bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation profiles in urothelial bladder cancer tissues and children with schistosomiasis from Eggua, Ogun State, Nigeria
Authors: Akpabio Cephas A. , Ebuh Rachael P. , Fatunla Oluwaseun E. , Awobode Henrietta O. , Anumudu Chiaka I. 
Published: November 2023

Abstract
Background
Squamous cell carcinoma has been attributed to chronic schistosomiasis and is the predominant type of bladder cancer in schistosomiasis endemic areas. The aim of this study was to assess early promoter DNA methylation in selected genes implicated in schistosomiasis-associated bladder cancer (SABC).

Methods
A total of 159 urine samples were collected from school-aged children in Eggua Community of Ogun State and examined by microscopy for Schistosoma haematobium eggs. From this sample, a subset of 34 (21.1%) urine samples positive for S. haematobium, age and sex-matched with negative urine control samples, and 16 formalin-fixed paraffin-embedded bladder cancer tissues obtained from the University College Hospital were subjected to DNA isolation and bisulphite DNA conversion. Quantitative methylation-specific PCR was used to determine the methylation status of APC, RARβ2, RASSF1A, and TIMP3 in the samples.

Results
High degrees of methylation of RARβ2(67.7%), RASSF1A (38.2%), and TIMP3(52.9%) was more common in urogenital schistosomiasis (UGS)-positive urine samples than negative urine (control) samples and in bladder cancer tissues. Promoter DNA methylation in the positive urine samples was 1.4-fold, 13.3-fold, 3.4-fold, and 3.8-fold higher in APC, RARβ2, RASSF1A, and TIMP3, respectively, than in the matched controls. The odds of promoter methylation were likely to increase with age group for APC (OR: 1.615) and TIMP3(OR: 2.000); sex for TIMP3(OR: 2.644); and haematuria for RARβ2(OR: 1.094), RASSF1A (OR: 1.143), and TIMP3(OR: 1.842), although there were no significant associations. Conclusions: Gene promoter DNA methylation in tumour suppressor genes was observed in schistosomiasis cases. Hence, promoter DNA methylation may occur during active schistosomiasis in children. This result may serve as an early non-invasive biomarker to detect and hint at the risk of developing SABC later in life.
Comparison of responses to neoadjuvant and adjuvant chemotherapies in muscle-invasive bladder cancer
Authors: Sekmek Serhat , Ucar Gökhan , Karahan Irfan , Bayram Dogan , Aktürk Esen Selin , Seven Ismet , Sendur Mehmet Ali Nahit , Uncu Dogan 
Published: November 2023

Abstract
Background
Bladder cancer surgery is critical for treatment, and systemic treatment before or after cystectomy may be necessary. We aimed to investigate the efficacy and response to neoadjuvant and adjuvant treatments.

Methods
Data on 93 patients with resectable muscle-invasive bladder cancer were analyzed retrospectively. Patients who received neoadjuvant and adjuvant chemotherapies were included. The neoadjuvant treatment group was divided into pathological responders and non-responders. Overall survival and disease-free survival were calculated.

Results
The median age was 61.5 years; there were 6 female and 87 male patients. Baseline characteristics were similar between the groups. While there was no difference in OS between the neoadjuvant and adjuvant treatment groups (20 months vs. not reached), DFS was significantly higher in the adjuvant group (20.6 vs. 25.3 months). While there was no significant difference in DFS between the responders and non-responders to neoadjuvant treatment (20.6 vs. 19.1 months), OS was significantly longer in the responders (Not reached vs. 12.3 months).

Conclusions
Our results concluded that neoadjuvant and adjuvant chemotherapies have similar survival rates, but no response was associated with poor outcomes. Determining the group for patient selection may be helpful for optimal management.
RecView: an interactive R application for locating recombination positions using pedigree data
Authors: Zhang Hongkai , Hansson Bengt 
Published: November 2023

Abstract
Background
Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chromosomes.

Results
We present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. RecView analyses and plots the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree, and infers recombination positions with either of two built-in algorithms: one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin. RecView handles multiple offspring and chromosomes simultaneously, and all putative recombination positions are reported in base pairs together with an estimated precision based on the local density of informative alleles. We demonstrate RecView using genotype data of a passerine bird with an available reference genome, the great reed warbler (Acrocephalus arundinaceus), and show that recombination events can be located to specific positions.

