bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of viral infection as an etiology of ME/CFS: a systematic review and meta-analysis
Authors: Hwang Jae-Hyun , Lee Jin-Seok , Oh Hyeon-Muk , Lee Eun-Jung , Lim Eun-Jin , Son Chang-Gue 
Published: October 2023

Abstract
Background
Myalgic encephalitis/chronic fatigue syndrome (ME/CFS) is a long-term disabling illness without a medically explained cause. Recently during COVID-19 pandemic, many studies have confirmed the symptoms similar to ME/CFS in the recovered individuals. To investigate the virus-related etiopathogenesis of ME/CFS, we conducted a systematic assessment of viral infection frequency in ME/CFS patients.

Methods
We conducted a comprehensive search of PubMed and the Cochrane Library from their inception through December 31, 2022, using selection criteria of viral infection prevalence in ME/CFS patients and controls. Subsequently, we performed a meta-analysis to assess the extent of viral infections' contribution to ME/CFS by comparing the odds ratio between ME/CFS patients and controls (healthy and/or diseased).

Results
Finally, 64 studies met our eligibility criteria regarding 18 species of viruses, including a total of 4971 ME/CFS patients and 9221 control subjects. The participants included healthy subjects and individuals with one of 10 diseases, such as multiple sclerosis or fibromyalgia. Two DNA viruses (human herpes virus (HHV)-7 and parvovirus B19, including their co-infection) and 3 RNA viruses (borna disease virus (BDV), enterovirus and coxsackie B virus) showed odds ratios greater than 2.0 compared with healthy and/or diseased subjects. Specifically, BDV exceeded the cutoff with an odds ratio of ≥ 3.47 (indicating a "moderate association" by Cohen’s d test) compared to both healthy and diseased controls.

Conclusion
This study comprehensively evaluated the risk of viral infections associated with ME/CFS, and identified BDV. These results provide valuable reference data for future studies investigating the role of viruses in the causation of ME/CFS.
Penile melanoma: a pathological report of two cases
Authors: Pósfai Boglárka , Szentkereszty Márton , Sánta Fanni , Bajory Zoltán , Simon Andrea , Kozéki Zsófia , Csányi Ildikó , Akgul Mahmut , Kuthi Levente 
Published: October 2023

Abstract
Background
Penile melanoma (PM) is a rare tumor, accounting for less than 2% of all penile cancers. PM can occur on the surface of the glans, foreskin, and opening of the urethra. Furthermore, PM primarily affects older individuals and is not associated with sun exposure. Currently, there is no specific staging system for genitourinary tract melanomas, so these tumors are typically staged using the criteria for cutaneous melanoma. Limited data in the literature suggests that PM generally has a poor clinical prognosis.

Case presentation
Here, we describe two cases of PM. The first case affected a 62-year-old male who presented with hematuria and a painful tumor in the distal urethra, leading to a suspicion of penile cancer. The second case involved a 68-year-old male who noticed a rapidly evolving dark spot on his foreskin. Histological analysis confirmed the presence of melanoma in both patients. The tumors showed a diffuse and strong PRAME-positivity and lacked BRAF mutation in both cases. Additionally, the second tumor harbored an activating CKIT mutation. An enhanced PD-L1 expression was observed in both tumors.

Conclusions
We presented two rare forms of mucosal melanoma and highlighted the entities in the differential diagnosis. Based on our experience PRAME is a helpful marker for making the diagnosis of PM, and PD-L1 can predict the success of the immunotherapy. We also emphasize the need for an organ-specific staging system for PMs.
Assessment of bony changes in temporomandibular joint in patients using cone beam computed tomography – a cross sectional study
Authors: Vasegh Zahra , Safi Yaser , azar Maryam Sanaei , Ahsaie Mitra Ghazizadeh , Arianezhad S. Marjan 
Published: October 2023

Abstract
Background and aim
The aim of this study is to evaluate the changes in the temporomandibular joint (TMJ) in patients with temporomandibular disorder (TMD) and the relationship between age, sex, and types of TMJ change using Cone Beam Computed Tomography (CBCT).

