A Cross-sectional Study to Identify Risk Factors for Hepatitis C in Punjab, India

BACKGROUND

Hepatitis C virus (HCV) antibody prevalence in Punjab, India (0.56%) is higher than the national average (0.32%), but primary drivers of local transmission are unclear.

OBJECTIVES

The objective of this study was to identify behavioral and demographic predictors of screening positive for HCV in Punjab.

MATERIALS AND METHODS

Interviews assessing exposure to potential HCV risk factors were administered cross-sectionally to persons screening for HCV across 10 treatment facilities. Risk ratios (RRs) were calculated using generalized estimating equation models accounting for clustering by health facility.

RESULTS

One thousand seven hundred and sixty-three patients tested anti-HCV positive; 595 were negative. 57.7% of respondents were male; the median age was 40 years. 13.8% reported injecting drugs. Males were more likely to test positive than females (RR: 1.14, 95% confidence interval [CI]: 1.07-1.21). Unmarried men were at higher risk of anti-HCV positivity compared with married men (RR: 1.16, 95% CI: 1.08-1.24), but unmarried women were at lower risk (RR: 0.65, 95% CI: 0.43-0.98). The strongest risk factors were history of injecting drugs (RR: 1.37, 95% CI: 1.24-1.51), incarceration (RR: 1.22, 95% CI: 1.12-1.33), acupuncture use (RR: 1.20, 95% CI: 1.09-1.33), having household member(s) with a history of incarceration (RR: 1.17, 95% CI: 1.08-1.26), and tattoos (RR: 1.16, 95% CI: 1.09-1.24). Additional risk factors among men included receiving injections in a public hospital or from unregistered medical practitioners and among women included a history of childbirth.

CONCLUSION

Injecting drugs was most strongly associated with anti-HCV positivity in this population. Greater attention to HCV prevention is needed, with a focus on people-centered harm reduction programs, behavioral change interventions, and increasing safety in potential transmission settings.

Data mining and machine learning in HIV infection risk research: An overview and recommendations

In the contemporary era, the applications of data mining and machine learning have permeated extensively into medical research, significantly contributing to areas such as HIV studies. By reviewing 38 articles published in the past 15 years, the study presents a roadmap based on seven different aspects, utilizing various machine learning techniques for both novice researchers and experienced researchers seeking to comprehend the current state of the art in this area. While traditional regression modeling techniques have been commonly used, researchers are increasingly adopting more advanced fully supervised machine learning and deep learning techniques, which often outperform the traditional methods in predictive performance. Additionally, the study identifies nine new open research issues and outlines possible future research plans to enhance the outcomes of HIV infection risk research. This review is expected to be an insightful guide for researchers, illuminating current practices and suggesting advancements in the field.

Risk Factors Associated with Human Brucellosis: A Systematic Review and Meta-Analysis

Background: Brucellosis is a zoonosis disease that can affect humans and a wide range of domestic and wild animals. Susceptibility to brucellosis in humans can be related to various factors, such as nutritional and occupational factors. This study evaluated factors related to brucellosis and identified influential risk factors for human infection. Methods: We performed a systematic literature review and meta-analysis of studies in PubMed, Web of Science, and Scopus. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to measure the strength of the association between some potential factors and the risk of brucellosis. Results: From 277 initial studies, 19 case-control studies were included in this review. Significant risk factors for brucellosis included occupation (OR 3.31, 95% CI 1.68-6.55), having aborted animals (OR 4.16, 95% CI 2.03-8.50), consumption of meat (OR 2.17, 95% CI 1.44-3.36), unpasteurized milk (OR 3.86, 95% CI 1.81-8.23), and raw cheese (OR 4.20, 95% CI 1.63-10.85). Conclusion: The results of this study advance the understanding of the etiology of brucellosis. In this meta-analysis, we found the association of different environmental factors with the risk of brucellosis. Additional high-quality prospective studies are needed to determine whether these factors cause brucellosis and to identify other factors.

Prevalence and risk factors of Hepatitis C virus infection in the Upper East Region of Ghana; a community-based cross-sectional study

Hepatitis C virus (HCV) infection remains a major cause of liver related morbidity and mortality worldwide. Epidemiologic data on seroprevalence, viremia prevalence and risk factors remain limited in sub-Saharan Africa. In Ghana, HCV-related deaths are estimated to have increased since 2015. Risk factors associated with HCV infection in Ghana are not well described. The aim of this study was to determine the prevalence of, and risk factors associated with hepatitis C virus infection in the Upper East Region located in the northern part of Ghana. A community-based cross-sectional study was conducted in 9 communities in the Upper East region of Ghana. A total of 1,769 participants aged ≥12 years were screened for HCV antibody (anti-HCV) using rapid diagnostic testing (RDT). Seventy-four participants undertook HCV RNA testing after a positive anti-HCV result. Multivariate logistic regression was used to determine risk factors associated with HCV seropositivity. The anti-HCV prevalence was 8.4%, with 149 out of 1,769 testing anti-HCV positive. Mean age (±SD) of seropositive persons was 45.4 (±16.3) years. The highest anti-HCV seroprevalence was amongst persons aged 60 years and above. Forty-four out of 74 (59.5%) seropositive cases had viremic infection and the estimated viremic prevalence in the screened population was 5.0%. Predictors of HCV seropositivity were age (OR 1.03 95% CI 1.01-1.04), history of female genital mutilation or circumcision (OR 1.63 95% CI 1.04-2.55), sexual activity (OR 2.57 95% CI 1.38-4.79), positive maternal HCV status (OR 10.38 95% CI 4.13-26.05) and positive HIV status (OR 4.03 95% CI 1.35-12.05). In conclusion, the Upper East Region demonstrates a high Hepatitis C antibody prevalence. Almost 60% of individuals have viremic infection, however the cost of RNA testing is a barrier to virological diagnosis. There is a need to educate the population about HCV-associated risk factors to reduce HCV transmission and burden of disease.

Clinical Characteristics, Functional Outcome, and Socioeconomic Impact of Ischemic Stroke among Young Egyptian Adults

BACKGROUND

Stroke in young patients results in disproportionately high societal cost given the productive life-years lost. Little is known about stroke in young Egyptian patients. We aimed to analyze clinicodemographic characteristics, functional outcome, and socioeconomic impact of ischemic stroke among young Egyptian adults.

METHODS

This is a prospective, observational cohort study of consecutively recruited patients with acute ischemic stroke (AIS), 18-50 years, between September 2022 and September 2023 at a tertiary stroke center in the south of Egypt. We recorded baseline demographic and cardiovascular risk factors, stroke severity, stroke subtype according to the TOAST classification, intravenous thrombolysis, employment, and ambulation status pre- and post-stroke, post-stroke complications, and 90-day functional outcome measured by the modified Rankin Scale (mRS).

RESULTS

Our cohort comprised 210 patients, 38.0 (±7.8) years, 89 (42%) females. Mean NIHSS score was 11.2 (±4.8); in-hospital case fatality was 9% (19 patients). Dyslipidemia (n = 105, 50%), smoking (n = 105, 50%), and hypertension (n = 67, 32%) were the most prevalent cardiovascular risk factors. At 90 days, 58 (29%) patients had a 90-day mRS 0-1 and 53 (26%) met criteria for depression diagnosis. Sixty-nine of the 116 employed individuals (59%) remained out of work after 90 days of stroke, 61 of whom were single earners in their household. 36/60 (60%) thrombolysis-eligible patients received it; an additional 98 otherwise thrombolysis-eligible patients presented >4.5 h from symptom onset. Patients receiving IV thrombolysis were significantly more likely to have resumed full-time work at 90 days (32% vs. 11%, p = 0.006) but with no significant difference in 90-day mRS.

CONCLUSIONS

Young adult AIS patients in Egypt experience high rates of post-stroke depression and face challenges in their ability to work and provide for their families. Since most patients have treatable cardiovascular risk factors and only about two-thirds of eligible patients receive thrombolysis, reinforcing primary prevention, education about early stroke signs, and benefits of acute can improve outcomes and have significant potential societal benefit.