Conclusions
RecView is an easy-to-use and highly effective application for locating recombination positions with high precision. RecView is available on GitHub (https://github.com/HKyleZhang/RecView.git).
Using published pathway figures in enrichment analysis and machine learning
Authors: Shin Min-Gyoung , Pico Alexander R. 
Published: November 2023

AbstractPathway Figure OCR (PFOCR) is a novel kind of pathway database approaching the breadth and depth of Gene Ontology while providing rich, mechanistic diagrams and direct literature support. Here, we highlight the utility of PFOCR in disease research in comparison with popular pathway databases through an assessment of disease coverage and analytical applications. In addition to common pathway analysis use cases, we present two advanced case studies demonstrating unique advantages of PFOCR in terms of cancer subtype and grade prediction analyses.
Characteristics of circulating immune cells in HBV-related acute-on-chronic liver failure following artificial liver treatment
Authors: Ju Tao , Jiang Daixi , Zhong Chengli , Zhang Huafen , Huang Yandi , Zhu Chunxia , Yang Shigui , Yan Dong 
Published: November 2023

Abstract
Background and aim
Liver failure, which is predominantly caused by hepatitis B (HBV) can be improved by an artificial liver support system (ALSS). This study investigated the phenotypic heterogeneity of immunocytes in patients with HBV-related acute-on-chronic liver failure (HBV-ACLF) before and after ALSS therapy.

Methods
A total of 22 patients with HBV-ACLF who received ALSS therapy were included in the study. Patients with Grade I according to the ACLF Research Consortium score were considered to have improved. Demographic and laboratory data were collected and analyzed during hospitalization. Immunological features of peripheral blood in the patients before and after ALSS were detected by mass cytometry analyses.

Results
In total, 12 patients improved and 10 patients did not. According to the immunological features data after ALSS, the proportion of circulating monocytes was significantly higher in non-improved patients, but there were fewer γδT cells compared with those in improved patients. Characterization of 37 cell clusters revealed that the frequency of effector CD8+ T (P = 0.003), CD4+ TCM (P = 0.033), CD4+ TEM (P = 0.039), and inhibitory natural killer (NK) cells (P = 0.029) decreased in HBV-ACLF patients after ALSS therapy. Sub group analyses after treatment showed that the improved patients had higher proportions of CD4+ TCM (P = 0.010), CD4+ TEM (P = 0.021), and γδT cells (P = 0.003) and a lower proportion of monocytes (P = 0.012) compared with the non-improved patients.

Conclusions
Changes in effector CD8+ T cells, effector and memory CD4+ T cells, and inhibitory NK cells are associated with ALSS treatment of HBV-ACLF. Moreover, monocytes and γδT cells exhibited the main differences when patients obtained different prognoses. The phenotypic heterogeneity of lymphocytes and monocytes may contribute to the prognosis of ALSS and future immunotherapy strategies.
Screening for poverty and related social determinants to improve knowledge of and links to resources (SPARK): development and cognitive testing of a tool for primary care
Authors: Adekoya Itunuoluwa , Delahunty-Pike Alannah , Howse Dana , Kosowan Leanne , Seshie Zita , Abaga Eunice , Cooney Jane , Robinson Marjeiry , Senior Dorothy , Zsager Alexander , Aubrey-Bassler Kris , Irwin Mandi , Jackson Lois , Katz Alan , Marshall Emily , Muhajarine Nazeem , Neudorf Cory , Pinto Andrew D. 
Published: November 2023

Abstract
Background
Healthcare organizations are increasingly exploring ways to address the social determinants of health. Accurate data on social determinants is essential to identify opportunities for action to improve health outcomes, to identify patterns of inequity, and to help evaluate the impact of interventions. The objective of this study was to refine a standardized tool for the collection of social determinants data through cognitive testing.

Methods
An initial set of questions on social determinants for use in healthcare settings was developed by a collaboration of hospitals and a local public health organization in Toronto, Canada during 2011–2012. Subsequent research on how patients interpreted the questions, and how they performed in primary care and other settings led to revisions. We administered these questions and conducted in-depth cognitive interviews with all the participants, who were from Saskatchewan, Manitoba, Ontario, and Newfoundland and Labrador. Cognitive interviewing was used, with participants invited to verbalize thoughts and feelings as they read the questions. Interview notes were grouped thematically, and high frequency themes were addressed.

