bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adult genitourinary sarcoma: Analysis using hospital-based cancer registry data in Japan
Authors: Nitta Satoshi , Kandori Shuya , Suzuki Shuhei , Hamada Kazuki , Chihara Ichiro , Shiga Masanobu , Kojo Kosuke , Sakka Shotaro , Nagumo Yoshiyuki , Kimura Tomokazu , Mathis Bryan J , Negoro Hiromitsu , Okuyama Ayako , Higashi Takahiro , Nishiyama Hiroyuki 
Published: November 2023

Abstract
Objectives We aimed to elucidate the clinical characteristics, survival outcomes and prognostic factors for overall survival of adult genitourinary sarcoma in Japan.Methods A hospital-based cancer registry data in Japan was used to identify and enroll patients diagnosed with genitourinary sarcoma in 2013. The datasets were registered from 121 institutions.Results A total of 116 men and 39 women were included, with a median age of 66 years. The most common primary site was the kidney in 47 patients, followed by the paratestis in 36 patients. The most common histological type was liposarcoma in 54 patients, followed by leiomyosarcoma in 25 patients. The 5-year overall survival rates were 57.6%. On univariate analysis, male gender, primary organ of paratestis, histological subtype of liposarcoma, and treatment with surgery were predictive of favorable survival while primary kidney, bladder or prostate gland, and treatment with chemotherapy or radiation were predictive of unfavorable survival. On multivariate analysis, primary paratestis and treatment with surgery were independent predictors of favorable survival while treatment with chemotherapy was an independent predictor of unfavorable survival.Conclusions We revealed clinical characteristics and survival outcomes of adult genitourinary sarcoma in Japan using a real-world large cohort database. Primary paratestis and treatment with surgery or chemotherapy were independent, significant factors for prognosis.
Saudi Billing System: designing a standardized health insurance billing system in Saudi Arabia to support a national health system transformation
Authors: Reka Husein , Mazevska Deniza , Pearse Jim , Maghrabi Abdullah Al , Young Susan E. , Ghamdi Shabab Al 
Published: November 2023

Abstract
Background The Saudi health transformation program entails a comprehensive reform of all health system functions. One of the pillars of this reform is the health care financing transformation. The Council of Health Insurance (CHI) aims to bring more transparency and understanding of case-mix through the introduction of patient classification and data standardization. Until recently, the private health insurance sector was using a variety of in-house non-standardized billing codes that impeded transparency and a value-based health care (VBHC) financing model. This study enabled the introduction of standardized billing codes known as the Saudi Billing System (SBS).
Methods We reviewed and assessed several patient classification and billing systems as part of the assessment phase, followed by data collection from eighty health care providers and the three largest health insurance companies, resulting in more than two million patient encounters for data analysis. A representative sample of 36,299 patient records were re-coded. Coding was undertaken using the Australian Classification of Health Interventions (ACHI) 10th Edition. Codes were assigned based on assessment by clinical coders using an established methodology and followed by an audit to confirm the assigned code or assign an alternative code where the coding could not be adequately completed by the initial coder.
Results 75% of records were mapped to an existing ACHI code, leaving 25% being a partial match, an approximate match or other (1%, 22% and 2% respectively). As part of this process, the original ACHI codes were modified, and additional codes were added, ensuring full compatibility with billing practices. We named the new code set the Saudi Billing System (SBS). As a result of this work, we created an additional 1,774 codes, bringing the total SBS code set to 7,947 codes (30% increase from ACHI 10th Edition).
Conclusions Patient classification and standardized billing systems are critical for transparency in providing health care and financing. Working within the existing national patient classification mandate and clinical coding standards required innovative ways to adapt these systems to a private health insurance market (specificity, familiarity, existing license with modification rights and ability to build fee schedule), to address the requirements of a reformed and more value-based insurance market.
Current mandated patient classification systems are a good basis for adaptation to serve the needs of the overall health care transformation in the country and a building block towards more transparency and VBHC.
Case Report:Sarcoidosis with Peripheral neuropathy
Authors: Li Jing , Yang Sha-Sha , Xue Min , Zhang Mei 
Published: November 2023