Adaptive Expression and ncRNA Regulation of Genes Related to Digestion and Metabolism in Stomach of Red Pandas during Suckling and Adult Periods

Red pandas evolved from carnivores to herbivores and are unique within Carnivora. Red pandas and carnivorous mammals consume milk during the suckling period, while they consume bamboo and meat during the adult period, respectively. Red pandas and carnivorous mammal ferrets have a close phylogenetic relationship. To further investigate the molecular mechanisms of dietary changes and nutrient utilization in red pandas from suckling to adult, comparative analysis of the whole transcriptome was performed on stomach tissues from red pandas and ferrets during the suckling and adult periods. The main results are as follows: (1) we identified ncRNAs for the first time in stomach tissues of both species, and found significant expression changes of 109 lncRNAs and 106 miRNAs in red pandas and 756 lncRNAs and 109 miRNAs in ferrets between the two periods; (2) up-regulated genes related to amino acid transport regulated by lncRNA-miRNA-mRNA networks may efficiently utilize limited bamboo amino acids in adult red pandas, while up-regulated genes related to amino acid degradation regulated by lncRNAs may maintain the balance of amino acid metabolism due to larger daily intakes in adult ferrets; and (3) some up-regulated genes related to lipid digestion may contribute to the utilization of rich nutrients in milk for the rapid growth and development of suckling red pandas, while up-regulated genes associated with linoleic acid metabolism regulated by lncRNA-miRNA-mRNA networks may promote cholesterol decomposition to reduce health risks for carnivorous adult ferrets. Collectively, our study offers evidence of gene expression adaptation and ncRNA regulation in response to specific dietary changes and nutrient utilization in red pandas during suckling and adult periods.

The association between hepatitis C virus infection status and blood pressure in adults in the United States: NHANES 1999-2012

Background

The Hepatitis C virus (HCV) infection is strongly associated with cardiovascular disease risk factors, but the relationship with blood pressure (BP) remains unclear.

Objectives

To assess the association between HCV infection status and BP in US adults.

Methods

Data for the study were obtained from the National Health and Nutrition Examination Survey (NHANES) between 1999 and 2012. The association of HCV infection status (including HCV infection, current HCV infection, and past HCV infection) with hypertension, systolic blood pressure (SBP), and diastolic blood pressure (DBP) were explored using logistic or linear regression analyses respectively.

Results

A total of 25,850 participants (age≥18 years) were enrolled in the current study, including 14,162 participants with hypertension. After adjusting for all covariates, HCV infection/current HCV infection was not associated with hypertension and SBP compared to participants with non-HCV infection (OR: 1.34,95% CI 0.96-1.87/1.31 95% CI 0.91,1.91, β: -0.92, 95% CI -2.7-0.86/-0.35 95% CI -2.51,1.81, respectively). HCV infection/current HCV infection was only associated with elevated DBP (β: 4.1,95% CI 2.57-5.63/4.24,95% CI 2.27-6.21). However, there was no correlation with past HCV infection in participants with hypertension, SBP, and DBP compared to those with non-HCV infection (OR: 1.23,95% CI 0.59-2.54; β: -3.79, 95% CI -7.67-0.08 and 2.28 95% CI -0.36-4.92, respectively).

Conclusion

In a representative sample of US adults, it was found that both HCV infection and current HCV infection were independently linked to higher DBP. However, there was no association between past HCV infection and DBP.

Target-specific requirements for RNA interference can arise through restricted RNA amplification despite the lack of specialized pathways

Since double-stranded RNA (dsRNA) is effective for silencing a wide variety of genes, all genes are typically considered equivalent targets for such RNA interference (RNAi). Yet, loss of some regulators of RNAi in the nematode C. elegans can selectively impair the silencing of some genes. Here we show that such selective requirements can be explained by an intersecting network of regulators acting on genes with differences in their RNA metabolism. In this network, the Maelstrom domain-containing protein RDE-10, the intrinsically disordered protein MUT-16, and the Argonaute protein NRDE-3 work together so that any two are required for silencing one somatic gene, but each is singly required for silencing another somatic gene, where only the requirement for NRDE-3 can be overcome by enhanced dsRNA processing. Quantitative models and their exploratory simulations led us to find that (1) changing cis-regulatory elements of the target gene can reduce the dependence on NRDE-3, (2) animals can recover from silencing in non-dividing cells and (3) cleavage and tailing of mRNAs with UG dinucleotides, which makes them templates for amplifying small RNAs, is enriched within 'pUG zones' matching the dsRNA. Similar crosstalk between pathways and restricted amplification could result in apparently selective silencing by endogenous RNAs.

Neglected etiologies of prolonged febrile illnesses in tropical and subtropical regions: A systematic review

BACKGROUND

Febrile illnesses that persist despite initial treatment are common clinical challenges in (sub)tropical low-resource settings. Our aim is to review infectious etiologies of "prolonged fevers" (persistent febrile illnesses, PFI) and to quantify relative contributions of selected neglected target diseases with limited diagnostic options, often overlooked, causing inadequate antibiotic prescriptions, or requiring prolonged and potentially toxic treatments.

METHODS

We performed a systematic review of articles addressing the infectious etiologies of PFI in adults and children in sub-/tropical low- and middle-income countries (LMICs) using the PRISMA guidelines. A list of target diseases, including neglected parasites and zoonotic bacteria (e.g., Leishmania and Brucella), were identified by infectious diseases and tropical medicine specialists and prioritized in the search. Malaria and tuberculosis (TB) were not included as target diseases due to well-established epidemiology and diagnostic options. Four co-investigators independently extracted data from the identified articles while assessing for risk of bias.

RESULTS

196 articles from 52 countries were included, 117 from Africa (33 countries), 71 from Asia (16 countries), and 8 from Central and -South America (3 countries). Target diseases were reported as the cause of PFI in almost half of the articles, most frequently rickettsioses (including scrub typhus), relapsing fever borreliosis (RF-borreliosis), brucellosis, enteric fever, leptospirosis, Q fever and leishmaniasis. Among those, RF-borreliosis was by far the most frequently reported disease in Africa, particularly in Eastern Africa. Rickettsioses (including scrub typhus) were often described in both Africa and Asia. Leishmaniasis, toxoplasmosis and amoebiasis were the most frequent parasitic etiologies. Non-target diseases and non-tropical organisms (Streptococcus pneumoniae, Escherichia coli, and non-typhoidal Salmonella spp) were documented in a fifth of articles.

CONCLUSIONS

Clinicians faced with PFI in sub-/tropical LMICs should consider a wide differential diagnosis including enteric fever and zoonotic bacterial diseases (e.g., rickettsiosis, RF-borreliosis and brucellosis), or parasite infections (e.g., leishmaniasis) depending on geography and syndromes. In the absence of adequate diagnostic capacity, a trial of antibiotics targeting relevant intra-cellular bacteria, such as doxycycline or azithromycin, may be considered.

A scoping review on the epidemiology and public significance of Brucella abortus in Chinese dairy cattle and humans

Brucellosis, caused by Brucella spp., is a re-emerging One Health disease with increased prevalence and incidence in Chinese dairy cattle and humans, severely affecting animal productivity and public health. In dairy cattle, B. abortus is the primary causative agent although infections with other Brucella species occur occasionally. However, the epidemiological and comparative importance of B. abortus in dairy cattle and humans remains inadequately understood throughout China due to the heterogeneity in locations, quality, and study methods. This scoping review aims to describe the changing status of B. abortus infection in dairy cattle and humans, investigate the circulating Brucella species and biovars, and identify factors driving the disease transmission by retrieving publicly accessible literature from four databases. After passing the prespecified inclusion criteria, 60 original articles were included in the final synthesis. Although the reported animal-level and farm-level prevalence of brucellosis in dairy cattle was lower compared to other endemic countries (e.g. Iran and India), it has been reported to increase over the last decade. The incidence of brucellosis in humans displayed seasonal increases. The Rose Bengal Test and Serum Agglutination Test, interpreted in series, were the most used serological test to diagnose Brucella spp. in dairy cattle and humans. B. abortus biovar 3 was the predominant species (81.9%) and biovar (70.3%) in dairy cattle, and B. melitensis biovar 3 was identified as the most commonly detected strain in human brucellosis cases. These strains were mainly clustered in Inner Mongolia and Shannxi Province (75.7%), limiting the generalizability of the results to other provinces. Live cattle movement or trade was identified as the key factor driving brucellosis transmission, but its transmission pattern remains unknown within the Chinese dairy sector. These knowledge gaps require a more effective One Health approach to be bridged. A coordinated and evidence-based research program is essential to inform regional or national control strategies that are both feasible and economical in the Chinese context.

