Miracle-dz/UniFAR-FTUs huggingface dataset:
Diabetes is associated with genotypically drug-resistant tuberculosis

Diabetes is associated with failure of tuberculosis (TB) treatment, but it is unclear whether this is related to genotypic drug resistance of the infecting mycobacteria. We used whole genome sequencing (WGS) to examine 1365 known drug resistance mutations in 896 Mycobacterium tuberculosis isolates from TB patients that were screened for diabetes using HbA1c testing as part of the TANDEM project [1]. Ethical approval was received from the London School of Hygiene and Tropical Medicine and institutional review boards in Indonesia and Peru. In Peru we selected all available M. tuberculosis isolates from TANDEM patients (44 with and 445 without diabetes), and in Indonesia we selected all available isolates from diabetic patients (n=115) plus a subset of isolates from non-diabetic patients (n=292) from the same clinics, during the same time period, frequency-matched by age. We used TB Profiler version 0.3. 8 [2] to determine M. tuberculosis lineage and drug resistance. A phylogeny was constructed using PhyML version 3.0 [3], and the minimum pairwise distance for isolates was calculated separately for patients with and without diabetes, stratified by country. In a study in Peru and Indonesia, diabetes was associated with an increased risk of tuberculosis caused by Mycobacterium tuberculosis strains with resistance mutations, particularly against rifampicin, and this was not explained by previous TB treatment http://bit.ly/2QCvUEM
Diagnosis and Management of Allergic Rhinitis in Children.

Allergic rhinitis is one of the most common chronic diseases managed by pediatricians. It can result in a significant burden of disease for the patient and their family. This article reviews classification of this condition as well as its pathophysiology, mediated by a Th2 lymphocyte response. Methods of diagnosis via elicitation of a thorough history, focused physical examination, and testing for specific allergen sensitization are discussed. Treatment of this condition is examined, focusing on allergen avoidance and a variety of available pharmacotherapies. Finally, allergen immunotherapy modalities and their potential for disease-modifying effects as well as their potential risks and benefits are outlined. [Pediatr Ann. 2019;48(12):e485-e488. ].
What is the structure of perceiver effects? On the importance of global positivity and trait-specificity across personality domains and judgment contexts.

When judging others' personalities, perceivers differ in their general judgment tendencies. These perceiver effects partly reflect a response bias but are also stable and psychologically important individual differences. However, current insights into the basic structure of perceiver effects are ambiguous with previous research pointing to either a unidimensional structure (i.e., people see others as globally positive vs. negative) or a multidimensional structure (i.e., people see others as high or low on specific traits). Here we provide a large scale investigation of the structure of perceiver effects that spans more than 100,000 personality judgments across 10 studies in which a total of N = 2,199 perceivers judged others on several trait domains (i.e., the Big Five, agency & communion) and in different judgment contexts (i.e., level of involvement with targets, level of exposure to targets). Results suggest that perceiver effects are hierarchically structured such that they reflect both a global tendency to view others positively versus negativity and specific tendencies to view others as high or low with respect to trait content. The relative importance of these components varied considerably across trait domains and judgment contexts: Perceiver effects were more specific for traits higher in observability and lower in evaluativeness and in context with less personal involvement and higher exposure to targets. Overall, results provide strong evidence for the hierarchical structure of perceiver effects and suggest that their meaning systematically varies depending on trait domain and possibly the judgment context. Implications for theory and assessment are discussed. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Shift work and use of psychotropic medicine: a follow-up study with register linkage

Objective This study aimed to investigate a prospective association between shift work and use of psychotropic medicine. Methods Survey data from random samples of the general working population of Denmark (N=19 259) were linked to data from national registers. Poisson regression was used for analyses of prospective associations between shift work and redeemed prescriptions of psychotropic medicine. Prevalent cases were excluded at baseline. In secondary analyses, we tested differential effects on subsets of psychotropic medicine and, cross-sectionally, we studied correspondence between estimates based on psychotropic medicine and self-reported mental health. According to the protocol we interpret results from the secondary analyses following the principles for nested hypothesis testing, if the primary analyses reject the null-hypothesis, and otherwise we regard it as hypothesis generating exploratory analyses. Results In the primary analysis, the rate ratio for incidence of psychotropic medicine among shift workers was 1.09 (95% confidence interval 0.99–1.21). Results from the secondary analyses suggested increased incidence of use of hypnotics, sedatives and antidepressants and decreased incidence of use of anxiolytics. Cross-sectional analysis suggested increased risk for use of psychotropic medicine (all kinds), but not for poor self-rated mental health. Conclusions Results did not support that working in shifts to the extent that is currently practiced in Denmark is associated with an increased incidence of overall psychotropic medicine use. Future studies should test, whether there is a differential incidence for different drugs among shift workers as suggested by the secondary analyses and how psychotropic medicine use and mental health are related.
Arginine methylation‐dependent LSD1 stability promotes invasion and metastasis of breast cancer

