bluuebunny/crossref_metadata_2025_split huggingface dataset:
expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer
Authors: Lee Jae Jun , Kang Hyun Ju , Kim Donghyo , Lim Si On , Kim Stephanie S. , Kim Gahyun , Kim Sanguk , Lee Jin-Ku , Kim Jinho 
Published: July 2024

Abstract
Background
Homologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy and poly ADP-ribose polymerase (PARP) inhibitors. One of the conventional approaches to HRD prognostication has generally centered on identifying deleterious mutations within the BRCA1/2 genes, along with quantifying the genomic scars, such as Genomic Instability Score (GIS) estimation with scarHRD. However, the scarHRD method has limitations in scenarios involving tumors bereft of corresponding germline data. Although several RNA-seq-based HRD prediction algorithms have been developed, they mainly support cohort-wise classification, thereby yielding HRD status without furnishing an analogous quantitative metric akin to scarHRD. This study introduces the expHRD method, which operates as a novel transcriptome-based framework tailored to n-of-1-style HRD scoring.

Results
The prediction model has been established using the elastic net regression method in the Cancer Genome Atlas (TCGA) pan-cancer training set. The bootstrap technique derived the HRD geneset for applying the expHRD calculation. The expHRD demonstrated a notable correlation with scarHRD and superior performance in predicting HRD-high samples. We also performed intra- and extra-cohort evaluations for clinical feasibility in the TCGA-OV and the Genomic Data Commons (GDC) ovarian cancer cohort, respectively. The innovative web service designed for ease of use is poised to extend the realms of HRD prediction across diverse malignancies, with ovarian cancer standing as an emblematic example.

Conclusions
Our novel approach leverages the transcriptome data, enabling the prediction of HRD status with remarkable precision. This innovative method addresses the challenges associated with limited available data, opening new avenues for utilizing transcriptomics to inform clinical decisions.
Association between antidepressant use and delirium in older adults: an analysis of the World Health Organization’s global pharmacovigilance database
Authors: Minoc Elise-Marie , Villain Cédric , Benbrika Soumia , Chrétien Basile , Descatoire Pablo , Heraudeau Marie , Sassier Marion , Pierre Mélissa , Martinaud Olivier , Dolladille Charles , Lelong-Boulouard Véronique 
Published: July 2024

Abstract
Background
Psychoactive drugs frequently cause delirium adverse events in older adults. However, few data on the relationship between antidepressants and delirium are available. Here, we investigated the association between antidepressant prescription and pharmacovigilance reports of delirium in older adults.

Methods
Using the World Health Organization’s VigiBase® global pharmacovigilance database from 1967 to 2022, we performed a disproportionality analysis in order to probe the putative associations between each antidepressant class (non-selective monoamine reuptake inhibitors (NSMRIs), selective serotonin reuptake inhibitors (SSRIs), serotonin-norepinephrine reuptake inhibitors (SNRIs), monoamine oxidase inhibitors (MAOIs), alpha-2-adrenergic receptor antagonists, and other antidepressants) and reports of delirium in people aged 65 or over. We calculated the reporting odds ratios (r-OR) and their 95% confidence interval ([95%CI]) with logistic regression models before and after adjustment for confounding factors. Secondary analyses were performed for each drug and within each class by age group (65-74, and 75 and over). We also studied the reports of concomitant delirium and hyponatremia.

Results
Our main analysis included 87,524 cases of delirium. After adjustment for confounders, a significant association was found between delirium and all antidepressant classes other than SNRIs. Intraclass disparities were found for the association between the most frequently prescribed antidepressants and reports of delirium. An elevated risk of reports of concomitant delirium and hyponatremia was found for SSRIs (4.46 [4.01-4.96]), SNRIs (1.25 [1.07-1.46]), MAOIs (1.72 [1.41-2.09]), and the “other antidepressants” class (1.47 [1.30-1.65]).

