bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is sexual misconduct training sufficient in the UK's medical schools: Results of a cross-sectional survey and opportunities for improvement
Authors: Dowling Tia , Steele Sarah 
Published: September 2023

Sexual misconduct adversely affects the mental and physical health of millions of people each year and has been declared a global pandemic. Incidence in both educational and clinical settings remains high. In the last 5 years, the NHS spent over £4 million settling sexual misconduct-related claims. Effective prevention requires training across all stages of career, beginning in clinical school. Here, we explore training in the UK's medical schools to identify provision and areas for improvement. Freedom of Information Act 2000 requests for data on training delivery and curricula content. 34 public UK universities offering medical education not applicable Provision and delivery of training, mode of delivery, theme, and continuation of training. All 34 universities responded. Twenty-two identified offering training. Seventeen made it compulsory. A review of curricula identified, however, only 18 did more just than mentioned sexual misconduct. Nine offered training more than once. Twelve did not offer training, of which three identified no plans to offer such training in the future. The most common delivery modes for training were workshops and lectures. The training was most often within the sexual health curriculum, disconnecting it from professionalism. There is no standardisation of sexual harassment training across the UK's public medical schools. Many future doctors will not have received relevant education when they assume posts in the NHS. Considering the magnitude of this issue and its critical connection to professionalism and collegiality, universities and professional bodies urgently should address this deficiency.
Atrophy of the Posterior Cricoarytenoid Muscle as an Indicator of a Recurrent Laryngeal Nerve Injury History Before Revision Anterior Cervical Spine Surgery
Authors: Seok Sang Yun , Lee Dong-Ho , Lee Hyung Rae , Cho Jae Hwan , Hwang Chang Ju , Park Sehan 
Published: September 2023

Study Design Retrospective study. Objectives In our recent study, we observed some cases of symptomatic normal vocal cord motility instead of asymptomatic vocal cord palsy (VCP) in preoperative laryngoscopy of a revision anterior cervical spine surgery (ACSS) cohort. We assumed the intrinsic muscle atrophy caused by recurrent laryngeal nerve injury could cause vocal cord-related symptoms. Thus, radiological examinations were reviewed in relation to the posterior cricoarytenoid (PCA) muscle, one of the intrinsic muscles. Methods We retrospectively analyzed 64 patients who underwent a revision ACSS. Patients with vocal cord-related symptoms were classified as symptomatic group (group S, n = 11), and those without symptoms as asymptomatic group (group AS, n = 53). The bilateral size and signal intensity of the PCA muscles in these patients were measured in the axial view with preoperative computed tomography (CT) and magnetic resonance imaging (MRI) evaluations. Since the size and signal intensity values were different on each image, the ratios of the contralateral and ipsilateral muscle values were analyzed for each modality. Results There was no VCP on laryngoscopy study. However, the mean ratio of the PCA muscle size on CT was 1.40 ± .37 in group S and 1.02 ± .12 in group AS ( P = .007). These values on the MRI were 1.49 ± .45 in group S and 1.02 ± .14 in group AS, which was also a significant difference ( P = .008). Conclusions Evaluating the size of the PCA muscle before revision ACSS may predict a previous recurrent laryngeal nerve injury. Careful planning for the appropriate approach should be undertaken if vocal cord-related symptoms and atrophy of PCA muscle are evident.
Assessing the Agreement of Light Microscopic Evaluation of Oral Lichen Planus Lesions With Associated Direct Immunofluorescence Evaluation
Authors: Hansen Blake T , Payne Jeffrey B , Samson Kaeli K , Giannini Peter J 
Published: September 2023

