Miracle-dz/UniFAR-FTUs huggingface dataset:
Diet Quality and the Risk of Impaired Speech Reception Threshold in Noise: The UK Biobank cohort

Objective: Previous studies have examined the association between several diet quality indexes and risk of hearing loss, based on self-reported information or on audiometry test, with inconsistent results. However, the impact of healthy diets on the capacity to listening in noise, a proxy of disability due to hearing loss, is unknown. This research assessed the prospective association between five diet quality indexes and the speech reception threshold in noise in the UK Biobank study. Design: Prospective cohort with 105,592 participants aged ≥40 years. At baseline, adherence to the Mediterranean Diet Adherence Screener, the alternate Mediterranean Diet score, the Dietary Approaches to Stop Hypertension, the Alternate Healthy Eating Index-2010, and the healthful Plant-Based Diet Index were assessed. Functional auditory capacity was measured with a digit triplet test, and impairment was defined as a speech reception threshold in noise >−3.5 dB in any physical exam during the follow-up. Results: Over a median follow-up of 3.2 (SD: 2.1) years, 1704 participants showed impaired speech reception threshold in noise. After adjusting for potential confounders, the hazard ratios (95% confidence interval) of impairment per 1-SD increase in the Mediterranean Diet Adherence Screener, alternate Mediterranean Diet score, Dietary Approaches to Stop Hypertension, Alternate Healthy Eating Index-2010 and healthful Plant-Based Diet Index scores were, respectively, 0.98 (0.94 to 1.03), 1.01 (0.96 to 1.06), 1.02 (0.97 to 1.07), 1.01 (0.96 to 1.06), and 1.00 (0.96 to 1.05). Results were similar when analyses were restricted to those >60 years, with British ethnicity, without chronic disease, without tinnitus or with optimal cognitive function. Conclusions: Adherence to a healthy diet did not show an association with the speech reception threshold in noise. More research is needed to identify the impact of individual foods or nutrients on this outcome.
Genome Sequence of VanLee, a Singleton Actinobacteriophage That Infects Multiple Gordonia Strains

VanLee is a singleton phage that was isolated from soil in Florida using Gordonia rubripertincta NRRL B-16540 as the host. The genome is 84,560 bp and has a GC content of 67.8%. VanLee has 164 predicted protein-coding genes and one tRNA. VanLee can infect Gordonia terrae with the same efficiency as G. rubripertincta. ABSTRACT VanLee is a singleton phage that was isolated from soil in Florida using Gordonia rubripertincta NRRL B-16540 as the host. The genome is 84,560 bp and has a GC content of 67.8%. VanLee has 164 predicted protein-coding genes and one tRNA. VanLee can infect Gordonia terrae with the same efficiency as G. rubripertincta.
Association between serum uric acid level and mortality in China

Supplemental Digital Content is available in the text Abstract Background: Whether there is an association between serum uric acid (SUA) level and risk of mortality in the general population remains unclear. Based on the China National Survey of Chronic Kidney Disease linked to mortality data, a population-based cohort study was performed to investigate the association between SUA level and all-cause mortality, cardiovascular disease (CVD) mortality, and cancer mortality in China. Methods: The survival status of participants in the cross-sectional survey was identified from January 1, 2006 to December 31, 2017. Only 33,268 individuals with complete SUA data among the 47,204 participants were included in the analysis. We determined the rates of all-cause mortality, CVD mortality, and cancer mortality. We used Cox proportional hazards regression models to evaluate the effect of the SUA level on mortality. Results: During a total of 297,538.4 person-years of follow-up, 1282 deaths occurred. In the Cox proportional hazards regression model, the rate of all-cause mortality, CVD mortality, and cancer mortality had a U-shaped association with SUA levels only in men, whereas no significant associations were detected in women. For all-cause mortality in men, the multivariable-adjusted hazard ratios (HRs) in the first, second, and fourth quartiles compared with the third quartile were 1.31 (95% confidence interval [CI] 1.04–1.67), 1.17 (95% CI 0.92–1.47), and 1.55 (95% CI 1.24–1.93), respectively. For CVD mortality, the corresponding HRs were 1.47 (95% CI 1.00–2.18), 1.17 (95% CI 0.79–1.75), and 1.67 (95% CI 1.16–2.43), respectively. For the cancer mortality rate, only a marginally significant association was detected in the fourth quartile compared with the third quartile with an HR of 1.43 (95% CI 0.99–2.08). Conclusions: The association between SUA and mortality differed by sex. We demonstrated a U-shaped association with SUA levels for all-cause and CVD mortalities among men in China.
Frequency and Outcome of Hepatic Arterial Thrombosis in Recipients of Living Donor Liver Transplantation.

