Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations between perceived stress and BMI and waist circumference in Chinese adults: data from the 2015 China Health and Nutrition Survey

Abstract Objectives: To assess the association between perceived stress and adiposity among Chinese adults. Design: Cross-sectional study. Perceived stress was assessed using the 14-item perceived stress scale. Associations between quintiles of perceived stress and BMI and waist circumference were assessed using linear regression models and multinomial regression models. Estimates were adjusted for sociodemographic characteristics. Setting: 2015 China Health and Nutrition Survey: 12 provinces covering a variety of geographic, economic development and health indicator situations. Participants: A total of 8385 adults of both sexes, aged 18–99 years, were included. Results: Overall, the mean perceived stress score was 22·7 (6·2), mean BMI was 24·3 (3·6) kg/m2 and prevalence of obesity (BMI ≥ 30 kg/m2) was 6·0 %. There were inverse associations between perceived stress quintiles with continuous BMI (P < 0·001), BMI categories (P = 0·015) and waist circumference (P = 0·047). Compared to adults in the lowest quintile of perceived stress, adults in the highest quintile of perceived stress had 0·44 kg/m2 lower mean BMI (95 % CI: −0·67, −0·21), 0·72 times the prevalence of obesity (95 % CI: 0·55, 0·94) and 0·73 times the prevalence of abdominal obesity (95 % CI: 0·61, 0·88). Results were similar when using Chinese-specific cut-points. Conclusion: Our results showed inverse associations between perceived stress quintiles and adiposity among Chinese adults. Future studies should aim to better understand the directionality of the observed associations and the potential biological and behavioural mechanisms underlying these associations in the Chinese population.
An AMPK-dependent, non-canonical p53 pathway plays a key role in adipocyte metabolic reprogramming

It has been known adipocytes increase p53 expression and activity in obesity, however, only canonical p53 functions (i.e. senescence and apoptosis) are attributed to inflammation-associated metabolic phenotypes. Whether or not p53 is directly involved in mature adipocyte metabolic regulation remains unclear. Here we show p53 protein expression can be up-regulated in adipocytes by nutrient starvation without activating cell senescence, apoptosis, or a death-related p53 canonical pathway. Inducing the loss of p53 in mature adipocytes significantly reprograms energy metabolism and this effect is primarily mediated through a AMP-activated protein kinase (AMPK) pathway and a novel downstream transcriptional target, lysosomal acid lipase (LAL). The pathophysiological relevance is further demonstrated in a conditional and adipocyte-specific p53 knockout mouse model. Overall, these data support a non-canonical p53 function in the regulation of adipocyte energy homeostasis and indicate that the dysregulation of this pathway may be involved in developing metabolic dysfunction in obesity.
Effects of dibenzothiophene, a sulfur‐containing heterocyclic aromatic hydrocarbon, and its alkylated congener, 2,4,7‐trimethyldibenzothiophene, on placental trophoblast cell function

Worldwide demand for petroleum products has resulted in increased oil and gas activities in many countries. Conventional and unconventional oil and gas extraction, production, and transport lead to increased levels of petroleum‐derived polycyclic aromatic hydrocarbons (PAHs) in the environment. PAH exposure has profound effects on reproduction by affecting pathways involved in placental trophoblast cell function and impairing normal placental development and function—key contributors to reproductive success. However, other components found in petroleum and wastewaters from oil and gas extraction, including the sulfur‐containing heterocyclic aromatic compounds such as dibenzothiophene (DBT) and its alkylated derivatives, may also impact reproductive success. The goal of this study was to examine the effect of exposure to DBT, a compound commonly detected in the environment, and one of its alkylated analogues, 2,4,7‐trimethyldibenzothiophene (2,4,7‐DBT), on steroidogenic and angiogenic pathways critical for mammalian development in placental trophoblast cells (HTR‐8/SVneo cells). 2,4,7‐DBT but not DBT increased estradiol output in association with increased tube‐like formation (surrogate for angiogenesis). These changes in angiogenesis did not appear to be related to altered expression of the key placental angiogenic gene targets (ANGPTL4, VEGFA, and PGF). Neither compound showed a concentration related effect on progesterone synthesis or its receptor expression. Our results suggest that 2,4,7‐DBT can disrupt key pathways important for placental trophoblast function and highlight the importance of determining the impact of exposure to both parent and alkylated compounds. Further, these data suggest that exposure to sulfur‐containing heterocyclic aromatic compounds may lead to placental dysfunction and impact reproductive success at environmentally relevant levels.
Human retinal pigment epithelial cells are protected against hypoxia by BNIP3

