Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporation of information diffusion model for enhancing analyses in HIV molecular surveillance

ABSTRACT Molecular surveillance of infections is essential in monitoring their transmission in the population. In this study, newly diagnosed HIV patients' phylogenetic, clinical and behavioural data were integrated, and an information diffusion model was incorporated in analysing transmission dynamics. A genetic network was constructed from HIV sequences, from which transmission cascades were extracted. From the transmission cascades, CRF01_AE had higher values of information diffusion metrics, including scale, speed and range, than that of B, signifying the distinct transmission patterns of two circulating subtypes in Hong Kong. Patients connected in the network, were more likely male, younger, of main circulating subtypes, to have acquired HIV infection locally, and a higher CD4 level at diagnosis. Genetic connections varied among men who have sex with men (MSM) who used different channels of sex networking and varied in their engagement in risk behaviours. MSM using recreational drugs for sex held positions of greater importance within the network. Significant differences in network metrics were observed among MSM as differentiated by their mobile apps usage patterns, evidencing the impact of social network on transmission networks. The applied model in the presence of consistently collected longitudinal data could enhance HIV molecular epidemiologic surveillance for informing future intervention planning.
Impact of forest plantation on methane emissions from tropical peatland

Tropical peatlands are a known source of methane (CH4) to the atmosphere, but their contribution to atmospheric CH4 is poorly constrained. Since the 1980s, extensive areas of the peatlands in Southeast Asia have experienced land‐cover change to smallholder agriculture and forest plantations. This land‐cover change generally involves lowering of groundwater level (GWL), as well as modification of vegetation type, both of which potentially influence CH4 emissions. We measured CH4 exchanges at the landscape scale using eddy covariance towers over two land‐cover types in tropical peatland in Sumatra, Indonesia: (a) a natural forest and (b) an Acacia crassicarpa plantation. Annual CH4 exchanges over the natural forest (9.1 ± 0.9 g CH4 m−2 year−1) were around twice as high as those of the Acacia plantation (4.7 ± 1.5 g CH4 m−2 year−1). Results highlight that tropical peatlands are significant CH4 sources, and probably have a greater impact on global atmospheric CH4 concentrations than previously thought. Observations showed a clear diurnal variation in CH4 exchange over the natural forest where the GWL was higher than 40 cm below the ground surface. The diurnal variation in CH4 exchanges was strongly correlated with associated changes in the canopy conductance to water vapor, photosynthetic photon flux density, vapor pressure deficit, and air temperature. The absence of a comparable diurnal pattern in CH4 exchange over the Acacia plantation may be the result of the GWL being consistently below the root zone. Our results, which are among the first eddy covariance CH4 exchange data reported for any tropical peatland, should help to reduce the uncertainty in the estimation of CH4 emissions from a globally important ecosystem, provide a more complete estimate of the impact of land‐cover change on tropical peat, and develop science‐based peatland management practices that help to minimize greenhouse gas emissions.
HIV infection confers distinct mechanisms in severe drug eruption: Endogenous virus activation with aberrant Th2/Th1 and CD8+ T cells function

