Miracle-dz/UniFAR-FTUs huggingface dataset:
Current co-morbidities burden in patients living with HIV in low- and middle-income countries

Purpose of review The present review aims to decipher common co-morbidities faced by people living with HIV in low- to middle-income countries, and in particular the sub-Saharan region, which hosts the majority of the HIV burden worldwide. Recent findings Well-controlled chronic HIV disease is strongly associated with an increased risk of developing cardiovascular disease. This is partly due to the natural aging process, however recent studies show that using antiretroviral therapy as well as the HIV disease itself may be predisposing factors to the development of cardiovascular diseases, creating a new burden for healthcare facilities in the region. Furthermore, newly completed studies assessing inflammation marker albuminuria and age-related syndrome frailty have been found in a higher prevalence than in non-HIV infected people, with increased morbidity and mortality. Summary As antiretroviral medication continues to be well supplied in the region and well tolerated by patients living with HIV, this group is now reckoning with cardiovascular ailments faced by all ageing population therefore there is a need for cardiovascular care systems to be better integrated within the existing, well-performing HIV care systems to address this burden.
Investigation into molecular mechanisms and high-frequency core TCM for pulmonary fibrosis secondary to COVID-19 based on network pharmacology and data mining.

BACKGROUND The complication, pulmonary fibrosis (PF) secondary to COVID-19, may have a second wave of late mortality, given the huge number of individuals infected by COVID-19. However, the molecular mechanisms of PF secondary to COVID-19 haven't been fully elucidated, making the identification of novel strategies for targeted therapy challenging. This study aimed to systematically identify the molecular mechanisms and high-frequency core traditional Chinese medicine (TCM) targeting PF secondary to COVID-19 through network pharmacology and data mining. METHODS The molecular mechanisms of PF secondary to COVID-19 were identified by mapping the COVID-19 differentially expressed gene and known targets associated with PF, protein-protein interactions network analysis, and enrichment pathway analysis; then the high-frequency core TCM targeting PF secondary to COVID-19 were identified by data mining and "Key targets related to PF secondary to COVID-19 - Ingredients" and "Key ingredients-key herbs" network analysis; and last we validated the interaction between the key ingredients and key targets by molecular docking. RESULTS The molecular mechanisms of PF secondary to COVID-19 were mainly related to tumor necrosis factor (TNF) signaling pathway, cytokine-cytokine receptor interaction pathway, and NF-κB signaling pathway. Among these, cytokines interleukin 6 (IL-6), TNF, and IL-1β were identified as the key targets associated with PF secondary to COVID-19. The high-frequency core TCM targeting these key targets were identified, including ingredients of quercetin, epigallocatechin-3-gallate, emodin, triptolide, resveratrol, and herb of Polygonum cuspidatum. Finally, our results were validated by quercetin and resveratrol both well docked to IL-6, TNF, and IL-1β protein, with the estimated docking energy <0 kcal/mol. CONCLUSIONS This study identified the cytokines-related molecular mechanisms of PF secondary to COVID-19, and the high-frequency core TCM against PF by targeting IL-6, TNF, and IL-1β. Which provides new ideas for the discovery of small molecular compounds with potential therapeutic effects on PF secondary to COVID-19.
Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress[OPEN]