Aim/objective: Assess agreement between light microscopy and direct immunofluorescence (DIF) for histopathologic evaluation of oral lichen planus (OLP). Methods: Records evaluated included 60 OLP, 16 lichenoid mucositis (LM), and 56 non-OLP/non-LM cases. Cases had both light microscopic and DIF evaluations. Histopathologic parameters of OLP included: (1) hydropic degeneration of the basal cell layer, (2) band-like lymphocytic infiltrate immediately subjacent to the epithelium, and (3) presence of Civatte bodies. Two calibrated examiners independently assessed light microscopic features. Examiners reviewed cases with discordant diagnoses to determine a consensus diagnosis. Intra-rater reliability (IRR), sensitivity, specificity, positive, and negative predictive values (PPV and NPV) were determined. Results: Of 132 patients, 72.7% were female, average age 61.9 (SD = 13.8). Most common sites were gingiva (37.9%), buccal mucosa (37.1%), and tongue (7.6%). IRR was 0.74 (95% CI: 0.40, 1.00) for the consensus diagnosis and 0.73 (95% CI: 0.39, 1.00) and 0.34 (95% CI: −0.03, 0.72) for the 2 examiners. Comparing consensus and definitive diagnoses: sensitivity of light microscopy: 0.32 (95% CI: 0.20, 0.45); specificity: 0.88 (95% CI: 0.78, 0.94); PPV: 0.68 (95% CI: 0.48, 0.84), and NPV: 0.61 (95% CI: 0.51, 0.70). Conclusion: Light microscopy alone is not a viable alternative to adjunctive DIF for diagnosis of OLP lesions.
High Positivity Rate of Urinary Mycobacterium tuberculosis Antigens Cocktail (ESAT-6, CFP-10, and MPT-64) in Active Tuberculosis Patients With and Without Human Immunodeficiency Virus Infection: A Cross-Sectional Study
Authors: Turbawaty Dewi Kartika , Surdjaja Novie Rahmawati , Indrati Agnes Rengga , Lismayanti Leni , Logito Verina 
Published: September 2023

Introduction: Human immunodeficiency virus (HIV) infection is a risk factor for the occurrence of a large of Mycobacterium tuberculosis (Mtb) antigen load in the body. The antigens cocktail namely early secretory antigenic target protein 6-kDa (ESAT-6), Culture filtrate protein 10 kDa (CFP-10), and Mycobacterium tuberculosis protein 64 (MPT-64) are secreted by Mtb during replication, hence, their concentration increase in patients with active Tuberculosis (TB). This increased levels facilitates their entry into the systemic circulation, followed by secretion by the glomerulus into the urine. The aim of this study was to determine the positivity rate of the urinary Mtb antigens cocktail between TB patients with and without HIV infection. Methods: This is an observational descriptive comparative study conducted with a cross-sectional design. Random urine samples were collected from patients diagnosed with active TB in Dr. Hasan Sadikin Bandung Hospital in 2021. The subjects were divided into 2 groups, TB-HIV group and TB without HIV group. The samples were tested using the quantitative immunochromatography method. Result: Sixty active TB patients consisting of TB patients with HIV infection (n = 30) and TB patients without HIV infection (n = 30). The positivity in the urinary Mtb antigens cocktail was 93.3% for TB-HIV group and 100% for TB without HIV group ( P = .492). The median concentration of urinary Mtb antigens cocktail in TB patients without HIV infection was higher than that of TB patients with HIV infection (137.73 ng/mL vs 96.69 ng/mL, respectively; P = .001). Conclusion: There was no significant difference in the positivity rate, meanwhile, there was a significant difference in concentration of the urinary Mtb antigens cocktail between active TB patients with and without HIV infection. Interestingly, this urinary Mtb antigens cocktail can be found in both groups without being affected by the patient’s immune condition, thus becoming a test to assist diagnose active TB.
BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data
Authors: Eagles Nicholas J. , Wilton Richard , Jaffe Andrew E. , Collado-Torres Leonardo 
Published: September 2023

Abstract
Background
Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generated by whole genome bisulfite sequencing (WGBS) requires several computational steps before it is ready for statistical analysis, and particular care is required to process data in a timely and memory-efficient manner. Alignment to a reference genome is one of the most computationally demanding steps in a WGBS workflow, taking several hours or even days with commonly used WGBS-specific alignment software. This naturally motivates the creation of computational workflows that can utilize GPU-based alignment software to greatly speed up the bottleneck step. In addition, WGBS produces raw data that is large and often unwieldy; a lack of memory-efficient representation of data by existing pipelines renders WGBS impractical or impossible to many researchers.

