Construction of a miRNA-mRNA Network Related to Exosomes in Colon Cancer

Background

The competing endogenous RNA (CeRNA) network plays important roles in the occurrence and development of colon cancer. This research is aimed at constructing a miRNA-mRNA network associated with exosomes in colon cancer.

Methods

We explored the GEO database and then analyzed the RNAs of 722 samples to obtain differentially expressed miRNAs (DEMs) and mRNAs (DEGs) alongside the progress of colon cancer. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEM target genes and DEGs were performed. In addition, a miRNA-mRNA network related to exosomes in colon cancer was constructed based on DEMs and DEGs. Finally, the expression of miRNA and mRNA in the network was verified by GEPIA2 on the base of TCGA database.

Results

Through our analysis, 19 DEMs (17 up and 2 down) and 1672 DEGs (954 up and 718 down) were screened. The GO and KEGG results show that these DEGs were mainly enriched in ribonucleoprotein complex biogenesis, noncoding RNA metabolic process, cell-substrate junction, cadherin binding, transcription coregulator activity, and regulation of the human T-cell leukemia virus 1 infection-related pathway. Besides, a miRNA-mRNA network, including 4 miRNAs (hsa-miR-623, hsa-miR-320c, hsa-miR-486-5p, and hsa-miR-1290) and 7 mRNAs (GNAI1, CADM1, PGRMC2, etc.), was constructed. Three of these seven mRNAs were downregulated in colon cancer. Ultimately, the GNAI1, CADM1, and PGRMC2 expression levels were verified by TCGA database.

Conclusions

This study reveals the network relationship between colon cancer exosome-derived miRNA and targeted mRNA. It deepens our understanding of new molecular mechanisms and pathways that may play a role in the occurrence and metastasis of colon cancer.

Anatomy of four human Argonaute proteins

MicroRNAs (miRNAs) bind to complementary target RNAs and regulate their gene expression post-transcriptionally. These non-coding regulatory RNAs become functional after loading into Argonaute (AGO) proteins to form the effector complexes. Humans have four AGO proteins, AGO1, AGO2, AGO3 and AGO4, which share a high sequence identity. Since most miRNAs are found across the four AGOs, it has been thought that they work redundantly, and AGO2 has been heavily studied as the exemplified human paralog. Nevertheless, an increasing number of studies have found that the other paralogs play unique roles in various biological processes and diseases. In the last decade, the structural study of the four AGOs has provided the field with solid structural bases. This review exploits the completed structural catalog to describe common features and differences in target specificity across the four AGOs.

Human Retrovirus Genomic RNA Packaging

Two non-covalently linked copies of the retrovirus genome are specifically recruited to the site of virus particle assembly and packaged into released particles. Retroviral RNA packaging requires RNA export of the unspliced genomic RNA from the nucleus, translocation of the genome to virus assembly sites, and specific interaction with Gag, the main viral structural protein. While some aspects of the RNA packaging process are understood, many others remain poorly understood. In this review, we provide an update on recent advancements in understanding the mechanism of RNA packaging for retroviruses that cause disease in humans, i.e., HIV-1, HIV-2, and HTLV-1, as well as advances in the understanding of the details of genomic RNA nuclear export, genome translocation to virus assembly sites, and genomic RNA dimerization.

A Single-Institute Cross-sectional Study of HCV-Positive Cancer Patients’ Quality of Life in Egypt

BACKGROUND: Egypt is the country with the greatest number of hepatitis C virus (HCV) genotype 4 infections. The latest mass screening campaign in Egypt in 2018 reported an overall HCV seroprevalence of 4.61% (95% confidence interval 4.61 to 4.62) among the 48,345,948 subjects tested. The prevalence of HCV in the cancer population is estimated to range from 1.5 to 32%. HCV per se might directly influence health-related quality of life (HRQoL), via colonization of microglia in the brain or, indirectly, via the effect of systemic inflammatory cytokines which, in turn, can trigger brain interleukin production. Thus, there is an increased interest about the effect of the dual burden of HCV in cancer patients and its impact on the patients’’ HRQoL. AIM: The study is conducted at the outpatient chemotherapy unit of a university hospital in Egypt, over a period of 6 months to estimate their quality of life (QoL) scores according to the European Organization for Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ)-C30 v3. MATERIALS AND METHODS: A cross-sectional study was conducted, including all patients referred to the chemotherapy clinic during the study period and proven to be HCV positive. Recruited patients were asked to fill the EORTC QLQ-C30 v3 questionnaire, and data regarding their medical conditions were collected from their medical files. RESULTS: One hundred and sixteen (8.8%) patients were HCV positive. QoL scores were statistically significantly lower from almost all reference values categories published in the EORTC manual.

Excretion and viability of SARS-CoV-2 in feces and its association with the clinical outcome of COVID-19

The main objective was to evaluate the viability of the SARS-CoV-2 viral particles excreted in stools. In addition, we aimed to identify clinical factors associated with the detection of SARS-CoV-2 RNA in feces, and to determine if its presence is associated with an unfavorable clinical outcome, defined as intensive care unit (ICU) admission and/or death. A prospective multicenter cohort study of COVID-19 adult patients, with confirmed SARS-CoV-2 infection by RT-PCR assay in nasopharyngeal (NP) swabs admitted to four hospitals in Spain, from March 2020 to February 2021. Sixty-two adult COVID-19 patients had stool samples collected at admission and/or during the follow up, with a total of 79 stool samples. SARS-CoV-2 RNA was detected in stool samples from 27 (43.5%) out of the 62 patients. Replicative virus, measured by the generation of cytopathic effect in cell culture and subsequent RT-PCR confirmation of a decrease in the Ct values, was not found in any of these stool samples. Fecal virus excretion was not associated with the presence of gastrointestinal symptoms, or with differences in the evolution of COVID-19 patients. Our results suggest that SARS-CoV-2 replicative capacity is null or very limited in stool samples, and thus, the fecal–oral transmission of SARS-CoV-2 as an alternative infection route is highly unlikely. In our study, the detection of SARS-CoV-2 RNA in feces at the beginning of the disease is not associated with any clinical factor nor with an unfavorable clinical outcome.

Seroprevalence of Hepatitis B, C and D in Vietnam: A systematic review and meta-analysis

Background

Vietnam has one of the greatest disease burdens from chronic viral hepatitis. Comprehensive prevalence data are essential to support its elimination as a public health threat.

Methods

We searched Medline and Embase from 1990 to 2021 for seroprevalence data relating to Hepatitis B (HBV), C (HCV) and D (HDV) in Vietnam. We estimated pooled prevalence with a DerSimonian-Laird random-effects model and stratified study populations into i) low-risk ii) high-risk exposure and iii) liver disease. We further estimated prevalence by decade and region and rates of HIV-coinfection.

Findings

We analysed 72 studies, including 120 HBV, 114 HCV and 23 HDV study populations. Pooled HBV prevalence was low in blood donors (1.86% [1.82-1.90]) but high in antenatal populations (10.8% [10.1-11.6]) and adults in the general population (10.5% [10.0-11.0]). It was similar or modestly increased in groups at highest risk of exposure, suggesting the epidemic is largely driven by chronic infections acquired in childhood. HCV pooled prevalence in the general population was lower than historical estimates: 0.26% (0.09-0.51) have active infection defined by detectable antigen or HCV RNA. In contrast, there is an extremely high prevalence of active HCV infection in people who inject drugs (PWID) (57.8% [56.5-59.1]), which has persisted through the decades despite harm-reduction interventions. HDV appears mainly confined to high-risk groups.

Interpretation

Blood safety has improved, but renewed focus on HBV vaccination at birth and targeted HCV screening and treatment of PWID are urgently required to meet elimination targets. Large cross-sectional studies are needed to better characterize HDV prevalence, but mass screening may not be warranted.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

miR-155-3p: processing by-product or rising star in immunity and cancer?