Profiling of 11 genome-wide outputs of gene regulation in response to hypoxia reveals multiple aspects of nuclear and whole-cell epigenetic and posttranscriptional gene regulation in Arabidopsis. Gene regulation is a dynamic process involving changes ranging from the remodeling of chromatin to preferential translation. To understand integrated nuclear and cytoplasmic gene regulatory dynamics, we performed a survey spanning the epigenome to translatome of Arabidopsis (Arabidopsis thaliana) seedlings in response to hypoxia and reoxygenation. This included chromatin assays (examining histones, accessibility, RNA polymerase II [RNAPII], and transcription factor binding) and three RNA assays (nuclear, polyadenylated, and ribosome-associated). Dynamic patterns of nuclear regulation distinguished stress-induced and growth-associated mRNAs. The rapid upregulation of hypoxia-responsive gene transcripts and their preferential translation were generally accompanied by increased chromatin accessibility, RNAPII engagement, and reduced Histone 2A.Z association. Hypoxia promoted a progressive upregulation of heat stress transcripts, as evidenced by RNAPII binding and increased nuclear RNA, with polyadenylated RNA levels only elevated after prolonged stress or reoxygenation. Promoters of rapidly versus progressively upregulated genes were enriched for cis-elements of ethylene-responsive and heat shock factor transcription factors, respectively. Genes associated with growth, including many encoding cytosolic ribosomal proteins, underwent distinct histone modifications, yet retained RNAPII engagement and accumulated nuclear transcripts during the stress. Upon reaeration, progressively upregulated and growth-associated gene transcripts were rapidly mobilized to ribosomes. Thus, multilevel nuclear regulation of nucleosomes, transcript synthesis, accumulation, and translation tailor transient stress responses.
Towards a paradigm shift in pediatric rehabilitation: accelerating the uptake of evidence on participation into routine clinical practice

Abstract Purpose Evidence for the importance of focusing on participation to promote health and wellbeing in childhood-onset disability exists, but practice is slow to change. This paper provides a knowledge translation roadmap to accelerate uptake of participation evidence into day-to-day practice. Materials and methods A structured roadmap to guide knowledge translation initiatives for implementing participation-based practices in co-creation with service users was developed based on elements from: the Five-factorframework for predicting implementation outcomes, the Cultural Cone framework, and the Knowledge-to-Action model. Results Guiding principles paired with examples of multi-component knowledge implementation strategies to facilitate readiness for change by stakeholders at the micro (e.g., client/family, service providers), meso (e.g., administrators within organisations such as rehabilitation centres, hospitals, schools) and macro (e.g., local and governmental policy, regulatory bodies) levels are introduced. Solution-based strategies are provided to facilitate “readiness to change” for each stakeholder group. The strategies are examples for successful implementation of evidence-based interventions/approaches that can be contextualized across settings. Conclusions The knowledge translation roadmap can assist children and families, service providers, administrators, and policymakers to bridge existing knowledge-to-practice gaps surrounding participation. Partnering and collaborating through a “family-clinician-manager-community leader-policymaker” synergy is key for achieving strategic practice change focussed on participation. Implications for Rehabilitation Sound evidence surrounding the topic of participation, including effective assessments and interventions, is available and ready for use. Shifting towards participation-focused practices for children and youth with disabilities requires a systemic multi-level KT approach. Our Participation-KT roadmap, comprised of a framework and a list of principles and strategies for implementation, can be used to guide all stakeholders to foster a shift in practice. Forming partnerships and working collaboratively with all stakeholders is key for successful implementation.
Morbidity and Mortality in the Obese Trauma Intensive Care Unit Patient

Introduction Obesity is an epidemic in the United States, known to be associated with comorbidities. However, some data show that obesity may be a protective factor in some instances. The purpose of this study is to determine if there are differences in morbidity and mortality when comparing the obese and non-obese critically ill trauma patient populations. Materials and Methods This was a retrospective study conducted at Prisma Health Upstate in Greenville, South Carolina, an Adult Level 1 Trauma Center. Patients over the age of 18 years admitted due to trauma from February 6, 2016 to February 28, 2019 were included in this study. Burn patients were excluded. An online trauma database was used to obtain age, sex, body mass index, Glasgow coma score (GCS), injury severity score (ISS), revised trauma score (RTS), days on mechanical ventilation, hospital length of stay (LOS), and intensive care unit (ICU) LOS. Results There were 2365 critically ill trauma patients who met inclusion criteria for this study. 1570 patients were men (66.38%) and mean age was 53.2 ± 20.9. Of the patients, 2166 patients had blunt trauma (91.59%). Median GCS was 15 (interquartilerange [IQR]: 12, 15), median RTS was 12 (IQR: 11, 12), and median ISS was 17 (IQR: 9, 22). Obese critically ill trauma patients had significantly lower odds of mortality than nonobese (OR .686, CI 0.473-.977). Penetrating traumas (OR: 4.206, CI: 2.478, 6.990), increased ISS (OR: 1.095, CI: .473, 1.112), and increased age (OR: 1.036, CI: 1.038, 1.045) were associated with significantly increased odds of mortality. Discussion The obesity paradox is observed in the obese critically ill trauma patient population.
Information Quality Frameworks for Digital Health Technologies: Systematic Review

