bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causal effects of gut microbiome on endometriosis: a two-sample mendelian randomization study
Authors: Liu Ziyu , Chen Peigen , Luo Liling , Liu Qianru , Shi Hao , Yang Xing 
Published: November 2023

Abstract
Background
Previous studies have shown observational associations between the gut microbiota and endometriosis; however, the causal nature of such associations remains unclear. This study aimed to analyze the genetic causal relationship between the two.

Methods
A gut microbiome genome-wide association study conducted by the MiBioGen consortium was used as exposure data, and summary statistics of endometriosis were obtained from the FinnGen consortium R8 release data. Inverse variance weighted, MR-Egger, weighted median, weighted model, and simple model analyses were applied to examine the causal relationship, and sensitivity analyses were conducted to validate the robustness of the results.

Results
The results showed that, out of 211 gut microbiome taxa, Clostridiales_vadin_BB60_group, Oxalobacteraceae, Desulfovibrio, Haemophilus, and Holdemania had protective effects on endometriosis, while Porphyromonadaceae and Anaerotruncus might contribute to the development of endometriosis. Heterogeneity and pleiotropy analyses confirmed the robustness of the results.

Conclusion
The two-sample Mendelian randomization analysis conducted in this study identified specific intestinal flora with a causal relationship with endometriosis at the genetic level, offering new insights into the gut microbiota-mediated development mechanism of endometriosis.
An association between ATP7B expression and human cancer prognosis and immunotherapy: a pan-cancer perspective
Authors: Zhang Zhanzhan , Zhang Aobo , Shi Yunpeng , Zhao Zijun , Zhao Zongmao 
Published: November 2023

Abstract
Background
ATP7B is a copper-transporting protein that contributes to the chemo-resistance of human cancer cells. It remains unclear what the molecular mechanisms behind ATP7B are in cancer, as well as its role in human pan-cancer studies.

Methods
Our study evaluated the differential expression of ATP7B in cancer and paracancerous tissues based on RNA sequencing data from the GTEx and TCGA. Kaplan–Meier and Cox proportional hazards regressions were used to estimate prognostic factors associated with ATP7B.The correlations between the expression of ATP7B and immune cell infiltration, tumor mutation burden, microsatellite instability and immune checkpoint molecules were analyzed. Co-expression networks and mutations in ATP7B were analyzed using the web tools. An analysis of ATP7B expression difference on drug sensitivity on tumor cells was performed using the CTRP, GDSC and CMap database.

Results
ATP7B expression differed significantly between cancerous and paracancerous tissues. The abnormal expression of ATP7B was linked to prognosis in LGG and KIRC. Infiltration of immune cells, tumor mutation burden, microsatellite instability and immunomodulators had all been linked to certain types of cancer. Cancer cells exhibited a correlation between ATP7B expression and drug sensitivity.

Conclusion
ATP7B might be an immunotherapeutic and prognostic biomarker based on its involvement in cancer occurrence and development.
Cytoreductive surgery is feasible in patients with limited regional platinum-resistant recurrent ovarian cancer
Authors: Zou Ruoyao , Jiang Qidi , Luo Xukai , Chen Mo , Yuan Lei , Yao Liangqing 
Published: November 2023

Abstract
Introduction
To evaluate the efficacy of cytoreductive surgery versus chemotherapy for the treatment of limited regional, platinum-resistant ovarian cancer (PROC).

Materials and methods
The clinical records of all patients with PROC treated in our center between March 2015 and March 2022 were retrospectively reviewed. We compared the oncology outcomes of patients who received cytoreduction or chemotherapy alone at relapse and presented information about postoperative adjuvant chemotherapy.

Results
Among 52 patients with limited regional recurrence, 40.4% (21/52) underwent cytoreduction because of platinum resistance, and 59.6% (31/52) received chemotherapy alone. No residual disease (R0) was achieved in 20 patients (95.2%). The severe morbidity rate within 30 days after the surgery was 15%. The median follow-up was 70.6 months. Compared with the chemotherapy alone group, the surgery group with R0 had better progression-free survival (PFS) (10.6 vs. 5.1 months; hazard ratio (HR) = 0.421; P = 0.0035) and post-relapse survival (PRS) (32.6 vs. 16.3 months; HR = 0.478; P = 0.047), but there was no difference in overall survival (OS) between the two groups. Laparoscopy is associated with lesser intraoperative blood loss with no differences in survival and postoperative complications compared to the open approach (P = 0.0042). Subgroup survival analysis showed that compared with chemotherapy alone, surgery prolonged PFS in patients regardless of tumor size (greater than or equal to 4 cm or less). Surgery group patients who achieved R0 had an objective response rate (ORR) of 36.8% (7/19), among whom 40% (4/10) received platinum rechallenge chemotherapy and 33.3% (3/9) were administered non-platinum chemotherapy.