MicroRNAs (miRNAs) are key players in gene regulation that target specific mRNAs for degradation or translational repression. Each miRNA is synthesized as a miRNA duplex comprising two strands (5p and 3p). However, only one of the two strands becomes active and is selectively incorporated into the RNA-induced silencing complex in a process known as miRNA strand selection. Recently, significant progress has been made in understanding the factors and processes involved in strand selection. Here, we explore the selection and functionality of the miRNA star strand (either 5p or 3p), which is generally present in the cell at low levels compared to its partner strand and, historically, has been thought to possess no biological activity. We also highlight the concepts of miRNA arm switching and miRNA isomerism. Finally, we offer insights into the impact of aberrant strand selection on immunity and cancer. Leading us through this journey is miR-155, a well-established regulator of immunity and cancer, and the increasing evidence that its 3p strand plays a role in these arenas. Interestingly, the miR-155-5p/-3p ratio appears to vary dependent on the timing of the immune response, and the 3p strand seems to play a regulatory role upon its partner 5p strand.

Specific Interaction of DARPin with HIV-1 CANTD Disturbs the Distribution of Gag, RNA Packaging, and Tetraspanin Remodelling in the Membrane

A designed repeat scaffold protein (Ank^GAG1D4) recognizing the human immunodeficiency virus-1 (HIV-1) capsid (CA) was formerly established with antiviral assembly. Here, we investigated the molecular mechanism of Ank^GAG1D4 function during the late stages of the HIV-1 replication cycle. By applying stimulated emission-depletion (STED) microscopy, Gag polymerisation was interrupted at the plasma membrane. Disturbance of Gag polymerisation triggered Gag accumulation inside producer cells and trapping of the CD81 tetraspanin on the plasma membrane. Moreover, reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) experiments were performed to validate the packaging efficiency of RNAs. Our results advocated that Ank^GAG1D4 interfered with the Gag precursor protein from selecting HIV-1 and cellular RNAs for encapsidation into viral particles. These findings convey additional information on the antiviral activity of Ank^GAG1D4 at late stages of the HIV-1 life cycle, which is potential for an alternative anti-HIV molecule.

Impact of sustained virologic response in regression of portal hypertension in Egyptian patients with hepatitis C virus-associated cirrhosis and portal hypertension

Background

Portal hypertension (PH) is a common consequence in hepatitis C virus cirrhotic patients. With interferon alpha-based therapy, SVR was linked to improved PH and fibrosis regression. SVR to oral antiviral regimens is linked to reduced portal pressure in patients with clinically significant portal hypertension (CSPH) at baseline. However, CSPH continues in most of the patients. This study aims to assess the reversibility and/or improvement of PH in Egyptian patients with HCV-related cirrhosis and CSPH after achieving SVR with DAAs. The second aim is to evaluate performance of the noninvasive markers of fibrosis in prediction of the presence and/or reversibility of the CSPH in correlation to radiological and endoscopic parameters.

Subjects and methods

We evaluated noninvasive parameters, radiological and endoscopic signs of PH at baseline, and/or SVR 24 and SVR 48 post-DAA therapy in 40 patients with cirrhosis and CSPH (group A) and another 40 patients with cirrhosis only (group B).

Results

In group A, the spleen diameter decreased from baseline (15.74 ± 1.53 cm), and SVR 24 (15.48 ± 1.51), to SVR 48 (15.35 ± 1.49 cm). No ascites detected at SVR 48 in 62.5%. Portal vein diameter and portal vein blood velocity reduced to 13.53 ± 1.07 mm and 14.14 ± 2.2 cm/s at SVR 48, with reversibility of hepatic vein waveform towards the triphasic pattern. Medium to large esophageal varices regressed from 52.5% to 2.5%, and up to 70% of patients showed no EVs at SVR 48. In group A, 24 patients showed complete reversibility of CSPH, and 16 patients showed improvement of CSPH. Child-Pugh score, FIB-4 index, King’s score, and Lok index revealed higher significance for detection of the presence of PH. Child-Pugh score, PC/SD ratio, and Lok index revealed higher significance for detection of reversibility of PH.

Conclusion

We concluded that CSPH improved after SVR with DAAs and completely regressed in some patients. Upon predicting the presence of PH, Child-Pugh score, FIB-4 index, King’s score, and Lok index were the most significant noninvasive scores. While for predicting the reversibility of PH, Child-Pugh score, PC/SD ratio, and Lok index were the most significant scores.

Cardiometabolic Health Status, Ethnicity and Health-Related Quality of Life (HRQoL) Disparities in an Adult Population: NutrIMDEA Observational Web-Based Study

Precision public health supported on online tools is increasingly emerging as a potential strategy to achieve health promotion and disease prevention. Our aim was to assess the relationships of sociodemographic variables, anthropometric data, dietary habits and lifestyle factors with health-related quality of life (HRQoL), cardiometabolic health status and ethnicity in an online recruited adult population (NutrIMDEA Study). NutrIMDEA Study is a web-based cross-sectional survey that included 17,333 adults. Self-reported sociodemographic characteristics, anthropometric data, clinical and family history of cardiometabolic illnesses, dietary habits, lifestyle factors and HRQoL features were collected. Diseased individuals showed significative poorer MedDiet and worse HRQoL than those in the healthy cardiometabolic status group (p < 0.05). In comparison, European/Caucasian individuals reported a significantly better HRQoL, higher MedDiet and HRQoL values compared with those of other ethnicities (p < 0.05). We obtained a total of 16.8% who reported poor/fair, 56.5% good and 26.6% very good/excellent HRQoL. Respondents with very good/excellent HRQoL showed lower BMI, greater adherence to a Mediterranean diet (MedDiet) and higher physical activity. The results suggest the presence of interactions between the mental and physical components of HRQoL with obesity, sedentarism and dietary intake, which were dependent on disease status and ethnicity. Online HRQoL assessment could contribute to wider implementation of precision public health strategies to promote health targeted interventions with policy implications to community health promotion.

Liver Disease Outcomes after Sustained Virological Response in Patients with Chronic Hepatitis C Infection Treated with Generic Direct-Acting Antivirals

The introduction of generic direct-acting antivirals (DAAs) in Egypt is associated with a superior cure rate of hepatitis C virus (HCV) infection. However, the course of progressive liver damage and developing liver related complications in patients with sustained virologic response (SVR) remain unclear. This study was designed to examine the long-term outcomes of generic DAA-induced virological cure in a real-life cohort of HCV patients with or without comorbid schistosomiasis. We prospectively enrolled a cohort of 506 recently cured HCV patients (437 Child-Pugh class A [Child-A] and 69 Child-Pugh class B [Child-B]). All patients were clinically evaluated at different time points during a 2-year follow-up (November 2018 to February 2021). Over the course of treatment and follow-up, 77 (15.2%) patients (42 [9.6%] Child-A and 35 [50.7%] Child-B) experienced complications at different time points. The overall mortality rate was approximately 1/1,000 person-years. The incidence of hepatic insufficiency was approximately 5.5/1,000 person-years, and that of de novo hepatocellular carcinoma (HCC) was approximately 8.3/1,000 person-years. A sustained improvement in liver indices up to 2 years of follow-up was observed. In the Cox regression model, pretreatment decompensated cirrhosis predicted the occurrence of adverse liver events and HCC after therapy. In conclusion, in HCV patients with advanced cirrhosis or coexisting hepatic schistosomiasis, generic DAA-induced SVR remains robust with favorable clinical outcomes although the risk of hepatocarcinogenesis cannot be eliminated. Surveillance of patients with treated HCV infection is an important aspect of postcure care for early detection and management of liver disease-related adverse events.

Advances in HIV-1 Assembly

The assembly of HIV-1 particles is a concerted and dynamic process that takes place on the plasma membrane of infected cells. An abundance of recent discoveries has advanced our understanding of the complex sequence of events leading to HIV-1 particle assembly, budding, and release. Structural studies have illuminated key features of assembly and maturation, including the dramatic structural transition that occurs between the immature Gag lattice and the formation of the mature viral capsid core. The critical role of inositol hexakisphosphate (IP6) in the assembly of both the immature and mature Gag lattice has been elucidated. The structural basis for selective packaging of genomic RNA into virions has been revealed. This review will provide an overview of the HIV-1 assembly process, with a focus on recent advances in the field, and will point out areas where questions remain that can benefit from future investigation.