Isoform-specific RNA structure determination using Nano-DMS-MaP

RNA structure determination is essential to understand how RNA carries out its diverse biological functions. In cells, RNA isoforms are readily expressed with partial variations within their sequences due, for example, to alternative splicing, heterogeneity in the transcription start site, RNA processing or differential termination/polyadenylation. Nanopore dimethyl sulfate mutational profiling (Nano-DMS-MaP) is a method for in situ isoform-specific RNA structure determination. Unlike similar methods that rely on short sequencing reads, Nano-DMS-MaP employs nanopore sequencing to resolve the structures of long and highly similar RNA molecules to reveal their previously hidden structural differences. This Protocol describes the development and applications of Nano-DMS-MaP and outlines the main considerations for designing and implementing a successful experiment: from bench to data analysis. In cell probing experiments can be carried out by an experienced molecular biologist in 3-4 d. Data analysis requires good knowledge of command line tools and Python scripts and requires a further 3-5 d.

Contemporary Insights into Hepatitis C Virus: A Comprehensive Review

Hepatitis C virus (HCV) remains a significant global health challenge. Approximately 50 million people were living with chronic hepatitis C based on the World Health Organization as of 2024, contributing extensively to global morbidity and mortality. The advent and approval of several direct-acting antiviral (DAA) regimens significantly improved HCV treatment, offering potentially high rates of cure for chronic hepatitis C. However, the promising aim of eventual HCV eradication remains challenging. Key challenges include the variability in DAA access across different regions, slightly variable response rates to DAAs across diverse patient populations and HCV genotypes/subtypes, and the emergence of resistance-associated substitutions (RASs), potentially conferring resistance to DAAs. Therefore, periodic reassessment of current HCV knowledge is needed. An up-to-date review on HCV is also necessitated based on the observed shifts in HCV epidemiological trends, continuous development and approval of therapeutic strategies, and changes in public health policies. Thus, the current comprehensive review aimed to integrate the latest knowledge on the epidemiology, pathophysiology, diagnostic approaches, treatment options and preventive strategies for HCV, with a particular focus on the current challenges associated with RASs and ongoing efforts in vaccine development. This review sought to provide healthcare professionals, researchers, and policymakers with the necessary insights to address the HCV burden more effectively. We aimed to highlight the progress made in managing and preventing HCV infection and to highlight the persistent barriers challenging the prevention of HCV infection. The overarching goal was to align with global health objectives towards reducing the burden of chronic hepatitis, aiming for its eventual elimination as a public health threat by 2030.

RNA-binding proteins and exoribonucleases modulating miRNA in cancer: the enemy within

Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.

SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity

The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5' tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.

Risk Assessment Tools from the One Health Perspective: A Narrative Review

Background

61% of the infections around the world that have emerged to date are zoonotic. Evidence warns that the threat posed by zoonoses is on the rise, and the risk of a new pandemic is higher now than ever. Early identification of risk, populations at risk, and risk of transmission are essential steps towards a prevention, preparation and response to outbreaks. This review aims to look at the tools available for identifying and estimating risks and threats from one health perspective and finally propose a list of indicators which could assess the risk of transmission of disease at the humans, animals and the environment intersection.

Methods

The databases like PubMed, google scholar, Embase and Scopus were used to extract the relevant articles. A search was carried out using a keyword. A total of 1311 articles were listed initially after the search and reviewed. Out of 1311, only 26 tools which assessed the risk of diseases mainly infectious or were relevant to risk of transmission of any infectious diseases were included in the review.

Results

The tools included in this review involve risk assessment at the environmental, animal and human dimensions. The tools are used to evaluate the contamination of the environment due to chemicals or toxins or the risk of transmission of infection due to environmental factors like air contamination, to identify the animal diseases like bovine respiratory disease and foot and mouth disease and to estimate the human health risk at the community or individual levels.

Conclusion

Risk assessment tools are an essential part of the prevention of pandemics. These tools are helpful in assessing the risk of transmission of infections either from human to human, between human and animals, between animals and animals and so on. Thus this review gives us an insight into the existing risk assessment tools and the need for a One Health risk assessment tools to prevent outbreaks in future. It also provides a list of factors that can be included in a one health risk assessment tool.

HIV-1 RNA genome packaging: it's G-rated

A member of the Retroviridae, human immunodeficiency virus type 1 (HIV-1), uses the RNA genome packaged into nascent virions to transfer genetic information to its progeny. The genome packaging step is a highly regulated and extremely efficient process as a vast majority of virus particles contain two copies of full-length unspliced HIV-1 RNA that form a dimer. Thus, during virus assembly HIV-1 can identify and selectively encapsidate HIV-1 unspliced RNA from an abundant pool of cellular RNAs and various spliced HIV-1 RNAs. Several "G" features facilitate the packaging of a dimeric RNA genome. The viral polyprotein Gag orchestrates virus assembly and mediates RNA genome packaging. During this process, Gag preferentially binds unpaired guanosines within the highly structured 5' untranslated region (UTR) of HIV-1 RNA. In addition, the HIV-1 unspliced RNA provides a scaffold that promotes Gag:Gag interactions and virus assembly, thereby ensuring its packaging. Intriguingly, recent studies have shown that the use of different guanosines at the junction of U3 and R as transcription start sites results in HIV-1 unspliced RNA species with 99.9% identical sequences but dramatically distinct 5' UTR conformations. Consequently, one species of unspliced RNA is preferentially packaged over other nearly identical RNAs. These studies reveal how conformations affect the functions of HIV-1 RNA elements and the complex regulation of HIV-1 replication. In this review, we summarize cis- and trans-acting elements critical for HIV-1 RNA packaging, locations of Gag:RNA interactions that mediate genome encapsidation, and the effects of transcription start sites on the structure and packaging of HIV-1 RNA.

HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures

Water molecules are integral to the structural stability of proteins and vital for facilitating molecular interactions. However, accurately predicting their precise position around protein structures remains a significant challenge, making it a vibrant research area. In this paper, we introduce HydraProt (deep Hydration of Proteins), a novel methodology for predicting precise positions of water molecule oxygen atoms around protein structures, leveraging two interconnected deep learning architectures: a 3D U-net and a Multi-Layer Perceptron (MLP). Our approach starts by introducing a coarse voxel-based representation of the protein, which allows for rapid sampling of candidate water positions via the 3D U-net. These water positions are then assessed by embedding the water-protein relationship in the Euclidean space by means of an MLP. Finally, a postprocessing step is applied to further refine the MLP predictions. HydraProt surpasses existing state-of-the-art approaches in terms of precision and recall and has been validated on large data sets of protein structures. Notably, our method offers rapid inference runtime and should constitute the method of choice for protein structure studies and drug discovery applications. Our pretrained models, data, and the source code required to reproduce these results are accessible at https://github.com/azamanos/HydraProt.

Prevalence, Trends and Correlates of HIV, Syphilis and HCV Infection Among Chinese Local and Cross-border Migrant Female Sex Workers in the Sino-Vietnam Border Area of Guangxi, 2016-2021

Female sex workers (FSWs) are considered a high-risk group for sexually transmitted infections (STIs). However, limited data exist on the prevalence and trends of HIV, syphilis and HCV among FSWs in the Sino-Vietnam border area. To determine the prevalence, trends and correlates of STIs among Chinese local FSWs (CL-FSWs) and cross-border migrant FSWs (CM-FSWs), we conducted consecutive cross-sectional surveys from 2016 to 2021, recruiting 7747 CL-FSWs and 932 CM-FSWs. The overall HIV, syphilis and HCV prevalence declined from 1.0%, 8.8% and 1.7% to 0.1%, 0.9% and 0.3%, respectively. There was no significant downward trend in the overall HIV and syphilis prevalence. However, HCV prevalence showed a decreasing trend among CL-FSWs. CM-FSWs had higher HIV prevalence (2.5% vs. 0.6%). Similarities and differences in STIs-related factors existed between CM-FSWs and CL-FSWs. For instance, receiving HIV-related services in the last year reduced the risk of HIV infection (for CM-FSWs: aOR = 0.234, 95% CI: 0.055-0.993; for CL-FSWs: aOR = 0.182, 95% CI: 0.058-0.567). Serving male clients at least 50 years old increased the risk of syphilis infection (for CM-FSWs: aOR = 4.277, 95% CI: 1.535-11.917; for CL-FSWs: aOR = 1.404, 95% CI: 1.087-1.815). Moreover, CM-FSWs with past-year STIs history had a higher risk of HIV (aOR = 34.976, 95% CI: 5.338-229.176) and HCV infection (aOR = 17.649, 95% CI: 1.846-168.846), both of which were associated with multiple factors in CL-FSWs. It is therefore necessary to develop effective, accessible, high-quality and targeted interventions for CM-FSWs and CL-FSWs.