Background Hypoxia has been implicated in the process of retinal pigment epithelium (RPE) dysfunction. However, recent studies suggest that hypoxia contributes to survival rather than cell death through induction of Bcl-2/adenovirus E1B 19-kDa interacting protein 3 (BNIP3)-dependent autophagy. In contrast, persistent oxidative stress was found to result in autophagy dysregulation in RPE cells. These seemingly contradictory findings led us to investigate the potential role of BNIP3, a crucial mediator of hypoxia-induced autophagy, in the context of hypoxic RPE cells. Methods Human RPE D407 cells were treated with low-oxygen conditions, and cell growth, apoptosis, and autophagy was assessed by Cell Counting Kit-8 assay, flow cytometry analysis and immunofluorescence staining, respectively. Results Hypoxic conditions simultaneously triggered a large amount of apoptosis and inhibited autophagy. Moreover, hypoxia led to severe impairments, including the stimulation of reactive oxygen species, and reduction of mitochondrial membrane potential, and adenosine triphosphate production. The stimulation of autophagy by rapamycin inhibited hypoxia-induced severe impairments to a great extent. Interestingly, similar results were observed for BNIP3 overexpression, which can be largely blocked by 3-MA, a well-defined inhibitor of autophagy. Moreover, BNIP3 knockdown further aggravated hypoxia-induced impairments in D407 cells, which can be reversed by rapamycin. Conclusions Collectively, these results indicated that BNIP3 can protect human retinal pigmented epithelial cells under hypoxic conditions by inducing autophagy.
Individual heterogeneity in the probability of hospitalization, skilled nursing facility admission and mortality.

BACKGROUND Multimorbidity is common in adults aged 65 and older, and associated with healthcare utilization, mortality, but most methods ignore the interrelationship among concurrent outcome nor provide person-specific probabilities. METHODS A longitudinal cohort of 5,300 older Americans from the 2011-2015 rounds of the National Health and Aging Study was linked to Center for Medicare and Medicaid Services claims. Odds ratios for 15 chronic conditions adjusted for sociodemographic factors were estimated using a joint model of hospitalization, SNF admission and mortality. Additionally, we estimated the person-specific probability of an outcome while currently at risk for other outcomes for different chronic disease combinations demonstrating the heterogeneity across persons with identical chronic conditions. RESULTS During the four-year follow-up period, 2,867 (54.1%) individuals were hospitalized, 1,029 (19.4%) were admitted to a SNF and 1,237 (23.3%) died. Chronic kidney disease, dementia, heart failure and chronic obstructive pulmonary disease had significant increased odds for all three outcomes. By incorporating a person-specific random intercept, there was considerable range of person-specific probabilities for individuals with hypertension, diabetes and depression with dementia, (hospitalization: 0.14-0.61; SNF admission: 0.04-0.28) and without dementia (hospitalization: 0.07-0.44; SNF admission: 0.02-0.15). Such heterogeneity was found among individuals with heart failure, ischemic heart disease, chronic kidney disease, hypertension, hyperlipemia and osteoarthritis with and without Medicare. CONCLUSIONS This approach of joint modeling of interrelated concurrent healthcare and mortality outcomes not only provides a cohort-level odds and probabilities but addresses the heterogeneity among otherwise similarly characterized persons identifying those with above average probability of poor outcomes.
EmhR is an indole-sensing transcriptional regulator responsible for the indole-induced antibiotic tolerance in Pseudomonas fluorescens.

