bluuebunny/crossref_metadata_2025_split huggingface dataset:
The HIV-1 gag p6: a promising target for therapeutic intervention
Authors: Chen Xiaowei , Wang Xiao 
Published: January 2024

AbstractThe p6 domain of the Gag precursors (Gag p6) in human immunodeficiency virus type 1 (HIV-1) plays multifunctional roles in the viral life cycle. It utilizes the endosomal sorting complex required for transport (ESCRT) system to facilitate viral budding and release from the plasma membrane through the interactions with the ESCRT-I component tumor susceptibility gene 101 (TSG101) and with the ALG-2 interacting protein X (ALIX). Moreover, Gag p6 contributes to viral replication by a range of posttranslational modifications such as SUMOylation, ubiquitination and phosphorylation. Additionally, Gag p6 also mediates the incorporation of the accessory protein Vpr into virions, thereby promoting Vpr-induced viral replication. However, less attention is focused on Gag p6 as therapeutic intervention. This review focuses on the structures and diverse functions of Gag p6 in viral replication, host cells, and pathogenesis. Additionally, several challenges were also discussed in studying the structure of Gag p6 and its interactions with partners. Consequently, it concludes that the Gag p6 represents an attractive target for the development of antiretroviral drugs, and efforts to develop p6-targeted antiretrovirals are expected to undergo significant growth in the forthcoming years.
The chemokine receptor CCR5: multi-faceted hook for HIV-1
Authors: Faivre Natacha , Verollet Christel , Dumas Fabrice 
Published: January 2024

AbstractChemokines are cytokines whose primary role is cellular activation and stimulation of leukocyte migration. They perform their various functions by interacting with G protein-coupled cell surface receptors (GPCRs) and are involved in the regulation of many biological processes such as apoptosis, proliferation, angiogenesis, hematopoiesis or organogenesis. They contribute to the maintenance of the homeostasis of lymphocytes and coordinate the function of the immune system. However, chemokines and their receptors are sometimes hijacked by some pathogens to infect the host organism. For a given chemokine receptor, there is a wide structural, organizational and conformational diversity. In this review, we describe the evidence for structural variety reported for the chemokine receptor CCR5, how this variability can be exploited by HIV-1 to infect its target cells and what therapeutic solutions are currently being developed to overcome this problem.
Genetic association of ACE2 and TMPRSS2 polymorphisms with COVID-19 severity; a single centre study from Egypt
Authors: Elnagdy Marwa H. , Magdy Alshimaa , Eldars Waleed , Elgamal Mohamed , El-Nagdy Ahmed Hazem , Salem Omnia , Elmowafy Mohamed Magdy , Elborsh Omar Ahmed , Elshafey Abdelrahman Walid , Kesba Muhammad Magdy , Abdulgalil Ahmed Elsaeed , Sobh Ali 
Published: January 2024

Abstract
Background
Since the emergence of the COVID-19 infection in China, it has caused considerable morbidity, mortality, and economic burden. It causes the vast majority of clinical manifestations, ranging from mild or even no symptoms to severe respiratory failure. There are many risk factors for severe COVID-19, such as old age, male gender, and associated comorbidities. A major role for genetic factors may exist. The SARS-CoV-2 virus enters the cell primarily through ACE2 receptors. rs2285666 is one of many polymorphisms found in the ACE2 receptor gene. To enable endosome-independent entry into target cells, the transmembrane protease serine-type 2 (TMPRSS2) is necessary to cleave the virus’ spike (S) glycoprotein. TMPRSS2 is characterized by an androgen receptor element. The rs12329760 polymorphism in TMPRSS2 may explain different genetic susceptibilities to COVID-19.

Method
This cross-sectional study was held in Mansoura University Hospitals during the period from June 2020 to April 2022 on patients who had mild and severe COVID-19. Demographic, clinical, and laboratory data were collected, and the TaqMan real-time polymerase chain was used for allelic discrimination in the genotyping of rs2285666 and rs12329760.

Results
This study included 317 Egyptian patients, aged from 0.2 to 87 years. Males were 146, while females were 171. They were divided into mild and severe groups (91 and 226 patients, respectively) based on their clinical symptoms. There was a significant association between COVID-19 severity and male gender, hypertension, diabetes mellitus, and high CRP. The genotype and allele frequency distributions of the ACE2 rs2285666 polymorphism showed no significant association with the severity of COVID-19 in both. In contrast, in TMPRSS2 rs12329760 minor T allele and CT, TT genotypes were significantly associated with a reduced likelihood of developing severe COVID-19.