Severe drug eruption (SDE), a common skin disease, becomes dangerous when it occurs in patients with human immunodeficiency virus (HIV). However, the molecular mechanisms are poorly understood. Forty patients including HIV+ SDE+ (n = 15), HIV− SDE+ (n = 15) and HIV+ SDE− (n = 10) subjects were enrolled in our study. All HIV+ patients were at acquired immune deficiency syndrome (AIDS) stage. Serum levels of TNF‐α, IFN‐γ, IL‐4, IL‐13, IL‐6, CXCL9, and CCL17 were quantified by ELISA. Epstein–Barr virus (EBV) and cytomegalovirus (CMV) loads were quantified by RT‐qPCR. CD4, CD8, Th1, Th2, TNF‐α‐CD8, and IFN‐γ‐CD8 T cell populations were measured by flow cytometry. Levels of biochemical indexes in HIV+ SDE+ patients were significantly different from in HIV− SDE+ patients (P < .05). EBV and CMV viral loads were significantly higher in HIV+ SDE+ patients, but not in HIV− SDE+ patients (P < .05). Inflammatory cytokines TNF‐α and IFN‐γ were significantly elevated in HIV+ SDE+ patients (P < .05). Th2/Th1 populations and TNF‐α secreting or IFN‐γ secreting CD8+ T cells, were significantly up‐regulated in HIV+ SDE+ patients compared to HIV− SDE+ patients (P < .05). Conversely, the CD4/CD8 ratio was significantly down‐regulated in HIV+ SDE+ patients compared to HIV− SDE+ patients (P < .05). HIV infection confers distinct clinical phenotypes and immune inflammatory mechanisms in SDE. Sustained EBV and CMV activation, unbalanced Th2/Th1 and overactive CD8+ T cells mediating a pro‐inflammatory response could act as distinct mechanisms in the aggravation of SDE in HIV+ SDE+ patients.
Independent Association Between Type of Intra-Operative Blood Transfusion and Post-Operative Delirium After Complex Spinal Fusion for Adult Deformity Correction.

STUDY DESIGN Retrospective cohort study. OBJECTIVE To determine whether type of intra-operative blood transfusion used is associated with increased incidence of post-operative delirium after complex spine fusion involving 5 levels or greater. SUMMARY OF BACKGROUND DATA Post-operative delirium after spine surgery has been associated with age, cognitive status, and several comorbidities. Intraoperative allogenic blood transfusions have previously been linked to greater complication risks and length of hospital stay. However, whether type of intra-operative blood transfusion used increases the risk for post-operative delirium after complex spinal fusion remains relatively unknown. METHODS The medical records of 130 adult (≥18 years old) spine deformity patients undergoing elective, primary complex spinal fusion (≥5 levels) for deformity correction at a major academic institution from 2010 to 2015 were reviewed. We identified 104 patients who encountered an intraoperative blood transfusion. Of the 104, 15 (11.5%) had Allogenic-only, 23 (17.7%) had Autologous-only, and 66 (50.8%) had Combined transfusions. The primary outcome investigated was the rate of post-operative delirium. RESULTS There were significant differences in estimated blood loss (Combined: 2155.5 ± 1900.7 mL vs. Autologous: 1396.5 ± 790.0 mL vs. Allogenic: 1071.3 ± 577.8 mL vs. None: 506.9 ± 427.3 mL, p < 0.0001) and amount transfused (Combined: 1739.7 ± 1127.6 mL vs. Autologous: 465.7 ± 289.7 mL vs. Allogenic: 986.9 ± 512.9 mL, p < 0.0001). The Allogenic cohort had a significantly higher proportion of patients experiencing delirium (Combined: 7.6% vs. Autologous: 17.4% vs. Allogenic: 46.7% vs. None: 11.5%, p = 0.002). In multivariate nominal-logistic regression analysis, Allogenic [OR: 24.81, 95%CI (3.930, 156.702), p = 0.0002) and Autologous [OR: 6.43, 95%CI (1.156, 35.772), p = 0.0335) transfusions were independently associated with post-operative delirium. CONCLUSIONS Our study suggests that there may be an independent association between intraoperative autologous and allogenic blood transfusions and post-operative delirium after complex spinal fusion. Further studies are necessary to identify the physiological effect of blood transfusions to better overall patient care and reduce healthcare expenditures. LEVELS OF EVIDENCE 3.
Call to action: a collaborative framework to better support female rugby league players

Women’s sports have seen a substantial increase in participation numbers and in their professionalism. There was a 29% increase in the number of Australian women who played rugby league in 20181 and there have been increased competition pathways for women in both Australia (ie, National Rugby League Women’s (NRLW) premiership) and England (ie, Women’s Super League (WSL)). Although female sporting teams and leagues struggle with participation, financial investment and spectatorship (ie, sociological factors),2 both the NRLW and WSL have major naming right sponsors. The Australian NRLW and State of Origin matches and the WSL grand final are also broadcast live on television. There is a paucity of sports science, clinical and medical literature on female rugby league players (n=8 articles; Scopus, July 2019). We attribute this to factors such as, participation numbers, limited years of professional women’s rugby league (ie, 2 years in Australia and 3 years in England) and a number of complex sociological factors. Much of the published research is outdated. Indeed the available injury surveillance research3 is over 10 years old and the types and rates of …
Exercise training attenuates angiotensin II‐induced vasoconstriction in the aorta of normotensive but not hypertensive rats