ABASTRACT Objective: To determine the frequency, risk factors, and management of hepatic arterial thrombosis (HAT) in recipients of living donor living transplantation. STUDY DESIGN Cohort study. PLACE AND DURATION OF STUDY Department of Liver Transplant, Pir Abdul Qadir Shah Jeelani Institute of Medical Sciences, Gambat, Sindh, Pakistan, from 1st January 2019 to 31st July 2020. METHODOLOGY Two hundred and forty living donor liver transplants (LDLT) recipients' data were evaluated. Frequencies of HAT were recorded, and various risk factors for the development of HAT were analysed by comparing HAT group (n = 12) and non-HAT group (n = 228). Management and outcome of HAT cases were also reviewed. Statistical analysis of this study was done with SPSS software version 21. RESULTS Out of 240 patients, 212 (88.3%) were males. Overall mean age was 39.40 ± 12.14 years. Mean model for end-stage liver disease (MELD) score was 18.70 ± 4.98. Overall male to female ratio was 7.5:1. The common indication for LDLT in these patients was chronic liver disease secondary to hepatitis B and C virus infection in 85% of patients. Postoperative HAT incidence was found as 5%. Risk factor found statistically significant was intraoperative platelet transfusion. CONCLUSION HAT is a deadly complication and needs early detection to avoid graft loss. The risk factor documented in this study should be avoided, if possible. Moreover, prompt and quick action is necessary for re-vascularisation to avoid re-transplantation. Key Words: Living donor, Hepatic arterial thrombosis, Liver transplantation.
The Fish Pathogen Aliivibrio salmonicida LFI1238 Can Degrade and Metabolize Chitin despite Gene Disruption in the Chitinolytic Pathway

The ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen is Aliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. ABSTRACT The fish pathogen Aliivibrio (Vibrio) salmonicida LFI1238 is thought to be incapable of utilizing chitin as a nutrient source, since approximately half of the genes representing the chitinolytic pathway are disrupted by insertion sequences. In the present study, we combined a broad set of analytical methods to investigate this hypothesis. Cultivation studies revealed that A. salmonicida grew efficiently on N-acetylglucosamine (GlcNAc) and chitobiose [(GlcNAc)2], the primary soluble products resulting from enzymatic chitin hydrolysis. The bacterium was also able to grow on chitin particles, albeit at a lower rate than on the soluble substrates. The genome of the bacterium contains five disrupted chitinase genes (pseudogenes) and three intact genes encoding a glycoside hydrolase family 18 (GH18) chitinase and two auxiliary activity family 10 (AA10) lytic polysaccharide monooxygenases (LPMOs). Biochemical characterization showed that the chitinase and LPMOs were able to depolymerize both α- and β-chitin to (GlcNAc)2 and oxidized chitooligosaccharides, respectively. Notably, the chitinase displayed up to 50-fold lower activity than other well-studied chitinases. Deletion of the genes encoding the intact chitinolytic enzymes showed that the chitinase was important for growth on β-chitin, whereas the LPMO gene deletion variants only showed minor growth defects on this substrate. Finally, proteomic analysis of A. salmonicida LFI1238 growth on β-chitin showed expression of all three chitinolytic enzymes and, intriguingly, also three of the disrupted chitinases. In conclusion, our results show that A. salmonicida LFI1238 can utilize chitin as a nutrient source and that the GH18 chitinase and the two LPMOs are needed for this ability. IMPORTANCE The ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen is Aliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. Due to extensive gene decay, many key enzymes in the chitinolytic pathway have been disrupted, putatively rendering this bacterium incapable of chitin degradation and utilization. In the present study, we demonstrate that A. salmonicida can degrade and metabolize chitin, the most abundant biopolymer in the ocean. Our findings shed new light on the environmental adaption of this fish pathogen.
Evaluating the impact of multivariate imputation by MICE in feature selection

