bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of clinical outcomes in critically ill COVID-19 patients on mechanical ventilation with nosocomial pneumonia between Alpha and Omicron variants
Authors: Sun Chuan-Yen , Huang Jhong-Ru , Shen Hsiao-Chin , Liao Ying-Ting , Ko Hung-Jui , Chang Chih-Jung , Chen Yuh-Min , Feng Jia-Yih , Chen Wei-Chih , Yang Kuang-Yao 
Published: November 2023

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a pandemic that has resulted in millions of deaths worldwide. Critically ill COVID-19 patients who require intubation and develop nosocomial pneumonia, commonly caused by gram-negative bacilli, have a higher mortality rate than those without nosocomial pneumonia. Objectives: The aim of this study is to compare the clinical characteristics and outcomes and associated risk factors of Alpha and Omicron SARS-CoV-2 variants in critically ill patients on mechanical ventilation (MV) with nosocomial pneumonia. Design: This is a retrospective single-center cohort study. Methods: This observational study was conducted at Taipei Veterans General Hospital, Taiwan from May 2021 to September 2022. Critically ill patients who had confirmed SARS-CoV-2 infection and intubated on a MV with bacterial pneumonia were enrolled. Demographic data, laboratory results, and treatment information were collected and analyzed. In addition, clinical outcomes among different SARS-CoV-2 variants were examined. Results: This study included 94 critically ill COVID-19 patients who required intubation and intensive care unit (ICU) admission. The Alpha group had a longer duration of SARS-CoV-2 viral shedding, MV days, and ICU stay, while the Omicron group had older age, more comorbidities, higher APACHE II scores, and higher in-hospital mortality (47.0% versus 25.0%, p = 0.047). However, independent risk factors for in-hospital mortality included malignancy, lower serum albumin levels, and lack of Remdesivir treatment, except for the SARS-CoV-2 variant. Conclusion: Our study discovered a higher in-hospital mortality rate in severe COVID-19 patients with MV and secondary pneumonia infected with the Omicron variant compared to the Alpha variant; however, real independent risk factors for in-hospital mortality are malignancy, lower serum albumin level, and lack of Remdesivir treatment.
The ensemble artificial intelligence (AI) method: Detection of hip fractures in AP pelvis plain radiographs by majority voting using a multi-center dataset
Authors: Beyaz Salih , Yayli Sahika Betul , Kılıc Ersin , Doktur Ugur 
Published: November 2023

Introduction This article was undertaken to explore the potential of AI in enhancing the diagnostic accuracy and efficiency in identifying hip fractures using X-ray radiographs. In the study, we trained three distinct deep learning models, and we utilized majority voting to evaluate their outcomes, aiming to yield the most reliable and precise diagnoses of hip fractures from X-ray radiographs. Methods An initial study was conducted of 10,849 AP pelvis X-rays obtained from five hospitals affiliated with Başkent University. Two expert orthopedic surgeons initially labeled 2,291 radiographs as fractures and 8,558 as non-fractures. The algorithm was trained on 6,943 (64%) radiographs, validated on 1,736 (16%) radiographs, and tested on 2,170 (20%) radiographs, ensuring an even distribution of fracture presence, age, and gender. We employed three advanced deep learning architectures, Xception (Model A), EfficientNet (Model B), and NfNet (Model C), with a final decision aggregated through a majority voting technique (Model D). Results For each model, we achieved the following metrics: For Model A: F1 Score 0.895, Accuracy 0.956, Specificity 0.973, Sensitivity 0.893. For Model B: F1 Score 0.900, Accuracy 0.960, Specificity 0.991, Sensitivity 0.845. For Model C: F1 Score 0.919, Accuracy 0.966, Specificity 0.984, Sensitivity 0.899. For Model D: F1 Score 0.929, Accuracy 0.971, Specificity 0.991, Sensitivity 0.897. We concluded that Model D (majority voting) achieved the best results in terms of the F1 score, accuracy, and specificity values. Conclusions Our study demonstrates that the results obtained by aggregating the decisions of multiple models through voting, rather than relying solely on the decision of a single algorithm, are more consistent. The practical application of these algorithms will be difficult due to ethical, legal, and confidentiality issues, despite the theoretical success achieved. Developing successful algorithms and methodologies should not be viewed as the ultimate goal; it is important to understand how these algorithms will be used in real-life situations. In order to achieve more consistent results, feedback from clinical practice will be helpful.
Kinematic Parameters Predictive of Pitch Velocity in Youth to Professional Baseball Pitchers: A Qualitative Systematic Review
Authors: Kew Michelle E. , Koo Alexander , Manzi Joseph E. , Coladonato Carlo , Estrada Jennifer , Dines Joshua S. , Carr James B. 
Published: November 2023