What is the central question of this study? What are the effects of exercise on Ang II‐induced vasoconstriction in aortas of normotensive rats and how do these effects occur in two‐kidney–one‐clip hypertensive animals? What is the main finding and its importance? In two‐kidney rats, exercise training improves the Ang II‐induced vasoconstriction by endothelium‐derived NO released through AT2R activation. This effect of exercise training on the Ang II‐induced vasoconstriction is blunted in two‐kidney–one‐clip hypertensive animals, possibly as a consequence of oxidative stress.
Prevalence and Factors Associated with Driving Under the Influence of Alcohol in Brazil: An Analysis by Macroregion

Objective: To analyze the prevalence and factors associated with driving under the influence of alcohol (DUIA) in Brazil, according to macroregion. Methods: A cross-sectional study was conducted using data from individuals aged 18 years or older who participated in the 2013 National Health Survey in Brazil. Subjects were selected by probabilistic sampling and interviewed through home visits. Prevalence of DUIA was estimated according to the number of drivers and/or motorcyclists who reported consuming alcohol in the previous 30 days (n = 9537). Poisson regression was used to analyze the factors associated with DUIA to Brazil and in each macroregion of the country. Results: The prevalence of DUIA was 27.5%, 29.4%, 29.6%, 22.9%, and 20.8% in the North, Northeast, Central-West, South, and Southeast macroregions, respectively. The overall prevalence of Brazil was 24.3%. In most macroregions, the main predictors of DUIA were male sex, high educational level, living in outside the capital or metropolitan regions (other regions), and binge drinking in the previous 30 days. Depression was a predictor in Brazil and two macroregions. Conclusion: A high prevalence of DUIA was observed in Brazil, especially in the Central-West, Northeast and, North macro-regions. Factors associated with DUIA can be incorporated to develop effective interventions to reduce this behavior in Brazil.
Pattern Recognition in Musculoskeletal Imaging Using Artificial Intelligence

Abstract Artificial intelligence (AI) has the potential to affect every step of the radiology workflow, but the AI application that has received the most press in recent years is image interpretation, with numerous articles describing how AI can help detect and characterize abnormalities as well as monitor disease response. Many AI-based image interpretation tasks for musculoskeletal (MSK) pathologies have been studied, including the diagnosis of bone tumors, detection of osseous metastases, assessment of bone age, identification of fractures, and detection and grading of osteoarthritis. This article explores the applications of AI for image interpretation of MSK pathologies.
Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation

Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.
Design, Synthesis, Molecular Modelling and Anticancer Activities of New Fused Phenanthrolines

Three series of fused pyrrolophenanthroline derivatives were designed as analogues of phenstatin and synthesized in two steps starting with 1,7-phenanthroline, 4,7-phenanthroline and 1,10-phenanthroline, respectively. Two (Compounds 8a and 11c) of the four compounds tested against a panel of sixty human cancer cell lines of the National Cancer Institute (NCI) exhibited significant growth inhibition activity on several cell lines. Compound 11c showed a broad spectrum in terms of antiproliferative efficacy with GI50 values in the range of 0.296 to 250 μM. Molecular docking studies indicated that Compounds 8a and 11c are accommodated in the colchicine binding site of tubulin in two different ways.
Maternal Milk and Relationships to Early Neurobehavioral Outcome in Preterm Infants