Conclusions
There was a significant association between reports of delirium and antidepressant classes (other than SNRIs). However, this association varied from one drug to another within a given antidepressant class. Moreover, this association could not always be explained by antidepressant-induced hyponatremia.
Comparison of FGM prevalence among Nigerian women aged 15–49 years using two household surveys conducted before and after the COVID-19 pandemic
Authors: Morlighem Camille , Visée Corentin , Nnanatu Chibuzor Christopher 
Published: July 2024

Abstract
Background
Due to its economic burden and change of focus, there is no gainsaying of the potential impacts of the COVID-19 pandemic on the progress of several female genital mutilation (FGM) interventions across the various countries. However, the magnitude of the potential changes in likelihood and prevalence should be more accurately explored and quantified using a statistically robust comparative study. In this study, we examined the differences in the likelihood and prevalence of FGM among 15-49 years old women before and after the pandemic in Nigeria.

Methods
We used advanced Bayesian hierarchical models to analyse post-COVID-19 datasets provided by the Multiple Indicator Cluster Surveys (MICS 2021) and pre-COVID-19 data from the Demographic and Health Surveys (DHS 2018).

Results
Results indicated that although there was an overall decline in FGM prevalence nationally, heterogeneities exist at state level and at individual-/community-level characteristics. There was a 6.9% increase in prevalence among women who would like FGM to continue within the community. FGM prevalence increased by 18.9% in Nasarawa, while in Kaduna there was nearly 40% decrease.

Conclusions
Results show that FGM is still a social norm issue in Nigeria and that it may have been exacerbated by the COVID-19 pandemic. The methods, data and outputs from this study would serve to provide accurate statistical evidence required by policymakers for complete eradication of FGM.
Preliminarily exploring the intraoperative ultrasonography characteristics of patients with degenerative cervical myelopathy
Authors: Liu Wenfen , Li Jiachun , Shu Tao , Ji Qiao , Wang Xianxiang , Li Renjie , Sui Yajuan , He Danni , Xu Zuofeng 
Published: July 2024

Abstract
Background
How to quickly read and interpret intraoperative ultrasound (IOUS) images of patients with degenerative cervical myelopathy (DCM) to obtain meaningful information? Few studies have systematically explored this topic.

Purpose
To systematically and comprehensively explore the IOUS characteristics of patients with DCM.

Materials and methods
This single-center study retrospectively included patients with DCM who underwent French-door laminoplasty (FDL) with IOUS guidance from October 2019 to March 2022. One-way ANOVA and Pearson’s /Spearman’s correlation analysis were used to analyze the correlations between the cross-sectional area of the spinal cord (SC) and individual characteristics; the relationships between the morphology, echogenicity, pulsation, decompression statuses, compression types of SC, location of the spinal cord central echo complex (SCCEC) and the disease severity (the preoperative Japanese Orthopedic Association score, preJOA score); the difference of the spinal cord pulsation amplitude(SCPA) and the SCCEC forward movement rate (FMR) between the compressed areas(CAs) and the non-compressed areas (NCAs).

Results
A total of 38 patients were successfully enrolled (30 males and 8 females), and the mean age was 57.05 ± 10.29 (27–75) years. The cross-sectional area of the SC was negatively correlated with age (r = − 0.441, p = 0.006). The preJOA score was significantly lower in the heterogeneous group than in the homogeneous group (P < 0.05, p = 0.005). The hyperechoic area (HEA) was negatively while the SCCEC FMR was positively correlated with the preJOA score (r = − 0.334, p = 0.020; r = 0.286, p = 0.041). The SCCEC FMR and SCPA in CAs were significantly greater than those in NCAs (p < 0.05, p = 0.007; P < 0.001, P = 0.000).