Conclusion
When well-selected PROC patients with limited regional recurrence achieved R0, their outcomes were superior to those of patients who received only chemotherapy with an acceptable morbidity rate. Laparoscope technology could be a reliable alternative surgical approach. The reintroduction of platinum agents may be considered following surgery. Further analyses in a larger population are warranted to elucidate the risks and benefits of this surgery and adjuvant chemotherapy strategy.
Evaluation of the performance of advantage P.f. malaria Card® and advantage malaria Pan + Pf Card®, two rapid diagnostic tests for parasitological confirmation of malaria cases in field situation in Togo
Authors: Teou Diwaba Carmel , Dorkenoo Ameyo Monique , Ataba Essoham , Alidou Smaila , Yakpa Kossi , Abdou-Kerim Agueregna , Maman Issaka , Agbonon Amegnona 
Published: November 2023

Abstract
Background
In Togo, malaria remains a major public health problem, and the management of suspected cases requires confirmation with appropriate biological methods. Malaria diagnosis has been improved by the introduction of rapid diagnostic tests (RDTs), recommended by the World Health Organization (WHO) for areas where microscopy is not available. To be used, these RDTs must meet performance criteria defined by the WHO. This study was conducted to evaluate the diagnostic performance of two RDTs: Advantage P.f. Malaria Card® detecting HRP2 antigen and Advantage Malaria Pan + Pf Card® detecting both HRP2 and pLDH antigens.

Methods
This was a cross-sectional analytical study conducted from December 2019 to February 2020 on malaria-suspected cases received in three sentinel sites in Togo and from whom capillary blood was collected to perform the two RDTs according to the manufacturer's instructions. Sensitivity and specificity were estimated by comparing to thick/thin blood smear, the gold standard, and to PCR, which is a more sensitive.

Results
A total of 390 participants (54.9% female) with a median age of 18 (± 0.8) years were included in the study. The sensitivity of both Advantage P.f. Malaria Card® and Advantage Malaria Pan + Pf Card® compared to thick/thin blood smear was 91.8% and 91.3%, respectively, and for both the specificity was 94.7%. Compared to PCR, the sensitivity was 84.2% and 83.8%, respectively, and the specificity 96.5%.

Conclusions
The performances of the Advantage P.f. Malaria Card® and Advantage Malaria PAN + Pf Card® compared to microscopy, considered the gold standard, were acceptable under the field conditions found in Togo. They can therefore be used for the biological diagnosis of malaria.

Graphical Abstract
Vertebral osteomyelitis caused by Campylobacter jejuni in an immunocompetent patient
Authors: Kirk Karina Frahm , Boel Jeppe , Nielsen Hans Linde 
Published: November 2023

Abstract
Background
Campylobacter jejuni is the leading cause of human bacterial gastroenteritis worldwide. However, systemic infection with C. jejuni is uncommon, and osteomyelitis caused by C. jejuni is extremely rare. Cultivation from spinal bone biopsies has not previously been reported in the literature.

Case presentation
A 79-year-old immunocompetent male was admitted to the emergency department at Aalborg University Hospital in Denmark with lower back pain, fever and diarrhoea. A FecalSwab obtained upon admission was PCR-positive for Campylobacter spp, while an aerobic blood culture bottle was positive for C. jejuni (Time to detection: 70.4 h). A MRI of columna totalis showed osteomyelitis at L1/L2 with an epidural abscess from L1 to L2 with compression of the dura sack. The patient underwent spinal surgery with spondylodesis and decompression of L1/L2. The surgery was uncomplicated and the discus material was also culture positive for C. jejuni. The patient was treated with meropenem for a total duration of four weeks, followed by four weeks of oral treatment with clindamycin in tapered dosage. The patient recovered quickly following surgery and targeted antibiotic treatment with decreasing lumbar pain and biochemical response and was fully recovered at follow-up three months after end of treatment.