Abstract

Background:Peripheral neuropathy is a broad term that encompasses various disorders of the peripheral nervous system. This includes granulomatous neuropathy and non- granulomatous small fiber neuropathy (SFN). The most prevalent clinical manifestations of granulomatous neuropathy are distal symmetric polyneuropathy and asymmetric polyradiculoneuropathy. Common causes of peripheral neuropathy include glycometabolic disturbance, infection, inflammation, and intoxication. However, cases of sarcoidosis are rare.
Case Presentation: A 58-year-old female driving instructor with no previous medical history presented to the hospital with initial numbness in her left foot, followed by numbness and weakness in her right foot and both feet. A month later, she experienced bilateral numbness below the wrist. The patient underwent a lumbar puncture and further testing for auto-antibodies in both the cerebrospinal fluid (CSF) and serum. The results showed negative findings for seventeen antibodies related to peripheral neuropathy and Anti-MAG antibody. Enhanced chest CT revealed multiple swollen lymph nodes in the neck, mediastinum, and bilateral hilar area. Ultrasonography also confirmed enlarged lymph nodes in the bilateral supraclavicular, subclavian region, and mediastinum. Electromyography (EMG) and Nerve conduction studies (NCS) indicated asymmetric motor and sensory polyneuropathy. Additionally, the histological examination of a supraclavicular lymph node revealed characteristic non-caseating granulomas (NCG).
Conclusion:This case report highlights the potential of peripheral neuropathy as a clinical manifestation of sarcoidosis. It emphasizes the importance of considering sarcoidosis as a possible diagnosis in patients presenting with peripheral neuropathy, thereby contributing to increased knowledge and reducing the risk of misdiagnosis.
Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes
Authors: Braun Asolina , Rowntree Louise , Huang Ziyi , Pandey Kirti , Thuesen Nikolas , Li Chen , Petersen Jan , Littler Dene , Raji Shabana , Nguyen Thi , Lange Emma Jappe Lange Jappe , Persson Gry , Klausen Michael Schantz , Kringelum Jens , Chung Shan Zou , Croft Nathan , Faridi Pouya , Ayala Rochelle , Rossjohn Jamie , Illing Patricia , Scull Katherine , Ramarathinam Sri , Mifsud Nicole , Kedzierska Katherine , Sørensen Anders , Purcell Anthony 
Published: November 2023

Abstract

Most COVID-19 vaccines have been designed to elicit immunity against the SARS-CoV-2 Spike protein. However, the repeated occurrence of new strains harbouring Spike protein mutations demonstrates ready immune evasion by the SARS-CoV-2 virus and the pressing need to develop more broadly targeting COVID-19 vaccines. To facilitate this, we used mass spectrometry to identify immunopeptides that are derived from seven structural and non-structural SARS-CoV-2 proteins that are relatively conserved across viral strains (N, E, Nsp1, Nsp4, Nsp5, Nsp8, Nsp9) and presented by prevalent Human Leukocyte Antigen (HLA) class I and class II molecules. Two different B-lymphoblastoid cell lines were chosen to map immunopeptidomes covering some of the major HLA types across the global human population. We used DNA plasmid transfection and direct antigen delivery approaches to sample different antigens. We found 248 unique HLA class I and HLA class II bound peptides with 71 derived from N, 12 from E, 28 from Nsp1, 19 from Nsp4, 73 from Nsp8 and 45 peptides derived from Nsp9. Over half of the viral peptides are reported for the first time. T cell responses were tested for 56 of the detected peptides and we show robust CD8+ and CD4+ T cell responses against several peptides from the N, E and Nsp9 proteins. Results from this study will aid the development of next-generation COVID vaccines targeting epitopes from across a number of SARS-CoV-2 proteins.
Development and validation of a nomogram for predicting sepsis-associated encephalopathy in ICU patients
Authors: Jin Jun , Zeng Mian , Zhou Qingshan , Yu Lei 
Published: November 2023