Background Digital health technologies (DHTs) generate a large volume of information used in health care for administrative, educational, research, and clinical purposes. The clinical use of digital information for diagnostic, therapeutic, and prognostic purposes has multiple patient safety problems, some of which result from poor information quality (IQ). Objective This systematic review aims to synthesize an IQ framework that could be used to evaluate the extent to which digital health information is fit for clinical purposes. Methods The review was conducted according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines. We searched Embase, MEDLINE, PubMed, CINAHL, Maternity and Infant Care, PsycINFO, Global Health, ProQuest Dissertations and Theses Global, Scopus, and HMIC (the Health Management Information Consortium) from inception until October 2019. Multidimensional IQ frameworks for assessing DHTs used in the clinical context by health care professionals were included. A thematic synthesis approach was used to synthesize the Clinical Information Quality (CLIQ) framework for digital health. Results We identified 10 existing IQ frameworks from which we developed the CLIQ framework for digital health with 13 unique dimensions: accessibility, completeness, portability, security, timeliness, accuracy, interpretability, plausibility, provenance, relevance, conformance, consistency, and maintainability, which were categorized into 3 meaningful categories: availability, informativeness, and usability. Conclusions This systematic review highlights the importance of the IQ of DHTs and its relevance to patient safety. The CLIQ framework for digital health will be useful in evaluating and conceptualizing IQ issues associated with digital health, thus forestalling potential patient safety problems. Trial Registration PROSPERO International Prospective Register of Systematic Reviews CRD42018097142; https://www.crd. york.ac. uk/prospero/display_record. php? RecordID=97142 International Registered Report Identifier (IRRID) RR2-10.1136/bmjopen-2018-024722
Father’s Bonding With an Infant Born Prematurely: A Qualitative Meta-synthesis

There is no current theory that explains the process of a fathers’ bonding with their infants born prematurely. Through meta-synthesis of 19 qualitative studies, we developed a conceptual framework to illustrate how fathers perceive the relationship with their premature infant formed over the first 18 months of life. It details the contextual factors that contribute to that process. Findings reveal a complex process comprised of five stages, derived from five core themes and related subthemes. Fathers progress through five sequential stages to establish their role as fathers and form emotional connections with their child. Stages include: (a) feeling alien and lacking emotional connection to the infant, (b) caregiving engagement and claiming the role as a father, (c) claiming the infant as their own, (d) adjusting to having the infant home, and (5) normalizing family life. This conceptual framework can inform future research and clinical interventions designed to foster father−infant bonding.
Maternal nutrient restriction in late pregnancy programs postnatal metabolism and pituitary development in beef heifers

Maternal undernutrition during pregnancy followed by ad libitum access to nutrients during postnatal life induces postnatal metabolic disruptions in multiple species. Therefore, an experiment was conducted to evaluate postnatal growth, metabolism, and development of beef heifers exposed to late gestation maternal nutrient restriction. Pregnancies were generated via transfer of in vitro embryos produced using X-bearing sperm from a single Angus sire. Pregnant dams were randomly assigned to receive either 100% (control; n = 9) or 70% (restricted; n = 9) of their total energy requirements from gestational day 158 to parturition. From post-natal day (PND) 301 until slaughter (PND485), heifers were individually fed ad libitum in a Calan gate facility. Calves from restricted dams were lighter than controls at birth (P<0.05) through PND70 (P<0.05) with no difference in body weight from PND105 through PND485 (P>0.10). To assess pancreatic function, glucose tolerance tests were performed on PND315 and PND482 and a diet effect was seen with glucose area under the curve being greater (P<0.05) in calves born to restricted dams compared to controls. At slaughter, total internal fat was greater (P<0.05) in heifers born to restricted dams, while whole pituitary weight was lighter (P<0.05). Heifers from restricted dams had fewer growth hormone-positive cells (somatotrophs) compared to controls (P<0.05). Results demonstrate an impaired ability to clear peripheral glucose in heifers born to restricted dams leading to increased deposition of internal fat. A reduction in the number of somatotrophs may contribute to the adipogenic phenotype of heifers born to restricted dams due to growth hormone’s known anabolic roles in growth, lipolysis, and pancreatic islet function.
Condition‐dependent interaction between mating success and competitive fertilization success in Drosophila melanogaster *