The purpose of this study was to (1) define medical and sociodemographic factors related to maternal milk feedings and (2) explore relationships between maternal milk feeding and early neurobehavioral outcome. Ninety-two preterm infants born ≤ 32 weeks gestation had maternal milk feeding and breastfeeding tracked in this retrospective analysis. At 34 to 41 weeks postmenstrual age (PMA), neurobehavior was assessed with the NICU Network Neurobehavioral Scale. Maternal milk feeding was often delayed by the use of total parenteral nutrition, administered for a median of 11 (7-26) days, impacting the timing of gastric feeding initiation. Seventy-nine (86%) infants received some maternal milk during neonatal intensive care unit (NICU) hospitalization. Twenty-one (27%) infants continued to receive maternal milk at 34 to 41 weeks PMA, with 10 (48%) of those receiving maternal milk exclusively. Among mothers who initiated maternal milk feeds, 20 (25%) put their infants directly at the breast at least once during hospitalization. Mothers who were younger (P = .02), non-Caucasian (P < .001), or on public insurance (P < .001) were less likely to provide exclusive maternal milk feedings by 34 to 41 weeks PMA. Infants who received maternal milk at 34 to 41 weeks PMA demonstrated better orientation (P = .03), indicating they had better visual and auditory attention to people and objects in the environment. Our findings demonstrate a relationship between maternal milk feedings and better neurobehavior, which is evident before the infant is discharged home from the NICU.
Arabidopsis tRNA-derived fragments as potential modulators of translation

ABSTRACT Transfer RNA-derived fragments (tRFs) exist in all branches of life. They are involved in RNA degradation, regulation of gene expression, ribosome biogenesis. In archaebacteria, kinetoplastid, yeast, and human cells, they were also shown to regulate translation. In Arabidopsis, the tRFs population fluctuates under developmental or environmental conditions but their functions are yet poorly understood. Here, we show that populations of long (30–35 nt) or short (19–25 nt) tRFs produced from Arabidopsis tRNAs can inhibit in vitro translation of a reporter gene. Analysing a series of oligoribonucleotides mimicking natural tRFs, we demonstrate that only a limited set of tRFs possess the ability to affect protein synthesis. Out of a dozen of tRFs, only two deriving from tRNAAla(AGC) and tRNAAsn(GUU) strongly attenuate translation in vitro. Contrary to human tRF(Ala), the 4 Gs present at the 5ʹ extremity of Arabidopsis tRF(Ala) are not implicated in this inhibition while the G18 and G19 residues are essential. Protein synthesis inhibition by tRFs does not require complementarity with the translated mRNA but, having the capability to be associated with polyribosomes, tRFs likely act as general modulation factors of the translation process in plants.
Hepatitis C Virus Infection in Pregnancy

Parenteral transmission is the major route of hepatitis C virus transmission in adults; however, vertical transmission is most common in children. There are several factors that have been shown to be associated with vertical transmission of hepatitis C virus, including hepatitis C virus RNA, human immunodeficiency virus coinfection, and peripheral blood mononuclear cell infection. As there is no effective vaccine to prevent hepatitis C virus infection, and there are no human data describing the safety of the new direct acting antiviral agents in pregnancy, the only preventive strategy for vertical transmission is to treat the hepatitis C virus infection before becoming pregnant. Direct acting antiviral agents are interferon-free, and many are also ribavirin-free. Based on animal studies, sofosbuvir plus ledipasvir may be the best safety profile during pregnancy for now; however, it is too early to recommend treating hepatitis C virus-infected pregnant women with these direct acting antiviral agents currently.
Scaling‐up biodiversity‐ecosystem functioning research

Abstract A rich body of knowledge links biodiversity to ecosystem functioning (BEF), but it is primarily focused on small scales. We review the current theory and identify six expectations for scale dependence in the BEF relationship: (1) a nonlinear change in the slope of the BEF relationship with spatial scale; (2) a scale‐dependent relationship between ecosystem stability and spatial extent; (3) coexistence within and among sites will result in a positive BEF relationship at larger scales; (4) temporal autocorrelation in environmental variability affects species turnover and thus the change in BEF slope with scale; (5) connectivity in metacommunities generates nonlinear BEF and stability relationships by affecting population synchrony at local and regional scales; (6) spatial scaling in food web structure and diversity will generate scale dependence in ecosystem functioning. We suggest directions for synthesis that combine approaches in metaecosystem and metacommunity ecology and integrate cross‐scale feedbacks. Tests of this theory may combine remote sensing with a generation of networked experiments that assess effects at multiple scales. We also show how anthropogenic land cover change may alter the scaling of the BEF relationship. New research on the role of scale in BEF will guide policy linking the goals of managing biodiversity and ecosystems.
Euphanoids A and B, two new lathyrane diterpenoids with nitric oxide (NO) inhibitory activity from Euphorbia kansuensis

