Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Patterns of Recombination across Human Viruses

Abstract Viral recombination is a major evolutionary mechanism driving adaptation processes, such as the ability of host-switching. Understanding global patterns of recombination could help to identify underlying mechanisms and to evaluate the potential risks of rapid adaptation. Conventional approaches (e.g., those based on linkage disequilibrium) are computationally demanding or even intractable when sequence alignments include hundreds of sequences, common in viral data sets. We present a comprehensive analysis of recombination across 30 genomic alignments from viruses infecting humans. In order to scale the analysis and avoid the computational limitations of conventional approaches, we apply newly developed topological data analysis methods able to infer recombination rates for large data sets. We show that viruses, such as ZEBOV and MARV, consistently displayed low levels of recombination, whereas high levels of recombination were observed in Sarbecoviruses, HBV, HEV, Rhinovirus A, and HIV. We observe that recombination is more common in positive single-stranded RNA viruses than in negatively single-stranded RNA ones. Interestingly, the comparison across multiple viruses suggests an inverse correlation between genome length and recombination rate. Positional analyses of recombination breakpoints along viral genomes, combined with our approach, detected at least 39 nonuniform patterns of recombination (i.e., cold or hotspots) in 18 viral groups. Among these, noteworthy hotspots are found in MERS-CoV and Sarbecoviruses (at spike, Nucleocapsid and ORF8). In summary, we have developed a fast pipeline to measure recombination that, combined with other approaches, has allowed us to find both common and lineage-specific patterns of recombination among viruses with potential relevance in viral adaptation.
Exploring the role of healthy dogs as hosts of enterohepatic Helicobacter species using cultivation‐dependent and ‐independent approaches

Enterohepatic Helicobacter (EHH) species have been increasingly associated with acute gastroenteritis, inflammatory bowel disease and hepatobiliary diseases in humans. However, their host range and transmission routes are poorly understood. Therefore, the aim of this study was to determine the presence of EHH in healthy dogs using both cultivation‐dependent and ‐independent methods. Three hundred and ninety faecal samples from domestic dogs without gastrointestinal symptoms were analysed between June 2018 and July 2019 in Valdivia (South of Chile). Samples were inoculated on selective medium and in parallel were filtrated over an antibiotic‐free blood agar. Both media were incubated in a microaerobic atmosphere at 37°C for 7 days. Colonies were identified by PCR and phylogenetic analysis. A subset of 50 samples (half of them positive for EHH by cultivation and the remaining half negative) was analysed by PCR‐Denaturing Gradient Gel Electrophoresis (PCR‐DGGE) for direct detection. Cultivation method detected EHH in 15.4% (60/390) of the samples, being the most prevalent species H. canis (5.8%, 23/390) and H. canicola (5.1%, 20/390), followed by H. bilis (3.6%, 14/390) and ‘H. winghamensis’ (1.3%, 5/390). In contrast, PCR‐DGGE method detected Helicobacter DNA in almost all (96%, 48/50) tested samples. On the other hand, the method used also allowed to isolate other Campylobacterales, in fact 44.3% (173/390) of the samples were positive for Campylobacter upsaliensis (43.3%, 169/390) followed by C. jejuni (2.0%, 8/390). Moreover, two strains that presented Campylobacter‐like morphology were finally identified as Anaerobiospirillum succiniciproducens. Our results indicate that healthy domestic dogs commonly carry EHH and other Campylobacter species. However, further studies are needed to determine whether and how these Helicobacter and Campylobacter species can be transmitted to humans.
Influence of regional white matter hyperintensity volume and apolipoprotein E ε4 status on hippocampal volume in healthy older adults