Handling missing values is a crucial step in preprocessing data in Machine Learning. Most available algorithms for analyzing datasets in the feature selection process and classification or estimation process analyze complete datasets. Consequently, in many cases, the strategy for dealing with missing values is to use only instances with full data or to replace missing values with a mean, mode, median, or a constant value. Usually, discarding missing samples or replacing missing values by means of fundamental techniques causes bias in subsequent analyzes on datasets. Aim: Demonstrate the positive impact of multivariate imputation in the feature selection process on datasets with missing values. Results: We compared the effects of the feature selection process using complete datasets, incomplete datasets with missingness rates between 5 and 50%, and imputed datasets by basic techniques and multivariate imputation. The feature selection algorithms used are well-known methods. The results showed that the datasets imputed by multivariate imputation obtained the best results in feature selection compared to datasets imputed by basic techniques or non-imputed incomplete datasets. Conclusions: Considering the results obtained in the evaluation, applying multivariate imputation by MICE reduces bias in the feature selection process.
Characteristics and effects of integrated nutrition and stimulation interventions to improve the nutritional status and development of children under 5 years of age: a systematic review and meta-analysis

Introduction Around 250 million children in low-income and middle-income countries are at risk of not fulfilling their developmental potential. There is a need to update syntheses investigating the effects of combined nutrition and stimulation interventions on children’s growth and development and identify intervention characteristics associated with positive effects. Methods We did a systematic review to: (1) understand the effects of integrated nutrition and stimulation interventions versus (i) usual care and (ii) standalone nutrition or stimulation interventions, on the growth and development of children under five; (2) explore intervention characteristics (delivery strategies, behaviour change techniques, intensity and personnel) associated with positive effects. We searched eight databases for studies published from inception to 16 November 2020. Eligible studies were randomised and non-randomised controlled trials of integrated nutrition and stimulation interventions examining growth and developmental outcomes. We performed meta-analyses for length-for-age/height-for-age, weight-for-age and weight-for-length/weight-for-height Z scores and cognitive, motor and language development scores, and subgroup analyses by intervention characteristics. We conducted random-effects metaregression to assess potential subgroup differences in outcomes by intervention characteristics. Results Twenty trials were included in the meta-analysis. Pooled effect sizes showed significant benefits of integrated interventions on developmental outcomes compared with usual care and standalone nutrition interventions (I2 >75%) but not on growth outcomes. Moreover, integrated interventions have non-significant effects on developmental outcomes compared with standalone stimulation interventions. Integrated interventions showed greater effects on cognitive (p=0.039) and language (p=0.040) outcomes for undernourished children compared with adequately nourished children. The effects of integrated interventions on developmental outcomes did not differ by intervention characteristics. Conclusion Integrated interventions have greater benefits for children’s development than usual care or standalone nutrition interventions, especially in settings with high levels of undernutrition. Future studies should use standardised reporting of implementation processes to identify intervention characteristics linked to positive effects.
Quantum Coherence for Light Harvesting