Methods and material
CBCT records of 200 patients (123 women and 67 men) were retrieved and assessed. Right and left TMJs were evaluated separately, resulting in a total of 400 TMJs. The images were analyzed using On demand 3D Application The radiographic findings were classified as erosion, proliferative changes mainly, including flattening and osteophytes of the condyle, sclerosis, Ely cyst, hypoplasia and hyperplasia of the condyles, ankylosis, and joint cavity. Data analysis was performed using descriptive statistics, paired T-tests, and repeated measure ANOVA (Analysis of Variance) in SPSS Software.

Results
The most prevalent types of condylar bony changes observed was osteophyte (63.5%) followed by flattening of the articular surface (42%), erosion (40%), ankylosis (10%) and sclerosis (10%). 7.5% of joints showed hyperplastic condyles but only 2% showed hypoplasia. The least prevalent change observed was Ely Cyst (1%). Osteophyte was the most prevalent change observed in all age groups and both sexes except for men aged 31 ~ 50, where flattening was more frequent. A statistically significant difference was found between sex and prevalence of erosion in the age group of 10 ~ 30 (P = 0.001); as well as between sex and condylar hyperplasia in the same age group.

Conclusion
Based on the findings of this research, the prevalence of bony changes of TMJ from highest to lowest is as follows: osteophyte, flattening of the articular surface, erosion, ankylosis, sclerosis, hyperplastic condyles, hypoplastic condyles and Ely Cyst. CBCT is an accurate 3 dimensional imaging modality for assessment of TMJ bony structures.
Application of non-invasive prenatal testing in screening chromosomal aberrations in pregnancies with different nuchal translucency cutoffs
Authors: Xu Yong , Hu Siqi , Chen Liyuan , Hao Ying , Zhang Hu , Xu Zhiyong , Wu Weiqing , Deng Liyanyan 
Published: October 2023

Abstract
Objective
To investigate the efficiency of non-invasive prenatal testing (NIPT) in cases with different cutoffs of nuchal translucency (NT).

Methods
The study retrospectively analyses pregnancies with NT ≥ 2.5 mm who underwent NIPT. Results of NT, NIPT, chromosomal diagnostic and pregnancy outcomes were collected.

Results
Study group was composed of 1470 single pregnancies, including 864 with NT 2.5–2.9 mm, 350 with NT 3.0–3.4 mm and 256 with NT ≥ 3.5 mm. Non-significant differences were found in the positive predictive value (PPV) of NIPT between different cutoffs of NT. There was one false positive case with NT 4.3 mm, screening for 47,XYY in NIPT showed normal in diagnostic testing. For cases with normal NIPT results, the residual risk is 1:20 (5%, 95%CI: 0.1–10.1%) in fetuses with NT 3.0–3.4 mm and 1:15 (6.5%, 95%CI: 1.4%-11.5%) in fetuses with NT ≥ 3.5 mm. These false negative cases included one trisomy 21, seven pathogenic CNVs, one uniparental disomy and one single gene disorders.

Conclusion
Our findings demonstrated that the PPV of NIPT for screening chromosomal aberrations were similarly in different NT cutoffs, while false positive case does exist. After normal in NIPT, risk for chromosomal aberrations remained, especially pathogenic CNV and even common trisomy. Therefore, prenatal diagnosis was recommended and CMA was suggested to apply in pregnancies with NT ≥ 3.0 mm.
CD28/PD1 co-expression: dual impact on CD8+ T cells in peripheral blood and tumor tissue, and its significance in NSCLC patients' survival and ICB response
Authors: Palermo Belinda , Franzese Ornella , Frisullo Giuseppe , D’Ambrosio Lorenzo , Panetta Mariangela , Campo Giulia , D’Andrea Daniel , Sperduti Isabella , De Nicola Francesca , Goeman Frauke , Gallina Filippo , Visca Paolo , Facciolo Francesco , Nisticò Paola 
Published: October 2023

Abstract
Background
Immune checkpoint blockade (ICB) has significantly prolonged survival of non-small cell lung cancer (NSCLC) patients, although most patients develop mechanisms of resistance. Recently single-cell RNA-sequencing (scRNA-Seq) revealed a huge T-cell phenotypic and (dys)functional state variability. Accordingly, T-cell exhaustion is recognized as a functional adaptation, with a dynamic progression from a long-lived “pre-exhausted stem-like progenitor” to a “terminally exhausted” state. In this scenario it is crucial to understand the complex interplay between co-stimulatory and inhibitory molecules in CD8+ T-cell functionality.