Abstract Two new lathyrane diterpenoids, euphanoids A and B (1 and 2), along with five known compounds (3–7) were isolated from the roots of Euphorbia kansuensis. Their structures were elucidated by spectroscopic analysis, and the absolute configuration of 1 was determined by single crystal X-ray diffraction. All of the isolates were screened for the inhibitory effects on nitric oxide (NO) production induced by lipopolysaccharide (LPS) in RAW264.7 cells, and compounds 1 and 2 showed pronounced inhibition on NO production with IC50 values of 4.7 and 9.5 μM, respectively, being more active than the positive control, quercetin (IC50 = 10.8 μM). Graphical Abstract
N‐acetyl‐seryl‐aspartyl‐lysyl‐proline is a valuable endogenous antifibrotic peptide for kidney fibrosis in diabetes: An update and translational aspects

N‐acetyl‐seryl‐aspartyl‐lysyl‐proline (AcSDKP) is an endogenous peptide that has been confirmed to show excellent organ‐protective effects. Even though originally discovered as a modulator of hemotopoietic stem cells, during the recent two decades, AcSDKP has been recognized as valuable antifibrotic peptide. The antifibrotic mechanism of AcSDKP is not yet clear; we have established that AcSDKP could target endothelial–mesenchymal transition program through the induction of the endothelial fibroblast growth factor receptor signaling pathway. Also, recent reports suggested the clinical significance of AcSDKP. The aim of this review was to update recent advances of the mechanistic action of AcSDKP and discuss translational research aspects.
Family History of Gastric Cancer and Helicobacter pylori Treatment.

BACKGROUND Helicobacter pylori infection and a family history of gastric cancer are the main risk factors for gastric cancer. Whether treatment to eradicate H. pylori can reduce the risk of gastric cancer in persons with a family history of gastric cancer in first-degree relatives is unknown. METHODS In this single-center, double-blind, placebo-controlled trial, we screened 3100 first-degree relatives of patients with gastric cancer. We randomly assigned 1838 participants with H. pylori infection to receive either eradication therapy (lansoprazole [30 mg], amoxicillin [1000 mg], and clarithromycin [500 mg], each taken twice daily for 7 days) or placebo. The primary outcome was development of gastric cancer. A prespecified secondary outcome was development of gastric cancer according to H. pylori eradication status, assessed during the follow-up period. RESULTS A total of 1676 participants were included in the modified intention-to-treat population for the analysis of the primary outcome (832 in the treatment group and 844 in the placebo group). During a median follow-up of 9.2 years, gastric cancer developed in 10 participants (1.2%) in the treatment group and in 23 (2.7%) in the placebo group (hazard ratio, 0.45; 95% confidence interval [CI], 0.21 to 0.94; P = 0.03 by log-rank test). Among the 10 participants in the treatment group in whom gastric cancer developed, 5 (50.0%) had persistent H. pylori infection. Gastric cancer developed in 0.8% of participants (5 of 608) in whom H. pylori infection was eradicated and in 2.9% of participants (28 of 979) who had persistent infection (hazard ratio, 0.27; 95% CI, 0.10 to 0.70). Adverse events were mild and were more common in the treatment group than in the placebo group (53.0% vs. 19.1%; P<0.001). CONCLUSIONS Among persons with H. pylori infection who had a family history of gastric cancer in first-degree relatives, H. pylori eradication treatment reduced the risk of gastric cancer. (Funded by the National Cancer Center, South Korea; ClinicalTrials.gov number, NCT01678027.).