Plasma-Derived HIV-1 Virions Contain Considerable Levels of Defective Genomes

Genetically-characterizing full-length HIV-1 RNA is critical for identifying genetically-intact genomes and for comparing these RNA genomes to proviral DNA. We have developed a method for sequencing plasma-derived RNA using long-range sequencing (PRLS assay; ∼8.3 kb from gag to the 3′ end or ∼5 kb from integrase to the 3′ end). We employed the gag-3′ PRLS assay to sequence HIV-1 RNA genomes from ART-naive participants during acute/early infection (n = 6) or chronic infection (n = 2). On average, only 65% of plasma-derived genomes were genetically-intact. Defects were found in all genomic regions but were concentrated in env and pol. We compared these genomes to near-full-length proviral sequences from paired peripheral blood mononuclear cell (PBMC) samples for the acute/early group and found that near-identical (>99.98% identical) sequences were identified only during acute infection. For three participants who initiated therapy during acute infection, we used the int-3′ PRLS assay to sequence plasma-derived genomes from an analytical treatment interruption and identified 100% identical genomes between pretherapy and rebound time points. The PRLS assay provides a new level of sensitivity for understanding the genetic composition of plasma-derived HIV-1 RNA from viremic individuals either pretherapy or after treatment interruption, which will be invaluable in assessing possible HIV-1 curative strategies.

IMPORTANCE We developed novel plasma-derived RNA using long-range sequencing assays (PRLS assay; 8.3 kb, gag-3′, and 5.0 kb, int-3′). Employing the gag-3′ PRLS assay, we found that 26% to 51% of plasma-derived genomes are genetically-defective, largely as a result of frameshift mutations and deletions. These genetic defects were concentrated in the env region compared to gag and pol, likely a reflection of viral immune escape in env during untreated HIV-1 infection. Employing the int-3′ PRLS assay, we found that analytical treatment interruption (ATI) plasma-derived sequences were identical and genetically-intact. Several sequences from the ATI plasma samples were identical to viral sequences from pretherapy plasma and PBMC samples, indicating that HIV-1 reservoirs established prior to therapy contribute to viral rebound during an ATI. Therefore, near-full-length sequencing of HIV-1 particles is required to gain an accurate picture of the genetic landscape of plasma HIV-1 virions in studies of HIV-1 replication and persistence.

Molecular and Physiological Aspects of SARS-CoV-2 Infection in Women and Pregnancy

Whilst scientific knowledge about SARS-CoV-2 and COVID-19 is rapidly increasing, much of the effects on pregnant women is still unknown. To accommodate pregnancy, the human endometrium must undergo a physiological transformation called decidualization. These changes encompass the remodeling of endometrial immune cells leading to immunotolerance of the semi-allogenic conceptus as well as defense against pathogens. The angiotensin converting enzyme 2 (ACE2) plays an important regulatory role in the renin-angiotensin-system (RAS) and has been shown to be protective against comorbidities known to worsen COVID-19 outcomes. Furthermore, ACE2 is also crucial for decidualization and thus for early gestation. An astounding gender difference has been found in COVID-19 with male patients presenting with more severe cases and higher mortality rates. This could be attributed to differences in sex chromosomes, hormone levels and behavior patterns. Despite profound changes in the female body during pregnancy, expectant mothers do not face worse outcomes compared with non-pregnant women. Whereas mother-to-child transmission through respiratory droplets during labor or in the postnatal period is known, another question of in utero transmission remains unanswered. Evidence of placental SARS-CoV-2 infection and expression of viral entry receptors at the maternal-fetal interface suggests the possibility of in utero transmission. SARS-CoV-2 can cause further harm through placental damage, maternal systemic inflammation, and hindered access to health care during the pandemic. More research on the effects of COVID-19 during early pregnancy as well as vaccination and treatment options for gravid patients is urgently needed.

Construction of Xinjiang metabolic syndrome risk prediction model based on interpretable models

Background

We aimed to construct simple and practical metabolic syndrome (MetS) risk prediction models based on the data of inhabitants of Urumqi and to provide a methodological reference for the prevention and control of MetS.

Methods

This is a cross-sectional study conducted in the Xinjiang Uygur Autonomous Region of China. We collected data from inhabitants of Urumqi from 2018 to 2019, including demographic characteristics, anthropometric indicators, living habits and family history. Resampling technology was used to preprocess the data imbalance problems, and then MetS risk prediction models were constructed based on logistic regression (LR) and decision tree (DT). In addition, nomograms and tree diagrams of DT were used to explain and visualize the model.

Results

Of the 25,542 participants included in the study, 3,267 (12.8%) were diagnosed with MetS, and 22,275 (87.2%) were diagnosed with non-MetS. Both the LR and DT models based on the random undersampling dataset had good AUROC values (0.846 and 0.913, respectively). The accuracy, sensitivity, specificity, and AUROC values of the DT model were higher than those of the LR model. Based on a random undersampling dataset, the LR model showed that exercises such as walking (OR=0.769) and running (OR= 0.736) were protective factors against MetS. Age 60 ~ 74 years (OR=1.388), previous diabetes (OR=8.902), previous hypertension (OR=2.830), fatty liver (OR=3.306), smoking (OR=1.541), high systolic blood pressure (OR=1.044), and high diastolic blood pressure (OR=1.072) were risk factors for MetS; the DT model had 7 depth layers and 18 leaves, with BMI as the root node of the DT being the most important factor affecting MetS, and the other variables in descending order of importance: SBP, previous diabetes, previous hypertension, DBP, fatty liver, smoking, and exercise.

Conclusions

Both DT and LR MetS risk prediction models have good prediction performance and their respective characteristics. Combining these two methods to construct an interpretable risk prediction model of MetS can provide methodological references for the prevention and control of MetS.

Epitranscriptomic regulation of HIV-1 full-length RNA packaging

During retroviral replication, the full-length RNA serves both as mRNA and genomic RNA. However, the mechanisms by which the HIV-1 Gag protein selects the two RNA molecules that will be packaged into nascent virions remain poorly understood. Here, we demonstrate that deposition of N6-methyladenosine (m6A) regulates full-length RNA packaging. While m6A deposition by METTL3/METTL14 onto the full-length RNA was associated with increased Gag synthesis and reduced packaging, FTO-mediated demethylation promoted the incorporation of the full-length RNA into viral particles. Interestingly, HIV-1 Gag associates with the RNA demethylase FTO in the nucleus and contributes to full-length RNA demethylation. We further identified two highly conserved adenosines within the 5'-UTR that have a crucial functional role in m6A methylation and packaging of the full-length RNA. Together, our data propose a novel epitranscriptomic mechanism allowing the selection of the HIV-1 full-length RNA molecules that will be used as viral genomes.

Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview

Retroviruses must selectively recognize their unspliced RNA genome (gRNA) among abundant cellular and spliced viral RNAs to assemble into newly formed viral particles. Retroviral gRNA packaging is governed by Gag precursors that also orchestrate all the aspects of viral assembly. Retroviral life cycles, and especially the HIV-1 one, have been previously extensively analyzed by several methods, most of them based on molecular biology and biochemistry approaches. Despite these efforts, the spatio-temporal mechanisms leading to gRNA packaging and viral assembly are only partially understood. Nevertheless, in these last decades, progress in novel bioimaging microscopic approaches (as FFS, FRAP, TIRF, and wide-field microscopy) have allowed for the tracking of retroviral Gag and gRNA in living cells, thus providing important insights at high spatial and temporal resolution of the events regulating the late phases of the retroviral life cycle. Here, the implementation of these recent bioimaging tools based on highly performing strategies to label fluorescent macromolecules is described. This report also summarizes recent gains in the current understanding of the mechanisms employed by retroviral Gag polyproteins to regulate molecular mechanisms enabling gRNA packaging and the formation of retroviral particles, highlighting variations and similarities among the different retroviruses.

Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55Gag and its maturation products

Maturation of the HIV-1 viral particles shortly after budding is required for infectivity. During this process, the Pr55^Gag precursor undergoes a cascade of proteolytic cleavages, and whilst the structural rearrangements of the viral proteins are well understood, the concomitant maturation of the genomic RNA (gRNA) structure is unexplored, despite evidence that it is required for infectivity. To get insight into this process, we systematically analysed the interactions between Pr55^Gag or its maturation products (NCp15, NCp9 and NCp7) and the 5ʹ gRNA region and their structural consequences, in vitro. We show that Pr55^Gag and its maturation products mostly bind at different RNA sites and with different contributions of their two zinc knuckle domains. Importantly, these proteins have different transient and permanent effects on the RNA structure, the late NCp9 and NCp7 inducing dramatic structural rearrangements. Altogether, our results reveal the distinct contributions of the different Pr55^Gag maturation products on the gRNA structural maturation.