Almost all life on Earth depends on the products of photosynthesis — the biochemical process whereby solar energy is stored as chemical-rich compounds. The energy of captured photons is transferred through a network of pigment-protein complexes towards the reaction center. The reaction center is responsible for trans-membrane charge separation, which generates a proton motive force which drives all subsequent biochemical reactions. The ultrafast (femtosecond) nature of the primary processes in photosynthesis is the main reason for its astonishing efficiency. On this timescale, quantum effects start to play a role and can appear in measured spectra as oscillations. It has been hypothesized that these are evidence of wave-like energy transfer. To unveil the fundamental principals of ultrafast excitation energy transfer in both natural and artificial light-harvesting systems, advanced spectroscopy techniques have been utilized. Coherent two-dimensional electronic spectroscopy is a state of the art technique which allows the most complete spectroscopic and temporal information to be extracted from the system under study. This technique has allowed us to identify a new photophysical process where the coherence of the initially excited state is shifted to the ground state upon an energy transfer step. Coherence dynamics caused by this process bear most of the signatures of pure electronic coherences, and can therefore be easily mistaken for coherent energy transfer. Our results imply that the wave-like energy transfer hypothesis should be reconsidered and tested against coherence shift mechanisms. Furthermore, we have demonstrated that the mixing between vibrational and electronic motions seem to be a general phenomenon in light-harvesting systems.
Non‐alcoholic fatty liver disease‐related risk of cardiovascular disease and other cardiac complications

Non‐alcoholic fatty liver disease (NAFLD) affects approximately 25% of the global adult population. The aim of this narrative review is to describe the associations between NAFLD and cardiovascular disease (CVD), arrhythmias, cardiac conduction defects, myocardial remodelling and heart failure. We also discuss the potential mechanisms that mediate or attenuate the strength of these associations, and briefly summarize the effect of treatments that both ameliorate NAFLD and decrease risk of CVD.
Impact of scaling up prenatal nutrition interventions on human capital outcomes in low- and middle-income countries: a modeling analysis

ABSTRACT Background Prenatal nutrition interventions can lead to improved birth outcomes, which in turn are associated with better education and human capital outcomes later in life. Objective We estimated the impact of scaling up iron–folic acid (IFA), calcium, multiple micronutrient (MMS), and balanced energy protein (BEP) supplementation for pregnant women, on human capital outcomes in low- and middle-income countries (LMIC). Methods We used mathematical modeling with proportional reductions in adverse birth outcomes to estimate the potential gains in school years and lifetime income due to scaling up each prenatal nutrition intervention. Estimates of intervention effects on birth outcomes were derived from meta-analyses of randomized trials. Estimates of the associations between birth outcomes and schooling and lifetime income were derived from de novo meta-analyses of observational studies. Results Across 132 LMIC, scaling up prenatal nutrition interventions to 90% coverage was estimated to increase school years and lifetime income per 5-yr birth cohort by: 2.28 million y (95% uncertainty intervals (UI): −0.44, 6.26) and $8.26 billion (95% UI: −1.60, 22.4) for IFA; 4.08 million y (95% UI: 0.12, 9.68) and $18.9 billion (95% UI: 0.59, 44.6) for calcium; 5.02 million y (95% UI: 1.07, 11.0) and $18.1 billion (95% UI: 3.88, 39.1) for MMS; and 0.53 million y (95% UI: −0.49, 1.70) and $1.34 billion (95% UI: −1.10, 3.10 billion) for BEP supplementation. South Asia and Sub-Saharan Africa tended to have the largest estimated regional gains in school years for scaling up each intervention due to the large population size and high burden of poor birth outcomes. Absolute income benefits for each intervention were estimated to be the largest in Latin America, where returns to education and incomes are higher relative to other regions. Conclusion Increasing coverage of prenatal nutrition interventions in LMIC may lead to substantial gains in schooling and lifetime income. Decision makers should consider the potential long-term human capital returns of investments in maternal nutrition.
Elevated Ras related GTP binding B (RRAGB) expression predicts poor overall survival and constructs a prognostic nomogram for colon adenocarcinoma