Conclusion
Our study indicates that the ACE2 rs2285666 polymorphism is not related to the severity of COVID-19, whether genotypes or alleles. In TMPRSS2 rs12329760, the dominant model and T allele showed significantly lower frequencies in severe cases, with a protective effect against severity. The discrepancies with previous results may be due to variations in other ACE2 receptor-related genes, inflammatory mediators, and coagulation indicators. Haplotype blocks and differences in racial makeup must be taken into consideration. Future research should be done to clarify how ethnicity affects these polymorphisms and how other comorbidities combine to have an additive effect.
Navigating the challenges of minimally invasive mitral valve surgery: a risk analysis and learning curve evaluation
Authors: Papadopoulos Nestoras , Ntinopoulos Vasileios , Dushaj Stak , Häussler Achim , Odavic Dragan , Biefer Hector Rodríguez Cetina , Dzemali Omer 
Published: January 2024

Abstract
Background
This study aimed to report the risk and learning curve analysis of a minimally invasive mitral valve surgery program performed through a right mini-thoracotomy at a single institution.

Methods
From January 2013 through December 2019, 266 consecutive patients underwent minimally invasive mitral valve surgery in our department and were included in the current study. Multiple logistic regression analysis was used for the adverse event outcome. Distribution over time of perioperative complications, defined as clinical endpoints in the Valve Academic Research Consortium-2 (VARC-2) consensus document, as well as CUSUM charts for assessment of cardiopulmonary bypass and aortic cross-clamping duration over time, has been performed for learning curve assessment.

Results
Overall incidences of postoperative stroke (1.1%), myocardial infarction (1.1%), and thirty-day mortality (1.5%) were low. The mitral valve reconstruction rate in our series was 95%. Multivariable analysis revealed that concomitant tricuspid valve surgery (OR 4.44; 95%CI 1.61–11.80; p = 0.003) was significantly associated with adverse event outcomes. Despite a trend towards adverse event outcomes in patients with preexisting active mitral valve endocarditis (OR 2.69; 95%CI 0.81–7.87; p = 0.082), mitral valve pathology did not significantly impact postoperative morbidity and mortality. Distribution over time of perioperative complications, defined as clinical endpoints in the VARC-2 consensus document, showed a trend towards an improved complication rate after the initial 65–100 procedures.

Conclusions
Mitral valve surgery via right-sided mini-thoracotomy can be implemented safely with low perioperative morbidity and mortality rates. Careful patient selection regarding isolated mitral valve surgery in the presence of degenerative mitral valve disease may represent a significant safety issue during the learning curve.
Trial Registration: The cantonal ethics commission of Zurich approved the study (registration ID 2020-00752, date of approval 24 April 2020).
The brain cytokine orchestra in multiple sclerosis: from neuroinflammation to synaptopathology
Authors: Amoriello Roberta , Memo Christian , Ballerini Laura , Ballerini Clara 
Published: January 2024

AbstractThe central nervous system (CNS) is finely protected by the blood–brain barrier (BBB). Immune soluble factors such as cytokines (CKs) are normally produced in the CNS, contributing to physiological immunosurveillance and homeostatic synaptic scaling. CKs are peptide, pleiotropic molecules involved in a broad range of cellular functions, with a pivotal role in resolving the inflammation and promoting tissue healing. However, pro-inflammatory CKs can exert a detrimental effect in pathological conditions, spreading the damage. In the inflamed CNS, CKs recruit immune cells, stimulate the local production of other inflammatory mediators, and promote synaptic dysfunction. Our understanding of neuroinflammation in humans owes much to the study of multiple sclerosis (MS), the most common autoimmune and demyelinating disease, in which autoreactive T cells migrate from the periphery to the CNS after the encounter with a still unknown antigen. CNS-infiltrating T cells produce pro-inflammatory CKs that aggravate local demyelination and neurodegeneration. This review aims to recapitulate the state of the art about CKs role in the healthy and inflamed CNS, with focus on recent advances bridging the study of adaptive immune system and neurophysiology.
HIF-2α/LINC02609/APOL1-mediated lipid storage promotes endoplasmic reticulum homeostasis and regulates tumor progression in clear-cell renal cell carcinoma
Authors: Xiao Haibing , Qu Yan , Li Haolin , Zhang Yi , Fei Mintian , Liang Chaozhao , Yang Hongmei , Zhang Xiaoping 
Published: January 2024

Abstract
Background
The VHL-HIF pathway and lipid droplet accumulation are the main characteristics of clear cell renal cell carcinoma (ccRCC). However, the connection between the two features is largely unknown.