Dietary restriction during development can affect adult body size and condition. In many species, larger (high‐condition) males gain higher mating success through male‐male competition and female choice, and female condition can affect the extent of both female mate choice and male investment in courtship or ejaculates. However, few studies have examined the joint effects and interplay of male and female condition during both the pre‐ and the postcopulatory phases of sexual selection. We therefore manipulated the larval diet of male and female Drosophila melanogaster to study how body size variation in both sexes biases competitive outcomes at different reproductive stages, from mating to paternity. We did not find a difference in mate preference or mating latency between females of different conditions, nor any interaction between male and female conditions. However, large males were more successful in gaining matings, but only when in direct competition, whereas mating latencies were shorter for low‐condition males in noncompetitive settings. Small males also transferred more sperm to nonvirgin females, displaced a larger proportion of resident sperm, and achieved higher paternity shares per mating than large males. In agreement with existing theory, we suggest that small males might partially compensate for their low mating success by strategically investing in larger sperm numbers and potentially other, unmeasured ejaculate traits, when they do have a mating opportunity.
Acute Bilateral Neuroretinitis and Panuveitis in A Patient with Coronavirus Disease 2019: A Case Report

ABSTRACT Purpose: Herein, we report a case of bilateral neuroretinitis and panuveitis in a patient recovered from coronavirus disease 2019 (COVID-19). Case presentation: A 37-year-old male patient with a history of recovered COVID-19, which was confirmed with nasopharyngeal reverse transcriptase polymerase chain reaction (RT-PCR) for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), about one-month ago was referred with one-week history of bilateral severe vision loss. Visual acuity was counting fingers, and bilateral retinitis and panuveitis were revealed in ocular examination. The result of the vitreous sample using RT-PCR was positive for SARS-CoV-2 and negative for Herpesviridae viruses and mycobacterium tuberculosis. The patient was successfully treated with corticosteroid. Conclusion: We report a case of bilateral neuroretinitis and panuveitisin a recovered COVID-19 patient and positive RT-PCR of the vitreous sample. It is suggested to apply intraocular sampling and evaluation for COVID-19 in patients with the new-onset of uveitis and/or retinitis during the pandemic.
The relationship between polymorphisms of microRNA and preeclampsia

Abstract Background: Preeclampsia has genetic correlation. Many studies have shown that microRNA (miRNA) polymorphism is highly associated with preeclampsia, but the results are inconsistent. The purpose of this study is to systematically evaluate the relationship between miRNA polymorphism and preeclampsia. Methods: In this study, the search time is set from the establishment of the database on January 2021. The search database include China National Knowledge Infrastructure (CNKI), Wanfang, VIP and China Biology Medicine disc (CBM), PubMed, EMBASE, and Web of Science, and the Cochrane Library. The subjects are case-control studies on the relationship between miRNA polymorphism and preeclampsia. The language is limited to English and Chinese. The data of the included study are extracted and the literature quality is evaluated by 2 researchers independently. The data are statistically analyzed through Stata 16.0 software. We also predicted the miRNA secondary structure and the binding sites of miRNA interaction with its target genes Results: This review will be disseminated in print by peer-review. Conclusion: This study will provide evidence-based medicine to elucidate the genetic tendency of preeclampsia. Ethics and dissemination: Private information from individuals will not be published. This systematic review also does not involve endangering participant rights. Ethical approval will not be required. The results may be published in a peer-reviewed journal or disseminated at relevant conferences. OSF Registration number: DOI 10.17605/OSF.IO/MJY2X.
Efficiency of fertilizer formulation, stock solution volume and media on chili (Capsicum annum kulai F1)