Conclusion
The cross-sectional area of the SC decreases with age in adults. More changes in intramedullary echogenicity and less moving forward of the SCCEC often indicate poor SC status, and the SCCEC FMR and SCPA are more pronounced in CAs.
Using fosfomycin to prevent infection following ureterorenoscopy in response to shortage of cephalosporins: a retrospective preliminary study
Authors: Etani Toshiki , Wachino Chiharu , Sakata Takuya , Aoki Maria , Gonda Masakazu , Shimizu Nobuhiko , Nagai Takashi , Unno Rei , Taguchi Kazumi , Naiki Taku , Hamamoto Shuzo , Okada Atsushi , Kawai Noriyasu , Nakamura Atsushi , Yasui Takahiro 
Published: July 2024

Abstract
Background
In 2019, the shortage of cefazolin led to the demand for cefotiam and cefmetazole exceeding the supply. The Department of Nephro-urology at Nagoya City University Hospital used fosfomycin as a substitute for perioperative prophylaxis. This retrospective preliminary study evaluated the efficacy of fosfomycin and cefotiam for preventing infections following ureterorenoscopy.

Methods
The study included 182 patients who underwent ureterorenoscopy between January 2018 and March 2021). Perioperative antibacterial treatment with fosfomycin (n = 108) or cefotiam (n = 74) was administered. We performed propensity score matching in both groups for age, sex, preoperative urinary catheter use, and preoperative antibiotic treatment.

Results
The fosfomycin and cefotiam groups (n = 69 per group) exhibited no significant differences in terms of patients’ median age, operative duration, preoperative urine white blood cell count, preoperative urine bacterial count, and the rate of preoperative antibiotic treatment. In the fosfomycin and cefotiam groups, the median duration of postoperative hospital stay was 3 and 4 days, respectively; the median maximum postoperative temperature was 37.3 °C and 37.2 °C, respectively. The fosfomycin group had lower postoperative C-reactive protein levels and white blood cell count than the cefotiam group. However, the frequency of fever > 38 °C requiring additional antibiotic administration was similar.

Conclusions
During cefotiam shortage, fosfomycin administration enabled surgeons to continue performing ureterorenoscopies without increasing the complication rate.
Unlocking the therapeutic potential of Nigella sativa extract: phytochemical analysis and revealing antimicrobial and antioxidant marvels
Authors: Rahman Anees Ur , Abdullah Abdullah , Faisal Shah , Mansour Basem , Yahya Galal 
Published: July 2024

AbstractThe growing global threat of antimicrobial resistance endangers both human and animal life, necessitating the urgent discovery of novel antimicrobial solutions. Medicinal plants hold promise as sources of potential antimicrobial compounds. In this study, we investigated the phytochemical constituents and microbicidal capabilities of the ethanolic extract from Nigella sativa (black seed). Gas chromatography analysis (GC) identified 11 compounds, among them thymoquinone, and thymol, contributing to antimicrobial and antioxidant properties. Antimicrobial assays demonstrated notable inhibition zones against broad spectra of bacteria, including Pseudomonas aeruginosa, Escherichia coli, Salmonella typhi, Staphylococcus aureus, Enterobacter, and Bacillus subtilis, along with potent antifungal activity against Aspergillus niger, Penicillium, and Candida albicans. Notably, when combined with antibiotics, the extract displayed exceptional synergistic antimicrobial efficacy. The black seed extract demonstrated membrane-damaging activity and disrupted virulence factors that protect microbes from antimicrobial agents, including the formation of bacterial biofilm and protease secretion. Thymoquinone, the primary active constituent of the extract, exhibited similar antimicrobial and ant virulence properties. In silico analysis targeting key regulators of quorum sensing and biofilm formation in P. aeruginosa, such as RhlG, LasR, and PqsR, showed a remarkable affinity of thymol and thymoquinone for these targets. Moreover, the N. sativa extract exhibited dose-dependent cytotoxicity against both the promastigote and amastigote forms of Leishmania tropica parasites, hinting at potential antiparasitic activity. In addition to its antimicrobial properties, the extract displayed potential antioxidant activity at a concentration of 400 μg/mL.
Evaluating the perceived impact and legacy of master’s degree level research in the allied health professions: a UK-wide cross-sectional survey
Authors: Cordrey Terry , Thomas Amanda , King Elizabeth , Gustafson Owen 
Published: July 2024

Abstract
Background
Post graduate master’s degree qualifications are increasingly required to advance allied health profession careers in education, clinical practice, leadership, and research. Successful awards are dependent on completion of a research dissertation project. Despite the high volume of experience gained and research undertaken at this level, the benefits and impact are not well understood. Our study aimed to evaluate the perceived impact and legacy of master’s degree training and research on allied health profession practice and research activity.

