bluuebunny/crossref_metadata_2025_split huggingface dataset:
The occurrence and development mechanisms of esophageal stricture: state of the art review
Authors: Yang Fang , Hu Yiwei , Shi Zewen , Liu Mujie , Hu Kefeng , Ye Guoliang , Pang Qian , Hou Ruixia , Tang Keqi , Zhu Yabin 
Published: January 2024

Abstract
Background
Esophageal strictures significantly impair patient quality of life and present a therapeutic challenge, particularly due to the high recurrence post-ESD/EMR. Current treatments manage symptoms rather than addressing the disease's etiology. This review concentrates on the mechanisms of esophageal stricture formation and recurrence, seeking to highlight areas for potential therapeutic intervention.

Methods
A literature search was conducted through PUBMED using search terms: esophageal stricture, mucosal resection, submucosal dissection. Relevant articles were identified through manual review with reference lists reviewed for additional articles.

Results
Preclinical studies and data from animal studies suggest that the mechanisms that may lead to esophageal stricture include overdifferentiation of fibroblasts, inflammatory response that is not healed in time, impaired epithelial barrier function, and multimethod factors leading to it. Dysfunction of the epithelial barrier may be the initiating mechanism for esophageal stricture. Achieving perfect in-epithelialization by tissue-engineered fabrication of cell patches has been shown to be effective in the treatment and prevention of esophageal strictures.

Conclusion
The development of esophageal stricture involves three stages: structural damage to the esophageal epithelial barrier (EEB), chronic inflammation, and severe fibrosis, in which dysfunction or damage to the EEB is the initiating mechanism leading to esophageal stricture. Re-epithelialization is essential for the treatment and prevention of esophageal stricture. This information will help clinicians or scientists to develop effective techniques to treat esophageal stricture in the future.
Outcomes of antiretroviral treatment for 0-14-year-old children living with HIV in Ganzhou, China, 2006–2023
Authors: Zeng Ting , Chen Xin , Zhang Xiao-Yi , Lian Chao-Xian , Yang Rong-Rong , Yu Li-Ling , Liao Xiao-Kang , Huang Dan-Dan , Zhang Yu-Ning , Cao Hong-Min 
Published: January 2024

Abstract
Background
Studies on antiretroviral therapy (ART) in children living with HIV (CLHIV) are limited due to the small population and low accession rate of ART.

Methods
All 0-14-year-old CLHIV admitted to the Ganzhou Center for Disease Control and Prevention from January 2006 to June 2023 were included retrospectively. The information of treatment regimens, disease progression, and laboratory tests of the patients under ART were used to explore the outcomes and impacts of long-term ART. The normality of all the data was tested by the Shapiro-Wilk test.

Results
From 2006 to 2023, 18 CLHIV were reported in Ganzhou. Among them, 11 received ART and were followed up for 60.0 ± 48.4 months. After receiving ART, the median viral load of them decreased from 89,600 copies/ml to 22 copies/ml (P = 0.007), the median CD4+ T cell count increased from 380.7 cells/µL to 661.9 cells/µL (P = 0.028), and the median CD8+ T cell count decreased from 1065.8 cells/µL to 983.3 cells/µL (P = 0.584). The laboratory test results regarding liver function, renal function, blood cell count, and glucolipid metabolism tended to be within normal reference ranges, and the mean height-for-age z-score and weight-for-age z-score increased. However, all the three CLHIV who received cotrimoxazole developed pneumocystis carinii pneumonia, upper respiratory infection, skin lesions, bacterial pneumonia and/or thrush; the mean body-mass-index-for-age z-score decreased from 0.52 to -0.63.

Conclusion
For CLHIV, ART could effectively inhibit the replication of HIV and improve the immune function of patients. More studies that focus on ART in CLHIV are urgently needed.
Experiences of people living with HIV in low- and middle-income countries and their perspectives in self-management: a meta-synthesis
Authors: Dadi Tegene Legese , Wiemers Anja M. C. , Tegene Yadessa , Medhin Girmay , Spigt Mark 
Published: January 2024

Abstract
Introduction
Availability of anti-retroviral treatment has changed HIV in to a manageable chronic disease, making effective self-management essential. However, only a few studies in low- and middle-income countries (LMICs) reported experiences of people living with HIV (PLWH) on self-management.