Results
Three hundred and seventy-five individuals responded to the study advertisements and 195 ultimately participated in the study. Although all interviews were conducted in English, participants were diverse. For many, the value of this information being collected in typical healthcare settings was unclear, and hence, we included descriptors for each question. In general, the questions were understood, but participants highlighted a number of ways the questions could be changed to be even clearer and more inclusive. For example, more response options were added to the question of sexual orientation and the “making ends meet” question was completely reworded in light of challenges to understand the informal phrasing cited by English as a Second Language (ESL) users of the tool.

Conclusion
In this work we have refined an initial set of 16 sociodemographic and social needs questions into a simple yet comprehensive 18-question tool. The changes were largely related to wording, rather than content. These questions require validation against accepted, standardized tools. Further work is required to enable community data governance, and to ensure implementation of the tool as well as the use of its data is successful in a range of organizations.
Polypharmacy, potentially inappropriate medications, and drug-drug interactions in older COVID-19 inpatients
Authors: Chen Zhaoyan , Tian Fangyuan , Zeng Ya 
Published: November 2023

Abstract
Objectives
The purpose of this study was to assess the impact of polypharmacy, potentially inappropriate medications, and drug-drug interactions on in-hospital mortality in older COVID-19 inpatients.

Methods
A cross-sectional study was conducted using electronic medical data from a tertiary hospital in Chengdu from December 2022 to January 2023. The 2019 AGS/Beers criteria was used to evaluate the potentially inappropriate mediation (PIM) status of older COVID-19 inpatients (age ≥ 65 years), the drug-drug interactions were evaluated on Medscape, and multivariate logistic regression was used to identify the risk factors associated with in-hospital mortality.

Results
A total of 206 older COVID-19 inpatients were included in the study. The mean number of drugs per day was 13.04. The prevalence of PIM use based on the 2019 AGS Beers Criteria was 66.99%. The prevalence of drug-drug interactions was 61.65%. Logistic regression demonstrated that age ≥ 80 (OR: 10.321, 95% CI: 1.649, 64.579, P = 0.013), renal insufficiency (OR: 4.740, 95% CI: 1.366, 16.447, P = 0.014), long-term hospitalization (OR: 6.637, 95% CI: 1.030, 42.779, P = 0.046), severe pneumonia (OR: 50.230, 95% CI: 5.180, 487.041, P = 0.001) were influencing factors associated with in-hospital mortality in older COVID-19 inpatients.

Conclusions
The polypharmacy, potentially inappropriate medications, and drug-drug interactions were seen in many older COVID-19 inpatients.
Therapeutic plasma exchange in the treatment of COVID-19 induced cytokine storm: the first Moroccan experience
Authors: Bouayed Mohamed Zakaria , Laaribi Ilyass , Benaini Iliass , Yeznasni Asmae , Berrajaa Sara , Oujidi Younes , Bkiyar Houssam , Abda Naima , Housni Brahim 
Published: November 2023

Abstract
Introduction
COVID-19 induced cytokine storm is a well-documented phenomena that contributes significantly in the disease’s evolution and prognosis. Therefore, therapies such as therapeutic plasma exchange, constitute a mainstay of therapeutic management especially for critically-ill patients.

Methods
We conducted a monocentric retrospective cohort study in the Resuscitation Department of the Mohammed VI University Hospital of Oujda-Morocco, to evaluate the efficiency of therapeutic plasma exchange on critically-ill COVID-19 patients over a 6 months period.
We divided our patients into two groups: patients who received TPE (Therapeutic Plasma Exchange) sessions (TPE group) and patients who only benefited from the standard protocol treatment (non TPE group).

Results
Our study included a total of 165 patients, 34.5% of which benefited from TPE sessions.
We observed an improvement of oxygenation parameters (SpO2 and PaO2/FiO2 ratio) and a progressive respiratory weaning, as well as a significant decrease of biomarkers indicative of inflammation (lymphocyte count, CRP (C Reactive Protein), IL-6, Ferritin) and coagulopathy (d-dimers, fibrinogen) in the TPE group after 5 consecutive TPE sessions.
In comparison with the non-TPE group, The TPE-group patients had a shorter ICU (Intensive Care Unit) length of stay, required less frequently mechanical ventilation, and we more likely to be extubated. Furthermore, the TPE group had a lower mortality rate.