Molecular Mechanisms of Neuroprotection after the Intermittent Exposures of Hypercapnic Hypoxia

The review introduces the stages of formation and experimental confirmation of the hypothesis regarding the mutual potentiation of neuroprotective effects of hypoxia and hypercapnia during their combined influence (hypercapnic hypoxia). The main focus is on the mechanisms and signaling pathways involved in the formation of ischemic tolerance in the brain during intermittent hypercapnic hypoxia. Importantly, the combined effect of hypoxia and hypercapnia exerts a more pronounced neuroprotective effect compared to their separate application. Some signaling systems are associated with the predominance of the hypoxic stimulus (HIF-1α, A1 receptors), while others (NF-κB, antioxidant activity, inhibition of apoptosis, maintenance of selective blood-brain barrier permeability) are mainly modulated by hypercapnia. Most of the molecular and cellular mechanisms involved in the formation of brain tolerance to ischemia are due to the contribution of both excess carbon dioxide and oxygen deficiency (ATP-dependent potassium channels, chaperones, endoplasmic reticulum stress, mitochondrial metabolism reprogramming). Overall, experimental studies indicate the dominance of hypercapnia in the neuroprotective effect of its combined action with hypoxia. Recent clinical studies have demonstrated the effectiveness of hypercapnic-hypoxic training in the treatment of childhood cerebral palsy and diabetic polyneuropathy in children. Combining hypercapnic hypoxia with pharmacological modulators of neuro/cardio/cytoprotection signaling pathways is likely to be promising for translating experimental research into clinical medicine.

Immunological relationship between Helicobacter pylori and anti-tumor necrosis factor α agents in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a group of diseases characterized by refractory and chronic inflammation of the bowel, which can be treated with biologics in clinical practice. Anti-tumor necrosis factor α (TNF-α) agents, which are among the most widely used biologics, alleviate the inflammatory activity in a variety of ways. Helicobacter pylori is a Gram-negative bacterium that colonizes the gastric mucosa, which could cause chronic inflammation and even induce gastric cancer. However, it has been suggested that H. pylori has a potential protective role in IBD patients. Yet there has been limited research on the mechanisms of the effect of H. pylori infection in IBD patients, and whether there is an interaction between H. pylori and anti-TNF-α agents. This review aims to summarize the possible mechanisms of H. pylori and anti-TNF-α agents in the development and treatment of IBD, and to explore the possible interaction between H. pylori infection and anti-TNF-α agents.

Impact of Helicobacter pylori and metabolic syndrome-related mast cell activation on cardiovascular diseases

Helicobacter pylori, a widely renowned bacterium, has recently gained attention owing to its potential impact on extragastric health. The emergence of research linking H. pylori infection with metabolic syndrome (MetS)-related cardiovascular diseases (CVDs) has raised intriguing questions about the pathogenic linkage and its translational implications for clinicians. MetS encompasses a collection of metabolic abnormalities that considerably elevate the risk of CVDs and cerebrovascular diseases. Emerging evidence supports a potential pathogenetic role of H. pylori for MetS-related disorders through mechanisms implicating chronic smoldering inflammation, insulin resistance (IR), and modulation of immune responses. One intriguing aspect of this possible connection is the role of mast cells (MCs), a subset of immune cells representing innate immune system effector cells. They play a fundamental role in innate immune responses and the modulation of adaptive immunity. Activated MCs are commonly found in patients with MetS-related CVD. Recent studies have also suggested that H. pylori infection may activate MCs, triggering the release of pro-inflammatory mediators that contribute to IR and atherosclerosis. Understanding these intricate interactions at the cellular level provides new insights into the development of therapeutic strategies targeting both H. pylori infection and MetS-related MCs activation. This review investigates the current state of research regarding the potential impact of H. pylori infection and MetS-related MCs activation on the pathophysiology of CVD, thereby opening up new avenues for related research and paving the way for innovative approaches to prevention and treatment in clinical practice

Increased oxidative stress in shoe industry workers with low-level exposure to a mixture of volatile organic compounds

This study aimed to assess the redox status and trace metal levels in 49 shoe industry workers (11 men and 38 women) occupationally exposed to a mixture of volatile organic compounds (VOCs), which includes aliphatic hydrocarbons, aromatic hydrocarbons, ketones, esters, ethers, and carboxylic acids. All measured VOCs were below the permitted occupational exposure limits. The control group included 50 unexposed participants (25 men and 25 women). The following plasma parameters were analysed: superoxide anion (O2 •-), advanced oxidation protein products (AOPP), total oxidative status (TOS), prooxidant-antioxidant balance (PAB), oxidative stress index (OSI), superoxide dismutase (SOD) and paraoxonase-1 (PON1) enzyme activity, total SH group content (SHG), and total antioxidant status (TAS). Trace metal levels (copper, zinc, iron, magnesium, and manganese) were analysed in whole blood. All oxidative stress and antioxidative defence parameters were higher in the exposed workers than controls, except for PON1 activity. Higher Fe, Mg, and Zn, and lower Cu were observed in the exposed vs control men, while the exposed women had higher Fe and lower Mg, Zn, and Cu than their controls. Our findings confirm that combined exposure to a mixture of VOCs, even at permitted levels, may result in additive or synergistic adverse health effects and related disorders. This raises concern about current risk assessments, which mainly rely on the effects of individual chemicals, and calls for risk assessment approaches that can explain combined exposure to multiple chemicals.

Molecular Insights of Nonalcoholic Fatty Liver Disease Pathogenesis

Nonalcoholic fatty liver disease (NAFLD) is now the most prevalent chronic liver disease. Many hepatic abnormalities are associated with NAFLD such as nonalcoholic steatohepatitis, progressive fibrosis, cirrhosis, and liver failure. Moreover, the pathogenesis of NAFLD has numerous etiologies and can be explained due to the existence of several of stimulus that act simultaneously on genetically susceptible patients. These stimuli include obesity, diabetes, and insulin resistance. In addition, identifying the role of gut microbiota on NAFLD progression has been illustrated. In this review, we clarified the several factors that lead to the development of NAFLD and identify those who are most at risk of developing liver end-stage disease. Highlighting the noninvasive diagnostic NAFLD markers could be helpful in the disease prevention and treatment approaches.

Association of Medicaid expansion with health insurance, unmet need for medical care and substance use disorder treatment among people who inject drugs in 13 US states

BACKGROUND AND AIMS

Impoverished people who inject drugs (PWID) are at the epicenter of US drug-related epidemics. Medicaid expansion is designed to reduce cost-related barriers to care by expanding Medicaid coverage to all US adults living at or below 138% of the federal poverty line. This study aimed to measure whether Medicaid expansion is (1) positively associated with the probability that participants are currently insured; (2) inversely related to the probability of reporting unmet need for medical care due to cost in the past year; and (3) positively associated with the probability that they report receiving substance use disorder (SUD) treatment in the past year, among PWID subsisting at ≤ 138% of the federal poverty line.

DESIGN

A two-way fixed-effects model was used to analyze serial cross-sectional observational data.

SETTING

Seventeen metro areas in 13 US states took part in the study.