Molecular pathways dysregulated by Pb2+ exposure prompts pancreatic beta-cell dysfunction

Type 2 diabetes mellitus (T2DM) is a metabolic disease characterized by reduced insulin sensitivity and dysfunction of β-cells. Although the increasing prevalence of diabetes worldwide is largely attributed to genetic predisposition or lifestyle factors (insufficient physical activity), and caloric intake. Environmental factors, exposure to xenobiotics and heavy metals have also been reported to be causative factors of T2DM. At this juncture, we, through our work unveil a plausible link between Pb²⁺ exposure and diabetes mellitus, and delineated a comprehensive understanding of the potential mechanisms of Pb²⁺-induced β-cells dysfunction. In our in vivo observations, we found that Pb²⁺ exposure strongly reduced glucose-stimulated insulin secretion and diminished functional pancreatic β-cell mass. Mechanistically, we found that Pb²⁺ downregulates intracellular cAMP level via hyper-activating Ca²⁺/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C and thereby reduces glucose-stimulated insulin secretion. Further, we report that Pb²⁺ inhibited mitochondrial adenosine triphosphate production and also identified Pb²⁺ as a negative regulator of β-cell proliferation via Ca²⁺/calmodulin-dependent protein kinase kinases-pAMPK-pRaptor axis. Together, our findings strongly reinforce Pb²⁺ to hijack the physiological role of calcium ions, by mimicking Ca²⁺ within pancreatic β-cell and thereby stands as a diabetogenic xenobiotic.

Evaluations of Clinical Utilization of Metagenomic Next-Generation Sequencing in Adults With Fever of Unknown Origin

Introduction

The diagnosis of infection-caused fever of unknown origin (FUO) is still challenging, making it difficult for physicians to provide an early effective therapy. Therefore, a novel pathogen detection platform is needed. Metagenomic next-generation sequencing (mNGS) provides an unbiased, comprehensive technique for the sequence-based identification of pathogenic microbes, but the study of the diagnostic values of mNGS in FUO is still limited.

Methods

In a single-center retrospective cohort study, 175 FUO patients were enrolled, and clinical data were recorded and analyzed to compare mNGS with culture or traditional methods including as smears, serological tests, and nucleic acid amplification testing (NAAT) (traditional PCR, Xpert MTB/RIF, and Xpert MTB/RIF Ultra).

Results

The blood mNGS could increase the overall rate of new organisms detected in infection-caused FUO by roughly 22.9% and 19.79% in comparison to culture (22/96 vs. 0/96; OR, ∞; p = 0.000) and conventional methods (19/96 vs. 3/96; OR, 6.333; p = 0.001), respectively. Bloodstream infection was among the largest group of those identified, and the blood mNGS could have a 38% improvement in the diagnosis rate compared to culture (19/50 vs. 0/50; OR, ∞; p = 0.000) and 32.0% compared to conventional methods (16/50 vs. 3/50; OR, 5.333; p = 0.004). Among the non-blood samples in infection-caused FUO, we observed that the overall diagnostic performance of mNGS in infectious disease was better than that of conventional methods by 20% (9/45 vs. 2/45; OR, 4.5; p = 0.065), and expectedly, the use of non-blood mNGS in non-bloodstream infection increased the diagnostic rate by 26.2% (8/32 vs. 0/32; OR, ∞; p = 0.008). According to 175 patients’ clinical decision-making, we found that the use of blood mNGS as the first-line investigation could effectively increase 10.9% of diagnosis rate of FUO compared to culture, and the strategy that the mNGS of suspected parts as the second-line test could further benefit infectious patients, improving the diagnosis rate of concurrent infection by 66.7% and 12.5% in non-bloodstream infection, respectively.

Conclusion

The application of mNGS in the FUO had significantly higher diagnostic efficacy than culture or other conventional methods. In infection-caused FUO patients, application of blood mNGS as the first-line investigation and identification of samples from suspected infection sites as the second-line test could enhance the overall FUO diagnosis rate and serve as a promising optimized diagnostic protocol in the future.

A Structural View of miRNA Biogenesis and Function

Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been the subject of deep study due to their involvement in many important biological processes. Compared with other ncRNAs, miRNAs are generated from devoted transcriptional units which are processed by a specific set of endonucleases. The contribution of structural biology methods for understanding miRNA biogenesis and function has been essential for the dissection of their roles in cell biology and human disease. In this review, we summarize the application of structural biology for the characterization of the molecular players involved in miRNA biogenesis (processors and effectors), starting from the X-ray crystallography methods to the more recent cryo-electron microscopy protocols.

Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging

RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55^Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5' untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5' UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS-SL1 interaction unexpectedly couples the PBS with dimerization and Pr55^Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.

Providing Asthma Management in the Retail Clinic Setting

Objective:

To determine whether there are differences in asthma management provided in the retail clinic setting versus in the primary care setting, and whether it would increase the number of well controlled asthmatics as determined by ACT score of 20 or greater, and less than or equal to 1 ED or hospital visit due to asthma, within 6 months.

Methods:

All asthma patients with an asthma control test (ACT) of 19 or less, received a new or updated asthma action plan (AAP) at the visit. If the patient presented to the retail clinic during an asthma exacerbation or with any asthma symptoms, they were not given an ACT and received usual care. Asthma quality data was retrospectively collected for primary care patients seen in the 6-months prior to as well as up to 6 months after the patient’s enrollment visit.

Results:

There was no significant difference in the number of admissions between locations in either the pre-implementation period or the post-implementation period for either the pediatric or adult cohort. There was a significant improvement in the percentage of pediatric and adult patients with at least 1 ACT in the post-implementation compared to pre-implementation for both retail clinic and primary care sites. The percentage of pediatric and adult patients with at least 1 AAP increased in the post-implementation compared to pre-implementation for both retail clinic and primary care sites.

Conclusion:

Retail clinics may be able to provide asthma management with similar outcomes to primary care settings.

Quantitative analysis of the formation of nucleoprotein complexes between HIV-1 Gag protein and genomic RNA using transmission electron microscopy

In HIV, the polyprotein precursor Gag orchestrates the formation of the viral capsid. In the current view of this viral assembly, Gag forms low-order oligomers that bind to the viral genomic RNA triggering the formation of high-ordered ribonucleoprotein complexes. However, this assembly model was established using biochemical or imaging methods that do not describe the cellular location hosting Gag-gRNA complex nor distinguish gRNA packaging in single particles. Here, we studied the intracellular localization of these complexes by electron microscopy and monitored the distances between the two partners by morphometric analysis of gold beads specifically labeling Gag and gRNA. We found that formation of these viral clusters occurred shortly after the nuclear export of the gRNA. During their transport to the plasma membrane, the distance between Gag and gRNA decreases together with an increase of gRNA packaging. Point mutations in the zinc finger patterns of the nucleocapsid domain of Gag caused an increase in the distance between Gag and gRNA as well as a sharp decrease of gRNA packaged into virions. Finally, we show that removal of stem loop 1 of the 5'-untranslated region does not interfere with gRNA packaging, whereas combined with the removal of stem loop 3 is sufficient to decrease but not abolish Gag-gRNA cluster formation and gRNA packaging. In conclusion, this morphometric analysis of Gag-gRNA cluster formation sheds new light on HIV-1 assembly that can be used to describe at nanoscale resolution other viral assembly steps involving RNA or protein-protein interactions.

Are Argonaute-Associated Tiny RNAs Junk, Inferior miRNAs, or a New Type of Functional RNAs?