While total white matter hyperintensity (WMH) volume on magnetic resonance imaging (MRI) has been associated with hippocampal atrophy, less is known about how the regional distribution of WMH volume may differentially affect the hippocampus in healthy aging. Additionally, apolipoprotein E (APOE) ε4 carriers may be at an increased risk for greater WMH volumes and hippocampal atrophy in aging. The present study sought to investigate whether regional WMH volume mediates the relationship between age and hippocampal volume and if this association is moderated by APOE ε4 status in a group of 190 cognitively healthy adults (APOE ε4 status [carrier/non‐carrier] = 59/131), ages 50–89. Analyses revealed that temporal lobe WMH volume significantly mediated the relationship between age and average bilateral hippocampal volume, and this effect was moderated by APOE ε4 status (−0.020 (SE = 0.009), 95% CI, [−0.039, −0.003]). APOE ε4 carriers, but not non‐carriers, showed negative indirect effects of age on hippocampal volume through temporal lobe WMH volume (APOE ε4 carriers: −0.016 (SE = 0.007), 95% CI, [−0.030, −0.003]; APOE ε4 non‐carriers: . 005 (SE = 0.006), 95% CI, [−0.006, 0.017]). These findings remained significant after additionally adjusting for sex, years of education, hypertension status and duration, cholesterol status, diabetes status, Body Mass Index, history of smoking, and the Wechsler Adult Intelligence Scale‐IV Full Scale IQ. There were no significant moderated mediation effects for frontal, parietal, and occipital lobe WMH volumes, with or without covariates. Our findings indicate that in cognitively healthy older adults, elevated WMH volume regionally localized to the temporal lobes in APOE ε4 carriers is associated with reduced hippocampal volume, suggesting greater vulnerability to brain aging and the risk for Alzheimer's disease.
Novel Variant Findings and Challenges Associated With the Clinical Integration of Genomic Testing: An Interim Report of the Genomic Medicine for Ill Neonates and Infants (GEMINI) Study.

Importance A targeted genomic sequencing platform focused on diseases presenting in the first year of life may minimize financial and ethical challenges associated with rapid whole-genomic sequencing. Objective To report interim variants and associated interpretations of an ongoing study comparing rapid whole-genomic sequencing with a novel targeted genomic platform composed of 1722 actionable genes targeting disorders presenting in infancy. Design, Setting, and Participants The Genomic Medicine in Ill Neonates and Infants (GEMINI) study is a prospective, multicenter clinical trial with projected enrollment of 400 patients. The study is being conducted at 6 US hospitals. Hospitalized infants younger than 1 year of age suspected of having a genetic disorder are eligible. Results of the first 113 patients enrolled are reported here. Patient recruitment began in July 2019, and the interim analysis of enrolled patients occurred from March to June 2020. Interventions Patient (proband) and parents (trios, when available) were tested simultaneously on both genomic platforms. Each laboratory performed its own phenotypically driven interpretation and was blinded to other results. Main Outcomes and Measures Variants were classified according to the American College of Medical Genetics and Genomics standards of pathogenic (P), likely pathogenic (LP), or variants of unknown significance (VUS). Chromosomal and structural variations were reported by rapid whole-genomic sequencing. Results Gestational age of 113 patients ranged from 23 to 40 weeks and postmenstrual age from 27 to 83 weeks. Sixty-seven patients (59%) were male. Diagnostic and/or VUS were returned for 51 patients (45%), while 62 (55%) had negative results. Results were concordant between platforms in 83 patients (73%). Thirty-seven patients (33%) were found to have a P/LP variant by 2 or both platforms and 14 (12%) had a VUS possibly related to phenotype. The median day of life at diagnosis was 22 days (range, 3-313 days). Significant alterations in clinical care occurred in 29 infants (78%) with a P/LP variant. Incidental findings were reported in 7 trios. Of 51 positive cases, 34 (67%) differed in the reported result because of technical limitations of the targeted platform, interpretation of the variant, filtering discrepancies, or multiple causes. Conclusions and Relevance As comprehensive genetic testing becomes more routine, these data highlight the critically important variant detection capabilities of existing genomic sequencing technologies and the significant limitations that must be better understood.
Evaluating WHO prescribed sanitary inspection templates for assessing contamination risks in tubewells with handpump – case of 9 Indian districts

Abstract WHO prescribes Sanitary Inspections in recommended formats for assessing contamination risks in Tubewells installed with handpump that often constitute primary drinking water sources in rural and remote areas. Sanitary inspections are easy alternatives to costlier and technically demanding laboratory water quality analysis. However, their efficacy remains uncertain despite decades of widespread usage. This study evaluates sanitary inspections by assessing contamination risk in 324 Tubewells with handpump across 9 districts in India. Results indicate that 62% of sampled sources were safe in lab analysis, despite sanitary inspections indicating varying risks. This implies that WHO prescribed inspections yield higher risks, and overestimated risk perception are likely to skew planning and policy, resulting in budgetary over-allocations and financial mismanagement in water-supplies. There is thus an urgent need to review and revise WHO prescribed sanitary inspection templates.
The Effectiveness of Levosimendan on Veno-Arterial Extracorporeal Membrane Oxygenation Management and Outcome: A Systematic Review and Meta-Analysis.