Discussion
Multiple studies have reported the safety and efficiency of therapeutic plasma exchange in the COVID-19 induced cytokine storm. Given the urgent character of the pandemic at the time, each center followed its own protocol in implementing plasma exchange.

Conclusion
Similar to the results reported in the literature, our study reports positive results after using TPE specifically in terms of respiratory weaning and an improvement of the cytokine storm biomarkers, and more importantly a lower mortality rate.
Neurosyphilis presenting with Guillain–Barre syndrome: a case report
Authors: Ung Hoameng , Ferrey Dominic 
Published: November 2023

Abstract
Background
Syphilis is associated with a wide variety of systemic presentations, earning it the moniker “The great mimicker”. Neurosyphilis is classically associated with meningovasculitis in the acute-subacute stage and tabes dorsalis and dementia paralytica in later stages. However, one of the less well described presentations include Guillain–Barre Syndrome. This case presents a patient with an ascending polyneuropathy suspicious for Guillain–Barre Syndrome who also had other atypical findings including a truncal sensory loss, optic disc swelling, and rash ultimately found to have neurosyphilis. Electrodiagnostic testing was consistent with demyelination, supporting a diagnosis of neurosyphilis associated Guillain–Barre Syndrome.

Case presentation
A 37-year-old female presented to the emergency department with a weakness and difficulty swallowing. She described a three-month history of symptoms, initially starting with a persistent headache followed by one month of a pruritic rash on her chest, palms, and soles. Two weeks prior to presentation, she developed progressive weakness in her arms, numbness in her arms and chest, and difficulty swallowing. Neurological exam was notable for multiple cranial neuropathies, distal predominant weakness in all extremities, length-dependent sensory loss, and hyporeflexia. Investigation revealed a positive Venereal Disease Research Laboratory in her cerebrospinal fluid without significant pleocytosis, contrast enhancement in cranial nerves V, VII, and VIII on MRI, and a demyelinating polyneuropathy on electrodiagnostic testing. She was diagnosed with Guillain–Barre syndrome, secondary to neurosyphilis. The patient acutely declined and required intubation, and ultimately made a full recovery after treatment with plasmapheresis and penicillin.

Conclusions
This case describes a clinical entity of syphilitic Guillain–Barre Syndrome and highlights the importance of including syphilis in the differential of any patient presenting with ascending polyradiculopathy, especially given the resurgence of syphilis.
Chromosome analysis of foetal tissue from 1903 spontaneous abortion patients in 5 regions of China: a retrospective multicentre study
Authors: Zhang Jian , Mu Fangxiang , Guo Zhongjie , Cai Zhuhua , Zeng Xianghui , Du Lirong , Wang Fang 
Published: November 2023

Abstract
Background
Abnormal foetal tissue chromosome karyotypes are one of the important pathogenic factors for spontaneous abortion (SA). To investigate the age and abnormal foetal karyotypes of 1903 couples who experienced SA.

Methods
A retrospective multicentre study collected age and foetal tissue karyotypes CNV-seq data of 1903 SA couples from 6 hospitals in 5 regions from January 2017 to March 2022. The distribution and correlation of abnormal foetal tissue karyotypes were evaluated by using regions and age.

Results
In our study, 1140 couples (60.5% of the total) had abnormal foetal tissue chromosome karyotypes in all regions. We found that there were differences in the number of abnormal foetal tissue chromosome karyotypes, of which the incidence of trisomy was higher. At the same time, the populations situated in the eastern region had a more triploid (15.5%) distribution, trisomy (58.1%) in the southern region, mosaicism (14.8%) and microduplication (31.7%) in the southwestern region, microdeletion (16.7%) in the northern region. There are variances across areas, and it is more common in the north. The incidence risk of prenatal chromosomal abnormalities varied according to age group.