Methods
This meta-synthesis of qualitative studies investigated perspectives of PLWH in LMICs on self-management. Various databases, including PubMed, EMBASE, EBSCO, and CINHAL, were searched through June 2022. Relevant additional articles were also included using cross-referencing of the identified papers. We used a thematic synthesis guided by the "Model of the Individual and Family Self-Management Theory" (IFSMT).

Result
PLWH in LIMICs experience a variety of challenges that restrict their options for effective self-management and compromises their quality of life. The main ones include: misconceptions about the disease, poor self-efficacy and self-management skills, negative social perceptions, and a non-patient-centered model of care that reduces the role of patients. The experiences that influenced the ability to practice self-management are summarized in context (the condition itself, physical and environmental factors, individual and family factors) and process factors (knowledge and beliefs, relationship with the health care worker, self-regulation skills and abilities, and social facilitation). Context and process greatly impacted quality of life through the self-management practices of the patients.

Conclusion and recommendation
PLWH encounter multiple challenges, are not empowered enough to manage their own chronic condition, and their needs beyond medical care are not addressed by service providers. Self-management practice of these patients is poor, and service providers do not follow service delivery approaches that empower patients to be at the center of their own care and to achieve an effective and sustainable outcome from treatment. These findings call for a comprehensive well thought self-management interventions.
ZNF148 inhibits HBV replication by downregulating RXRα transcription
Authors: Yao Xinyan , Xu Kexin , Tao Nana , Cheng Shengtao , Chen Huajian , Zhang Dapeng , Yang Minli , Tan Ming , Yu Haibo , Chen Peng , Zhan Zongzhu , He Siyi , Li Ranran , Wang Chunduo , Wu Daiqing , Ren Jihua 
Published: January 2024

Abstract
Background
Progressive hepatitis B virus (HBV) infection can result in cirrhosis, hepatocellular cancer, and chronic hepatitis. While antiviral drugs that are now on the market are efficient in controlling HBV infection, finding a functional cure is still quite difficult. Identifying host factors involved in regulating the HBV life cycle will contribute to the development of new antiviral strategies. Zinc finger proteins have a significant function in HBV replication, according to earlier studies. Zinc finger protein 148 (ZNF148), a zinc finger transcription factor, regulates the expression of various genes by specifically binding to GC-rich sequences within promoter regions. The function of ZNF148 in HBV replication was investigated in this study.

Methods
HepG2-Na+/taurocholate cotransporting polypeptide (HepG2-NTCP) cells and Huh7 cells were used to evaluate the function of ZNF148 in vitro. Northern blotting and real-time PCR were used to quantify the amount of viral RNA. Southern blotting and real-time PCR were used to quantify the amount of viral DNA. Viral protein levels were elevated, according to the Western blot results. Dual-luciferase reporter assays were used to examine the transcriptional activity of viral promoters. ZNF148’s impact on HBV in vivo was investigated using an established rcccDNA mouse model.

Results
ZNF148 overexpression significantly decreased the levels of HBV RNAs and HBV core DNA in HBV-infected HepG2-NTCP cells and Huh7 cells expressing prcccDNA. Silencing ZNF148 exhibited the opposite effects in both cell lines. Furthermore, ZNF148 inhibited the activity of HBV ENII/Cp and the transcriptional activity of cccDNA. Mechanistic studies revealed that ZNF148 attenuated retinoid X receptor alpha (RXRα) expression by binding to the RXRα promoter sequence. RXRα binding site mutation or RXRα overexpression abolished the suppressive effect of ZNF148 on HBV replication. The inhibitory effect of ZNF148 was also observed in the rcccDNA mouse model.

Conclusions
ZNF148 inhibited HBV replication by downregulating RXRα transcription. Our findings reveal that ZNF148 may be a new target for anti-HBV strategies.
Lactylation stabilizes DCBLD1 activating the pentose phosphate pathway to promote cervical cancer progression
Authors: Meng Qingfei , Sun Huihui , Zhang Yanghe , Yang Xiangzhe , Hao Shiming , Liu Bin , Zhou Honglan , Xu Zhi-Xiang , Wang Yishu 
Published: January 2024

Abstract
Background
Discoidin, CUB, and LCCL domain-containing type I (DCBLD1) is identified as an oncogene involved in multiple regulation of tumor progression, but specific mechanisms remain unclear in cervical cancer. Lactate-mediated lactylation modulates protein function. Whether DCBLD1 can be modified by lactylation and the function of DCBLD1 lactylation are unknown. Therefore, this study aims to investigate the lactylation of DCBLD1 and identify its specific lactylation sites. Herein, we elucidated the mechanism by which lactylation modification stabilizes the DCBLD1 protein. Furthermore, we investigated DCBLD1 overexpression activating pentose phosphate pathway (PPP) to promote the progression of cervical cancer.