Indole is well-known as an interspecies signaling molecule to modulate bacterial physiology, however, it is not clear how the indole signal is perceived and responded to by plant growth promoting rhizobacteria (PGPR) in the rhizosphere. Here, we demonstrated that indole enhanced the antibiotic tolerance of Pseudomonas fluorescens 2P24, a PGPR well known for its biocontrol capacity. Proteomic analysis revealed that indole influenced the expression of multiple genes including the emhABC operon encoding a major multidrug efflux pump. The expression of emhABC was regulated by a TetR-family transcription factor EmhR, which was demonstrated to be an indole-responsive regulator. Molecular dynamics simulation showed that indole allosterically affected the distance between the two DNA-recognizing helices within the EmhR dimer, leading to diminished EmhR-DNA interaction. It was further revealed the EmhR ortholog in Pseudomonas syringae was also responsible for indole-induced antibiotic tolerance, suggesting this EmhR-dependent, indole-induced antibiotic tolerance is likely to be conserved among Pseudomonas species. Taken together, our results elucidated the molecular mechanism of indole-induced antibiotic tolerance in Pseudomonas species and had important implications on how rhizobacteria sense and respond to indole in the rhizosphere. This article is protected by copyright. All rights reserved.
Species-specific effects of biocrust-forming lichens on soil properties under simulated climate change are driven by functional traits.

(1) Biocrusts are key drivers of ecosystem functioning in drylands, yet our understanding of how climate change will affect the chemistry of biocrust-forming species and their impacts on carbon (C) and nitrogen (N) cycling is still very limited. (2) Using a manipulative experiment conducted with common biocrust-forming lichens with distinct morphology and chemistry (Buellia zoharyi, Diploschistes diacapsis, Psora decipiens and Squamarina lentigera), we evaluated changes in lichen total and isotopic C and N and several soil C and N variables after 50 months of simulated warming and rainfall reduction. (3) Climate change treatments reduced δs13 C and C:N ratio in B. zoharyi, and increased δ15 N in S. lentigera. Lichens had species-specific effects on soil dissolved organic N (DON), NH 4 + , β-glucosidase and acid phosphatase activity regardless of climate change treatments, while these treatments changed how lichens affected several soil properties regardless of biocrust species. Changes in thallus δ13 C, N and C:N drove species-specific effects on DON, NH 4 + , β-glucosidase and acid phosphatase activity. (4) Our findings indicate that warmer and drier conditions will alter the chemistry of biocrust-forming lichens, affecting soil nutrient cycling, and emphasize their key role as modulators of climate change impacts in dryland soils.
Simultaneous Directed Evolution of Coupled Enzymes for Efficient Asymmetric Synthesis of l-Phosphinothricin