Methods
We used transcriptional sequencing and TCGA database analysis to identify APOL1 as a novel therapeutic target for ccRCC. The oncogenic functions of APOL1 were investigated by cell proliferation, colony formation, migration and invasion assays in ccRCC cells in vitro and xenografts derived from ccRCC cells in vivo. Oil red O staining and quantification were used to detect lipid droplets. Chromatin immunoprecipitation (ChIP) assays and luciferase reporter assays were carried out to identify HIF-2α bound to the promoter of APOL1 and lncRNA LINC02609. RNA-FISH and luciferase reporter assays were performed to determine that LncRNA LINC02609 functions as a competing endogenous RNA to regulate APOL1 expression by sponging miR-149-5p.

Findings
RNA-seq data revealed that HIF2α can regulate APOL1 and lncRNA LINC02609 expression. We also found that HIF-2α can bind to the promoter of APOL1 and lncRNA LINC02609 and transcriptionally regulate their expression directly. We further demonstrated that LncRNA LINC02609 functions as a competing endogenous RNA to regulate APOL1 expression by sponging miR-149-5p in ccRCC. Mechanistically, APOL1-dependent lipid storage is required for endoplasmic reticulum (ER) homeostasis and cell viability and metastasis in ccRCC. We also showed that high APOL1 expression correlated with worse clinical outcomes, and knockdown of APOL1 inhibited tumor cell lipid droplet formation, proliferation, metastasis and xenograft tumor formation abilities. Together, our studies identify that HIF2α can regulate the expression of the lipid metabolism related gene APOL1 by direct and indirect means, which are essential for ccRCC tumorigenesis.

Interpretation
Based on the experimental data, in ccRCC, the HIF-2α/LINC02609/APOL1 axis can regulate the expression of APOL1, thus interfering with lipid storage, promoting endoplasmic reticulum homeostasis and regulating tumor progression in ccRCC. Together, our findings provide potential biomarkers and novel therapeutic targets for future studies in ccRCC.
Machine learning for risk stratification in the emergency department (MARS-ED) study protocol for a randomized controlled pilot trial on the implementation of a prediction model based on machine learning technology predicting 31-day mortality in the emergency department
Authors: van Dam Paul M.E.L. , van Doorn William P.T.M. , van Gils Floor , Sevenich Lotte , Lambriks Lars , Meex Steven J.R. , Cals Jochen W.L. , Stassen Patricia M. 
Published: January 2024

Abstract
Background
Many prediction models have been developed to help identify emergency department (ED) patients at high risk of poor outcome. However, these models often underperform in clinical practice and their actual clinical impact has hardly ever been evaluated. We aim to perform a clinical trial to investigate the clinical impact of a prediction model based on machine learning (ML) technology.

Methods
The study is a prospective, randomized, open-label, non-inferiority pilot clinical trial. We will investigate the clinical impact of a prediction model based on ML technology, the RISKINDEX, which has been developed to predict the risk of 31-day mortality based on the results of laboratory tests and demographic characteristics. In previous studies, the RISKINDEX was shown to outperform internal medicine specialists and to have high discriminatory performance. Adults patients (18 years or older) will be recruited in the ED. All participants will be randomly assigned to the control group or the intervention group in a 1:1 ratio. Participants in the control group will receive care as usual in which the study team asks the attending physicians questions about their clinical intuition. Participants in the intervention group will also receive care as usual, but in addition to asking the clinical impression questions, the study team presents the RISKINDEX to the attending physician in order to assess the extent to which clinical treatment is influenced by the results.

Discussion
This pilot clinical trial investigates the clinical impact and implementation of an ML based prediction model in the ED. By assessing the clinical impact and prognostic accuracy of the RISKINDEX, this study aims to contribute valuable insights to optimize patient care and inform future research in the field of ML based clinical prediction models.

Trial registration
ClinicalTrials.gov NCT05497830. Machine Learning for Risk Stratification in the Emergency Department (MARS-ED). Registered on August 11, 2022. URL: https://clinicaltrials.gov/study/NCT05497830.
Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions
Authors: Xie Fei , Zhao Shengwei , Zhan Xiaoxiu , Zhou Yang , Li Yin , Zhu Weiyun , Pope Phillip B. , Attwood Graeme T. , Jin Wei , Mao Shengyong 
Published: January 2024

AbstractBackgroundMethanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains.ResultsHere, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12exchanges could enable them to occupy ecological niches that possibly alter the direction of H2utilization.ConclusionsWe provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2flow.
Working under short timescales to deliver a national trial: a case study of the ComFluCOV trial from a statistician’s perspective
Authors: Harris Rosie , Thirard Russell , Baos Sarah , Lazarus Rajeka , Todd Rachel , Kirwan Jana , Joyce Katherine , Hutton David , Clout Maddie , Cappel-Porter Heike , Culliford Lucy , Rogers Chris A. 
Published: January 2024

Abstract
Background
In early 2021, the Department of Health and Social Care in the UK called for research on the safety and immunogenicity of concomitant administration of COVID-19 and influenza vaccines. Co-administration of these vaccines would facilitate uptake and reduce the number of healthcare visits required. The ComFluCOV trial was designed to deliver the necessary evidence in time to inform the autumn (September–November) 2021 vaccination policy. This paper presents the statistical methodology applied to help successfully deliver the trial results in 6 months.

Methods
ComFluCOV was a parallel-group multicentre randomised controlled trial managed by the Bristol Trials Centre. Two study statisticians, supported by a senior statistician, worked together on all statistical tasks. Tools were developed to aid the pre-screening process. Automated data monitoring reports of clinic data and electronic diaries were produced daily and reviewed by the trial team and feedback provided to sites. Analyses were performed independently in parallel, and derivations and results of all outcomes were compared.

Results
Set-up was achieved in less than a month, and 679 participants were recruited over 8 weeks. A total of 537 [at least] daily reports outlining recruitment, protocol adherence, and data quality, and 695 daily reports of participant electronic diaries identifying any missed diary entries and adverse events were produced over a period of 16 weeks. A preliminary primary outcome analysis of validated data was reported to the Department of Health and Social Care in May 2021. The database was locked 6 weeks after the final participant follow-up and final analyses completed 3 weeks later. A pre-print publication was submitted within 14 days of the results being made available. The results were reported 6 months after first discussions about the trial.

Conclusion
The statistical methodologies implemented in ComFluCOV helped to deliver the study in the timescale set. Working in a new clinical area to tight timescales was challenging. Having two statisticians working together on the study provided a quality assurance process that enabled analyses to be completed efficiently and ensured data were interpreted correctly. Processes developed could be applied to other studies to maximise quality, reduce the risk of errors, and overall provide enhanced validation methods.

Trial registration
ISRCTN14391248, registered on 30 March 2021
Pragmatic randomized controlled trials: strengthening the concept through a robust international collaborative network: PRIME-9—Pragmatic Research and Innovation through Multinational Experimentation
Authors: Omerovic Elmir , Petrie Mark , Redfors Björn , Fremes Stephen , Murphy Gavin , Marquis-Gravel Guillaume , Lansky Alexandra , Velazquez Eric , Perera Divaka , Reid Christopher , Smith Julian , van der Meer Peter , Lipsic Eric , Juni Peter , McMurray John , Bauersachs Johann , Køber Lars , Rouleau Jean L. , Doenst Torsten 
Published: January 2024

AbstractIn an era focused on value-based healthcare, the quality of healthcare and resource allocation should be underpinned by empirical evidence. Pragmatic clinical trials (pRCTs) are essential in this endeavor, providing randomized controlled trial (RCT) insights that encapsulate real-world effects of interventions. The rising popularity of pRCTs can be attributed to their ability to mirror real-world practices, accommodate larger sample sizes, and provide cost advantages over traditional RCTs. By harmonizing efficacy with effectiveness, pRCTs assist decision-makers in prioritizing interventions that have a substantial public health impact and align with the tenets of value-based health care. An international network for pRCT provides several advantages, including larger and diverse patient populations, access to a broader range of healthcare settings, sharing knowledge and expertise, and overcoming ethical and regulatory barriers. The hypothesis and study design of pRCT answers the decision-maker’s questions. pRCT compares clinically relevant alternative interventions, recruits participants from diverse practice settings, and collects data on various health outcomes. They are scarce because the medical products industry typically does not fund pRCT. Prioritizing these studies by expanding the infrastructure to conduct clinical research within the healthcare delivery system and increasing public and private funding for these studies will be necessary to facilitate pRCTs. These changes require more clinical and health policy decision-makers in clinical research priority setting, infrastructure development, and funding. This paper presents a comprehensive overview of pRCTs, emphasizing their importance in evidence-based medicine and the advantages of an international collaborative network for their execution. It details the development of PRIME-9, an international initiative across nine countries to advance pRCTs, and explores various statistical approaches for these trials. The paper underscores the need to overcome current challenges, such as funding limitations and infrastructural constraints, to leverage the full potential of pRCTs in optimizing healthcare quality and resource utilization.