Methods
To gain a baseline landscape of the composition, functional states, and transcriptomic signatures predictive of prognosis, we analyzed CD8+ T-cell subsets characterized by the presence/absence of PD1 and CD28 from periphery, adjacent non-tumor tissue and tumor site of a cohort of treatment-naïve NSCLC patients, by integrated multiparametric flow cytometry, targeted multi-omic scRNA-seq analyses, and computational pipelines.

Results
Despite the increased PD1 levels, an improved PD1+CD28+ T-cell polyfunctionality was observed with the transition from periphery to tumor site, associated with lack of TIGIT, TIM-3 and LAG-3, but not with Ag-experienced-marker CD11a. Differently from CD28+ T cells, the increased PD1 levels in the tumor were associated with reduced functionality in PD1+CD28− T cells. CD11ahigh, although expressed only in a small fraction of this subset, still sustained its functionality. Absence of TIGIT, TIM-3 and CTLA-4, alone or combined, was beneficial to CD28− T cells. Notably, we observed distinct TRM phenotypes in the different districts, with CD28+ T cells more capable of producing TGFβ in the periphery, potentially contributing to elevated CD103 levels. In contrast CD28− TRM mainly produced CXCL13 within the tumor.
ScRNA-seq revealed 5 different clusters for each of the two subsets, with distinctive transcriptional profiles in the three districts. By interrogating the TCGA dataset of patients with lung adenocarcinoma (LUAD) and metastatic NSCLC treated with atezolizumab, we found signatures of heterogeneous TRM and "pre-exhausted" long-lived effector memory CD8+ T cells associated with improved response to ICB only in the presence of CD28.

Conclusions
Our findings identify signatures able to stratify survival of LUAD patients and predict ICB response in advanced NSCLC. CD28 is advocated as a key determinant in the signatures identified, in both periphery and tumor site, thus likely providing feasible biomarkers of ICB response.

Graphical Abstract
The effects of aerobic exercises compared to conventional chest physiotherapy on pulmonary function, functional capacity, sputum culture, and quality of life in children and adolescents with cystic fibrosis: a study protocol for randomized controlled trial study
Authors: Hamedi Nadia , Kajbafvala Mehrnaz , ShahAli Shabnam , Pourahmadi MohammadReza , Eshghi Alireza , Estahbanati MohammadReza Modaresi 
Published: October 2023

Abstract
Background
Cystic fibrosis (CF) is an autosomal recessive disorder caused by abnormal function of the chloride ion channels and characterized by pancreatic insufficiency and chronic endobronchial airway infection. Pulmonary dysfunction is very common and could lead to a reduction in the quality of life. Airway clearance techniques (ACT) and physical exercises are introduced as one of the main components of treatment. Therefore, it will be of interest to examine the effect of aerobic exercises compared to conventional chest physiotherapy (CPT) on pulmonary function, functional capacity, sputum culture, and quality of life in patients with CF.

Methods
Thirty patients with CF will participate in a double-blind parallel controlled trial containing 18 sessions of treatment. Group A consists of CPT and placebo aerobic exercise, and group B includes aerobic exercise and placebo CPT. Pulmonary function, functional capacity, sputum culture, and quality of life will be evaluated with a spirometry test, 6-min walk test (6MWT), sputum culture test, and the Cystic Fibrosis Questionnaire-Revised (CFQ-R), respectively, before and after the intervention.

Discussion
We will evaluate and compare the effectiveness of aerobic exercises and conventional chest physiotherapy on pulmonary function, functional capacity, sputum culture, and quality of life. Comparing these two treatment patterns can contribute to a better understanding of the effectiveness. Therefore, if there is a significant difference between the two treatments, the superior treatment will be prioritized clinically.