PARTICIPANTS

Participants were PWID who took part in any of the three waves (2012, 2015, 2018) of data gathered in the Center for Disease Control and Prevention's National HIV Behavioral Surveillance (NHBS), were aged ≤ 64 years and had incomes ≤ 138% of the federal poverty line. For SUD treatment analyses, the sample was further limited to PWID who used drugs daily, a proxy for SUD.

MEASUREMENTS

State-level Medicaid expansion was measured using Kaiser Family Foundation data. Individual-level self-report measures were drawn from the NHBS surveys (e.g. health insurance coverage, unmet need for medical care because of its cost, SUD treatment program participation).

FINDINGS

The sample for the insurance and unmet need analyses consisted of 19 946 impoverished PWID across 13 US states and 3 years. Approximately two-thirds were unhoused in the past year; 41.6% reported annual household incomes < $5000. In multivariable models, expansion was associated with a 19.0 [95% confidence interval (CI) = 9.0, 30.0] percentage-point increase in the probability of insurance coverage, and a 9.0 (95% CI = -15.0, -0.2) percentage-point reduction in the probability of unmet need. Expansion was unrelated to SUD treatment among PWID who used daily (n = 17 584).

CONCLUSIONS

US Medicaid expansion may curb drug-related epidemics among impoverished people who inject drugs by increasing health insurance coverage and reducing unmet need for care. Persisting non-financial barriers may undermine expansion's impact upon substance use disorder treatment in this sample.

Sex-Biased Expression and Response of microRNAs in Neurological Diseases and Neurotrauma

Neurological diseases and neurotrauma manifest significant sex differences in prevalence, progression, outcome, and therapeutic responses. Genetic predisposition, sex hormones, inflammation, and environmental exposures are among many physiological and pathological factors that impact the sex disparity in neurological diseases. MicroRNAs (miRNAs) are a powerful class of gene expression regulator that are extensively involved in mediating biological pathways. Emerging evidence demonstrates that miRNAs play a crucial role in the sex dimorphism observed in various human diseases, including neurological diseases. Understanding the sex differences in miRNA expression and response is believed to have important implications for assessing the risk of neurological disease, defining therapeutic intervention strategies, and advancing both basic research and clinical investigations. However, there is limited research exploring the extent to which miRNAs contribute to the sex disparities observed in various neurological diseases. Here, we review the current state of knowledge related to the sexual dimorphism in miRNAs in neurological diseases and neurotrauma research. We also discuss how sex chromosomes may contribute to the miRNA sexual dimorphism phenomenon. We attempt to emphasize the significance of sexual dimorphism in miRNA biology in human diseases and to advocate a gender/sex-balanced science.

Molecular mechanism of microRNA-mediated hypoglycemic effect of whole grain highland barley

As a non-coding RNA, microRNA (miRNA) has been proven to play an important role in the development and progression of type 2 diabetes mellitus (T2DM). Highland barley is a whole grain from the Tibetan areas of China. Our previous studies have demonstrated its hypoglycemic effect. To further explore the underlining molecular mechanism, we investigated the effect of highland barley intervention on liver miRNA expression profiles in diabetic mice. Our results showed that ten differentially expressed miRNA among different groups were identified and their target genes were predicted. Remarkably, many glycometabolism-associated genes, including Foxo3, Nras, Rptor, Igf1r, Tsc2 and Braf, were negatively regulated by miR-122-5p, miR-503-5p, miR-455-5p and miR-210-3p, respectively. Pathway enrichment analysis revealed these target genes were mainly involved in AMPK, MAPK and FOXO signaling pathways. Thereby, these miRNA and mRNA were validated using qRT-PCR, and the results were consistent with the small RNA-seq and expectations. Highland barley could regulate the MAPK, AMPK, and FOXO signaling pathways by regulating critical miRNA-mRNA pairs, e.x. miR-210-3p-Tsc2/Braf, miR-122-5p-Foxo3, and miR-455-5p-Igf1r, thereby improving blood glucose metabolism in diabetic mice. The present study preliminarily explored the hypoglycaemic effects of highland barley based on transcriptomics, and more detailed and in-depth studies on this topic are needed in the future.

Revaccination for Hepatitis B in Previous Nonresponders Following Hepatitis C Eradication

BACKGROUND

Patients with chronic hepatitis C virus (HCV) do not respond to hepatitis B virus (HBV) vaccination as efficiently as the general population. We assessed if revaccination after HCV treatment resulted in improved response.

METHODS

Previous HBV vaccine nonresponders were prospectively recruited for revaccination after HCV eradication. Hepatitis B surface antibody (HBsAb) testing was performed 1 month after series completion.

RESULTS

Follow-up HBsAb testing was performed in 31 of 34 enrolled patients with 21 (67.7%) reactive results. There were no significant differences in HBsAb reactivity based on age, sex, race, or advanced fibrosis presence.

CONCLUSIONS

HBV vaccine nonresponders should be considered for revaccination following HCV cure.

Association between urbanization and metabolic syndrome in low- and middle-income countries: A systematic review and meta-analysis

AIMS

The prevalence of metabolic syndrome (MetS) is on the rise in an increasingly urbanized world. The study aimed to review the association between urbanization and MetS in low- and middle-income countries (LMICs).

DATA SYNTHESIS

A comprehensive search of five databases (MEDLINE, Web of Science, Scopus, EMBASE, and CENTRAL) was performed in January 2022 and updated in October 2022. Peer-reviewed studies that met the eligibility selection criteria were included. Search terms were used for the main concepts which are MetS, dietary patterns, and urbanization in LMICs. Study selection was done in two stages and in duplicate. Random effects models were used to calculate the overall pooled prevalence and main study-level characteristics. Out of 9,773 identified studies, nineteen were included in the systematic review and meta-analysis. The studies were done on 313,644 participants (149,616 urban and 164,028 rural). The pooled risk ratio (RR, 95% confidence interval) of MetS between urban and rural dwellers was RR = 1.24; 95%CI [1.15, 1.34] (I2 = 96.0%, P < 0.0001). A relatively higher prevalence of MetS among urban than rural residents has been observed, especially with the International Diabetes Federation criteria (RR = 1.54; 95%CI [1.21, 1.96]; I2 = 65.0%), and in the population in India (RR = 2.19; 95%CI = 1.24, 3.88, I2 = 85%). Overall, the role of dietary patterns in the development of MetS was inconsistent, and few studies showed a lower risk of MetS with adherence to recommended healthy dietary patterns.

CONCLUSIONS

There was an association between urbanization and the high prevalence of MetS. Interventions and policies to reduce the risk of MetS are needed.

Examining County-Level Associations between Federally Qualified Health Centers and Sexually Transmitted Infections: A Political Ecology of Health Framework

Federally Qualified Health Centers (FQHCs) are the largest providers of healthcare for sexually transmitted infections (STIs) in medically underserved communities in the United States (US). Through the Affordable Care Act (ACA), FQHCs have grown in number, but the impact of this growth on STIs is poorly understood. This ecological study seeks to quantify the association between FQHCs and STI prevalence in all US counties. Variables were described utilizing medians and interquartile ranges, and distributions were compared using Kruskal-Wallis tests. Median rates of chlamydia in counties with high, low, and no FQHCs were 370.3, 422.6, and 242.1 cases per 100,000 population, respectively. Gonorrhea rates were 101.9, 119.7, and 49.9 cases per 100,000 population, respectively. Multivariable linear regression models, adjusted for structural and place-based characteristics (i.e., Medicaid expansion, social vulnerability, metropolitan status, and region), were used to examine county-level associations between FQHCs and STIs. Compared to counties with no FQHCs, counties with a high number of FQHCs had chlamydia rates that were an average of 68.6 per 100,000 population higher (β = 68.6, 95% CI: 45.0, 92.3) and gonorrhea rates that were an average of 25.2 per 100,000 population higher (β = 25.2, 95% CI: 13.2, 37.2). When controlled for salient factors associated with STI risks, greater FQHC availability was associated with greater diagnosis and treatment of STIs. These findings provide empirical support for the utility of a political ecology of health framework and the critical role of FQHCs in confronting the STI epidemic in the US.