Methods
DCBLD1 expression was examined in human cervical cancer cells and adjacent non-tumorous tissues using quantitative reverse transcription-polymerase chain reaction, western blotting, and immunohistochemistry. In vitro and in vivo studies were conducted to investigate the impact of DCBLD1 on the progression of cervical cancer. Untargeted liquid chromatography-tandem mass spectrometry (LC–MS/MS) metabolomics studies were used to characterize DCBLD1-induced metabolite alterations. Western blot, immunofuorescence and transmission electron microscopy were performed to detect DCBLD1 degradation of G6PD by activating autophagy. Chromatin immunoprecipitation, dual luciferase reporter assay for detecting the mechanism by which lactate increases DCBLD1 transcription. LC–MS/MS was employed to verify specific modification sites within the DCBLD1 protein.

Results
We found that lactate increased DCBLD1 expression, activating the PPP to facilitate the proliferation and metastasis of cervical cancer cells. DCBLD1 primarily stimulated PPP by upregulating glucose-6-phosphate dehydrogenase (G6PD) expression and enzyme activity. The mechanism involved the increased enrichment of HIF-1α in the DCBLD1 promoter region, enhancing the DCBLD1 mRNA expression. Additionally, lactate-induced DCBLD1 lactylation stabilized DCBLD1 expression. We identified DCBLD1 as a lactylation substrate, with a predominant lactylation site at K172. DCBLD1 overexpression inhibited G6PD autophagic degradation, activating PPP to promote cervical cancer progression. In vivo, 6-An mediated inhibition of G6PD enzyme activity, inhibiting tumor proliferation.

Conclusions
Our findings revealed a novel post-translational modification type of DCBDL1, emphasizing the significance of lactylation-driven DCBDL1-mediated PPP in promoting the progression of cervical cancer.

Graphical Abstract
Schematic illustration of DCBLD1-induced G6PD-mediated reprogramming of PPP metabolism in promoting cervical cancer progression.
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc
Authors: Antonello Alice , Bergamin Riccardo , Calonaci Nicola , Househam Jacob , Milite Salvatore , Williams Marc J. , Anselmi Fabio , d’Onofrio Alberto , Sundaram Vasavi , Sosinsky Alona , Cross William C. H. , Caravagna Giulio 
Published: January 2024

AbstractCopy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.
RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci
Authors: Fazal Sarah , Danzi Matt C. , Xu Isaac , Kobren Shilpa Nadimpalli , Sunyaev Shamil , Reuter Chloe , Marwaha Shruti , Wheeler Matthew , Dolzhenko Egor , Lucas Francesca , Wuchty Stefan , Tekin Mustafa , Züchner Stephan , Aguiar-Pulido Vanessa 
Published: January 2024

AbstractExpansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing number of TR expansions are being identified, and interpreting them is a challenge. We present RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), a machine learning tool for distinguishing pathogenic from benign TR expansions. Our results demonstrate that an ensemble approach classifies TRs with an average precision of 93% and recall of 83%. RExPRT’s high precision will be valuable in large-scale discovery studies, which require prioritization of candidate loci for follow-up studies.
A cell atlas of the larval Aedes aegypti ventral nerve cord
Authors: Yin Chang , Morita Takeshi , Parrish Jay Z. 
Published: January 2024