Trial registration
https://www.irct.ir, IRCT20210505051181N5. Registered on 19 February 2023.
Molecular-phylogenetic analyses of Ixodes species from South Africa suggest an African origin of bird-associated exophilic ticks (subgenus Trichotoixodes)
Authors: Hornok Sándor , Kontschán Jenő , Takács Nóra , Heyne Heloise , Kovács Áron Botond , Plantard Olivier , Keve Gergő , Fedorov Denis , Gyuranecz Miklós , Halajian Ali 
Published: October 2023

Abstract
Background
Among hard ticks (Acari: Ixodidae), the genus Ixodes comprises the highest number of species, which in turn are most numerous in the Afrotropical zoogeographic region. In South Africa extensive morphological studies have been performed on Ixodes species but only few reports included molecular analyses.

Methods
In this study, 58 Ixodes spp. ticks, collected from ten mammalian and eight avian host species in South Africa, were molecularly and phylogenetically analyzed. In addition, a newly collected sample of the Palearctic Ixodes trianguliceps was included in the analyses.

Results
Among the ticks from South Africa, 11 species were identified morphologically. The majority of ticks from mammals represented the Ixodes pilosus group with two species (n = 20), followed by ticks resembling Ixodes rubicundus (n = 18) and Ixodes alluaudi (n = 3). In addition, single specimens of Ixodes rhabdomysae, Ixodes ugandanus, Ixodes nairobiensis and Ixodes simplex were also found. Considering bird-infesting ticks, Ixodes theilerae (n = 7), Ixodes uriae (n = 4) and ticks most similar to Ixodes daveyi (provisionally named I. cf. daveyi, n = 2) were identified. Molecular analyses confirmed two species in the I. pilosus group and a new species (I. cf. rubicundus) closely related to I. rubicundus sensu stricto. Phylogenetic trees based on concatenated mitochondrial or mitochondrial and nuclear gene sequences indicated that the subgenus Afrixodes forms a monophyletic clade with bird-associated exophilic ticks (subgenus Trichotoixodes). Ixodes trianguliceps clustered separately whereas I. alluaudi with their morphologically assigned subgenus, Exopalpiger.

Conclusions
Phylogenetic analyses shed new lights on the relationships of Ixodes subgenera when including multiple sequences from subgenus Afrixodes and African as well as Palearctic species of subgenera Trichotoixodes and Exopalpiger. Subgenera Afrixodes and bird-associated Trichotoixodes share common ancestry, suggesting that the latter might have also originated in Africa. Regarding the subgenus Exopalpiger, I. alluaudi is properly assigned as it clusters among different Australian Ixodes, whereas I. trianguliceps should be excluded.

Graphical Abstract
Acute osteomyelitis, thrombophlebitis, and pulmonary embolism: a case report
Authors: Sheikh Najeeb Mohammad , Alshwaiki Afif , Martini Nafiza , Alsuliman Tamim , Alkharat Banan , Alrstom Ali 
Published: October 2023

Abstract
Background
Septic pulmonary embolism (SPE), deep vein thrombophlebitis (DVT), and acute osteomyelitis (AOM) form a triad that is rarely seen in children and is usually associated with a history of trauma on long bones. Unfortunately, a delay in diagnosis is frequently observed in this syndrome, which places the patient at risk of life-threatening complications. This delay can largely be attributed to the failure to consider osteomyelitis as a potential underlying cause of DVT.

Case presentation
In this case report, we present the case of a 16-year-old Arabian male who presented with limb trauma and fever. The patient had a delayed diagnosis of osteomyelitis, which resulted in the formation of an abscess and subsequent joint destruction. Surgical drainage and joint replacement surgery were deemed necessary for treatment.

Conclusions
persistent fever along with a history of trauma on a long bone with signs of DVT of the limb in a child should raise concern for osteomyelitis and an MRI evaluation of the limb should be obtained.
DNA methylation of insulin signaling pathways is associated with HOMA2-IR in primary myoblasts from older adults
Authors: Burton Mark A. , Garratt Emma S. , Hewitt Matthew O. , Sharkh Hanan Y. , Antoun Elie , Westbury Leo D. , Dennison Elaine M. , Harvey Nicholas C. , Cooper Cyrus , MacIsaac Julia L. , Kobor Michael S. , Patel Harnish P. , Godfrey Keith M. , Lillycrop Karen A. 
Published: October 2023

Abstract
Background
While ageing is associated with increased insulin resistance (IR), the molecular mechanisms underlying increased IR in the muscle, the primary organ for glucose clearance, have yet to be elucidated in older individuals. As epigenetic processes are suggested to contribute to the development of ageing-associated diseases, we investigated whether differential DNA methylation was associated with IR in human primary muscle stem cells (myoblasts) from community-dwelling older individuals.