Background: Specific kinematic factors have been found to contribute to faster pitch speeds, with poor mechanics leading to injury. Purpose: To discuss the kinematic parameters that predict faster ball velocity among baseball pitchers. Study Design: Systematic review. Methods: Using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, the authors utilized the Cochrane Database of Systematic Reviews, PubMed (2008-2019), and OVID/MEDLINE (2008-2019) databases. Eligible articles included those that reported on kinematic factors predictive of ball velocity across youth, high school, collegiate, and professional levels of play. The quality of all included studies was evaluated by 2 reviewers using the Appraisal tool for Cross-Sectional Studies (AXIS). The lack of consistent study design or outcome variables precluded meta-analysis. Results: A total of 584 studies were identified from the initial search with 12 included in final analysis (930 pitchers in total; 429 [46.1%] youth, 164 [17.6%] high school, 153 [16.5%] collegiate and 184 [19.8%] professional) with mean ball velocity of 71.1 mph (114.4 km/h). The average AXIS score was 16 out of a possible 20. The shoulder played a significant role in the generation of velocity-induced torques. Hip and shoulder separation was associated with a 2.6 ± 0.5 mph (4.1 ± 0.8 km/h) increase in velocity, whereas increased shoulder movement of the nonthrowing arm was negatively correlated with initial ball velocity ( r2 = 0.798). Furthermore, hip/shoulder separation, decreased movement of the nonthrowing shoulder, trunk power and timing of maximum trunk rotation, increased contralateral trunk tilt and increased sagittal-plane trunk tilt, and decreased knee flexion at ball release were all associated with higher fastball speeds. Conclusion: Multiple upper extremity and trunk kinematic parameters affect ball velocity, with significant contributions from the throwing shoulder and trunk, as well as nondominant arm. Understanding kinematic predictors of faster ball velocity can help guide training regimens.
Clinical Implication of Glenohumeral and Subacromial Synovitis in Rotator Cuff Tears
Authors: Gimm Geunwu , Yoon Jeong Yong , Ahn Eunmi , Oh Sohee , Jo Chris Hyunchul 
Published: November 2023

Background: Synovitis of the glenohumeral (GH) joint and the subacromial (SA) space is commonly observed during arthroscopic rotator cuff surgery. Purpose: To investigate the distribution, severity, and clinical implications of synovitis in the GH joint and SA space in patients with a full-thickness rotator cuff tear (RCT). Study Design: Case series; Level of evidence, 4. Methods: Data were retrospectively collected from 207 patients with a full-thickness RCT who underwent arthroscopic repair. Preoperative parameters used in the clinical assessment included pain, range of motion (ROM), muscle strength, and functional scores. Macroscopic assessment of synovitis was performed intraoperatively in the 3 regions of interest (ROIs) of the GH joint and 4 ROIS of the SA space using an evaluation system. The distribution and severity of synovitis and the association between synovitis and clinical assessment were evaluated. Results: Synovitis was more severe in the GH joint than in the SA space ( P < .001). Synovitis in the posterior GH joint and the lateral SA space, where most of the rotator cuff was located, was the most severe area among the ROIs of the GH joint and the SA space, respectively ( P < .05). All types of pain, except for pain at rest, were associated with synovitis in the posterior GH joint ( P < .05). All ROM measures were associated with synovitis in the posterior and inferior GH joint (| r| > 0.20; P < .05 for both). The strength of the supraspinatus and the infraspinatus was associated with synovitis in the posterior GH joint ( P < .05). Shoulder function was associated with synovitis in the posterior and inferior GH joint and more in the posterior GH joint ( P < .05 for both). Synovitis in the SA space was not associated with any of the clinical parameters. Conclusion: Synovitis in the posterior GH joint was the most severe form of synovitis in the GH joint in patients with a full-thickness RCT. Synovitis in the posterior GH joint was closely associated with increased pain and decreased ROM, muscle strength, and functional score. Synovitis in the SA space was milder and not associated with any clinical parameters.
A model for community-led peer-facilitated advance care planning workshops for the public
Authors: Carter Rachel Z , Hassan Eman , Porterfield Pat , Barwich Doris 
Published: November 2023