Results
We present BiocMAP, a Bioconductor-friendly methylation analysis pipeline consisting of two modules, to address the above concerns. The first module performs computationally-intensive read alignment using Arioc, a GPU-accelerated short-read aligner. Since GPUs are not always available on the same computing environments where traditional CPU-based analyses are convenient, the second module may be run in a GPU-free environment. This module extracts and merges DNA methylation proportions—the fractions of methylated cytosines across all cells in a sample at a given genomic site. Bioconductor-based output objects in R utilize an on-disk data representation to drastically reduce required main memory and make WGBS projects computationally feasible to more researchers.

Conclusions
BiocMAP is implemented using Nextflow and available at http://research.libd.org/BiocMAP/. To enable reproducible analysis across a variety of typical computing environments, BiocMAP can be containerized with Docker or Singularity, and executed locally or with the SLURM or SGE scheduling engines. By providing Bioconductor objects, BiocMAP’s output can be integrated with powerful analytical open source software for analyzing methylation data.
A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)
Authors: Diesel Jose , Molano Gary , Montecinos Gabriel J. , DeWeese Kelly , Calhoun Sara , Kuo Alan , Lipzen Anna , Salamov Asaf , Grigoriev Igor V. , Reed Daniel C. , Miller Robert J. , Nuzhdin Sergey V. , Alberto Filipe 
Published: September 2023

AbstractMacrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
Temporal variation in oral microbiome composition of patients undergoing autologous hematopoietic cell transplantation with keratinocyte growth factor
Authors: Bohn Bruno , Chalupova Miroslava , Staley Christopher , Holtan Shernan , Maakaron Joseph , Bachanova Veronika , El Jurdi Najla 
Published: September 2023

Abstract
Introduction
Autologous hematopoietic cell transplantation (AHCT) is a well-established treatment for lymphoma. Unintended effects of this therapy include oral mucositis (OM) and gastrointestinal toxicities, resulting in poor clinical outcomes. The gut microbiome has been previously linked to transplant toxicities among allogeneic recipients, but little is known about the effects of AHCT on the oral microbiome.

Methods
Seven patients with non-Hodgkin or Hodgkin lymphoma undergoing AHCT with palifermin (keratinocyte growth factor) were included. Buccal swab samples were collected at baseline and 14- and 28-days post-treatment. Oral microbial communities were characterized with 16 S rRNA amplicon sequencing. Temporal trends in community composition, alpha diversity, and beta diversity were investigated.

Results
A significant reduction in the relative abundance of the genera Gemella and Actinomyces were observed from baseline. No significant temporal differences in alpha diversity were observed. Significant changes in beta diversity were recorded.

Conclusion
Results of this pilot study suggest treatment with AHCT and palifermin affects the oral microbiome, resulting in temporal shifts in oral microbial community composition. Future studies are warranted to confirm these trends and further investigate the effects of AHCT on the oral microbiome and how these shifts may affect health outcomes.
Analysis of the association between dietary patterns and nonalcoholic fatty liver disease in a county in Guangxi
Authors: Xiao Song , Chen Ziqi , Mai Tingyu , Cai Jiansheng , Chen Yulu , Tang Xu , Gou Ruoyu , Luo Tingyu , He Kailian , Li Tingjun , Qin Jian , Zhang Zhiyong , Li You 
Published: September 2023

Abstract
Background
This study aims to investigate the relationship between different dietary patterns and non-alcoholic fatty liver disease (NAFLD).

