacent read alignments flanking the TE locus. When applied to diverse single-cell omics datasets, MATES shows improved performance over existing methods, enhancing the accuracy of TE quantification and aiding in the identification of marker TEs for identified cell populations. This development facilitates the exploration of single-cell heterogeneity and gene regulation through the lens of TEs, offering an effective transposon quantification tool for the single-cell genomics community.
mgikit: Demultiplexing toolkit for MGI fastq files
Authors: Bkhetan Ziad Al , Wang Sen 
Published: January 2024

AbstractMGI sequencing is reported to be an inexpensive solution to obtain genomics information. There is a growing need for software and tools to analyse MGI’s outputs efficiently.mgikitis a tool collection to demultiplex MGI fastq data and reformat it effectively. The tool and its documentation are available at:https://sagc-bioinformatics.github.io/mgikit/.
Opportunistic screening for coronary artery calcium deposition using chest radiographs – a multi-objective models with multi-modal data fusion
Authors: Jeong Jiwoong , Chao Chieh-Ju , Arsanjani Reza , Ayoub Chadi , Lester Steven J. , Pereyra Milagros , Said Ebram F , Roarke Michael , Tagle-Cornell Cecilia , Koepke Laura M. , Tsai Yi-Lin , Jung-Hsuan Chen , Chang Chun-Chin , Farina Juan M. , Trivedi Hari , Patel Bhavik N. , Banerjee Imon 
Published: January 2024

AbstractBackgroundTo create an opportunistic screening strategy by multitask deep learning methods to stratify prediction for coronary artery calcium (CAC) and associated cardiovascular risk with frontal chest x-rays (CXR) and minimal data from electronic health records (EHR).MethodsIn this retrospective study, 2,121 patients with available computed tomography (CT) scans and corresponding CXR images were collected internally (Mayo Enterprise) with calculated CAC scores binned into 3 categories (0, 1-99, and 100+) as ground truths for model training. Results from the internal training were tested on multiple external datasets (domestic (EUH) and foreign (VGHTPE)) with significant racial and ethnic differences and classification performance was compared.FindingsClassification performance between 0, 1-99, and 100+ CAC scores performed moderately on both the internal test and external datasets, reaching average f1-score of 0.66 for Mayo, 0.62 for EUH and 0.61 for VGHTPE. For the clinically relevant binary task of 0 vs 400+ CAC classification, the performance of our model on the internal test and external datasets reached an average AUCROC of 0.84.InterpretationThe fusion model trained on CXR performed better (0.84 average AUROC on internal and external dataset) than existing state-of-the-art models on predicting CAC scores only on internal (0.73 AUROC), with robust performance on external datasets. Thus, our proposed model may be used as a robust, first-pass opportunistic screening method for cardiovascular risk from regular chest radiographs. For community use, trained model and the inference code can be downloaded with an academic open-source license fromhttps://github.com/jeong-jasonji/MTL_CAC_classification.FundingThe study was partially supported by National Institute of Health 1R01HL155410-01A1 award.
Recreational and occupational physical activity and risk of adverse events in truncatingMYBPC3founder variant carriers
Authors: Hassanzada Fahima , Jansen Mark , van Lint Freyja H.M. , Bosman Laurens P. , Schmidt Amand F. , Dooijes Dennis , van de Sande Danny , Miah Bristi , van der Crabben Saskia N. , Wilde Arthur A.M. , Lekanne Deprez Ronald H. , de Boer Rudolf A. , Christiaans Imke , Jongbloed Jan D.H. , Jorstad Harald T. , Asselbergs Folkert W. , van Tintelen J. Peter , Baas Annette F. , te Riele Anneline S.J.M. 
Published: January 2024

AbstractBackgroundMYBPC3founder variants cause hypertrophic cardiomyopathy (HCM) leading to heart failure (HF) and malignant ventricular arrhythmias (MVA). Exercise is typically regarded a risk factor for disease expression, although evidence is conflicting. Stratifying by type of exercise may discriminate low-from high-risk activities in these patients.Objective(s)Evaluate effects of exercise, stratified by high-static and high-dynamic component, on risk of major cardiomyopathy-related events (MCE) and cardiomyopathy penetrance amongMYBPC3founder variant carriers.MethodsWe interviewed 188 carriers (57% male, 43.4±14.8 years) on exercise participation since age ten. Exercise was quantified as metabolic equivalent task (MET)-hours/week before presentation. MCE was defined as a composite of MVA (sustained ventricular tachycardia/fibrillation), HF (HF hospitalizations or transplantation), and septal reduction therapy. Static and dynamic exercise were defined per Bethesda classification. Associations of exercise with MCE and cardiomyopathy penetrance were adjusted for sex and assessed using Cox regression.ResultsOverall, 40 (21%) subjects experienced MCE and 139 (74%) were diagnosed with cardiomyopathy. No association was found for overall physical activity and high-static activity with MCE (p=0.900 overall; p=0.274 high-static) or cardiomyopathy penetrance (p=0.787 overall; p=0.774 high-static). In contrast, high-dynamic activity was associated with MVA (dichotomized at 75thpercentile: adjusted hazard ratio 2.70, 95% confidence interval 1.01-7.24, p=0.049).ConclusionsOverall exercise participation does not generally increase the risk of adverse events amongMYBPC3founder variant carriers. Nonetheless, an increased risk of MVA was observed among those engaged in the highest quartile of high-dynamic-sports, suggesting that high-level high-intensity exercise activities should be entertained with caution.
SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network
Authors: Timme Ruth E. , Woods Jacquelina , Jones Jessica L , Calci Kevin R , Rodriguez Rachel , Barnes Candace , Leard Elizabeth , Craven Mark , Chen Haifeng , Boerner Cameron , Grim Christopher , Windsor Amanda M. , Ramachandran Padmini , Muruvanda Tim , Rand Hugh , Tesfaldet Bereket , Amirzadegan Jasmine , Kayikcioglu Tunc , Walsky Tamara , Allard Marc , Balkey Maria , Bias C. Hope , Brown Eric , Judy Kathryn , Pfefer Tina , Tallent Sandra M , Hoffmann Maria , Pettengill James ,   the GenomeTrakr Laboratory consortium
Published: January 2024

ABSTRACTWastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA’s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA’s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA.IMPORTANCEThis manuscript serves two primary objectives. Firstly, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA’s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Secondly, it outlines best practices for gathering and organizing population-level Next Generation Sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.