Associations of five blood heavy metals with hepatitis B virus infection and immunity in adults: a cross-sectional study

BACKGROUND

Heavy metal pollution has emerged as a significant concern for human health, prompting increased awareness of its potential adverse effects. While previous research has established a connection between heavy metals and liver function biomarkers, the specific relationship between heavy metals and HBV infection remains unexplored. This cross-sectional study aims to investigate the potential correlations between five blood heavy metals - lead, cadmium, mercury, manganese, and selenium - and the presence of HBsAg, HBsAb, and HBcAb in adults.

METHODS

The study utilized data from NHANES 2007-2018. Participants were classified into four groups based on their infectious status, and the association between heavy metals and HBV infection was analyzed using multiple logistic regression and stratification analysis.

RESULTS

A total of 8431 participants were included, with 5 436 classified as Susceptible, 1 765 as Vaccinated, 865 as Natural Infection, and 103 as Acute/Chronic HBV Infection. The Vaccinated group exhibited a lower mean age (34.52 ± 14.16 years) compared to the other groups. Statistically significant differences in heavy metal concentrations (except selenium) were observed among the groups (P < 0.001). After adjusting for covariates, lead was significantly associated with HBV infection (Q2: OR 2.37, 95%CI 1.04-5.39; Q3: OR 2.34, 95%CI 1.01-5.40), and positive trends were observed for high blood concentrations of mercury (Q4: OR 3.03, 95%CI 1.31-7.04) and manganese (Q4: OR 2.52, 95%CI 1.20-5.28). Furtherly, the presence of lead reduced the protection of HBsAb (Q2: OR 0.84, 95%CI 0.73-0.97; Q3: OR 0.77, 95%CI 0.66-0.90; Q4: OR 0.83, 95%CI 0.70-0.98). Subgroup analysis indicated that cadmium was associated with an increased risk of HBV infection in Asians (OR 1.36, 95%CI 1.03-1.78) and individuals with a BMI range of 25 to 30 (OR 1.60, 95%CI 1.17-2.18).

CONCLUSIONS

The study's findings suggest a correlation between elevated blood Pb concentrations and reduced immunization rates against hepatitis B. Individuals with a positive HBsAg exhibit lower blood Se concentrations and higher blood Hg and Mn concentrations.

Interventions to mitigate the risks of COVID-19 for people experiencing homelessness and their effectiveness: a systematic review

Objectives

People experiencing homelessness also experience poorer clinical outcomes of COVID-19. Various interventions were implemented for people experiencing homelessness in 2020-2022 in different countries in response to varied national guidance to limit the impact of COVID-19. It is important to understand what was done and the effectiveness of such interventions. This systematic review aims to describe interventions to mitigate the risks of COVID-19 in people experiencing homelessness and their effectiveness.

Methods

A protocol was developed and registered in PROSPERO. Nine databases were searched for studies on interventions to mitigate the impact of COVID-19 on people experiencing homelessness. Included studies were summarised with narrative synthesis.

Results

From 8,233 references retrieved from the database searches and handsearching, 15 were included. There was a variety of interventions, including early identification of potential COVID-19 infections, provision of isolation space, healthcare support, and urgent provision of housing regardless of COVID-19 infection.

Conclusion

The strategies identified were generally found to be effective, feasible, and transferable. This review must be interpreted with caution due to the low volume of eligible studies and the low quality of the evidence available.

Assessing the impact of the COVID-19 pandemic on latex glove usage and latex allergy complaints among nurses: A descriptive study

BACKGROUND

The coronavirus 2019 (COVID-19) pandemic has led to a significant increase in the use of latex gloves among nurses. However, concerns about the rise in latex allergies and related complaints due to this increase remain uncertain.

OBJECTİVE

This study aims to assess the rates of latex glove usage and allergy-related complaints among nurses working in hospitals during the COVID-19 pandemic.

METHODS

Between May 15 and June 15, 2021, ethical approvals were obtained for a cross-sectional study involving 448 volunteer nurses. Descriptive statistics were used to represent categorical values as counts (n) and percentages (%), while continuous values were represented as mean±standard deviation. The normal distribution of the data was assessed using the Kolmogorov-Smirnov and Shapiro-Wilk tests. Comparative analyses were conducted using paired sample t-test, Pearson's chi-squared (x2) test, McNemar's chi-squared (x2) test, and Spearman correlation analysis.

RESULTS

Before the pandemic, the average number of invasive procedures was 45.13±26.48, whereas during the pandemic, this rate increased to 50.23±29.14. The average glove usage duration went from 7.69±3.13 hours to 14.73±3.68 hours during the pandemic. Among nurses, the rate of allergic symptoms, which was previously at 31.5%, rose to 33.3% during the pandemic.

CONCLUSİON

This study revealed a significant increase in daily invasive procedures and the use of latex gloves among nurses during the pandemic period. Simultaneously, the frequency of allergic symptoms also rose. These findings underscore the importance of awareness and preventive measures, particularly regarding latex allergies, in the healthcare field.

When Argonaute takes out the ribonuclease sword

Argonaute (AGO) proteins in all three domains of life form ribonucleoprotein or deoxyribonucleoprotein complexes by loading a guide RNA or DNA, respectively. Since all AGOs retain a PIWI domain that takes an RNase H fold, the ancestor was likely an endoribonuclease (i.e., a slicer). In animals, most miRNA-mediated gene silencing occurs slicer independently. However, the slicer activity of AGO is indispensable in specific events, such as development and differentiation, which are critical for vertebrates and thus cannot be replaced by the slicer-independent regulation. This review highlights the distinctions in catalytic activation mechanisms among slicing-competent AGOs, shedding light on the roles of two metal ions in target recognition and cleavage. The precision of the target specificity by the RNA-induced silencing complexes is reevaluated and redefined. The possible coevolutionary relationship between slicer-independent gene regulation and AGO-binding protein, GW182, is also explored. These discussions reveal that numerous captivating questions remain unanswered regarding the timing and manner in which AGOs employ their slicing activity.

Neurological Complications Caused by Human Immunodeficiency Virus (HIV) and Associated Opportunistic Co-infections: A Review on their Diagnosis and Therapeutic Insights

Neurocognitive disorders associated with human immunodeficiency virus (HIV) infected individuals increase the risk of mortality and morbidity that remain a prevalent clinical complication even in the antiretroviral therapy era. It is estimated that a considerable number of people in the HIV community are developing neurological complications at their early stages of infection. The daily lives of people with chronic HIV infections are greatly affected by cognitive declines such as loss of attention, learning, and executive functions, and other adverse conditions like neuronal injury and dementia. It has been found that the entry of HIV into the brain and subsequently crossing the blood-brain barrier (BBB) causes brain cell damage, which is the prerequisite for the development of neurocognitive disorders. Besides the HIV replication in the central nervous system and the adverse effects of antiretroviral therapy on the BBB, a range of opportunistic infections, including viral, bacterial, and parasitic agents, augment the neurological complications in people living with HIV (PLHIV). Given the immuno-compromised state of PLHIV, these co-infections can present a wide range of clinical syndromes with atypical manifestations that pose challenges in diagnosis and clinical management, representing a substantial burden for the public health system. Therefore, the present review narrates the neurological complications triggered by HIV and their diagnosis and treatment options. Moreover, coinfections that are known to cause neurological disorders in HIV infected individuals are highlighted.

Structural and computational studies of HIV-1 RNA

Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.

The Effect of Coronavirus Disease 2019 on the Quality of Associated Care in Patients with Gastric Cancer

Coronavirus is a new virus that has affected human life on a large scale; it has infected millions of people and killed hundreds of thousands of people. In contrast, among cancers, stomach neoplasia is the most common cancer of the upper gastrointestinal (UGI) tract. COVID-19 disease has disrupted the optimal management of patients with cancer. Metastasis, deterioration of the patient's nutritional status, UGI bleeding, and increased surgical complications are all consequences of delayed treatment of patients with gastric cancer. However, there is still insufficient evidence on the immunogenicity of the vaccine and the protection provided by coronavirus vaccines in patients with cancer, especially those with immunodeficiency or those who are treated for certain types of cancers. Also, as part of the prevention and control of COVID-19 disease, nutritional support for patients with gastrointestinal cancer is particularly important, and the psychological and physiological limitations caused by the disease duration are hurting the well-being of patients. Therefore, the assessment of the impact of the coronavirus on cancer should be treated as an important issue, and healthcare professionals should be prepared to deal with the long-term effects of the coronavirus disease.