Histone lysine demethylase 1 (LSD1), the first identified histone demethylase, is overexpressed in multiple tumor types, including breast cancer. However, the mechanisms that cause LSD1 dysregulation in breast cancer remain largely unclear. Here, we report that protein arginine methyltransferase 4 (PRMT4 or CARM1) dimethylates LSD1 at R838, which promotes the binding of the deubiquitinase USP7, resulting in the deubiquitination and stabilization of LSD1. Moreover, CARM1‐ and USP7‐dependent LSD1 stabilization plays a key role in repressing E‐cadherin and activating vimentin transcription through promoter H3K4me2 and H3K9me2 demethylation, respectively, which promotes invasion and metastasis of breast cancer cells. Consistently, LSD1 arginine methylation levels correlate with tumor grade in human malignant breast carcinoma samples. Our findings unveil a unique mechanism controlling LSD1 stability by arginine methylation, also highlighting the role of the CARM1‐USP7‐LSD1 axis in breast cancer progression.
The Au/Ag alloy nanoshuttle-TiO2 nanostructure with enhanced H2 production under visible light and inactivation analysis

Plasmonic noble metal has been applied in photocatalytic materials, and TiO2 with plasmonic noble metal has been studied for a long time. In this work, we have fabricated incomplete covered Au/Ag alloy nanoshuttle-TiO2 nanomaterials with 268.7 μmol g−1 h−1 H2-evolution in a simple solution method. The considerable photocatalytic performance is mainly due to the enhanced surface plasmon resonance effect of Au/Ag alloy nanoshuttles. It has been found that TiO2 clusters attached to the Au/Ag nanoshuttles surface migrate under electrons irradiation and cover the exposed Au/Ag NS surface to achieve thermodynamic stability, which results in instability of photocatalytic performance. The mechanism has been discussed in detail.
The Reciprocal Relationship of Pain and Movement in African American Older Adults With Multi-Joint Osteoarthritis.

Pain with movement is a common issue for older adults with osteoarthritis; however, there has been insufficient attention within populations at increased risk for disabling pain, such as African American older adults. Accordingly, using a mixed methods approach, the purpose of the current study is to describe the nature of chronic joint pain and movement and its impact on physical function in African American older adults with symptomatic osteoarthritis. The authors accrued a sample of 110 African American older adults who completed cross-sectional surveys; from this sample, the authors interviewed 18 participants. Findings suggest that patterns of movement are uniquely influenced by pain. Specifically, three dynamic themes emerged: The Impact of Pain on Movement; The Importance and Impact of Movement on Pain; and The Adaptation of Personal Behaviors to Minimize Pain With Movement. Function-focused nursing care rests on addressing challenges and opportunities that African American older adults face in maintaining healthy movement when managing osteoarthritis pain. [Research in Gerontological Nursing, xx(x), xx-xx. ].
Use of allometry and skinfold thicknesses to estimate the fat mass of circumpubertal boys

Abstract Background: In the pubertal period, each part of the body grows at different rates. This makes the relationship between the parts nonlinear. Particularly, the fat mass (FM) of boys tends to decrease, further exacerbating the issue of linearity in growth. Aim: To propose predictive models of FM from skinfolds (SF) adjusted allometrically. Subjects and methods: 75 pubertal boys (14.4 ± 0.9 years) composed the sample by self-selected pubic hair. FM was determined by DXA (FMDXA) (kg), stature (cm), body mass (kg) and nine SF (mm) by anthropometric measurements. The SF were individually adjusted allometrically. FMDXA (Y) values and each anthropometric independent variable-IV (X) underwent logarithmic transformation. Linear regressions were used. The significance of the prediction of the FMDXA of each model (ANOVA) and the concordance analysis (Bland-Altman) were performed. Results: Predictive allometric models of FMDXA showed high determination coefficients (r2) and reduced standard errors of estimation (SEE). The adjusted model involved reduced agreement limits, demonstrating its accuracy. Conclusions: It was possible to propose models with allometric adjustments to estimate FM of pubertal boys. Allometry may aid in the development of predictive linear models of body composition, since it has an indicative capacity of the variables for estimation.
Predicting Reduced Tinnitus Burden After Cochlear Implantation in Adults.