Background: The core to successful advance care planning (ACP) facilitation is helping people determine their values, beliefs and wishes, and understand substitute decision-making. Recognizing the potential for community members to support public awareness and education we developed a model of ACP education, whereby peer facilitators associated with community organizations host workshops that educate and assist members of the public with ACP. Objectives: Describe the development and evaluation of the model for community-led peer-facilitated ACP workshops for the public. Design: Descriptive mixed methods. Methods: A training curriculum and program model were co-developed with two community organizations that had been successful in delivering ACP workshops independently in their communities. Herein we describe a mixed-methods evaluation of three cycles of implementation and improvement of the model. Results: The model centers on three key concepts; the right content (based around three steps Think, Talk, Plan), the right facilitator, and the right approach. A suite of tools was designed to support the three groups involved in the delivery of the ACP workshops: the public participants, the peer facilitators, and the community-based organizations. The peer-facilitator training addresses the facilitator’s learning needs of ACP content knowledge, facilitation skills, and understanding change behavior. Training evaluation data from 106 facilitators confirmed that the curriculum prepared them to facilitate the workshops. Qualitative data revealed that support from organizations with established reputations in their community is critical, with mentoring from more experienced facilitators beneficial. Conclusion: Our model demonstrates the potential of community-led, peer-facilitated ACP initiatives to enhance the capacity of community to upstream ACP conversations. Reaching a broader audience and creating a supportive, inclusive environment for individuals to comfortably learn about ACP can drive the much-needed culture shift to normalize ACP. Meaningful community engagement, empowerment, and partnerships are essential for the successful development and widespread impact of these initiatives.
Genomic landscape of patients with germline RUNX1 variants and familial platelet disorder with myeloid malignancy
Authors: Yu Kai , Deuitch Natalie , Merguerian Matthew , Cunningham Lea , Davis Joie , Bresciani Erica , Diemer Jamie , Andrews Elizabeth , Young Alice , Donovan Frank , Sood Raman , Craft Kathleen , Chong Shawn , Chandrasekharappa Settara , Mullikin Jim , Liu Paul P. 
Published: November 2023

Abstract
Familial platelet disorder with associated myeloid malignancies (FPDMM) is caused by germline RUNX1 mutations and characterized by thrombocytopenia and increased risk of hematologic malignancies. We recently launched a longitudinal natural history study for patients with FPDMM. Among 27 families with research genomic data by the end of 2021, 26 different germline RUNX1 variants were detected. Besides missense mutations enriched in Runt homology domain and loss-of-function mutations distributed throughout the gene, splice-region mutations and large deletions were detected in 6 and 7 families, respectively. In 25 of 51 (49%) patients without hematologic malignancy, somatic mutations were detected in at least 1 of the clonal hematopoiesis of indeterminate potential (CHIP) genes or acute myeloid leukemia (AML) driver genes. BCOR was the most frequently mutated gene (in 9 patients), and multiple BCOR mutations were identified in 4 patients. Mutations in 6 other CHIP- or AML-driver genes (TET2, DNMT3A, KRAS, LRP1B, IDH1, and KMT2C) were also found in ≥2 patients without hematologic malignancy. Moreover, 3 unrelated patients (1 with myeloid malignancy) carried somatic mutations in NFE2, which regulates erythroid and megakaryocytic differentiation. Sequential sequencing data from 19 patients demonstrated dynamic changes of somatic mutations over time, and stable clones were more frequently found in older adult patients. In summary, there are diverse types of germline RUNX1 mutations and high frequency of somatic mutations related to clonal hematopoiesis in patients with FPDMM. Monitoring changes in somatic mutations and clinical manifestations prospectively may reveal mechanisms for malignant progression and inform clinical management. This trial was registered at www.clinicaltrials.gov as #NCT03854318.
Knock-in mice expressing a humanized arachidonic acid 15-lipoxygenase (Alox15) carry a partly dysfunctional erythropoietic system
Authors: Reisch Florian , Heydeck Dagmar , Schäfer Marjann , Rothe Michael , Yang Jiaxing , Stehling Sabine , Püschel Gerhard P. , Kuhn Hartmut 
Published: November 2023