The biosynthesis pathways of microRNAs (miRNAs) have been well characterized with the identification of the required components. miRNAs are synthesized from the transcripts of miRNA genes and other RNAs, such as introns, transfer RNAs, ribosomal RNAs, small nucleolar RNAs, and even viral miRNAs. These small RNAs are loaded into Argonaute (AGO) proteins and recruit the effector complexes to target mRNAs, repressing their gene expression post-transcriptionally. While mature miRNAs were defined as 19–23 nucleotides (nt), tiny RNAs (tyRNAs) shorter than 19 nt have been found to bind AGOs as equivalent or lesser miRNAs compared to their full-length mature miRNAs. In contrast, my recent study revealed that when human AGO3 loads 14 nt cleavage-inducing tyRNAs (cityRNAs), comprised of the first 14 nt of their corresponding mature miRNA, it can become a comparable slicer to AGO2. This observation raises the possibility that tyRNAs play distinct roles from their mature form. This minireview focuses on human AGO-associated tyRNAs shorter than 19 nt and discusses their possible biosynthesis pathways and physiological benefits, including how tyRNAs could avoid target-directed miRNA degradation accompanied by AGO polyubiquitination.

Unique situation of hepatocellular carcinoma in Egypt: A review of epidemiology and control measures

Hepatocellular carcinoma (HCC) is the sixth most common primary malignancy worldwide, and the third most common cause of death among cancers worldwide. HCC occurs in several pre-existing conditions, including hepatitis C, hepatitis B virus, and non-alcoholic cirrhosis. Egypt used to be the country with the heaviest hepatitis C virus (HCV) burden. The relationship between HCV and HCC is an important research area. In Egypt, HCC is a significant public health problem. A possible cause for the increasing rates of detection of HCC in Egypt is the mass screening program that was carried by the government for detecting and treating HCV. A multidisciplinary approach is now widely applied to HCC management in health centers all over Egypt. Different treatment modalities are available in Egypt, with success rates comparable to global rates. The Egyptian health authorities have made the elimination of HCV from Egypt a special priority, and this approach should lead to a decrease in number of HCC cases in the near future. In this article we review the current situation of HCC in Egypt, including epidemiological aspects, relevant risk factors for HCC development, strategies, and efforts established by health authorities for the screening and prevention of both HCV and HCC in Egypt. We highlight the different modalities for HCC treatment.

Selective packaging of HIV-1 RNA genome is guided by the stability of 5' untranslated region polyA stem

To generate infectious virus, HIV-1 must package two copies of its full-length RNA into particles. HIV-1 transcription initiates from multiple, neighboring sites, generating RNA species that only differ by a few nucleotides at the 5' end, including those with one (1G) or three (3G) 5' guanosines. Strikingly, 1G RNA is preferentially packaged into virions over 3G RNA. We investigated how HIV-1 distinguishes between these nearly identical RNAs using in-gel chemical probing combined with recently developed computational tools for determining RNA conformational ensembles, as well as cell-based assays to quantify the efficiency of RNA packaging into viral particles. We found that 1G and 3G RNAs fold into distinct structural ensembles. The 1G RNA, but not the 3G RNA, primarily adopts conformations with an intact polyA stem, exposed dimerization initiation site, and multiple, unpaired guanosines known to mediate Gag binding. Furthermore, we identified mutants that exhibited altered genome selectivity and packaged 3G RNA efficiently. In these mutants, both 1G and 3G RNAs fold into similar conformational ensembles, such that they can no longer be distinguished. Our findings demonstrate that polyA stem stability guides RNA-packaging selectivity. These studies also uncover the mechanism by which HIV-1 selects its genome for packaging: 1G RNA is preferentially packaged because it exposes structural elements that promote RNA dimerization and Gag binding.

Health education interventions to promote health literacy in adults with selected non-communicable diseases living in low-to-middle income countries: A systematic review and meta-analysis

RATIONALE, AIMS AND OBJECTIVES

Health illiteracy is an important contributor to the burden of non-communicable diseases (NCDs); in particular in settings where health illiteracy is part of a perpetuating system of risk factors. Interventions that promote health literacy may provide an important tool in the primary and secondary prevention of NCDs. The objective of this systematic review was to evaluate the effectiveness of health literacy interventions on health literacy in the management of patients with selected NCDs living in low-to-middle income countries (LMIC).

METHODS

Seven electronic databases were searched (October 29, 2020) for RCTs aimed at improving health literacy in adults with NCDs in LMICs. Eligible NCDs included those pertaining to cancer, cardiovascular disease (CVD), chronic respiratory disease (CRD) or Diabetes. Studies were included that explicitly focussed on improving health literacy, and reported comprehensive measures of health literacy, or components thereof (ie, knowledge, attitude or behaviour). Random-effect meta-analyses were conducted for continuous outcome measures (Hedges-g).

RESULTS

The completed search yielded 2573 unique results of which 53 unique studies met the inclusion criteria. Studies included patients with cancer (n = 1, 2%), CRD (n = 8, 15%), CVD (n = 11, 21%) or Diabetes (n = 33, 62%). A significant (P < .01) summary effect was found for disease knowledge (SES = 1.27 [n = 23, 95%CI = 1.05-1.49]), attitude (SES = 1.17 [n = 20, 95%CI = 0.88-1.47]), and behaviour (SES = 1.20 [n = 31, 95%CI = 0.94-1.46]).

CONCLUSIONS

These results support the conclusion that there is compelling evidence, in particular, for patients with Diabetes, that health-literacy interventions are effective in promoting disease knowledge, attitude and behaviour across four chronic conditions that drive the burden of NCDs.

Disposal of Waste from Tattoo and Beauty Parlors in Poland: A Survey-Based Analysis on Epidemiological Safety

Appropriate waste management is increasingly relevant due to environmental and infectious disease transmission concerns. An anonymous observational cross-sectional study was conducted from 2013-2017 of 262 tattooists and 824 beauticians throughout Poland. Knowledge, attitudes, behavior, and compliance with blood-borne infection controls and correct waste disposal were assessed. Tattooists correctly addressed hazardous waste significantly more often than did beauticians (83.3% vs. 44.8%). Medical waste was collected by a specialist company in 90.1% of tattoo parlors and 63.3%of beauty parlors. Tattooists correctly used and disposed of sharps more frequently than beauticians (93.1% vs. 68.9%); however, 46.4% of beauticians and 12.4% of tattooists discarded waste into municipal trash, including sharps (27.1% and 2.6%, respectively). Incorrect collection and labeling of biological waste present occupational risk to waste disposal personnel. Education and instructional controls could improve health safety in this industry. Biological waste management processes are restrictive for medical services and liberal for beauty services, an industry for which they should also be applied more comprehensively.

Molecular characterization and antimicrobial susceptibility testing of clinical and non-clinical Brucella melitensis and Brucella abortus isolates from Egypt

Brucellosis is a highly contagious and incapacitating disease of humans, livestock and wildlife species globally. Treatment of brucellosis in animals is not recommended, and in humans, combinations of antibiotics recommended by the World Health Organization are used. However, sporadic antimicrobial-resistant (AMR) isolates and relapse cases have been reported from different endemic regions. In the current study, molecular characterization and antibiotic susceptibility testing using the microdilution method for 35 B. abortus and B. melitensis strains isolated from humans, milk and animal were carried out. Additionally, Next-Generation-Sequencing (NGS) technology was applied to confirm Brucella at the species level and investigate AMR and pathogenicity-associated determinants. MALDI-TOF seemed to be a rapid and reliable tool for routine identification of brucellae to the genus level; however, DNA-based identification is indispensable for accurate species identification. Brucella abortus strains were isolated from two human cases and a sheep. Such infections are uncommon in Egypt. Egyptian Brucella strains are still in-vitro susceptible to doxycycline, tetracyclines, gentamicin, ciprofloxacin, levofloxacin, chloramphenicol, streptomycin, trimethoprim/sulfamethoxazole and tigecycline. Probable (no CLSI/EUCAST breakpoints have been defined yet) in-vitro resistance to rifampicin and azithromycin was observed. WGS failed to determine classical AMR genes, and no difference in the distribution of virulence-associated genes in all isolates was found. Isolates of human and non-human origins were still susceptible to the majority of antibiotics used for treatment in humans. The absence of classical AMR genes in genomes of "resistant" Brucella strains may reflect a lack of information in databases, or resistance might not be encoded by single resistance genes. The One Health approach is necessary for tackling brucellosis. Continuous susceptibility testing, updating of breakpoints, assessing mutations that lead to resistance are needed.