OBJECTIVES Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) provides a temporary support system for patients with cardiogenic shock refractory to conventional medical therapies. It has been reported that levosimendan may facilitate VA-ECMO weaning and improve survival. The primary objective of this review was to examine the effect of levosimendan use on VA-ECMO weaning and mortality in critically ill patients on VA-ECMO. DESIGN MEDLINE, EMBASE, and CENTRAL were searched. A pair of reviewers identified eligible clinical trials. Two reviewers extracted data and independently assessed the risk of bias. A random-effect model was used to combine data. The primary outcome was the success of weaning from VA-ECMO. MEASUREMENTS AND MAIN RESULTS Seven studies of observational design, including a total of 630 patients, were selected in the final analysis. The sample size ranged from ten-to-240 patients, with a mean age between 53 and 65 years, and more than half of them underwent cardiac surgeries. The VA-ECMO durations varied between four and 11.6 days. Overall, levosimendan use was significantly associated with successful weaning compared with control (odds ratio [OR] 2.89, 95% CI, 1.53-5.46; poverall effect = 0.001); I2 = 49%). For survival, six studies (n = 617) were included in the meta-analysis involving 326 patients in the levosimendan group and 291 in the comparator group. Pooled results showed a significantly higher survival rate in the levosimendan group (OR 0.46, 95% CI, 0.30-0.71; poverall effect = 0.0004; I2 = 20%). CONCLUSIONS Levosimendan therapy was significantly associated with successful weaning and survival benefit in patients with cardiogenic or postcardiotomy shock needing VA-ECMO support for severe cardiocirculatory compromise. To date, there is limited literature and absence of evidence from randomized trials addressing the use of levosimendan in VA-ECMO weaning. This study may be considered a hypothesis-generating research for randomized controlled trials to confirm its findings.
DEVELOPMENT OF A GRID SEARCH MOLECULAR MECHANICS MODELING STRATEGY TO STUDY ELUTION BEHAVIOR IN CYCLODEXTRIN MODIFIED CAPILLARY ELECTROPHORESIS

Novel methods to use molecular mechanics (MM) in modeling solute-receptor interactions are developed that are pertinent to computational studies of dynamic separation or sensing processes. Specifically, a grid search MM modeling approach is used to study separation behavior in cyclodextrin (CD)-modified capillary electrophoresis (CE). Laboratory CE separations of di-substituted naphthalene compounds are accomplished employing an anionic, single isomer carboxymethyl-CD as a running buffer additive. Computational work involved the docking of these solutes into the cavity of this CD using a systematic grid search to probe the interaction space. It was discovered that the size of incremental changes in position and dimensional freedom in defining the grid are significant parameters. At each grid position the configuration of the atoms in the complex is altered in a process to minimize energy. It was discovered that comprehensive minimization involving many iterations of the process is extremely important in locating true low energy conformers. Interaction energy contours, involving translation and rotation of the solute into the CD cavity, are produced that graphically reveals the strength of the CD-solute interaction. Increasing the number of minimization iterations from 100s to1000s resulted in remarkable changes in those contours, and improved the correlation between computationally determined and experimental distribution coefficients. The correct ordering of distribution coefficients was achieved with a few approaches, but with the comprehensive minimization approach experimental and computational coefficients were generally within a factor of 4 of each other. Moreover, the comprehensive minimization approach resulted in many points in the grid search, micro-positional states, that minimized to a single conformer. Consideration of the degeneracy of these states is also shown to be significant.
MiR-191 downregulation protects against isoflurane-induced neurotoxicity through targeting BDNF