AbstractArachidonic acid 15-lipoxygenases (ALOX15) play a role in mammalian erythropoiesis but they have also been implicated in inflammatory processes. Seven intact Alox genes have been detected in the mouse reference genome and the mouse Alox15 gene is structurally similar to the orthologous genes of other mammals. However, mouse and human ALOX15 orthologs have different functional characteristics. Human ALOX15 converts C20 polyenoic fatty acids like arachidonic acid mainly to the n-6 hydroperoxide. In contrast, the n-9 hydroperoxide is the major oxygenation product formed by mouse Alox15. Previous experiments indicated that Leu353Phe exchange in recombinant mouse Alox15 humanized the catalytic properties of the enzyme. To investigate whether this functional humanization might also work in vivo and to characterize the functional consequences of mouse Alox15 humanization we generated Alox15 knock-in mice (Alox15-KI), in which the Alox15 gene was modified in such a way that the animals express the arachidonic acid 15-lipoxygenating Leu353Phe mutant instead of the arachidonic acid 12-lipoxygenating wildtype enzyme. These mice develop normally, they are fully fertile but display modified plasma oxylipidomes. In young individuals, the basic hematological parameters were not different when Alox15-KI mice and outbred wildtype controls were compared. However, when growing older male Alox15-KI mice develop signs of dysfunctional erythropoiesis such as reduced hematocrit, lower erythrocyte counts and attenuated hemoglobin concentration. These differences were paralleled by an improved ex vivo osmotic resistance of the peripheral red blood cells. Interestingly, such differences were not observed in female individuals suggesting gender specific effects. In summary, these data indicated that functional humanization of mouse Alox15 induces defective erythropoiesis in aged male individuals.
Graphical Abstract
Fecal microbiota transplantation as a therapy for treating ulcerative colitis: an overview of systematic reviews
Authors: Liu Haixia , Li Jing , Yuan Jiaxin , Huang Jinke , Xu Youqi 
Published: November 2023

Abstract
Aim
The current overview on published systematic reviews (SRs) and meta-analysis (MAs) aimed to systematically gather, evaluate, and synthesize solid evidence for using fecal microbiota transplantation (FMT) to treat ulcerative colitis (UC).

Methods
Relevant articles published before January 2023 were collected from Web of Science, Embase, PubMed, and Cochrane Library. Two authors used Assessment of Multiple Systematic Reviews 2 (AMSTAR-2) tool, PRISMA checklists, and Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system were applied by two authors to independently evaluate the methodological quality, reporting quality, and evidence quality, respectively. Re-meta-analysis on the primary RCTs was conducted after excluding overlapping randomized controlled trials (RCTs).

Results
Six SRs/MAs involving 12 primary RCTs and 544 participants were included. According to the AMSTAR-2 tool and PRISMA checklist, methodological quality and reporting quality of the included studies was overall satisfactory. The evidence quality of a great majority of outcomes was rated as moderate to high according to the GRADE system. Compared to placebo, the re-meta-analysis found a great advantage of use FMT in inducing combined clinical and endoscopic remission (OR 3.83 [2.31, 6.34]), clinical remission (3.31 [2.09, 5.25]), endoscopic remission (OR 3.75 [2.20, 6.39]), clinical response (OR 2.56 [1.64, 4.00]), and endoscopic response (OR 2.18 [1.12, 4.26]). Pooled data showed no significant difference in serious adverse events between patients receiving FMT and those receiving placebo (OR 1.53 [0.74, 3.19]). Evidence quality of the outcomes derived from re-meta-analysis was significantly higher after overcoming the limitations of previous SRs/MAs.