Abstract
Background: Sepsis-associated encephalopathy (SAE) is associated with systemic inflammation caused by sepsis. It is estimated that a majority of sepsis patients develop severe acute effects (SAE) during their stay in the intensive care unit (ICU), and a significant number of survivors have persistent cognitive impairment even after they have recovered from the illness. The aim of this study was to develop a useful predictive nomogram for patients with ICU sepsis and screen for SAE risk factors.
Methods: We conducted a retrospective cohort study using the Medical Information Mart for Intensive Care IV (MIMIC-IV) database, defining SAE as a Glasgow Coma Scale (GCS) score of ≤15 or delirium. We randomly divided patients into training and validation cohorts, and used least absolute shrinkage and selection operator (LASSO) regression modeling to optimize feature selection. The independent risk factors were determined through a multivariable logistic regression analysis, and a prediction model was built. Nomogram performance was evaluated using the area under the receiver operating characteristic curve (AUC), calibration plots, Hosmer-Lemeshow test, decision curve analysis (DCA), net reclassification improvement (NRI) and integrated discrimination improvement (IDI).
Results: Among 4476 sepsis patients screened, 2781 (62.1%) developed SAE. In-hospital mortality was higher in the SAE group than in the non-SAE group (9.5% vs 3.7% p<0.001). A number of variables were screened, such as the patient's age, gender, BMI on the first day of admission, the mean arterial pressure, the body temperature, the platelet count, the sodium level, and the use of midazolam. The variables that were assessed encompassed the patient's age, gender, BMI upon admission, initial mean arterial pressure, body temperature, platelet count, sodium level, utilization of midazolam, and SOFA score. These were used to construct and validate a nomogram. Comparisons between the nomogram's AUC, NRI, IDI, and DCA with those of the conventional SOFA score in conjunction with delirium revealed superior performance. The nomogram's calibration plots and the results of the Hosmer-Lemeshow test indicated accurate calibration. Enhanced NRI and IDI values demonstrated that our scoring system surpassed traditional diagnostic approaches. Furthermore, the DCA curve indicated favorable clinical applicability of the nomogram.
Conclusion: This study identified independent risk factors for the development of SAE in sepsis patients and used them to construct a predictive model. The findings of this study can provide a clinical reference for the early diagnosis of SAE in patients.
Genetic confounding in health disparities research
Authors: Gupta Sonali , Sharma Shivam , Jordan I. King , Mariño-Ramírez Leonardo 
Published: November 2023

Abstract
Background
Health disparities are defined as health differences that adversely affect socially disadvantaged populations, and health disparities research is focused primarily on social and environmental determinants of health. We hypothesized that unmeasured genetic differences between population groups are likely to be a major source of hidden confounding for observational studies of health disparities.
Results
Our study cohort consisted of 26,912 UK Biobank participants from Asian, Black, and White ethnic groups. We analyzed outcomes for 1,536 diseases and discovered numerous health disparities that affect socially disadvantaged Asian and Black UK ethnic groups. We modeled outcomes for the top twenty Asian-White and Black-White health disparities using genetic and socioenvironmental risk factors to test for genetic confounding. We found that genetic diversity and differences in socioenvironmental risk factors are correlated between UK ethnic groups and demonstrate how genetic confounding can lead to spurious associations between social disadvantage and genetically influenced disease disparities. Specifically, inclusion of genetic data in disease risk models attenuates the effect of socioeconomic deprivation (SED) on most of the top health disparities, including spurious associations of SED with sickle cell disease and skin cancer. Moreover, comparisons of disease models with SED alone versus models with SED and genetic data together indicate that all the top health disparities analyzed here are more accurately modeled when genetic confounders are included.
Conclusions
Our results support an integrated approach to health disparities research that incorporates genetic, social, and environmental data whenever possible.
High transmission of endemic human coronaviruses before and during the COVID-19 pandemic in adolescents in Cebu, Philippines
Authors: Joseph Janet O. , Ylade Michelle , Daag Jedas Veronica , Aogo Rosemary , Crisostomo Maria Vinna , Mpingabo Patrick , Premkumar Lakshmanane , Deen Jacqueline , Katzelnick Leah 
Published: November 2023