Methods
A cross-sectional online survey design was used to collect data from allied health professionals working in the United Kingdom who had completed a postgraduate master’s degree. Participants were recruited voluntarily using social media and clinical interest group advertisement. Data was collected between October and December 2022 and was analysed using descriptive statistics and narrative content analysis. Informed consent was gained, and the study was approved by the university research ethics committee.

Results
Eighty-four responses were received from nine allied health professions with paramedics and physiotherapists forming the majority (57%) of respondents. Primary motivation for completion of the master’s degree was for clinical career progression (n = 44, 52.4%) and formation of the research dissertation question was predominantly sourced from individual ideas (n = 58, 69%). Formal research output was low with 27.4% (n = 23) of projects published in peer reviewed journal and a third of projects reporting no output or dissemination at all. Perceived impact was rated highest in individual learning outcomes, such as improving confidence and capability in clinical practice and research skills. Ongoing research engagement and activity was high with over two thirds (n = 57, 67.9%) involved in formal research projects.

Conclusion
The focus of master's degree level research was largely self-generated with the highest perceived impact on individual outcomes rather than broader clinical service and organisation influence. Formal output from master’s research was low, but ongoing research engagement and activity was high suggesting master’s degree training is an under-recognised source for AHP research capacity building. Future research should investigate the potential benefits of better coordinated and prioritised research at master’s degree level on professional and organisational impact.
A retrospective cohort study to evaluate disease burden, health care resource utilization, and costs in patients with breast cancer in Dubai, UAE
Authors: Hamza DMM , Zayed MWA , Tahoun N , Farghaly M , Kumaresan S , Ramachandrachar BC , Ali A 
Published: July 2024

Abstract
Background
The current study evaluated the disease burden, health care resource utilization and analyzed the cost burden due to events of special interest among patients with breast cancer (BC) diagnosed and treated in Dubai, United Arab Emirates (UAE), in general and in the subset of patients treated with cyclin-dependent kinase (CDK) 4/6 inhibitors.

Methods
This retrospective cohort study, using insurance e-claims data from Dubai Real-World Database, was conducted from 01 January 2014 to 30 September 2021. Female patients aged ≥ 18 years with at least 1 diagnosis claim for BC and with continuous enrollment during the index period were included.

Results
Overall, 8,031 patients were diagnosed with BC (median age: 49.0 years), with the majority (68.1%) being in 41–60-year age group. During the post-index period, BC-specific costs contributed to 84% of the overall disease burden among patients with BC. Inpatient costs (USD 16,956.2) and medication costs (USD 10,251.3) contributed significantly to BC-specific costs. In the subgroup of patients in whom CDK4/6 inhibitors were part of the treatment regimen (n = 174), CDK4/6 inhibitors were commonly prescribed in combination with aromatase inhibitors (41.4%) and estrogen receptor antagonists (17.9%). In patients with BC, health care costs due to events of special interest (n = 1,843) contributed to 17% of the overall disease cost burden.