ABSTRACT The growth of the greenhouse chili industry is rapidly increasing in the world including Malaysia. Currently, compost is the most popular growing media. Four fertilizer formulations commonly used by farmers (Local), including the recommended Cooper, Bennoit and Cooper Modified formulation, were evaluated in combination with two volumes (400 and 750 L) for enhancement fruit yield of chili in soilless culture. The results indicate that, the day of blooming and fruiting was reduced by 91% and 50% in media containing coconut dust (CD) + empty fruit bunch (EFB) compared with CD alone. Yield with CD+EFB was increased 36% compared with CD while volume of water shows insignificant difference. Interestingly, Cooper, Local and Cooper Modified formulation enhanced 32, 28 and 19% of yield, respectively. As conclusion, combination of CD+EFB with Cooper, Local and Cooper Modified were more efficient in yield production compared with CD alone for future research.
Prevalence and Persistent Shedding of Fecal SARS-CoV-2 RNA in Patients With COVID-19 Infection: A Systematic Review and Meta-analysis

INTRODUCTION: The prevalence and shedding of fecal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA indicate coronavirus disease 2019 (COVID-19) infection in the gastrointestinal (GI) tract and likely infectivity. We performed a systemic review and meta-analysis to evaluate the prevalence and the duration of shedding of fecal RNA in patients with COVID-19 infection. METHODS: PubMed, Embase, Web of Science, and Chinese databases Chinese National Knowledge Infrastructure and Wanfang Data up to June 2020 were searched for studies evaluating fecal SARS-CoV-2 RNA, including anal and rectal samples, in patients with confirmed COVID-19 infection. The pooled prevalence of fecal RNA in patients with detectable respiratory RNA was estimated. The days of shedding and days to loss of fecal and respiratory RNA from presentation were compared. RESULTS: Thirty-five studies (N = 1,636) met criteria. The pooled prevalence of fecal RNA in COVID-19 patients was 43% (95% confidence interval [CI] 34%–52%). Higher proportion of patients with GI symptoms (52.4% vs 25.9%, odds ratio = 2.4, 95% CI 1.2–4.7) compared with no GI symptoms, specifically diarrhea (51.6% vs 24.0%, odds ratio = 3.0, 95% CI 1.9–4.8), had detectable fecal RNA. After loss of respiratory RNA, 27% (95% CI 15%–44%) of the patients had persistent shedding of fecal RNA. Days of RNA shedding in the feces were longer than respiratory samples (21.8 vs 14.7 days, mean difference = 7.1 days, 95% CI 1.2–13.0). Furthermore, days to loss of fecal RNA lagged respiratory RNA by a mean of 4.8 days (95% CI 2.2–7.5). DISCUSSION: Fecal SARS-CoV-2 RNA is commonly detected in COVID-19 patients with a 3-fold increased risk with diarrhea. Shedding of fecal RNA lasted more than 3 weeks after presentation and a week after last detectable respiratory RNA.
TGF‐β as a driver of fibrosis: physiological roles and therapeutic opportunities

Many chronic diseases are marked by fibrosis, which is defined by an abundance of activated fibroblasts and excessive deposition of extracellular matrix, resulting in loss of normal function of the affected organs. The initiation and progression of fibrosis are elaborated by pro‐fibrotic cytokines, the most critical of which is transforming growth factor‐β1 (TGF‐β1). This review focuses on the fibrogenic roles of increased TGF‐β activities and underlying signaling mechanisms in the activated fibroblast population and other cell types that contribute to progression of fibrosis. Insight into these roles and mechanisms of TGF‐β as a universal driver of fibrosis has stimulated the development of therapeutic interventions to attenuate fibrosis progression, based on interference with TGF‐β signaling. Their promise in preclinical and clinical settings will be discussed. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.