Abstract

Background.
SARS-CoV-2, the causative agent of COVID-19, is a betacoronavirus belonging to the same genus as endemic human coronaviruses (hCoVs) OC43 and HKU1 and is distinct from alpha hCoVs 229E and NL63. In a study of adolescents in the Philippines, we evaluated the seroprevalence to hCoVs, whether pre-pandemic hCoV immunity modulated subsequent risk of SARS-CoV-2 infection, and if SARS-CoV-2 infection affected the transmission of the hCoVs.
Methods.
From 499 samples collected in 2021 and screened by SARS-CoV-2 receptor binding domain (RBD) enzyme-linked immunosorbent assay (ELISA), we randomly selected 59 SARS-CoV-2 negative and 61 positive individuals for further serological evaluation. We measured RBD and spike antibodies to the four hCoVs and SARS-CoV-2 by ELISA in samples from the same participants collected pre-pandemic (2018–2019) and mid-pandemic (2021), before COVID-19 vaccination.
Results.
We observed over 72% seropositivity to the four hCoVs pre-pandemic. Binding antibodies increased with age to 229E and OC43, suggesting endemic circulation, while immunity was flat across ages for HKU1 and NL63. During the COVID-19 pandemic, antibody level increased significantly to the RBDs of OC43, NL63, and 229E and spikes of all four hCoVs in both SARS-CoV-2 negative and positive adolescents. Those aged 12–15 years old in 2021 had higher antibodies to RBD and spike of OC43, NL63, and 229E than adolescents the same age in 2019, further demonstrating intense transmission of the hCoVs during the pandemic.
Conclusions.
We observe a limited impact of the COVID-19 pandemic on endemic hCoV transmission. This study provides insight into co-circulation of hCoVs and SARS-CoV-2.
The Impact of Acupuncture on The Brain Function of Patients With Mild to Moderate Depressive Disorders: A Study Protocol
Authors: Yang Bin , Miao Runqing , Wang Tianyu , Zhu Fengya , Li Wuyu , Liu Yang , Wu Jie 
Published: November 2023

Abstract
Introduction:
Depressive disorders are common mental disease that significantly impact the daily lives of those affected. Acupuncture has shown promising therapeutic effects in the treatment of depressive disorders, but its underlying mechanisms remain unclear. This study aims to evaluate the therapeutic effects of acupuncture on mild to moderate depressive disorders and its influence on the brain function of patients with mild to moderate depressive disorders.
Methods
This study plans to recruit 118 participants, who will be randomly allocated to either the acupuncture group or the sham acupuncture group in a 1:1 ratio. Both groups will undergo 8 weeks of treatment, consisting of three sessions per week, with each session lasting for 30 minutes. A follow-up period of 3 months will be conducted after the treatment. Assessments will be conducted at weeks 0, 8, 12, 16, and 20 in this study. The primary outcome measure will be self-rating depression scale (SDS), while secondary outcome measures will include the self-rating anxiety scale (SAS), quality of life scale (SF-36), traditional Chinese medicine syndrome score, symptom elimination rate and functional near-infrared spectroscopy (fNIRS) brain imaging.
Discussion
While acupuncture has been confirmed to have a certain degree of therapeutic efficacy in the treatment of depressive disorders, research on the mechanisms underlying acupuncture's treatment of depression remains limited, particularly with regards to its impact on the brain function of individuals with depression. This study aims to explore both the clinical effectiveness and treatment mechanisms of acupuncture for depressive disorders, with a specific focus on its influence on brain function. This research endeavors to provide new insights into the potential of acupuncture as a therapeutic approach for the treatment of depression in the future.
Oral Microbiota and Porphyromonas Gingivalis Kgp Genotypes Altered in Parkinson’s Disease with Mild Cognitive Impairment
Authors: Li Dongcheng , Ren Tengzhu , Li Hao , Huang Mingdi , Chen Jiaxin , He Qishan , Lv Wei , Liu Hailing , Xu Renshi , Zhang Xiong 
Published: November 2023