Conclusion
The study highlights the significant cost burden among patients with BC, with BC-specific costs contributing to 84% of the overall disease cost burden. Despite few limitations such as study population predominantly comprising of privately insured expatriate patients and only direct healthcare costs being assessed in the current study, most indicative costs have been captured in the study, by careful patient selection and cost comparisons, as applicable. The findings can guide key health care stakeholders (payers and providers) on future policy measures aiming to reduce the cost burden among patients with BC.
Knowledge in motion: temporal dynamics of wild food plant use in the Polish-Lithuanian-Belarusian border region
Authors: Prakofjewa Julia , Sartori Matteo , Šarka Povilas , Kalle Raivo , Pieroni Andrea , Sõukand Renata 
Published: July 2024

Abstract
Background
Understanding how Local Ecological Knowledge (LEK) evolves over time is crucial for fostering social and environmental responsibility. This study aims to develop a conceptual model of plant knowledge circulation, providing insights into the temporal dynamics of LEK in the Polish-Lithuanian-Belarusian border region. It explores the key patterns and driving forces behind changes in the use of wild plants for food.

Methods
Field research was conducted in 60 rural settlements across Podlasie Voivodeship (Poland), Vilnius Region (Lithuania), and Hrodna Region (Belarus). This included 200 semi-structured interviews and participant observation among two local communities, Lithuanians and Poles. To assess the temporal dynamics of wild food use, we performed a cross-ethnic, cross-border analysis over time, dividing the data into three major temporal dimensions: past, continuous, and recently acquired uses.

Results
Of the 72 wild plant taxa reported by Poles or Lithuanians in the Polish-Lithuanian-Belarusian borderland, 47 were continuously used for food, 58 were utilised in the past, and 41 were recently acquired. Cross-country trends were similar, with Poland showing more past uses. Diachronic comparisons between Poles and Lithuanians in each studied country revealed no significant differences. Recently acquired taxa overlapped considerably with those used continuously and in the past. The most diversely utilised taxa showed the greatest overlaps. By observing the movement of specific plant taxa within various time dimensions, we distinguished overlapping flow variations: retention (3 taxa), decay (11), invention (8), stagnation (17), revitalisation (6), re-invention (3), and knowledge in motion (24). Shifts in the use of wild food plants were influenced by changes in environmental conditions, governmental policies, cultural practices, and economic factors.

Conclusion
The findings of this study have important implications for improving methods of tracking changes in LEK and enhancing our understanding of the relationship between people and nature. Our results underscore the importance of considering knowledge circulation over time in different directions. Recognising the various stages of knowledge circulation might help in pursuing sustainable solutions that balance the needs of human communities with environmental protection.
The effect of large channel-based foraminoplasty on lumbar biomechanics in percutaneous endoscopic discectomy: a finite element analysis
Authors: Sun Wei , Li Duohua , Zhao Sicong , Fu Hao , Tian Jiayu , Zhang Feng , Feng Hu , Wu Dongying 
Published: July 2024

Abstract
Background
This study aimed to evaluate the effect of foraminoplasty using large-channel endoscopy during TESSYS on the biomechanics of the lumbar spine.

Methods
A complete lumbar spine model, M1, was built using 3D finite elements, and models M2 and M3 were constructed to simulate the intraoperative removal of the superior articular process of L5 using a trephine saw with diameters of 5 mm and 8.5 mm, respectively, and applying normal physiological loads on the different models to simulate six working conditions—anterior flexion, posterior extension, left-right lateral bending, and left-right rotation—to investigate the displacement and facet joint stress change of the surgical segment, and the disc stress change of the surgical and adjacent segments.

Results
Compared with the M1 model, the M2 and M3 models showed decreased stress at the L4-5 left FJ and a significant increase in stress at the right FJ in forward flexion. In the M2 and M3 models, the L4-5 FJ stresses were significantly greater in left lateral bending or left rotation than in right lateral bending or right rotation. The right FJ stress in M3 was greater during left rotation than that in M2, and that in M2 was greater than that in M1. The L4-5disc stress in the M3 model was greater during posterior extension than that in the M1 and M2 models. The L4-5disc stress in the M3 model was greater in the right rotation than in the M2 model, and that in the M2 model was greater than that in the M1 model.

Conclusion
Foraminoplasty using large-channel endoscopy could increase the stress on the FJ and disc of the surgical segment, which suggested unnecessary and excessive resection should be avoided in PTED to minimize biomechanical disruption.