Abstract Background Isoflurane inhalation can cause nerve damage, and miR-191 is abnormally expressed in nerve crush injuries. This study aimed to explore the effect of miR-191 on isoflurane-induced cognition impairment and neurotoxicity in vivo and in vitro, as well as its potential mechanism. Methods Sprague-Dawley male rats and primary hippocampal neurons were applied and exposed to 2% isoflurane. The level of miR-191 was regulated both in vitro and in vivo to investigate the role of miR-191 in isoflurane-induced neurotoxicity. Morris water maze assay was used to evaluate the neurological function of rats. The level of miR-191 was measured by qRT-PCR. CCK-8 assay and Flow cytometry were applied to detect the cell viability and apoptosis. Dual luciferase reporter gene detection was used for the target gene analysis. Results miR-191 was up-regulated in the hippocampal tissues of rats exposed to isoflurane. Downregulation of miR-191 ameliorated isoflurane-induced cognition impairment, including the increase of the neurological score and the escape latency, and the decrease of the time spent in the original quadrant for the rats exposed to isoflurane. Isoflurane exposure inhibited hippocampal neuron viability and promoted cell apoptosis, which was reversed by down-regulation of miR-191. BDNF is a target gene of miR-191. Conclusions Isoflurane causes some neurotoxic effect which is mediated through miR-191 abnormal expression targeting BDNF. Downregulation of miR-191 has a protective role against isoflurane-induced neurotoxicity, regulates the vitality and slows down neuronal cell apoptosis.
Systematic review of pharmacokinetics and potential pharmacokinetic interactions of flavonolignans from silymarin

Silymarin is an extract from the seeds (fruits) of Silybum marianum that contains flavonolignans and flavonoids. Although it is frequently used as a hepatoprotective agent, its application remains somewhat debatable, in particular, due to the low oral bioavailability of flavonolignans. Moreover, there are claims of its potential interactions with concomitantly used drugs. This review aims at a systematic summary and critical assessment of known information on the pharmacokinetics of particular silymarin flavonolignans. There are two known major reasons for poor systemic oral bioavailability of flavonolignans: (1) rapid conjugation in intestinal cells or the liver and (2) efflux of parent flavonolignans or formed conjugates back to the lumen of the gastrointestinal tract by intestinal cells and rapid excretion by the liver into the bile. The metabolism of phase I appears to play a minor role, in contrast to extensive conjugation and indeed the unconjugated flavonolignans reach low plasma levels after common doses. Only about 1%–5% of the administered dose is eliminated by the kidneys. Many in vitro studies tested the inhibitory potential of silymarin and its components toward different enzymes and transporters involved in the absorption, metabolism, and excretion of xenobiotics. In most cases, effective concentrations are too high to be relevant under real biological conditions. Most human studies showed no silymarin–drug interactions explainable by these suggested interferences. More interactions were found in animal studies, likely due to the much higher doses administered.
Characterizing a two-pronged epidemic in Mexico of non-communicable diseases and SARS-Cov-2: factors associated with increased case-fatality rates

Abstract Background People with a previous diagnosis of non-communicable diseases (NCDs) are more likely to develop serious forms of COVID-19 or die. Mexico is the country with the fourth highest fatality rate from SARS-Cov-2, with high mortality in younger adults. Objectives To describe and characterize the association of NCDs with the case-fatality rate (CFR) adjusted by age and sex in Mexican adults with a positive diagnosis for SARS-Cov-2. Methods We studied Mexican adults aged ≥20 years who tested positive for SARS-Cov-2 during the period from 28 February to 31 July 2020. The CFR was calculated and associations with history of NCDs (number of diseases and combinations), severity indicators and type of institution that treated the patient were explored. The relative risk (RR) of death was estimated using Poisson models and CFR was adjusted using logistic models. Results We analysed 406 966 SARS-Cov-2-positive adults. The CFR was 11.2% (13.7% in men and 8.4% in women). The CFR was positively associated with age and number of NCDs (p trend <0.001). The number of NCDs increased the risk of death in younger adults when they presented three or more NCDs compared with those who did not have any NCDs [RR, 46.6; 95% confidence interval (CI), 28.2, 76.9 for women; RR, 16.5; 95% CI, 9.9, 27.3 for men]. Lastly, there was great heterogeneity in the CFR by institution, from 4.6% in private institutions to 18.9% in public institutions. Conclusion In younger adults, higher CFRs were associated with the total number of NCDs and some combinations of type 2 diabetes, chronic kidney disease, chronic obstructive pulmonary disease and cardiovascular disease.
Characterization of an NDM-5-producing hypervirulent Klebsiella pneumoniae sequence type 65 clone from a lung transplant recipient