Abstract
Cognitive impairment (CI) is a common complication of the non-motor symptoms in Parkinson’s disease (PD), including PD with mild cognitive impairment (PD-MCI) and PD dementia. Recent studies reported the oral dysbiosis in PD and CI, respectively. Porphyromonas gingivalis (P. gingivalis), a pathogen of oral dysbiosis, play an important role in PD, whose lysine-gingipain (Kgp) could lead to AD-type pathologies. No previous study investigated the composition of oral microbiota and role of P. gingivalisin PD-MCI. This study aimed to investigates the differences of oral microbiota composition, P. gingivalis copy number, and Kgp genotypes among PD-MCI, PD with normal cognition(PD-NC) and periodontal status-matched control (PC) groups. The oral bacteria composition, the copy number of P. gingivalisand the Kgp genotypes in gingival crevicular fluid from PD-MCI, PD-NC, and PC were analyzed using 16S ribosomal RNA sequencing, quantitative real-time PCR, and MseⅠ restriction. We found that the structures of oral microbiota in PD-MCI group were significantly different compared to that in PD-NC and PC group. The relative abundances of Prevotella, Lactobacillus, Megasphaera, Atopobium and Howardella were negatively correlated with cognitive score. Moreover, there was a significant difference of Kgp genotypes among the three groups. The predominant Kgp genotypes of P. gingivalis in the PD-MCI group was primarily Kgp Ⅱ, whereas in the PD-NC group was mainly Kgp Ⅰ. The Kgp Ⅱ correlated with lower MMSE and MoCA scores, suggested that PD-CI may be related to Kgp genotypes Ⅱ.
Why are star dunes rarely recognised in the rock record?
Authors: Bristow Charles , Duller Geoff 
Published: November 2023

Abstract
Star dunes are the tallest dunes on Earth and are amongst the largest and most spectacular dynamic landforms. Although they are widespread in modern sandy deserts star dunes are rarely recognised in the rock record probably due to a lack of suitable models. This stratigraphic study of a star dune in the Sahara Desert shows that the dune has developed recently and grown rapidly to create a 100 m high dune within the past thousand years. At the base of the dune there is a period of around eight thousand years that appears to lack sand accumulation, probably due to stabilization of the dunes during the African humid period (AHP). The star dune accumulation post-dates the end of the AHP. We present a new model for the structure of a star dune based on a geophysical and geochronological investigation. Individual structural features in star dunes are similar to those from linear or barchanoid dunes, likely leading to misidentification in the rock record, but the suite of features we describe will permit identification of star dunes in future studies of the rock record.
Identification and Experimental Validation of Genes Associated with Programmed Cell Death in Dendritic Cells of the Thyroid Tissue in Hashimoto's Thyroiditis
Authors: Yang Dongyu , Wang Xichang , Sun Ying , Shao Ying , Shi Xiaoguang 
Published: November 2023

Abstract
Introduction:
Hashimoto's thyroiditis (HT) is a chronic autoimmune disorder. Being antigen-presenting cells, dendritic cells induce various types of programmed cell death (PCD), resulting in immune disorders. This study aimed to identify genes associated with various PCD pathways in dendritic cells within the thyroid tissue of HT patients.
Methods
We downloaded the single-cell RNA-sequencing dataset HRA001684 from the National Genomics Data Center (NGDC) database to calculate the area under the curve (AUC) scores for PCD-related genes. We obtained the mRNA sequencing datasets GSE138198 and HRA001684 from Gene Expression Omnibus and NGDC, respectively. Differentially expressed genes (DEGs) were identified by comparing the normal and HT groups in GSE138198 and HRA001684. The intersection of these DEGs with PCD-related genes led to the identification of 17 PCDDEGs.
Results
The AUC scores showed that dendritic cells exhibited significantly high levels of necroptosis, ferroptosis, pyroptosis, autophagy, and PANoptosis and expressed six PCDDEGs: TNFAIP3, CYBB, PTPN6, STAT1, TGFB1, and NLRP3. These genes displayed an AUC > 0.8 for HT in the GSE29315, GSE138198, and HRA001684 datasets and clinical thyroid samples, confirming their diagnostic accuracy. Moreover, their expression was positively correlated with the serum levels of thyroid peroxidase and thyroglobulin antibodies. Finally, all PCDDEGs were inversely associated with thyroid follicular epithelial cells.
Discussion
These findings suggest that dendritic cells play a crucial role in mediating PCD within the thyroid tissues of HT patients. Moreover, TNFAIP3, CYBB, PTPN6, STAT1, TGFB1, and NLRP3 may crucially contribute to the pathogenesis of HT through PCD pathways.