Injection Behaviors and Use of Syringe Service Programs over Time among People Who Inject Drugs in Baltimore, Maryland

Introduction: People who inject drugs (PWID) are at increased risk for infectious disease transmission, including hepatitis C and HIV. Understanding trends in injection risk behaviors and syringe service program (SSP) use over time can help improve infectious disease prevention and other harm reduction services. Methods: Using National HIV Behavioral Surveillance System data from Baltimore, Maryland, we examined changes in receptive sharing of (1) syringes, (2) injection equipment, (3) syringes to divide drugs; and (4) receipt of syringes from SSPs among PWID from 2009 to 2018 (n = 518 in 2009, n = 638 in 2012, n = 586 in 2015, and n = 575 in 2018) using unadjusted and adjusted logistic models calculated across time for the total sample. Results: The conditional probability of receptive sharing of syringes and receipt of syringes from SSPs remained relatively stable, while receptive sharing of injection equipment and receptive sharing of syringes to divide drugs dropped substantially after 2009. White race and daily injection frequency were positively associated with sharing syringes and injection equipment and negatively associated with SSP use over time. In 2015, there was a notable shift such that women were twice as likely as men to receive syringes from SSPs and less likely than men to report the use of shared syringes or equipment. Conclusion: Findings indicate overall steady or decreasing trends in injection risk and steady trends in SSP usage over time, with some notable improvements among women and indications of shifting drug market patterns. Injection-related risk behaviors remain high among White PWID and may require targeted outreach and interventions.

Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging

The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5' end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure-function relationship approaches. Our mutational analysis revealed that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2' hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80-92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA-Pr50Gag interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.

The role of m6A epigenetic modifications in tumor coding and non-coding RNA processing

BACKGROUND

Epigenetic modifications of RNA significantly contribute to the regulatory processes in tumors and have, thus, received considerable attention. The m6A modification, known as N6-methyladenosine, is the predominant epigenetic alteration found in both eukaryotic mRNAs and ncRNAs.

MAIN BODY

m6A methylation modifications are dynamically reversible and are catalyzed, removed, and recognized by the complex of m6A methyltransferase (MTases), m6A demethylase, and m6A methyl recognition proteins (MRPs). Published evidence suggests that dysregulated m6A modification results in abnormal biological behavior of mature mRNA, leading to a variety of abnormal physiological processes, with profound implications for tumor development in particular.

CONCLUSION

Abnormal RNA processing due to dysregulation of m6A modification plays an important role in tumor pathogenesis and potential mechanisms of action. In this review, we comprehensively explored the mechanisms by which m6A modification regulates mRNA and ncRNA processing, focusing on their roles in tumors, and aiming to understand the important regulatory function of m6A modification, a key RNA epigenetic modification, in tumor cells, with a view to providing theoretical support for tumor diagnosis and treatment. Video Abstract.

microRNAs in action: biogenesis, function and regulation

Ever since microRNAs (miRNAs) were first recognized as an extensive gene family >20 years ago, a broad community of researchers was drawn to investigate the universe of small regulatory RNAs. Although core features of miRNA biogenesis and function were revealed early on, recent years continue to uncover fundamental information on the structural and molecular dynamics of core miRNA machinery, how miRNA substrates and targets are selected from the transcriptome, new avenues for multilevel regulation of miRNA biogenesis and mechanisms for miRNA turnover. Many of these latest insights were enabled by recent technological advances, including massively parallel assays, cryogenic electron microscopy, single-molecule imaging and CRISPR-Cas9 screening. Here, we summarize the current understanding of miRNA biogenesis, function and regulation, and outline challenges to address in the future.

Seroconversion of hepatitis B vaccine among patients from outpatient clinic in Georgia

Introduction

Hepatitis B virus (HBV) is a serious global health challenge with vaccination being the most effective preventive measure. However, several risk-factors may impact HBV vaccine immunogenicity. We aimed to evaluate the immunogenicity of the HBV vaccine.

Methods

Participants' socio-demographic data were obtained from medical records. Anti-HBs testing was performed. Descriptive and bivariate analyses were performed.

Results

Among 431 participants, 62.2 % (n = 268) were males. In all, 43.2 % (n = 186) had normal weight, 24.8 % (n = 107) were overweight, and 17.6 % (n = 76) had obesity. Seroconversion after 3-dose HBV vaccination was 74.7 %. Participants with normal weight had higher seroprevalence (n = 156/186, 83.9 %), compared with those with overweight (n = 72/107, 67.3 %) or obesity (n = 48/76, 63.2 %) (Normal weight vs overweight: aOR = 2.44, 95 % CI: 1.38-4.32 and normal weight vs obesity: aOR = 2.97, 95 % CI:1.61-5.47).

Conclusion

BMI is an independent factor impairing the vaccine response. These findings urge for more tailored vaccination strategies with focus on higher risk populations.

The predictive accuracy of coronary heart disease risk prediction models in rural Northwestern China

Cardiovascular risk models developed may have limitations when applied to rural Chinese. This study validated and compared the Framingham Risk Score (FRS) and Prediction for Atherosclerotic Cardiovascular Disease Risk in China (PAR) models in predicting 10-year risk of coronary heart disease (CHD) in a rural cohort in Ningxia, China from 2008 to 2019. The FRS and PAR models were validated by estimating predicted events, C index, calibration χ2 and plots. 1381 adults without CHD at baseline were followed up for 9.75 years on average. 168 CHD cases were observed. The FRS and PAR underestimated CHD events by 22 % and 46 % for the total population, while overestimated for males by 152 % and 78 %, respectively. The C index was slightly higher for PAR than FRS. Both models showed weak calibration with chi-square values above 20 (p < 0.001). Bland-Altman plots indicated FRS predicted higher CHD risk than PAR, lacking consistency. Overall, FRS and PAR demonstrated limited performance in predicting 10-year CHD risk in this rural population. PAR had slightly better discrimination than FRS, but require further improvement in calibration and individual risk estimation to suit the rural population in Northwest China.

Determining the defining lengths between mature microRNAs/small interfering RNAs and tinyRNAs

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are loaded into Argonaute (AGO) proteins, forming RNA-induced silencing complexes (RISCs). The assembly process establishes the seed, central, 3' supplementary, and tail regions across the loaded guide, enabling the RISC to recognize target RNAs for silencing. This guide segmentation is caused by anchoring the 3' end at the AGO PAZ domain, but the minimum guide length required for the conformation remains to be studied because the current miRNA size defined by Dicer processing is ambiguous. Using a 3' → 5' exonuclease ISG20, we determined the lengths of AGO-associated miR-20a and let-7a with 3' ends that no longer reach the PAZ domain. Unexpectedly, miR-20a and let-7a needed different lengths, 19 and 20 nt, respectively, to maintain their RISC conformation. This difference can be explained by the low affinity of the PAZ domain for the adenosine at g19 of let-7a, suggesting that the tail-region sequence slightly alters the minimum guide length. We also present that 17-nt guides are sufficiently short enough to function as tinyRNAs (tyRNAs) whose 3' ends are not anchored at the PAZ domain. Since tyRNAs do not have the prerequisite anchoring for the standardized guide segmentation, they would recognize targets differently from miRNAs and siRNAs.

Correlation between mitral valve area and left atrial function in rheumatic mitral valve stenosis patients

BACKGROUND

Rheumatic heart disease (RHD) continues to be one of the leading causes of cardiovascular morbidity and mortality. The mitral valve frequently develops mitral stenosis (MS), and it is the most prevalent valve lesion in patients with chronic RHD. Left atrial (LA) functional impairment is associated with rheumatic MS.

AIM

The aim of this study was to evaluate the association between LA function and mitral valve area (MVA) in rheumatic MS patients, and to assess the echocardiographic parameters in sinus rhythm and atrial fibrillation (AF) patients.

METHODS

This was a cross-sectional, descriptive study that involved patients with rheumatic MS. Patients underwent a standard 12-lead electrocardiogram and echocardiographic examination. MVA was assessed and correlated with LA function. Comparison was made between sinus rhythm and AF patients.