ABSTRACT The emergence of New Delhi Metallo-β-lactamase (NDM)-producing Klebsiella pneumoniae has aroused critical concern worldwide. Herein, we reported the first emergence of NDM-5-producing K. pneumoniae isolates in a 68-year-old lung transplant recipient, who died of septic shock 13 days after surgery. The K. pneumoniae strain KP22937 isolated from the bloodstream of the patient was analyzed for phenotypes and genotypes. KP22937 belonged to sequence type (ST) 65 and capsule serotype K2, contained iucABCDiutA and iroBCDN virulence clusters, showed high virulence to mice, and was therefore considered a hypervirulent K. pneumoniae. The bla NDM-5 gene was located on a genomic island region of the IncX3-type plasmid pNDM22937, which was successfully transferred to Escherichia coli EC600 with insignificant fitness costs. The transconjugant demonstrated similar antimicrobial susceptibility and growth kinetics to the recipient E. coli EC600. The plasmid pNDM22937 was almost identical to the bla NDM-5-carrying IncX3 plasmids previously reported in K. pneumoniae strains with different ST types and in other species. Our findings raise concerns about the horizontal spread of bla NDM-5 gene mediated by IncX3 plasmid, where hypervirulent K. pneumoniae strains are also involved. Stricter control measures are needed to prevent the dissemination of the novel clone in hospital settings.
Deciphering nucleotide modification-induced structure and stability changes

ABSTRACT Nucleotide modification in RNA controls a bevy of biological processes, including RNA degradation, gene expression, and gene editing. In turn, misregulation of modified nucleotides is associated with a host of chronic diseases and disorders. However, the molecular mechanisms driving these processes remain poorly understood. To partially address this knowledge gap, we used alchemical and temperature replica exchange molecular dynamics (TREMD) simulations on an RNA duplex and an analogous hairpin to probe the structural effects of modified and/or mutant nucleotides. The simulations successfully predict the modification/mutation-induced relative free energy change for complementary duplex formation, and structural analyses highlight mechanisms driving stability changes. Furthermore, TREMD simulations for a hairpin-forming RNA with and without modification provide reliable estimations of the energy landscape. Illuminating the impact of methylated and/or mutated nucleotides on the structure-function relationship and the folding energy landscape, the simulations provide insights into modification-induced alterations to the folding mechanics of the hairpin. The results here may be biologically significant as hairpins are widespread structure motifs that play critical roles in gene expression and regulation. Specifically, the tetraloop of the probed hairpin is phylogenetically abundant, and the stem mirrors a miRNA seed region whose modification has been implicated in epilepsy pathogenesis.
Torque Teno Virus Load Is Associated With Subclinical Alloreactivity in Kidney Transplant Recipients: A Prospective Observational Trial

Supplemental Digital Content is available in the text. Background. Nonpathogenic torque teno viruses (TTVs) are highly prevalent in transplant recipients and associated with immunosuppression. Studies in kidney transplant patients have proposed assessment of TTV load for risk stratification of clinically overt graft rejection. The value of TTV quantification in the context of subclinical rejection has not been evaluated. Methods. In this prospective trial, 307 consecutive kidney transplant recipients were subjected to per-protocol monitoring of plasma TTV. TTV was analyzed in the context of protocol biopsies (n = 82), scheduled 1 year posttransplantation. Results. TTV load at the time of biopsy was lower in recipients with rejection (n = 19; according to Banff, including borderline changes suspicious for acute T cell-mediated rejection) than those without rejection (n = 63) whereby each log increase in TTV copies/mL decreased the risk for rejection by 9% (risk ratio 0.91, 95% confidence interval, 0.85-0.97; P = 0.004). Development of chronic lesions (cg, cv, ci, ct, ah, ptcml) was associated with the number of days with a TTV load <1 × 106 copies/mL between months 3 and 12 posttransplant (β 0.07, 95% confidence interval, 0.01-0.14; P = 0.02). Conclusions. This trial demonstrates an association between TTV and subclinical graft rejection in kidney transplant recipients. A TTV load <1 × 106 copies/mL suggests suboptimal immunosuppression.