AbstractMosquito-borne diseases account for nearly 1 million human deaths annually, yet we have a limited understanding of developmental events that influence host-seeking behavior and pathogen transmission in mosquitoes. Mosquito-borne pathogens are transmitted during blood meals, hence adult mosquito behavior and physiology have been intensely studied. However, events during larval development shape adult traits, larvae respond to many of the same sensory cues as adults, and larvae are susceptible to infection by many of the same disease-causing agents as adults. Hence, a better understanding of larval physiology will directly inform our understanding of physiological processes in adults. Here, we use single cell RNA sequencing (scRNA-seq) to provide a comprehensive view of cellular composition in the Aedes aegypti larval ventral nerve cord (VNC), a central hub of sensory inputs and motor outputs which additionally controls multiple aspects of larval physiology. We identify more than 35 VNC cell types defined in part by neurotransmitter and neuropeptide expression. We also explore diversity among monoaminergic and peptidergic neurons that likely control key elements of larval physiology and developmental timing, and identify neuroblasts and immature neurons, providing a view of neuronal differentiation in the VNC. Finally, we find that larval cell composition, number, and position are preserved in the adult abdominal VNC, suggesting studies of larval VNC form and function will likely directly inform our understanding adult mosquito physiology. Altogether, these studies provide a framework for targeted analysis of VNC development and neuronal function in Aedes aegypti larvae.
Ixodid ticks and zoonotic tick-borne pathogens of the Western Balkans
Authors: Kapo Naida , Zuber Bogdanović Ivana , Gagović Ema , Žekić Marina , Veinović Gorana , Sukara Ratko , Mihaljica Darko , Adžić Bojan , Kadriaj Përparim , Cvetkovikj Aleksandar , Djadjovski Igor , Potkonjak Aleksandar , Velo Enkelejda , Savić Sara , Tomanović Snežana , Omeragić Jasmin , Beck Relja , Hodžić Adnan 
Published: January 2024

AbstractIxodid ticks are distributed across all countries of the Western Balkans, with a high diversity of species. Many of these species serve as vectors of pathogens of veterinary and medical importance. Given the scattered data from Western Balkan countries, we have conducted a comprehensive review of available literature, including some historical data, with the aim to compile information about all recorded tick species and associated zoonotic pathogens in this region. Based on the collected data, the tick fauna of the Western Balkans encompasses 32 tick species belonging to five genera: Ixodes, Haemaphysalis, Dermacentor, Rhipicephalus and Hyalomma. A range of pathogens responsible for human diseases has also been documented, including viruses, bacteria and parasites. In this review, we emphasize the necessity for integrated surveillance and reporting, urging authorities to foster research by providing financial support. Additionally, international and interdisciplinary collaborations should be encouraged that include the exchange of expertise, experiences and resources. The present collaborative effort can effectively address gaps in our knowledge of ticks and tick-borne diseases.
Graphical Abstract
Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis
Authors: Kim Seongryong , Leem Galam , Choi Junjeong , Koh Yongjun , Lee Suho , Nam Sang-Hee , Kim Jin Su , Park Chan Hee , Hwang Ho Kyoung , Min Kyoung Il , Jo Jung Hyun , Lee Hee Seung , Chung Moon Jae , Park Jeong Youp , Park Seung Woo , Song Si Young , Shin Eui-Cheol , Kang Chang Moo , Bang Seungmin , Park Jong-Eun 
Published: January 2024

Abstract
Background
Recent studies using single-cell transcriptomic analysis have reported several distinct clusters of neoplastic epithelial cells and cancer-associated fibroblasts in the pancreatic cancer tumor microenvironment. However, their molecular characteristics and biological significance have not been clearly elucidated due to intra- and inter-tumoral heterogeneity.

Methods
We performed single-cell RNA sequencing using enriched non-immune cell populations from 17 pancreatic tumor tissues (16 pancreatic cancer and one high-grade dysplasia) and generated paired spatial transcriptomic data from seven patient samples.

Results
We identified five distinct functional subclusters of pancreatic cancer cells and six distinct cancer-associated fibroblast subclusters. We deeply profiled their characteristics, and we found that these subclusters successfully deconvoluted most of the features suggested in bulk transcriptome analysis of pancreatic cancer. Among those subclusters, we identified a novel cancer cell subcluster, Ep_VGLL1, showing intermediate characteristics between the extremities of basal-like and classical dichotomy, despite its prognostic value. Molecular features of Ep_VGLL1 suggest its transitional properties between basal-like and classical subtypes, which is supported by spatial transcriptomic data.

Conclusions
This integrative analysis not only provides a comprehensive landscape of pancreatic cancer and fibroblast population, but also suggests a novel insight to the dynamic states of pancreatic cancer cells and unveils potential therapeutic targets.