Conclusions
While C. jejuni osteomyelitis is rare, it should still be suspected as a possible causative bacterial aetiology in patients with vertebral osteomyelitis, in particular when symptoms of diarrhoea is involved in the clinical presentation. Susceptibility testing is crucial due to emerging resistance, and targeted treatment strategies should rely upon such tests.
Survival of Trial-Like and Non–Trial-Like Patients With Immunotherapy in Advanced Hepatocellular Carcinoma in Real World: A Collaborative Multicenter Indian Study (IMHEP)
Authors: Ramaswamy Anant , Kulkarni Anand , John George , Rauthan Amit , Patil Shekhar , Duseja Ajay , Talwar Vineet , Rajappa Senthil J. , Ghadyalpatil Nikhil , Wadhawan Manav , Shukla Akash , Krishna Vamshi M. , Srinivas Sujay , Taneja Sunil , Sravani K. Mary , Rathi Sahaj , Bhargava Prabhat , Ostwal Vikas 
Published: November 2023

PURPOSE Immune checkpoint inhibitors (ICIs) is the initial line of management in advanced hepatocellular carcinoma (HCC), but survivals in the real world are not known. MATERIALS AND METHODS A retrospective study of patients with advanced HCC receiving ICIs (as first-line therapy or as later lines of therapy) across 11 Indian institutions was conducted. Patients were divided into either cohort 1 (trial-like receiving ICI as first-line therapy), with a Child Pugh score (CTP) of ≤6, an Eastern Cooperative Oncology Group performance status (ECOG PS) of 0/1, and no VP4 (main portal vein thrombosis [MPVT]) or cohort 2 (trial unlike) who did not satisfy at least one of the above criteria. The primary end point was 12-month overall survival (OS). RESULTS Between January 2017 and January 2022, 133 patient data were analyzed. The presence of MPVT was seen in 33 patients (25%). The ICIs used were atezolizumab-bevacizumab, nivolumab, and pembrolizumab in 89 (66%), 44 (33%), and one (1%) patients, respectively. With a median follow-up of 13.8 months, the 12-month OS for the entire cohort was 33.4% (95% CI, 23.6 to 43.2). Patients in cohort 1 (n = 31) had a significantly improved OS compared with patients in cohort 2 (n = 102; 12-month OS, 57.9% [95% CI, 38.5 to 77.3] v 24% [95% CI, 13.4 to 34.6]; P = .005). Patients with CTP A as compared with CTP B (9.7 v 4.3 months; P < .001) and an ECOG PS of 0/1 as compared with a PS of ≥2 (8.7 v 7.2 months; P = .04) and without MPVT (9.4 v 4.0; P < .001) had superior survivals. CONCLUSION Patients with advanced HCC in the real world, trial-like have survivals in consonance with trial data, whereas patients with features excluding them from trials, such as main portal vein thrombosis, poor ECOG PS, and child Pugh B status, have markedly inferior survivals, despite good tolerance to immunotherapy.
Normative Measurements of L1–S1 Segmental Angulation, Disk Space Height, and Neuroforaminal Dimensions Using Computed Tomography
Authors: Razzouk Jacob , Case Trevor , Brandt Zachary , Marciniak Mary , Sajdak Grant , Nguyen Kai , Small Easton , Petersen Garrett , Kagabo Whitney , Ramos Omar , Shaffrey Christopher I. , Cheng Wayne , Danisa Olumide 
Published: November 2023

BACKGROUND AND OBJECTIVES:
To establish normative anatomic measurements of lumbar segmental angulation (SA) and disk space height (DSH) in relation to neuroforaminal dimensions (NFDs), and to uncover the influence of patient demographic and anthropometric characteristics on SA, DSH, and NFDs.

METHODS:
NFDs, SA, and anterior, middle, and posterior DSH were measured using computed tomography of 969 patients. NFDs were defined as sagittal anterior-to-posterior width, foraminal height, and area. Statistical analyses were performed to assess associations among SA, DSH, NFDs, and patient height, weight, body mass index, sex, and ethnicity.

RESULTS:
SA and DSH measurements increased moving caudally from L1 to S1. Foraminal width decreased moving caudally from L1 to S1. Foraminal height and area demonstrated unimodal distribution patterns with the largest values clustered at L2–L3 on the right side and L3–L4 on the left. Significant differences in SA, DSH, and NFD measurements were observed based on the disk level. Inconsistent, marginal NFD differences were observed based on laterality. Across all disk levels, only weak-to-moderate correlations were observed between SA and DSH in relation to NFDs. Patient height, weight, and body mass index were only weakly associated with SA, DSH, and NFDs. Based on patient sex, significant differences were observed for SA, DSH, and NFD measurements from L1 to S1, with males demonstrating consistently larger values compared with females. Based on patient race and ethnicity, significant differences in SA and NFD measurements were observed from L1 to S1.