Methods
Residents over 30 years old in the ecological longevity cohort in Gongcheng Yao Autonomous County, Guangxi Province were the research objects selected from 2018 to 2019. Physical examination, baseline population survey, and food frequency questionnaire (FFQ) survey were conducted. Dietary patterns were analyzed by factor analysis. Influencing factors of NAFLD were analyzed by multiple logistic regression.

Results
NAFLD was diagnosed in 241 of 2664 participants based on ultrasonography, and the detection rate was 9.0%. Factor analysis yielded a total of three dietary patterns, namely, traditional Chinese, Western, and cereal-potato dietary patterns. Results of multivariate logistic regression analysis showed that after adjusting for confounding factors, participants in the highest quartile of the Western dietary pattern exhibited a higher prevalence of NAFLD (OR = 2.799; 95% CI: 1.620–4.837; p < 0.05) than participants in the lowest quartile. Participants in the highest quartile of the cereal-potato pattern exhibited a decreased risk of NAFLD compared with those in the lowest quartile (OR = 0.581; 95% CI: 0.371–0.910, p < 0.05). The traditional Chinese patterns did not show any association with the risk of NAFLD.

Conclusions
The Western dietary pattern increases the risk of NAFLD, whereas the cereal-potato dietary pattern reduces the risk of NAFLD. It is important for the prevention and control of NAFLD to adhere to the cereal-potato dietary.
Clinical Data based XGBoost Algorithm for infection risk prediction of patients with decompensated cirrhosis: a 10-year (2012–2021) Multicenter Retrospective Case-control study
Authors: Zheng Jing , Li Jianjun , Zhang Zhengyu , Yu Yue , Tan Juntao , Liu Yunyu , Gong Jun , Wang Tingting , Wu Xiaoxin , Guo Zihao 
Published: September 2023

AbstractObjectivesTo appraise effective predictors for infection in patients with decompensated cirrhosis (DC) by using XGBoost algorithm in a retrospective case-control study.MethodsClinical data were retrospectively collected from 6,648 patients with DC admitted to five tertiary hospitals. Indicators with significant differences were determined by univariate analysis and least absolute contraction and selection operator (LASSO) regression. Further multi-tree extreme gradient boosting (XGBoost) machine learning-based model was used to rank importance of features selected from LASSO and subsequently constructed infection risk prediction model with simple-tree XGBoost model. Finally, the simple-tree XGBoost model is compared with the traditional logical regression (LR) model. Performances of models were evaluated by area under the receiver operating characteristic curve (AUROC), sensitivity, and specificity.ResultsSix features, including total bilirubin, blood sodium, albumin, prothrombin activity, white blood cell count, and neutrophils to lymphocytes ratio were selected as predictors for infection in patients with DC. Simple-tree XGBoost model conducted by these features can predict infection risk accurately with an AUROC of 0.971, sensitivity of 0.915, and specificity of 0.900 in training set. The performance of simple-tree XGBoost model is better than that of traditional LR model in training set, internal verification set, and external feature set (P < 0.001).ConclusionsThe simple-tree XGBoost predictive model developed based on a minimal amount of clinical data available to DC patients with restricted medical resources could help primary healthcare practitioners promptly identify potential infection.
PFAS concentrations in early and mid-pregnancy and risk of gestational diabetes mellitus in a nested case-control study within the ethnically and racially diverse PETALS cohort
Authors: Peterson Alicia K. , Zhu Yeyi , Fuller Sophia , Feng Juanran , Alexeeff Stacey , Mitro Susanna D. , Kannan Kurunthachalam , Robinson Morgan , Padula Amy , Ferrara Assiamira 
Published: September 2023

Abstract
Background
Per- and polyfluoroalkyl substances (PFAS) are persistent synthetic chemicals and are commonly found in everyday items. PFAS have been linked to disrupting glucose homeostasis, however, whether they are associated with gestational diabetes mellitus (GDM) risk remains inconclusive. We examined prospective associations of PFAS concentrations measured twice in pregnancy with GDM risk.