Graphical Abstract
Prevalence of autoimmune diseases in an admixed population of patients with type 1 diabetes: a multicenter study in Brazil
Authors: Gomes Marilia Brito , Braga Fernanda Oliveira , Drummond Karla Guerra , Pinheiro André , Leal Franz , Porto Luís Cristóvão , Ferreira Livia Leite , Pinheiro Geraldo da Rocha Castelar , Negrato Carlos Antonio 
Published: January 2024

Abstract
Background/objectives
The primary aim of this study was to evaluate the prevalence of autoimmune diseases (AIDs) and its associated factors in an admixed Brazilian population of patients with type 1 diabetes (T1D). The secondary one was to determine the relationship between AIDs and the occurrence of diabetes-related chronic complications (DRCC).

Methods
This cross-sectional, nationwide survey was conducted in 13 public clinics in 11 Brazilian cities. Overall, 1,760 patients were included; 967 females (55.9%), 932 (54%) Caucasians, aged 29.9 ± 11.9 years, age at diagnosis 14.8 ± 8.9 years, diabetes duration 15.5 ± 9.3 years and 12.2 ± 3.8 years of school attendance. AIDs were retrieved from medical records or self-report and stratified as follows: absence of AIDs, only autoimmune thyroid disease (AITD), and other AIDs including the combination with AITD (hyper or hypothyroidism).

Results
The prevalence of AIDs was 19.5% being AITDs (16.1%), the most frequently found. A higher prevalence of hypertension, dyslipidemia and overweight or obesity was found in patients who had exclusively AITDs. A higher prevalence of diabetic retinopathy (DR) was observed in patients with AITDs and patients with other AIDs in combination with AITDs. Chronic kidney disease (CKD) was more prevalent in patients with only AITDs. Lower levels of HbA1C, were observed in patients with isolated AITDs or with other AIDs, regardless of the presence of AITD. Hierarchical multivariate analysis, showed that AIDs were associated with female gender, older age, and longer diabetes duration, self-reported color-race (White and Brown), geographic region (Brazilian North/Northeast region) and higher anti-TPO levels (≥ 35 UI/ml).

Conclusions
In conclusion, Brazilian patients with T1D, belonging to a highly ethnically admixed population, had an important prevalence of AIDs, mostly AITDs, that was associated with female gender, self-reported color-race, older age and longer diabetes duration. Moreover, these patients also had a higher prevalence of DRCC. Even though we highlight the importance of investigating the presence of AIDs at diagnosis and at regular intervals, it is unclear whether screening and early detection of additional AIDs may improve the clinical outcomes in individuals with T1D. Future prospective studies are necessary to establish the interplay between T1D, AIDs and DRCC.
Monitoring modifiable injury risk factors over an in-season mesocycle in semi-professional female field hockey players
Authors: Sánchez-Migallón Violeta , Moreno-Pérez Víctor , Terrón-Manrique Pablo , Fernández-Ruiz Vicente , Blake Catherine , Navandar Archit , Samanes Álvaro López 
Published: January 2024

Abstract
Objective
This study aimed to determine changes of modifiable injury risk factors and fatigue parameters during a mesocycle (4 months of the competitive season) in semi-professional female field hockey players (Spanish 2nd Division).

Methods
Fourteen female field hockey players (age: 22.6 ± 4.9 years) participated in the study over 4 months of the competitive season (September–December 2019). The players were tested each month for their: maximal isometric knee flexion, hip adduction, and abduction muscle strength; passive straight leg raise and ankle dorsiflexion range of motion (ROM); countermovement jump height; and perceptual fatigue (through a perceived well-being questionnaire).

Results
Statistical differences were reported in isometric knee flexion torque in the dominant and non-dominant limb (p = < 0.001, ηp2 = 0.629,0.786 respectively), non-dominant isometric hip abductors torque (p = 0.016, ηp2 = 0.266) and isometric hip adductors torque in dominant and non-dominant limbs (p = < 0.001, ηp2 = 0.441–546). Also, significant differences were reported in the straight leg raise test (p = < 0.001, ηp2 = 0–523, 0.556) and ankle dorsiflexion (p = 0.001, ηp2 = 0.376, 0.377) for the dominant and non-dominant limb respectively. Finally, the jump height measured showed significant differences (p = <.001, ηp2 = 0.490), while no differences were reported in perceived well-being parameters (p = 0.089–0.459).

Conclusion
Increments in isometric muscle strength and fluctuations in ROM values and vertical jumping capacity are reported over an in-season mesocycle (i.e., 4 months of the competitive season). This information can be used to target recovery strategies to make them more efficient.