CONCLUSION:
This study describes 48 450 normative measurements of L1–S1 SA, DSH, and NFDs. These measurements serve as representative models of normal anatomic dimensions necessary for several applications including surgical planning and diagnosis of foraminal stenosis. Normative values of SA and DSH are not moderately or strongly associated with NFDs. SA, DSH, and NFDs are influenced by sex and ethnicity, but are not strongly or moderately influenced by patient anthropometric factors.
Spinal Cord Injury Management Policies in High School Sports as Reported by Athletic Administrators
Authors: Scarneo-Miller Samantha E. , Swartz Erik E. , Register-Mihalik Johna K. , Coleman Kelly A. , Emrich Christina M. , DiStefano Lindsay J. 
Published: November 2023

ABSTRACT

Introduction/Purpose
Athletic administrators (AA) in U.S. high schools are uniquely positioned to provide guidance and endorsement for the prevention and management of common sport-related catastrophic injuries, such as the development of a spinal cord injury management (SCIM) policy. The purpose of this project was to evaluate AA’s knowledge of comprehensive SCIM policies in U.S. high schools. Secondarily, we aimed to investigate the factors, facilitators, and barriers to the development and adoption of comprehensive policies.

Methods
An online questionnaire was distributed to 6423 AA working in U.S.-based high school athletics, with 366 included in the final data analysis. The questionnaire evaluated AA’s knowledge of comprehensive SCIM policies addressing components of adoption, documentation, and communication. The questionnaire was developed based on the 2002 “National Athletic Trainers’ Association Position Statement: Acute Management of the Cervical Spine-Injured Athlete.” The questionnaire also inquired about facilitators and barriers to developing and adopting comprehensive policies. Proportions were calculated for policy adoption, and independent-samples t-tests evaluated the influence of athletic training services on comprehensive SCIM policies.

Results
About half of AA (49.2%, n = 180/366) reported having all recommended components of a written SCIM policy. AA who had access to an athletic trainer (yes = 62.9%, no = 18.1%, unknown = 19%) were more likely to have a comprehensive SCIM policy compared with those without access (80.6% vs 19.4%, χ
2
1 = 7.091, P = 0.008, prevalence ratio = 1.24, 95% confidence interval = 1.03–1.50). The most commonly reported facilitator (49.9%) was “having a medical professional at the school,” and the main barrier (30.2%) was “my school would need more information, resources, assistance, etc.”

Conclusions
The findings identify areas for improvement in supporting the health and safety of children in high school participating in interscholastic athletics. Future dissemination and implementation research should develop strategies tailored to individual school community and need to improve SCIM policy adoption and implementation.
Seamless Multimodal Transportation Scheduling
Authors: Raghunathan Arvind U. , Bergman David , Hooker John N. , Serra Thiago , Kobori Shingo 
Published: November 2023

Ride-hailing services have expanded the role of shared mobility in passenger transportation systems, creating new markets and creative planning solutions for major urban centers. In this paper, we consider their use for the first-mile or last-mile passenger transportation in coordination with a mass transit service to provide a seamless multimodal transportation experience for the user. A system that provides passengers with predictable information on travel and waiting times in their commutes is immensely valuable. We envision that the passengers will inform the system of their desired travel and arrival windows so that the system can jointly optimize the schedules of passengers. The problem we study balances minimizing travel time and the number of trips taken by the last-mile vehicles, so that long-term planning, maintenance, and environmental impact are all taken into account. We focus on the case where the last-mile service aggregates passengers by destination. We show that this problem is NP-hard, and we propose a decision diagram–based branch-and-price decomposition model that can solve instances of real-world size (10,000 passengers spread over an hour, 50 last-mile destinations, 600 last-mile vehicles) in computational time (∼1 minute) that is orders of magnitude faster than the solution times of other methods appearing in the literature. Our experiments also indicate that aggregating passengers by destination on the last-mile service provides high-quality solutions to more general settings. History: Accepted by Pascal Van Hentenryck, Area Editor for Computational Modeling: Methods and Analysis. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplemental Information ( https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2019.0163 ) as well as from the IJOC GitHub software repository ( https://github.com/INFORMSJoC/2019.0163 ). The complete IJOC Software and Data Repository is available at https://informsjoc.github.io/ .
Variants of IL6, IL10, FCN2, RNASE3, IL12B and IL17B loci are associated with Schistosoma mansoni worm burden in the Albert Nile region of Uganda
Authors: Nyangiri Oscar Asanya , Mulindwa Julius , Namulondo Joyce , Kitibwa Anna , Nassuuna Jacent , Elliott Alison , Kimuda Magambo Phillip , Boobo Alex , Nerima Barbara , Adriko Moses , Dunton Nathan J. , Madhan Gaganjit Kaur , Kristiansen Mark , Casacuberta-Partal Miriam , Noyes Harry , Matovu Enock ,   on behalf of the TrypanoGEN+ Research group of the H3Africa consortium
Published: November 2023