OBJECTIVE Explore patient characteristics associated with tinnitus improvement after cochlear implantation. STUDY DESIGN Retrospective cohort. SETTING Tertiary referral. PATIENTS Adults with bilateral severe-to-profound hearing loss and tinnitus. INTERVENTIONS Unilateral cochlear implantation. RESULTS From 1996 to 2018, 358 patients endorsed pre-implant tinnitus and had ascertainable tinnitus status at 1-year. Clinically significant improvement in Tinnitus Handicap Inventory (THI) (reduction by at least 7-points) was observed in 262 (73.2%) patients, of whom 155 (59.2%) reported complete resolution. Of the 24 characteristics explored, four were identified as independent predictors of improved tinnitus in logistic regression models. In a multivariable model including identified independent predictors, each 10-percentage point increase in baseline hearing in noise test was associated with an 14% reduction in odds of tinnitus resolution or clinically significant improvement (odds ratio [OR] 0.86, 95% confidence limits [CL] 0.77, 0.96) and preoperative use of a hearing aid in the contralateral ear was associated with a 72% reduction (OR 0.28; 95% CL 0.11, 0.73). Each 10-point increase in baseline Hearing Handicap Inventory for Adults (HHI) score was associated with a 28% increase in odds of tinnitus improvement (OR 1.28; 95% CL 1.07, 1.54). Higher baseline burden of tinnitus was associated with higher odds of tinnitus improvement (OR 1.21 per 10-point THI increase, 95% CL 1.04, 1.40). CONCLUSIONS Worse residual hearing and higher baseline hearing and tinnitus handicap are associated with higher odds of tinnitus improvement. Expectations of patients seeking reduced tinnitus burden following cochlear implantation should be managed by counselling regarding odds of tinnitus improvement compared to those with similar residual hearing and tinnitus burden.
Draft Genome Sequence of an Escherichia coli Sequence Type 410 Isolate Harboring blaNDM-5 Genes with gyrA and parE Mutations, Isolated from Urine Culture in China

Escherichia coli sequence type 410 (ST410) is now an international high-risk clone and is responsible for a large number of clinical infections. Here, we report the draft genome sequence of an ST410 clinical isolate harboring multiple blaNDM-5 genes that was obtained from urine culture in China. ABSTRACT Escherichia coli sequence type 410 (ST410) is now an international high-risk clone and is responsible for a large number of clinical infections. Here, we report the draft genome sequence of an ST410 clinical isolate harboring multiple blaNDM-5 genes that was obtained from urine culture in China.
Draft Whole-Genome Sequences of Two Western European Borrelia miyamotoi Isolates

We report the draft whole-genome sequences of two Borrelia miyamotoi strains isolated in The Netherlands. Using next-generation sequencing, we determined the complete sequence of the chromosomes and several plasmids. The two strains show a genotype typical of European strains, distinct from the genomes of strains from Asia or the United States. ABSTRACT We report the draft whole-genome sequences of two Borrelia miyamotoi strains isolated in The Netherlands. Using next-generation sequencing, we determined the complete sequence of the chromosomes and several plasmids. The two strains show a genotype typical of European strains, distinct from the genomes of strains from Asia or the United States.
Diffusion Properties of Normal-Appearing White Matter Microstructure and Severity of Motor Impairment in Acute Ischemic Stroke

BACKGROUND AND PURPOSE: The effect of white matter hyperintensities as measured by FLAIR MR imaging on functional impairment and recovery after ischemic stroke has been investigated thoroughly. However, there has been growing interest in investigating normal-appearing white matter microstructural integrity following ischemic stroke onset with techniques such as DTI. MATERIALS AND METHODS: Fifty-two patients with acute ischemic stroke and 36 without stroke were evaluated with a DTI and FLAIR imaging protocol and clinically assessed for the severity of motor impairment using the Motricity Index within 72 hours of suspected symptom onset. RESULTS: There were widespread decreases in fractional anisotropy and increases in mean diffusivity and radial diffusivity for the acute stroke group compared with the nonstroke group. There was a significant positive association between fractional anisotropy and motor function and a significant negative association between mean diffusivity/radial diffusivity and motor function. The normal-appearing white matter ROIs that were most sensitive to the Motricity Index were the anterior/posterior limb of the internal capsule in the infarcted hemisphere and the splenium of the corpus callosum, external capsule, posterior limb/retrolenticular part of the internal capsule, superior longitudinal fasciculus, and cingulum (hippocampus) of the intrahemisphere/contralateral hemisphere. CONCLUSIONS: The microstructural integrity of normal-appearing white matter is a significant parameter to identify neural differences not only between those individuals with and without acute ischemic stroke but also correlated with the severity of acute motor impairment.
Collaboration Between Maternal and Child Health and Chronic Disease Epidemiologists to Identify Strategies to Reduce Hypertension-Related Severe Maternal Morbidity