HIV-1 Packaging Visualised by In-Gel SHAPE

HIV-1 packages two copies of its gRNA into virions via an interaction with the viral structural protein Gag. Both copies and their native RNA structure are essential for virion infectivity. The precise stepwise nature of the packaging process has not been resolved. This is largely due to a prior lack of structural techniques that follow RNA structural changes within an RNA-protein complex. Here, we apply the in-gel SHAPE (selective 2'OH acylation analysed by primer extension) technique to study the initiation of HIV-1 packaging, examining the interaction between the packaging signal RNA and the Gag polyprotein, and compare it with that of the NC domain of Gag alone. Our results imply interactions between Gag and monomeric packaging signal RNA in switching the RNA conformation into a dimerisation-competent structure, and show that the Gag-dimer complex then continues to stabilise. These data provide a novel insight into how HIV-1 regulates the translation and packaging of its genome.

HIV-1 integrase binding to genomic RNA 5'-UTR induces local structural changes in vitro and in virio

BACKGROUND

During HIV-1 maturation, Gag and Gag-Pol polyproteins are proteolytically cleaved and the capsid protein polymerizes to form the honeycomb capsid lattice. HIV-1 integrase (IN) binds the viral genomic RNA (gRNA) and impairment of IN-gRNA binding leads to mis-localization of the nucleocapsid protein (NC)-condensed viral ribonucleoprotein complex outside the capsid core. IN and NC were previously demonstrated to bind to the gRNA in an orthogonal manner in virio; however, the effect of IN binding alone or simultaneous binding of both proteins on gRNA structure is not yet well understood.

RESULTS

Using crosslinking-coupled selective 2'-hydroxyl acylation analyzed by primer extension (XL-SHAPE), we characterized the interaction of IN and NC with the HIV-1 gRNA 5'-untranslated region (5'-UTR). NC preferentially bound to the packaging signal (Psi) and a UG-rich region in U5, irrespective of the presence of IN. IN alone also bound to Psi but pre-incubation with NC largely abolished this interaction. In contrast, IN specifically bound to and affected the nucleotide (nt) dynamics of the apical loop of the transactivation response element (TAR) and the polyA hairpin even in the presence of NC. SHAPE probing of the 5'-UTR RNA in virions produced from allosteric IN inhibitor (ALLINI)-treated cells revealed that while the global secondary structure of the 5'-UTR remained unaltered, the inhibitor treatment induced local reactivity differences, including changes in the apical loop of TAR that are consistent with the in vitro results.

CONCLUSIONS

Overall, the binding interactions of NC and IN with the 5'-UTR are largely orthogonal in vitro. This study, together with previous probing experiments, suggests that IN and NC binding in vitro and in virio lead to only local structural changes in the regions of the 5'-UTR probed here. Accordingly, disruption of IN-gRNA binding by ALLINI treatment results in local rather than global secondary structure changes of the 5'-UTR in eccentric virus particles.

The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation

A growing number of studies indicate that mRNAs and long ncRNAs can affect protein populations by assembling dynamic ribonucleoprotein (RNP) granules. These phase-separated molecular ‘sponges’, stabilized by quinary (transient and weak) interactions, control proteins involved in numerous biological functions. Retroviruses such as HIV-1 form by self-assembly when their genomic RNA (gRNA) traps Gag and GagPol polyprotein precursors. Infectivity requires extracellular budding of the particle followed by maturation, an ordered processing of ∼2400 Gag and ∼120 GagPol by the viral protease (PR). This leads to a condensed gRNA-NCp7 nucleocapsid and a CAp24-self-assembled capsid surrounding the RNP. The choreography by which all of these components dynamically interact during virus maturation is one of the missing milestones to fully depict the HIV life cycle. Here, we describe how HIV-1 has evolved a dynamic RNP granule with successive weak–strong–moderate quinary NC-gRNA networks during the sequential processing of the GagNC domain. We also reveal two palindromic RNA-binding triads on NC, KxxFxxQ and QxxFxxK, that provide quinary NC-gRNA interactions. Consequently, the nucleocapsid complex appears properly aggregated for capsid reassembly and reverse transcription, mandatory processes for viral infectivity. We show that PR is sequestered within this RNP and drives its maturation/condensation within minutes, this process being most effective at the end of budding. We anticipate such findings will stimulate further investigations of quinary interactions and emergent mechanisms in crowded environments throughout the wide and growing array of RNP granules.

A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions

Simian immunodeficiency virus (SIV) is an important lentivirus used as a non-human primate model to study HIV replication, and pathogenesis of human AIDS, as well as a potential vector for human gene therapy. This study investigated the role of single-stranded purines (ssPurines) as potential genomic RNA (gRNA) packaging determinants in SIV replication. Similar ssPurines have been implicated as important motifs for gRNA packaging in many retroviruses like, HIV-1, MPMV, and MMTV by serving as Gag binding sites during virion assembly. In examining the secondary structure of the SIV 5' leader region, as recently deduced using SHAPE methodology, we identified four specific stretches of ssPurines (I-IV) in the region that harbors major packaging determinants of SIV. The significance of these ssPurine motifs were investigated by mutational analysis coupled with a biologically relevant single round of replication assay. These analyses revealed that while ssPurine II was essential, the others (ssPurines I, III, & IV) did not significantly contribute to SIV gRNA packaging. Any mutation in the ssPurine II, such as its deletion or substitution, or other mutations that caused base pairing of ssPurine II loop resulted in near abrogation of RNA packaging, further substantiating the crucial role of ssPurine II and its looped conformation in SIV gRNA packaging. Structure prediction analysis of these mutants further corroborated the biological results and further revealed that the unpaired nature of ssPurine II is critical for its function during SIV RNA packaging perhaps by enabling it to function as a specific binding site for SIV Gag.

Case study: risk associated to wearing silver or graphene nanoparticle-coated facemasks for protection against COVID-19

The world is living a pandemic situation derived from the worldwide spreading of SARS-CoV-2 virus causing COVID-19. Facemasks have proven to be one of the most effective prophylactic measures to avoid the infection that has made that wearing of facemasks has become mandatory in most of the developed countries. Silver and graphene nanoparticles have proven to have antimicrobial properties and are used as coating of these facemasks to increase the effectivity of the textile fibres. In the case of silver nanoparticles, we have estimated that in a real scenario the systemic (internal) exposure derived from wearing these silver nanoparticle facemasks would be between 7.0 × 10^–5 and 2.8 × 10^–4 mg/kg bw/day. In addition, we estimated conservative systemic no effect levels between 0.075 and 0.01 mg/kg bw/day. Therefore, we estimate that the chronic exposure to silver nanoparticles derived form facemasks wearing is safe. In the case of graphene, we detected important gaps in the database, especially regarding toxicokinetics, which prevents the derivation of a systemic no effect level. Nevertheless, the qualitative approach suggests that the risk of dermal repeated exposure to graphene is very low, or even negligible. We estimated that for both nanomaterials, the risk of skin sensitisation and genotoxicity is also negligible.

A Review of the Evidence and Recommendations on Communication Skills and the Patient-Provider Relationship: A Rome Foundation Working Team Report

BACKGROUND & AIMS

Over several decades, changes in health care have negatively impacted meaningful communication between the patient and provider and adversely affected their relationship. Under increasing time pressure, physicians rely more on technology than face-to-face time gathering data to make clinical decisions. As a result, they find it more challenging to understand the illness context and fully address patient needs. Patients experience dissatisfaction and a diminution of their role in the care process. For patients with disorders of gut-brain interaction, stigma leads to greater care dissatisfaction, as there is no apparent structural basis to legitimize the symptoms. Recent evidence suggests that practical communication skills can improve the patient-provider relationship (PPR) and clinical outcomes, but these data are limited.

METHODS

The Rome Foundation convened a multidisciplinary working team to review the scientific evidence with the following aims: a) to study the effect of communication skills on patient satisfaction and outcomes by performing an evidence-based review; b) to characterize the influence of sociocultural factors, health care system constraints, patient perspective, and telehealth on the PPR; c) to review the measurement and impact of communication skills training on these outcomes; and d) to make recommendations to improve communication skills training and the PPR.

RESULTS

Evidence supports the fact that interventions targeting patient-provider interactions improve population health, patient and provider experience, and costs. Communication skills training leads to improved patient satisfaction and outcomes. The following are relevant factors to consider in establishing an effective PPR: addressing health care system constraints; incorporating sociocultural factors and the role of gender, age, and chronic illness; and considering the changing role of telehealth on the PPR.