Methods
We measured DNA methylation (Infinium HumanMethylationEPIC BeadChip) in myoblast cultures from vastus lateralis biopsies (119 males/females, mean age 78.24 years) from the Hertfordshire Sarcopenia Study extension (HSSe) and examined differentially methylated cytosine phosphate guanine (CpG) sites (dmCpG), regions (DMRs) and gene pathways associated with HOMA2-IR, an index for the assessment of insulin resistance, and levels of glycated hemoglobin HbA1c.

Results
Thirty-eight dmCpGs (false discovery rate (FDR) < 0.05) were associated with HOMA2-IR, with dmCpGs enriched in genes linked with JNK, AMPK and insulin signaling. The methylation signal associated with HOMA2-IR was attenuated after the addition of either BMI (6 dmCpGs), appendicular lean mass index (ALMi) (7 dmCpGs), grip strength (15 dmCpGs) or gait speed (23 dmCpGs) as covariates in the model. There were 8 DMRs (Stouffer < 0.05) associated with HOMA2-IR, including DMRs within T-box transcription factor (TBX1) and nuclear receptor subfamily-2 group F member-2 (NR2F2); the DMRs within TBX1 and NR2F2 remained associated with HOMA2-IR after adjustment for BMI, ALMi, grip strength or gait speed. Forty-nine dmCpGs and 21 DMRs were associated with HbA1c, with cg13451048, located within exoribonuclease family member 3 (ERI3) associated with both HOMA2-IR and HbA1c. HOMA2-IR and HbA1c were not associated with accelerated epigenetic ageing.

Conclusions
These findings suggest that insulin resistance is associated with differential DNA methylation in human primary myoblasts with both muscle mass and body composition making a significant contribution to the methylation changes associated with IR.
Forecasting emergency department arrivals using INGARCH models
Authors: Reboredo Juan C. , Barba-Queiruga Jose Ramon , Ojea-Ferreiro Javier , Reyes-Santias Francisco 
Published: October 2023

Abstract
Background
Forecasting patient arrivals to hospital emergency departments is critical to dealing with surges and to efficient planning, management and functioning of hospital emerency departments.

Objective
We explore whether past mean values and past observations are useful to forecast daily patient arrivals in an Emergency Department.

Material and methods
We examine whether an integer-valued generalized autoregressive conditional heteroscedastic (INGARCH) model can yield a better conditional distribution fit and forecast of patient arrivals by using past arrival information and taking into account the dynamics of the volatility of arrivals.

Results
We document that INGARCH models improve both in-sample and out-of-sample forecasts, particularly in the lower and upper quantiles of the distribution of arrivals.

Conclusion
Our results suggest that INGARCH modelling is a useful model for short-term and tactical emergency department planning, e.g., to assign rotas or locate staff for unexpected surges in patient arrivals.
Ris-aided integrated satellite duplex UAV relay terrestrial networks with imperfect hardware and co-channel interference
Authors: Sun Jiu , Guo Kefeng , Zhou Feng , Wang Xueling , Zhu Mingfu 
Published: October 2023

AbstractIncreasing the spectrum and time utilization rate is the goal of the next wireless communication networks. This work studies the outage performance of the reconfigurable intelligent surface (RIS)-aided integrated satellite duplex unmanned-aerial-vehicle relay terrestrial networks. Especially, the RIS is installed in the tall building to enhance the communication. To further increase the time utilization rate, the duplex unmanned aerial vehicle is utilized to enhance the time utilization efficiency. However, owing to the practical reasons, the imperfect hardware and co-channel interference are further researched in this paper. Particularly, the accurate expression for the outage probability (OP) is gotten to confirm the effects of RIS parameters, channel parameters and imperfect hardware on the considered network. To gain more insights of the OP at high signal-to-noise ratios, the asymptotic analysis for the OP is derived. Finally, some Monte Carlo simulations are provided to verify the rightness of the theoretical analysis. The simulations indicate that the OP is mainly judged by the satellite transmission link. The results also indicate that although RIS can enhance the system performance, the system performance is not decided by RIS.