Introduction Maternal and child health (MCH) and chronic disease programs at state health agencies may not routinely collaborate. The objective of this study was to describe a project that enhanced relationships between MCH and chronic disease epidemiologists at the Florida Department of Health, increased epidemiologic capacity, and informed both programs. Methods We collaborated to assess hypertension-related severe maternal morbidity (H-SMM) and hypertensive disorders (preexisting hypertension, gestational hypertension, and preeclampsia) among women at delivery of their live birth to help determine the burden on health care systems in Florida. We identified ways to improve the health of women before they conceive and to help them manage any chronic diseases during the perinatal period. Results We found differences by maternal characteristics in H-SMM rates among 979,660 women who delivered live births. We proposed strategies to support collaboration between state MCH and chronic disease staff. First, increase the screening, monitoring, and management of hypertension before, during, and after pregnancy. Second, examine H-SMM concurrently with maternal mortality to help find prevention strategies. Third, include reproductive-aged women in ongoing hypertension prevention and intervention efforts. Fourth, expand team-based care to include obstetricians, midwives, and doulas who can work together with primary care providers for hypertension management. And fifth, create and share data products that guide various groups about hypertension and related risk factors among reproductive-aged women. Conclusion The collaboration between the Florida Department of Health MCH and chronic disease epidemiologists produced 1) a program-relevant indicator, H-SMM and 2) strategies for enhancing program and clinical activities, communication, and surveillance to reduce H-SMM rates.
AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Abstract Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio. slu.se.
SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function

MOTIVATION Most proteins perform their biological functions through interactions with other proteins in cells. Amino acid mutations, especially those occurring at protein interfaces, can change the stability of protein-protein interactions (PPIs) and impact their functions, which may cause various human diseases. Quantitative estimation of the binding affinity changes (ΔΔGbind) caused by mutations can provide critical information for protein function annotation and genetic disease diagnoses. RESULTS We propose SSIPe, which combines protein interface profiles, collected from structural and sequence homology searches, with a physics-based energy function for accurate ΔΔGbind estimation. To offset the statistical limits of the PPI structure and sequence databases, amino acid-specific pseudocounts were introduced to enhance the profile accuracy. SSIPe was evaluated on large-scale experimental data containing 2204 mutations from 177 proteins, where training and test datasets were stringently separated with the sequence identity between proteins from the two datasets below 30%. The Pearson correlation coefficient (PCC) between estimated and experimental ΔΔGbind is 0.61 with a root-mean-square-error (RMSE) 1.93 kcal/mol, which was significantly better than the other methods. Detailed data analyses revealed that the major advantage of SSIPe over other traditional approaches lies in the novel combination of the physical energy function with the new knowledge-based interface profile. SSIPe also considerably outperformed a former profile-based method (BindProfX) due to the newly introduced sequence profiles and optimized pseudocount technique that allows for consideration of amino acid-specific prior mutation probabilities. AVAILABILITY Web-server/standalone program, source code and datasets are freely available at https://zhanglab.ccmb. med.umich. edu/SSIPe and https://github.com/tommyhuangthu/SSIPe. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Plasmacytoid dendritic cell and myeloid dendritic cell function in ageing: A comparison between elderly and young adult women

Ageing is associated with a changing immune system, leading to inflammageing (increased levels of inflammation markers in serum) and immunosenescence (reduced immune cells and reduced responses towards pathogens). This results in reduced vaccination responses and increased infections in elderly. Much is known about the adaptive immune system upon ageing, but less is known about the innate immune system. Therefore, the aim of this study was to compare innate immune function of Toll like receptor (TLR)-mediated responses between elderly and young adult women. To this end, elderly and young adult women were compared to study the effect of ageing on the relative prevalence and reactivity to TLR-mediated responses of myeloid- and plasmacytoid dendritic cells (mDC, pDC). In addition, TLR expression and inflammatory markers in serum were investigated. Elderly women had reduced numbers of circulating pDCs. In addition, pDCs and mDCs of elderly women responded differently towards TLR stimulation, especially TLR7/8 mediated stimulation was reduced, compared to young adults. In serum, markers involved in inflammation were generally increased in elderly. In conclusion, this study confirms and extends the knowledge about immunosenescence and inflammageing on innate immunity in elderly women.