CONCLUSIONS

We concluded that effective communication skills can improve the PPR and health outcomes. This is an achievable goal through training and system change. More research is needed to confirm these findings.

Utility of positron emission tomography-computed tomography in the evaluation of fever of unknown origin in a resource-limited tropical nation

Positron emission tomography–computed tomography (PET-CT) has been used as an imaging modality in workup of fever of unknown origin (FUO). The aim of our study is to evaluate the diagnostic utility of PET-CT in FUO workup in a resource-limited setting. We also looked at laboratory parameters as predictors of contributory PET-CT scans and propose an algorithm for evaluation of FUO in resource-limited tropical regions. This retrospective observational study included patients admitted for FUO workup under general medicine in a teaching hospital in South India from June 2013 to May 2016. PET-CT was done when the patient remained undiagnosed after a detailed clinical assessment and first- and second-tier investigations. Among 43 patients included in our study, a definite diagnosis was established in 74% (32). Noninfectious inflammatory diseases, infections, malignancies, and miscellaneous diseases were diagnosed in 37.2% (16/43), 23.3% (10/43), 9.3% (4/43), and 4.7% (2/43), respectively. Tuberculosis was the single most common disease seen in 20.9% (9/43). PET-CT scans were contributory toward establishment of final diagnosis in 90.7% (39/43). High C-reactive protein (CRP) and aspartate aminotransferase (AST) levels were associated with contributory PET-CT scans (P = 0.006 and 0.011, respectively). PET-CT delineating organ/tissue for diagnostic biopsy was associated with final diagnosis of infectious disease (P = 0.001). Sensitivity, specificity, and positive and negative predictive value of PET-CT scans were 76.9% (20/26), 33.3% (2/6), 83% (20/24), and 25% (2/8), respectively. High CRP and AST were predictors of contributory PET-CT scans. PET-CT scans have high sensitivity and positive predictive value when used in evaluation of FUO. Although it is a useful tool in FUO workup, especially in the diagnosis of tropical infections, PET-CT should be done after a comprehensive clinical assessment and basic investigations.

NAFLD mark: an accurate model based on microRNA-34 for diagnosis of non-alcoholic fatty liver disease patients

BACKGROUND

It remains essential for non-alcoholic fatty liver (NAFLD) patients, to develop a sensitive and specific diagnostic model. Data regarding the use of micro (mi)RNA-34 for NAFLD diagnosis are few. Routine clinical assessment, laboratory tests were done for Egyptian individuals (n = 314) were included (100 healthy individuals and 214 NAFLD patients). Quantification of miRNA-34 was done using real-time PCR. Extremely significant variables were entered into stepwise logistic regression. The diagnostic power of variables was estimated by the area under the ROC (AUC).

RESULTS

MiRNA-34 levels were higher in NAFLD patients than healthy individuals with a significant difference (P< 0.0001). The multivariate analysis was used to evaluate the NAFLD-associated variables (CRP, cholesterol, body mass index (BMI), ALT had p< 0.0001 while mRNA-34 had (p=0.0004). The AUCs (CI) of candidate NAFLD markers were in the order of miRNA-34 0.72 (0.66-0.77) < ALT 0.73 (0.67-0.79) < BMI 0.81 (0.76-0.86) < cholesterol < 0.85 (0.79-0.90) < CRP 0.88 (0.84-0.92). We developed a novel index for discriminating patients with NAFLD named NAFLD Mark. AUC was jumped to 0.98 (0.93-0.99) when five markers were combined. The AUC of NAFLD mark for NAFLD detection was higher than the AUCs of seven common NAFLD indexes (0.44-0.86).

CONCLUSIONS

The NAFLD mark is a non-invasive and highly sensitive and specific model for NAFLD diagnosis.

Case Report: Metagenomic Next-Generation Sequencing Confirmed a Case of Central Nervous System Infection With Brucella melitensis in Non-endemic Areas

Brucellosis is a highly contagious zoonotic disease caused by bacteria that belong to the genus Brucella. It is a major endemic disease in northern China. We reported a rare case of central nervous system (CNS) infection caused by Brucella melitensis in a patient living in non-endemic areas. The medical history of the patient included chronic headache and trunk numbness. Based on the presented clinical symptoms and medical examinations, a clinical diagnosis of binocular uveo-encephalitis was made in the local hospital. The patient's symptoms were unrelieved after being treated with empiric therapy. Soon after, the patient was admitted to our hospital because of the obnubilation and coma in the trip. We ran a few examinations and sent the cerebrospinal fluid (CSF) for metagenomic next-generation sequencing (mNGS) immediately. The Magnetic resonance imaging (MRI) examination was unremarkable, and bilateral mastoid inflammation was attached. Metagenomic next-generation sequencing suggested a CNS infection caused by Brucella melitensis. Then, the results of the serum agglutination test and quantitative polymerase chain reaction assay also confirmed that. After being treated with doxycycline, rifampin, and cefatriaxone, consciousness of the patient was restored and headache diminished. Two months later, a lumbar puncture was used to check the pressure of the CSF, and the total course of treatment was more than 6 months. This case highlighted the potential value of mNGS in early clinal diagnosis. We believe that mNGS may be a complementary method for rapid identification of infection of CNS caused by the pathogen.

Recommendations for development of acute seizure action plans (ASAPs) from an expert panel

PURPOSE OF REVIEW

Disease-related treatment action plans for acute exacerbations providing information that may be helpful for self-management for patients and caregivers are commonly used for chronic conditions such as asthma and diabetes. However, among patients with epilepsy, a review of the literature suggested that the majority did not have an action plan in place for acute seizure treatment.

RECENT FINDINGS

Currently, there is a lack of unified guidance on seizure action plans (SAPs) in the literature. In the authors' opinion, available formats have limitations for practical use and may not be easily customizable to individual patients, and they are not often designed to provide simple-to-follow steps for rapid immediate steps to determine and initiate appropriate treatment of seizure emergencies. Our group reviewed current examples of SAPs and provided guidance on the development of acute seizure action plans (ASAPs) designed to facilitate rapid, appropriate acute care in the community and to be as useful as possible for a wide range of care partners, including those with limited experience.

SUMMARY

This paper provides agreed upon expert opinion recommendations and considerations for goals, development process, types of content, and format for an ASAP.

The Zinc Content of HIV-1 NCp7 Affects Its Selectivity for Packaging Signal and Affinity for Stem-Loop 3

The nucleocapsid (NC) protein of human immunodeficiency (HIV) is a small, highly basic protein containing two CCHC zinc-finger motifs, which is cleaved from the NC domain of the Gag polyprotein during virus maturation. We previously reported that recombinant HIV-1 Gag and NCp7 overexpressed in an E. coli host contains two and one zinc ions, respectively, and Gag exhibited much higher selectivity for packaging signal (Psi) and affinity for the stem-loop (SL)-3 of Psi than NCp7. In this study, we prepared NCp7 containing 0 (⁰NCp7), 1 (NCp7) or 2 (²NCp7) zinc ions, and compared their secondary structure, Psi-selectivity and SL3-affinity. Along with the decrease of the zinc content, less ordered conformations were detected. Compared to NCp7, ²NCp7 exhibited a much higher Psi-selectivity and SL3-affinity, similar to Gag, whereas ⁰NCp7 exhibited a lower Psi-selectivity and SL3-affinity, similar to the H23&H44K double mutant of NCp7, indicating that the different RNA-binding property of Gag NC domain and the mature NCp7 may be resulted, at least partially, from their different zinc content. This study will be helpful to elucidate the critical roles that zinc played in the viral life cycle, and benefit further investigations of the functional switch from the NC domain of Gag to the mature NCp7.

RNA Structures and Their Role in Selective Genome Packaging

To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.

Syndromic surveillance of female sexually transmitted infections in primary care: a descriptive study in Monastir, Tunisia, 2007─2017

BACKGROUND

Sexually Transmitted Infections (STIs) are a public health problem, especially for reproductive-age women. The aim of this study was to determine the incidence and trend of STIs during 11 years in Tunisia (2007-17).