Conclusion
In conclusion, moderate- to high-quality evidence supported a promising use of FMT to safely induce remission in UC. However, further trials with larger sample size are still required to comprehensively analyze the delivery route, total dosage, frequency, and donor selection in FMT.
Molecular characterisation of Staphylococcus aureus in school-age children in Guangzhou: associations among agr types, virulence genes, sequence types, and antibiotic resistant phenotypes
Authors: Cai Hao , Li Xueying , Zhang Chao , Zhong Huamin , Xie Yongqiang , Huang Lianfen , Zhang Baidu , Long Yan , Zhou Zhenwen , Liang Bingshao 
Published: November 2023

Abstract
Background
Staphylococcus aureus, one of the most prevalent opportunistic pathogens, mainly colonizes the nasal cavity and is a risk factor for severe infections. Virulence factors and accessory gene regulator (agr) are key to the severity and diversity of staphylococcal infection. In this study, we aimed to characterise S. aureus agr-types and virulence genes and correlated them with genetic background and antibiotic-resistant phenotypes.

Results
Agr types were identified in 704 isolates (98.5%), with only 11 isolates were negative for agr type. Most of our isolates were classified as agr type I, followed by types III, II and IV. The enterotoxin c gene (sec) was detected in 48.6% of isolates, showing the highest prevalence among the five enterotoxin genes detected. The positivity rates for the lukS/F-PV and tsst genes were 4% and 2.2%, respectively, while neither sed nor SasX were detected. ST45, ST59, ST338, ST188, ST6, ST7, ST22, ST25, ST398, and ST944 belonged to agr I group, while ST5 and ST15 belonged to agr II group. ST30 and ST1 were classified into agr III group, and ST121 was assigned into agr IV group. The tsst gene was found exclusively within agr I and III types belonging to ST7 and ST30 isolates, while the lukS/F-PV was predominantly carried by agr I type isolates primarily within CC59 and CC22 clones. Among the methicillin-resistant S. aureus (MRSA) isolates, 89.7% belonged to agr I group, and 97.8% of rifampicin-resistant or intermediate isolates were assigned to agr I group. MRSA isolates harboured more tested virulence genes compared to methicillin-susceptible S. aureus isolates.

Conclusions
We characterized the distributions of agr types and eight major virulence genes of 715 S. aureus isolates, and our findings revealed clear associations between agr types and STs, as well as virulence genes, and drug resistant phenotypes.
Genome-wide identification of bZIP gene family and expression analysis of BhbZIP58 under heat stress in wax gourd
Authors: Liu Wei , Wang Min , Zhong Min , Luo Chen , Shi Shaoqi , Qian Yulei , Kang Yunyan , Jiang Biao 
Published: November 2023

Abstract
Background
The basic leucine zipper (bZIP) transcription factor family is one of the most abundant and evolutionarily conserved gene families in plants. It assumes crucial functions in the life cycle of plants, including pathogen defense, secondary metabolism, stress response, seed maturation, and flower development. Although the genome of wax gourd has been published, little is known about the functions, evolutionary background, and gene expression patterns of the bZIP gene family, which limits its utilization.

Results
A total of 61 bZIP genes (BhbZIPs) were identified from wax gourd (Benincasa hispida) genome and divided into 12 subgroups. Whole-genome duplication (WGD) and dispersed duplication (DSD) were the main driving forces of bZIP gene family expansion in wax gourd, and this family may have undergone intense purifying selection pressure during the evolutionary process. We selected BhbZIP58, only one in the member of subgroup B, to study its expression patterns under different stresses, including heat, salt, drought, cold stress, and ABA treatment. Surprisingly, BhbZIP58 had a dramatic response under heat stress. BhbZIP58 showed the highest expression level in the root compared with leaves, stem, stamen, pistil, and ovary. In addition, BhbZIP58 protein was located in the nucleus and had transcriptional activation activity. Overexpression of BhbZIP58 in Arabidopsis enhanced their heat tolerance.

Conclusions
In this study, bZIP gene family is systematically bioinformatically in wax gourd for the first time. Particularly, BhbZIP58 may have an important role in heat stress. It will facilitate further research on the bZIP gene family regarding their evolutionary history and biological functions.