Conclusion
The findings of this study suggest that the karyotypes of patients with abnormal foetal tissue chromosome abortion in different regions were different. Meanwhile, patients ≥ 35 years old had a higher risk of abnormal foetal tissue chromosome abortion.
Impact of sex on treatment-related adverse effects and prognosis in nasopharyngeal carcinoma
Authors: Cui Linchong , Chen Zilu , Zeng Fangfang , Jiang Xiaolan , Han Xiaoyan , Yuan Xiaofei , Wu Shuting , Feng Huiru , Lin Danfan , Lu Wenxuan , Liu Xiong , Peng Xiaohong , Yu Bolong 
Published: November 2023

Abstract
Background
In nasopharyngeal cancer (NPC), women have a lower incidence and mortality rate than men. Whether sex influences the prognosis of NPC patients remains debatable. We retrospectively examined the influence of sex on treatment-related side effects and prognosis in NPC.

Methods
Clinical data of 1,462 patients with NPC treated at the Southern Hospital of Southern Medical University from January 2004 to December 2015 were retrospectively examined. Statistical analysis was performed to assess differences in overall survival (OS), distant metastasis-free survival (DMFS), local recurrence-free survival(LRFS), and progression-free survival(PFS), as well as treatment-related adverse effects, including myelosuppression, gastrointestinal responses, and radiation pharyngitis and dermatitis, between men and women.

Results
Women had better 5-year OS (81.5% vs. 87.1%, P = 0.032) and DMFS (76.2% vs. 83.9%, P = 0.004) than men. Analysis by age showed that the prognoses of premenopausal and menopausal women were better than those of men, whereas prognoses of postmenopausal women and men were not significantly different. Additionally, women had a better prognosis when stratified by treatment regimen. Furthermore, chemotherapy-related adverse effects were more severe in women than in men; however, the incidences of radiation laryngitis and dermatitis were not significantly different between the sexes. Logistic regression analysis revealed that the female sex was an independent risk factor for severe myelosuppression and gastrointestinal reactions.

Conclusions
Chemotherapy-related side effects are more severe but the overall prognosis is better in women with NPC than in men with NPC. Patients may benefit from a personalized treatment approach for NPC.

Trial registration
This study was approved by the Medical Ethics Committee of Nanfang Hospital of the Southern Medical University (NFEC-201,710-K3).
Prevalence of age-related macular degeneration in Iran and its projections through 2050: a systematic review and meta-analysis
Authors: Roshanshad Amirhossein , Roshanshad Romina , Moosavi Seyed Ali , Ardekani Ali , Nabavizadeh Sara Sadat , Fereidooni Reza , Ashraf Hossein , Vardanjani Hossein Molavi 
Published: November 2023

Abstract
Background
Age-related Macular Degeneration (AMD) is one of the most common causes of vision loss. A substantial increase in the burden of AMD is expected in the aging populations, including the Iranians. We investigated the age and gender-specific prevalence of AMD and its determinants in Iran.

Methods
We systematically searched international (PubMed, Scopus, Embase, etc.) and local (IranDoc, Magiran, etc.) online databases. We included cross-sectional or cohort studies, either clinic- or population-based, published on the prevalence of AMD among Iranians, with no limitation on age. Joanna Briggs Institute (JBI) tools for critical appraisal were used. Prevalence estimates are pooled by applying random-effects modeling. Subgroup analysis and meta-regression were performed.

Results
Seventeen studies with 16,120 participants were included. Based on studies in general population, the pooled prevalence of AMD was 10.8% (95% CI: 6.5-16.2%) in males, and 9.8% (95% CI: 4.7-16.4%) in females. 8.5% of moderate vision impaired, 13.6% of severe vision impaired, and 15.7% of blind participants were affected by AMD. The prevalence of AMD was 2% in 40–49, and 32.3% in the ≥ 80 population. The prevalence of AMD was 11.9% among the visually impaired vs. 8.7% in the general population. The study’s sampling method, location, and mean age were correlated with the heterogeneities of the prevalence. We observed an increasing trend in the number of AMD cases (average annual percent change = 3.66%; 95% CI: 3.65–3.67%) from 1990 to 2050. The expected number of AMD cases in Iran will be near 5.5 million by 2050.

Conclusion
The prevalence of AMD in Iran was somewhere between the prevalence of Asians and Europeans. Given the aging trend of the Iranian community and an average annual percent change of 3.66%, it is indispensable to adopt preventive and screening policies to diminish the burden of the disease in the future decades.