RESULTS

Eighty-one patients with rheumatic MS were included in this study, with 71.6% of them having associated MR. MVA showed a statistically highly significant positive correlation with LA and right ventricular (RV) function, and a statistically significant/highly significant negative correlation with their dimensions. A higher percentage of patients with severe MS was in AF (58.1%).

CONCLUSIONS

There was a positive correlation between LA function and MVA in rheumatic MS patients. AF was related to the severity of MS.

Risk transboundary transmission areas and driving factors of brucellosis along the borders between China and Mongolia

OBJECTIVE

Brucellosis is a common and neglected zoonotic infectious disease worldwide caused by Brucella. However, transboundary transmissions among countries, particularly those with high incidences, are seldom investigated. In the present study, by taking China and Mongolia as examples, we aim to identify transboundary transmission risk and driving factors of brucellosis along borders.

METHODS

167 brucellosis outbreak locations along the border between China and Mongolia were collected. Wildlife distribution and cross-border activities were mapped. Maximum entropy approach modeling was conducted to predict the potential risk of prevalence of brucellosis with meteorological factors, geographical environment, economic development, living habits et al. The accuracy of the models was assessed by the area under the receiver operating characteristic (ROC) curve (AUC), Kappa test, and correctly classified instances (CCI).

RESULTS

The spatial model performed excellent predictive performance with the predictor variables of soils, pastures, goat density, mean precipitation of the wettest month, temperature seasonality, and population density, which with the contribution and permutation important in 27.2 %, 31.9; 23.3 %, 6.8; 18.0 %, 17.2; 11.2 %, 18.1; 10. 3 %, 15.2; 10.0 %, 10.8. The calculated AUC, SD, Kappa, and CCI are 0.870, 0.001, 0.882, and 0.883, respectively. The distribution map of brucellosis showed high-risk areas along the borders.

CONCLUSIONS

Our study identified high-risk areas and the driving effect of brucellosis along the borders between China and Mongolia. Moreover, there is the possibility of cross-border wildlife activities in high-risk areas, which increases the risk of cross-border brucellosis transmission. The funding provides clues for cooperative prevention and control of brucellosis by reducing transboundary transmission.

Risk Factors for Recent HIV Infections among Adults in 14 Countries in Africa Identified by Population-Based HIV Impact Assessment Surveys, 2015-2019

Identifying persons who have newly acquired HIV infections is critical for characterizing the HIV epidemic direction. We analyzed pooled data from nationally representative Population-Based HIV Impact Assessment surveys conducted across 14 countries in Africa for recent infection risk factors. We included adults 15-49 years of age who had sex during the previous year and used a recent infection testing algorithm to distinguish recent from long-term infections. We collected risk factor information via participant interviews and assessed correlates of recent infection using multinomial logistic regression, incorporating each survey's complex sampling design. Compared with HIV-negative persons, persons with higher odds of recent HIV infection were women, were divorced/separated/widowed, had multiple recent sex partners, had a recent HIV-positive sex partner or one with unknown status, and lived in communities with higher HIV viremia prevalence. Prevention programs focusing on persons at higher risk for HIV and their sexual partners will contribute to reducing HIV incidence.

Determining the defining lengths between mature microRNAs/small interfering RNAs and tinyRNAs

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are loaded into Argonaute (AGO) proteins, forming RNA-induced silencing complexes (RISCs). The assembly process establishes the seed, central, 3' supplementary, and tail regions across the loaded guide, enabling the RISC to recognize and cleave target RNAs. This guide segmentation is caused by anchoring the 3' end at the AGO PAZ domain, but the minimum guide length required for the conformation remains to be studied because there was no method by which to do so. Using a 3'→5' exonuclease ISG20, we determined the lengths of AGO-associated miR-20a and let-7a with 3' ends that no longer reach the PAZ domain. Unexpectedly, miR-20a and let-7a needed different lengths, 19 and 20 nt, respectively, to maintain their RISC conformation. This difference can be explained by the low affinity of the PAZ domain for the adenosine at g19 of let-7a, suggesting that the tail-region sequence slightly alters the minimum guide length. We also present that 17-nt guides are sufficiently short enough to function as tinyRNAs (tyRNAs) whose 3' ends are not anchored at the PAZ domain. Since tyRNAs do not have the prerequisite anchoring for the standardized guide segmentation, they would recognize targets differently from miRNAs and siRNAs.

Post-transcriptional gene silencing in a dynamic RNP world

MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.

The effect of drop-in centers on access to HIV testing, case finding, and condom use among female sex workers in Addis Ababa, Ethiopia

Background

Varied HIV prevention interventions involving multiple strategies has been instrumental in the effort to contain and lessen the prevalence of HIV around the globe. However, female sex workers (FSWs) often face stigma and discriminatory challenges, resulting in lower access to the HIV prevention initiatives. This study has aimed to assess the effect of one of the HIV service delivery models, the Drop-in Centers (DICs), which is designed to overcome the service uptake barriers of FSWs.

Method

A quasi-experimental study design was employed. A respondent-driven sampling technique was used to recruit 1,366 FSWs from January to June 2020. A propensity score matching technique was used to balance the potential confounders between FSWs who had access to DICs and those who had never accessed DICs. Comparisons of the effect of DIC on the outcome of interest was made using a logit regression model at a 5% level of significance.

Results

A total of 1,366 FSWs took part in the study. The analysis estimated the average treatment effects of access to DICs on four key outcomes: ever-testing to know HIV status, finding HIV-positive FSWs, awareness of HIV-positive status, and consistent condom use. A significant effect of DIC was seen at a 95% confidence interval on each outcome. Access to DIC produced a 7.58% increase in the probability of testing to know HIV status (P < 0.001), a 7.02% increment in finding HIV-positive FSWs (P = 0.003), an increase of 6.93% in awareness of HIV status among HIV positive FSWs (P = 0.001), and a 4.39% rise in consistent condom use (P = 0.01).

Conclusions

Ensuring access of FSWs to DICs has led to an upsurge in HIV testing among FSWs, raising HIV status awareness among those who are HIV positive, and encouraged consistent condom use. To provide effective HIV prevention services, particularly to those FSWs living with HIV, it is essential to strengthen the services provided in DICs and expand the centers. This will ensure that the entire network of FSWs is reached with appropriate HIV prevention services.

Structural diversity of the region encompassing DIS, SD and Psi hairpins in HIV and SIV genomes

We investigated in silico the secondary structure of the region encompassing DIS, SD and Psi hairpins in HIV-1 genomes of rare groups N, O and P, HIV-2 genomes and SIV genomes from chimpanzees, gorillas and monkeys. We found that the structure of this region in SIVcpzptt genomes of the 1st and the 2nd clusters is similar to that in HIV-1 genomes of groups M and N, respectively. Further, the structure of the region encompassing DIS, SD and Psi hairpins is similar in HIV-1 genomes of groups O and P and SIVgor genomes. Here we report that the DIS hairpin and truncated Psi hairpin are conserved in all HIV-1 and SIVcpz/gor genomes studied, while only the sequence of the splice donor site, but not the architecture of the SD hairpin involving this signal is conserved in HIV-1N/O/P and SIVcpz/gor genomes. A study on the 5' leader structure in genomes of 28 different SIV lineages infecting monkeys showed that the domain closed by U5-AUG duplex can form in all these genomes. This domain mainly consists of 2 subdomains, one of which includes the signal PBS (PBS subdomain) and another contains a putative DIS hairpin (DIS subdomain). DIS subdomains contain 1-8 hairpins. None of them is similar to those in HIV-1 or SIVcpz/gor genomes. The palindrome GUGCAC was found only in SIVdrl/mnd-2, the GACGC-GCGUC duplex (Sakuragi et al., 2012) - only in SIVrcm/drl/mnd-2 and a putative 5' G-quadruplex - in SIVdeb/drl/rcm/stm genomes. In genomes of eight SIV lineages, DIS hairpin has palindrome UGCGCA. Studies on the 5' leader in 64 HIV-2 genomes of different subtypes showed, in particular, that this region has sequences of a putative 5' G-quadruplex and a putative duplex similar to the GACGC-GCGUC duplex. The secondary structures of the region encompassing DIS, SD and Psi hairpins in HIV-2 genomes of subtype B and recombinant 01_AB are similar and differ from that in genomes of subtype A.