ABSTRACT Currently, no articles have explored the roles of RRAGB gene in the occurrence and development of cancer. By means of The Cancer Genome Atlas (TCGA) data mining, we found that this gene might be a novel prognostic predictor for colon adenocarcinoma (COAD). Hence, this article was carried out to explore its roles in COAD and associations with immunity. RRAGB single-gene expression matrix and corresponding clinical information were extracted from TCGA database. Univariate/multivariate cox regression analyses and gene set enrichment analysis (GSEA) were utilized to identify independent prognostic factors and RRAGB related pathways, respectively. Relationships between RRAGB and immunity were also analyzed. Boxplot and K-M survival analysis indicated that RRAGB was not only differently expressed in COAD (P < 0.05), but also significantly associated with overall survival (OS; P < 0.05). Univariate and multivariate Cox hazard regression analyses indicated that RRAGB could serve as an independent prognostic factor for COAD (both P < 0.05). GSEA identified five signaling pathways significantly enriched in the high-RRAGB expression phenotype. Moreover, a RRAGB-based nomogram was successfully constructed and displayed a satisfactory performance. In addition, RRAGB expression was found to be significantly associated with microsatellite instability (MSI), tumor mutational burden (TMB) and immunity. Our results revealed that RRAGB could be a prognostic biomarker for COAD in terms of OS and markedly related to MSI, TMB, and immunity. We also constructed an RRAGB-based nomogram with a satisfactory performance. Further researches should be carried out to validate our findings. GRAPHICAL ABSTRACT
A specific promoter-type in ribonuclease L gene is associated with phagocytic activity in pigs

We have previously generated Large White pigs with high immune competence using a selection strategy based on phagocytic activity (PA), capacity of alternative complement pathway, and antibody response after vaccination against swine erysipelas. In this study, to identify the genetic changes caused by the immune selection pressure, we compared gene expression and polymorphisms in the promoter region between pigs subjected to the immune selection (immune-selected pigs) and those that were not (non-selected pigs). After lipid A stimulation, using a microarray analysis, 37 genes related to immune function and transcription factor activity showed a greater than three-fold difference in expression between macrophages derived from immune-selected and non-selected pigs. We further performed a polymorphic analysis of the promoter region of the differentially expressed genes, and elucidated the predominant promoter-types in the immune-selected and non-selected pigs, respectively, in the genes encoding ribonuclease L (RNASEL), sterile α motif and histidine-aspartate domain containing deoxynucleoside triphosphate triphosphohydrolase 1, signal transducer and activator of transcription 3, and tripartite motif containing 21. Analysis of the association between these promoter genotypes and the immune phenotypes revealed that the immune-selected promoter-type in RNASEL was associated with increased PA and was inherited recessively. Considering that RNASEL has been reported to be involved in antimicrobial immune response of mice, it may be possible to enhance the PA of macrophages and improve disease resistance in pig populations using RNASEL promoter-type as a DNA marker for selection.
Running head: DISENTANGLING INDIRECT EFFECTS THROUGH MULTIPLE MEDIATORS 1 Disentangling indirect effects through multiple mediators without assuming any causal structure among the mediators

When multiple mediators exist on the causal pathway from treatment to outcome, path analysis prevails for disentangling indirect effects along paths linking possibly several mediators. However, separately evaluating each indirect effect along different posited paths demands stringent assumptions, such as correctly specifying the mediators’ causal structure, and no unobserved confounding among the mediators. These assumptions may be unfalsifiable in practice and, when they fail to hold, can result in misleading conclusions about the mediators. Nevertheless, these assumptions are avoidable when substantive interest is in inference about the indirect effects specific to each distinct mediator. In this article, we introduce a new definition of indirect effects called interventional indirect effects from the causal inference and epidemiology literature. Interventional indirect effects can be unbiasedly estimated without the assumptions above while retaining scientifically meaningful interpretations. We show that under a typical class of linear and additive mean models, estimators of interventional indirect effects adopt the same analytical form as prevalent product-of-coefficient estimators assuming a parallel mediator model. Prevalent estimators are therefore unbiased when estimating interventional indirect effects even when there are unknown causal effects among the mediators but require a different causal interpretation. When other mediators moderate the effect of each mediator on the outcome, and the mediators’ covariance is affected by treatment, such an indirect effect due to the mediators’ mutual dependence (on one another) cannot be attributed to any mediator alone. We exploit the proposed definitions of interventional indirect effects to develop novel estimators under such settings.