METHODS

We conducted a descriptive study including all women with curable STIs (chlamydia, gonorrhea, syphilis and trichomoniasis) diagnosed with the syndromic approach in all basic health care centers of the Governorate of Monastir (Tunisia) from 2007 to 2017. Syndromes included, Pelvic Pain (PP), Vaginal Discharge (VD) and Genital Ulceration (GU).

RESULTS

We analyzed 40,388 episodes of curable STIs with a crude incidence rate and age standardized incidence rate of 1393 (95% Confidence Interval (CI); 1348-1438) / 100,000 Person Year (PY) and 1328 (95%CI; 1284-1372) /100,000 PY respectively. The incidence rate showed a positive trend over 11 years for all age groups and syndromes. VD was the most common syndrome with a crude incidence rate of 1170/100,000 PY. For all syndromes, women aged 20 to 39 were the most affected age group (p < 0.001).

CONCLUSION

In conclusion, the incidence rate of STIs episodes among women diagnosed with the syndromic approach was high, consistent with the global evidence. Focusing on reviewing STIs surveillance system in low and middle-income countries could allow the achievement of the ending of STIs epidemics by 2030.

Awareness of Rheumatic Heart Disease in Egypt: A National Multicenter Study

Background: While the prevalence of rheumatic heart disease (RHD) in Egypt is relatively high, data on the awareness of Egyptians about the cause of RHD are lacking. Methods: Using a pre-tested questionnaire, we performed a multicenter survey of outpatients attending 15 university hospitals across Egypt. Results: A total of 6958 participants were interviewed. Most subjects (81.7%) reported a previous experience of sore throat. Seeking treatment, most patients (69.3%) consulted a medical professional, while the others relied on self/peer medication. Individuals consulting a physician received antibiotics more frequently than those who did not (89.1 vs. 38.7%; OR: 12.4, 95% CI 10.8–14.1). The median RHD knowledge score in our sample was 4 (IQR = 6). While most subjects (56.3%) claimed knowledge of the complications of an untreated sore throat, only a third (34%) were aware of the association between sore throat and RHD. In a multivariate analysis, older age (Mean Difference [MD]: 1.58, 95% CI 1.37–1.79), female gender (MD: 0.89, 95% CI 0.75–1.04), higher education (MD: 1.10, 95% CI 0.90–1.30), and being interviewed outside Cairo (MD: 0.67, 95% CI 0.51–0.82) were significant predictors of knowledge about RHD. Conclusion: The current study showed low levels of awareness on the cause of RHD among Egyptians and highlights a pressing need for interventions to address this public knowledge gap.

Structural basis for piRNA targeting

PIWI proteins use PIWI-interacting RNAs (piRNAs) to identify and silence transposable elements and thereby maintain genome integrity between metazoan generations1. The targeting of transposable elements by PIWI has been compared to mRNA target recognition by Argonaute proteins2,3, which use microRNA (miRNA) guides, but the extent to which piRNAs resemble miRNAs is not known. Here we present cryo-electron microscopy structures of a PIWI-piRNA complex from the sponge Ephydatia fluviatilis with and without target RNAs, and a biochemical analysis of target recognition. Mirroring Argonaute, PIWI identifies targets using the piRNA seed region. However, PIWI creates a much weaker seed so that stable target association requires further piRNA-target pairing, making piRNAs less promiscuous than miRNAs. Beyond the seed, the structure of PIWI facilitates piRNA-target pairing in a manner that is tolerant of mismatches, leading to long-lived PIWI-piRNA-target interactions that may accumulate on transposable-element transcripts. PIWI ensures targeting fidelity by physically blocking the propagation of piRNA-target interactions in the absence of faithful seed pairing, and by requiring an extended piRNA-target duplex to reach an endonucleolytically active conformation. PIWI proteins thereby minimize off-targeting cellular mRNAs while defending against evolving genomic threats.

Predictive Factors for Positive HIV Test Results in a Hospital Setting

Background: Hospital admission for any reason provides the situation for voluntary HIV testing and consultation. Identifying the predictors of positivity may lead to a cost-effective method while enhancing professionalism. Objectives: To find the predictors of HIV-positive test result in a general hospital in Shiraz compared to a control group. Methods: In this case-control study, the records of all patients who received HIV testing upon their hospitalization in a general hospital in Shiraz, south of Iran, from January 2017 to the end of December 2017 were reviewed. For each HIV-positive case, at least one control from the same ward in the hospital with negative HIV test result was randomly selected. Based on the best-fitted model of logistic regression, the probability of positive HIV test results was estimated for each participant according to the risk factors, and a receiver operating characteristic (ROC) curve was drawn. Results: Out of 7333 persons who accepted to be tested, 77 patients tested positive for HIV, of whom 55 (71.4%) were male with the mean age of 41.5 ± 9.5 years. None of the HIV-positive patients were intravenous drug users, nor had they a history of imprisonment. The odds ratio (OR) was 21 for hepatitis-positive patients (hepatitis B and/or C) compared to negative ones, which was seven times higher in opium addicts than non-opium addicts. We developed a model using age, sex, opium addiction, and HBV and HCV status to predict the probability of being positive for HIV with an AUC of 0.853 (95% confidence interval 0.797 to 0.909). Conclusions: Hospital admission could be an appropriate momentum for providing voluntary counseling and testing. Infection with HBV and HCV are important risk factors for HIV infection, and additional testing should be offered, especially to these patients.

RNA Binding Properties of the Ty1 LTR-Retrotransposon Gag Protein

A universal feature of retroelement propagation is the formation of distinct nucleoprotein complexes mediated by the Gag capsid protein. The Ty1 retrotransposon Gag protein from Saccharomyces cerevisiae lacks sequence homology with retroviral Gag, but is functionally related. In addition to capsid assembly functions, Ty1 Gag promotes Ty1 RNA dimerization and cyclization and initiation of reverse transcription. Direct interactions between Gag and retrotransposon genomic RNA (gRNA) are needed for Ty1 replication, and mutations in the RNA-binding domain disrupt nucleation of retrosomes and assembly of functional virus-like particles (VLPs). Unlike retroviral Gag, the specificity of Ty1 Gag-RNA interactions remain poorly understood. Here we use microscale thermophoresis (MST) and electrophoretic mobility shift assays (EMSA) to analyze interactions of immature and mature Ty1 Gag with RNAs. The salt-dependent experiments showed that Ty1 Gag binds with high and similar affinity to different RNAs. However, we observed a preferential interaction between Ty1 Gag and Ty1 RNA containing a packaging signal (Psi) in RNA competition analyses. We also uncover a relationship between Ty1 RNA structure and Gag binding involving the pseudoknot present on Ty1 gRNA. In all likelihood, the differences in Gag binding affinity detected in vitro only partially explain selective Ty1 RNA packaging into VLPs in vivo.

Establishment of a novel scoring model for mortality risk prediction in HIV-infected patients with cryptococcal meningitis

Background

Cryptococcal meningitis (CM) remains a leading cause of death in HIV-infected patients, despite advances in CM diagnostic and therapeutic strategies. This study was performed with the aim to develop and validate a novel scoring model to predict mortality risk in HIV-infected patients with CM (HIV/CM).

Methods

Data on HIV/CM inpatients were obtained from a Multicenter Cohort study in China. Independent risk factors associated with mortality were identified based on data from 2013 to 2017, and a novel scoring model for mortality risk prediction was established. The bootstrapping statistical method was used for internal validation. External validation was performed using data from 2018 to 2020.

Results

We found that six predictors, including age, stiff neck, impaired consciousness, intracranial pressure, CD4⁺ T-cell count, and urea levels, were associated with poor prognosis in HIV/CM patients. The novel scoring model could effectively identify HIV/CM patients at high risk of death on admission (area under curve 0.876; p<0.001). When the cut-off value of 5.5 points or more was applied, the sensitivity and specificity was 74.1 and 83.8%, respectively. Our scoring model showed a good discriminatory ability, with an area under the curve of 0.879 for internal validation via bootstrapping, and an area under the curve of 0.886 for external validation.

Conclusions

Our developed scoring model of six variables is simple, convenient, and accurate for screening high-risk patients with HIV/CM, which may be a useful tool for physicians to assess prognosis in HIV/CM inpatients.