Background
Individuals genetically susceptible to high schistosomiasis worm burden may contribute disproportionately to transmission and could be prioritized for control. Identifying genes involved may guide development of therapy.

Methodology/Principal findings
A cohort of 606 children aged 10–15 years were recruited in the Albert Nile region of Uganda and assessed for Schistosoma mansoni worm burden using the Up-Converting Particle Lateral Flow (UCP-LF) test detecting circulating anodic antigen (CAA), point-of-care Circulating Cathodic Antigen (POC-CCA) and Kato-Katz tests. Whole genome genotyping was conducted on 326 children comprising the top and bottom 25% of worm burden. Linear models were fitted to identify variants associated with worm burden in preselected candidate genes. Expression quantitative trait locus (eQTL) analysis was conducted for candidate genes with UCP-LF worm burden included as a covariate. Single Nucleotide Polymorphism loci associated with UCP-LF CAA included IL6 rs2066992 (OR = 0.43, p = 0.0006) and rs7793163 (OR = 2.0, p = 0.0007); IL21 SNP kgp513476 (OR 1.79, p = 0.0025) and IL17B SNP kgp708159 (OR = 0.35, p = 0.0028). A haplotype in the IL10 locus was associated with lower worm burden (OR = 0.53, p = 0.015) and overlapped SNPs rs1800896, rs1800871 and rs1800872. Significant haplotypes (p<0.05, overlapping significant SNP) associated with worm burden were observed in IL6 and the Th17 pathway IL12B and IL17B genes. There were significant eQTL in the IL6, IL5, IL21, IL25 and IFNG regions.

Conclusions
Variants associated with S. mansoni worm burden were in IL6, FCN2, RNASE3, IL10, IL12B and IL17B gene loci. However only eQTL associations remained significant after Bonferroni correction. In summary, immune balance, pathogen recognition and Th17 pathways may play a role in modulating Schistosoma worm burden. Individuals carrying risk variants may be targeted first in allocation of control efforts to reduce the burden of schistosomiasis in the community.
Teaching-learning in clinical education based on epistemological orientations: A multi-method study
Authors: Khani Hamed , Ahmady Soleiman , Sabet Babak , Namaki Ali , Zandi Shirdel , Niakan Somayeh 
Published: November 2023

Introduction
Teaching-learning is the heart of medical education in the clinical setting. The objective of this research was to develop a conceptual model of effective clinical teaching in undergraduate medical education and conceptualize its operational framework based on the best fit approach.

Materials and methods
This research consisted of three sub-studies conducted using a multi-method approach. The first sub-study was conducted using a qualitative meta-synthesis approach. The second sub-study used Clarke’s situational analysis approach as a postmodern version of grounded theory. Finally, the third sub-study was designed in two stages. First, it was conducted using the expert panel, in the second step, framework of synthesis based on best fit, and the framework of Ottenhoff- de Jonge et al., which formed the basis of this study.

Results
In the first sub-study, qualitative evidence on the factors of effective teaching-learning in clinical education was synthesized into five dimensions. Based on the second sub-study, the clinical teaching-learning situation in undergraduate medical education in Iran was represented in three maps, including situational, social worlds/arenas, and positional. Finally, in the third sub-study, based on model modification and development in the expert panel, the effective teaching-learning dimensions were developed into behavioral, social, pedagogical, technology, contextual, educational leadership, and financial dimensions. In the second step, based on the framework of Ottenhoff- de Jonge et al., a three-dimensional matrix was developed concerning epistemological orientations about teaching and learning.

Discussion
Moving from a single teaching-centered and learning-centered orientation to a teaching-learning-centered orientation is required for effective teaching-learning in clinical medical education.