Methods
In the PETALS pregnancy cohort, a nested case–control study which included 41 GDM cases and 87 controls was conducted. PFAS analytes were measured in blood serum collected in both early and mid-pregnancy (mean [SD]: 13.9 [2.2] and 20.2 [2.2] gestational weeks, respectively), with cumulative exposure calculated by the area-under-the-curve (AUC) to integrate both the PFAS concentration and the timing of the exposure. Individual adjusted weighted unconditional logistic regression models examined seven PFAS in association with GDM risk. P-values were corrected using the false-discovery-rate (FDR). Mixture models were analyzed with Bayesian kernel machine regression (BKMR).

Results
PFDA, PFNA and PFOA were individually associated with higher GDM risk per interquartile range (IQR) in early pregnancy (OR [95% CI]: 1.23 [1.09, 1.38]), 1.40 [1.24, 1.58]), and 1.15 [1.04, 1.27], respectively), mid-pregnancy (1.28 [1.15, 1.43], 1.16 [1.05, 1.28], and 1.20 [1.09, 1.33], respectively), and with cumulative exposure (1.23 [1.09, 1.38], 1.21 [1.07, 1.37], and 1.19 [1.09, 1.31], respectively). PFOS in mid-pregnancy and with cumulative exposure was associated with increased GDM risk (1.41 [1.17, 1.71] and 1.33 [1.06, 1.58], respectively). PFUnDA in early pregnancy was associated with lower GDM risk (0.79 [0.64, 0.98]), whereas mid-pregnancy levels were associated with higher risk (1.49 [1.18, 1.89]). PFHxS was associated with decreased GDM risk in early and mid-pregnancy (0.48 [0.38, 0.60] and 0.48 [0.37, 0.63], respectively) and with cumulative exposure (0.49 [0.38,0.63]). PFPeA was not associated with GDM. Similar conclusions were observed in BKMR models; however, overall associations in these models were not statistically significant.

Conclusions
Higher risk of GDM was consistently observed in association with PFDA, PFNA, and PFOA exposure in both early and mid-pregnancy. Results should be corroborated in larger population-based cohorts and individuals of reproductive age should potentially avoid known sources of PFAS.
Evaluation of allylestrenol for clinical pregnancies in patients treated with assisted reproductive techniques: a retrospective, propensity score matched, observational study
Authors: Yu Yuexin , Yu Tingting , Ding Weiping , Xiu Yinling , Zhao Mengsi , Sun Kaixuan , Zhang Qian , Xu Xiaohang 
Published: September 2023

Abstract
Background
Allylestrenol is an oral progestogen being increasingly used for luteal phase support in assisted reproductive techniques. However, evidence of the clinical efficacy of allylestrenol in luteal phase support is lacking. Dydrogesterone is a representative drug used for luteal phase support, the efficacy of which has been clinically confirmed. As such, we aimed to compare the effects of allylestrenol with the standard dydrogesterone on clinical pregnancy rates and pregnancy outcomes.

Methods
This retrospective study included 3375 assisted reproductive technique cycles using either allylestrenol or dydrogesterone between January 2015 and March 2020. Patients using either allylestrenol or dydrogesterone were matched in a 1:1 ratio using propensity scores. The primary outcomes were clinical pregnancy rate and pregnancy outcomes.

Results
No significant difference was found in the clinical pregnancy rate (53.5% vs. 53.2%, P = 0.928) and pregnancy outcomes (all P > 0.05) between allylestrenol and dydrogesterone. Compared with dydrogesterone, the use of allylestrenol significantly reduced the rate of biochemical pregnancies (6.4% vs. 11.8%, P < 0.001) and multiple gestation rate (16.8% vs. 26.3%, P = 0.001). Moreover, endometrial thickness, morphology, and blood flow were significantly improved by allylestrenol treatment (all P < 0.05).

Conclusions
Allylestrenol exhibited similar effects on clinical pregnancy rates and pregnancy outcomes as dydrogesterone. Moreover, allylestrenol can significantly reduce the biochemical pregnancy rate and improve the endometrial receptivity.