The traditional strategy to improve multienzyme-catalyzed reaction efficiencies may lead to enhanced single-enzyme catalytic efficiencies but may also result in the loss of coordination among enzymes. We describe a directed evolution strategy for an entire coupled-enzyme system to simultaneously enhance enzyme coordination and catalytic efficiency. ABSTRACT The traditional strategy to improve the efficiency of an entire coupled-enzyme system relies on the separate direction of the evolution of enzymes involved in their respective enzymatic reactions. This strategy can lead to enhanced single-enzyme catalytic efficiency but may also lead to a loss of coordination among enzymes. This study aimed to overcome such shortcomings by executing a directed evolution strategy on multiple enzymes in one combined group that catalyzes the asymmetric biosynthesis of l-phosphinothricin. The genes of a glutamate dehydrogenase from Pseudomonas moorei (PmGluDH) and a glucose dehydrogenase from Exiguobacterium sibiricum (EsGDH), along with other gene parts (promoters, ribosomal binding sites [RBSs], and terminators), were simultaneously evolved. The catalytic efficiency of PmGluDH was boosted by introducing the beneficial mutation A164G (from 1.29 s−1 mM−1 to 183.52 s−1 mM−1), and the EsGDH expression level was improved by optimizing the linker length between the RBS and the start codon of gdh. The total turnover numbers of the bioreaction increased from 115 (GluDH_WTNADPH [NADPH-dependent wild-type GluDH]) to 5,846 (A164GNADPH coupled with low expression of EsGDH) and to 33,950 (A164GNADPH coupled with high expression of EsGDH). The coupling efficiency was increased from ∼30% (GluDH_WT with low expression of GDH) to 83.3% (GluDH_A164G with high expression of GDH). In the batch production of l-phosphinothricin utilizing whole-cell catalysis, the strongest biocatalytic reaction exhibited a high space-time yield (6,410 g · liter−1 · day−1) with strict stereoselectivity (>99% enantiomeric excess). IMPORTANCE The traditional strategy to improve multienzyme-catalyzed reaction efficiencies may lead to enhanced single-enzyme catalytic efficiencies but may also result in the loss of coordination among enzymes. We describe a directed evolution strategy for an entire coupled-enzyme system to simultaneously enhance enzyme coordination and catalytic efficiency. The simultaneous-evolution strategy was applied to a multienzyme-catalyzed reaction for the asymmetric synthesis of l-phosphinothricin, which not only enhanced the catalytic efficiency of GluDH but also improved the coordination between GluDH and GDH. Since this strategy is enzyme independent, it may be applicable to other coupled-enzyme systems for chiral chemical synthesis.
Development of semitransparent wood‐polymer composites

A new material has been developed consisting of pieces of wood embedded within a matrix of acrylic polymer, resulting in a transparent or semitransparent wood‐based product. This material presents quite appealing aesthetic features, thereby opening new possibilities for decorative applications. Because acrylic and methacrylic monomers are in the liquid state at room temperature, it is possible to introduce wood (in the current case, walnut wood) into a mixture of acrylic (hydroxypropyl acrylate) and/or methacrylic monomers (methyl methacrylate and 2‐hydroxyethyl methacrylate) along with a plasticizer (dioctyl phthalate) in the presence of a chemical initiator (benzoyl peroxide). A transparent polymeric matrix with dispersed wood is then obtained through bulk free‐radical polymerization. Introducing this reaction mixture along with pieces of wood into a mold results in a wood‐polymer composite. A 24−1 experimental fractional factorial design was implemented to study the importance of the composition of these materials on several relevant properties. The sheets produced were characterized by tensile testing, dynamic mechanical thermal analysis, thermal gravimetric analysis, and heat deflection temperature. The models obtained for predicting each property pointed to valuable insights regarding the influential constituents. In particular, our results suggested that monomers to be used in future applications of this material should be selected in terms of their cost and the desired flexibility for the final product, not in terms of their polarity. J. VINYL ADDIT. TECHNOL. , 2012. © 2012 Society of Plastics Engineers
Stability of conventional and machine learning-based tumor auto-segmentation techniques using undersampled dynamic radial bSSFP acquisitions on a 0.35 T hybrid MR-linac system.

PURPOSE Hybrid MRI-linear accelerator systems (MR-linacs) allow for the incorporation of MR images with high soft-tissue contrast into the radiation therapy procedure prior to, during or post irradiation. This allows for optimization of the treatment planning, but also for real-time monitoring of the tumor position using cine MRI, from which intrafractional motion can be compensated. Fast imaging and accurate tumor tracking are crucial for effective compensation. This study investigates the application of cine MRI with a radial acquisition scheme on a low-field MR-linac to accelerate the acquisition rate and evaluates the effect on tracking accuracy. METHODS An MR sequence using tiny golden-angle radial k-space sampling was developed and applied to cine imaging on patients with liver tumors on a 0.35 T MR-linac. Tumor tracking was assessed for accuracy and stability from the cine images with increasing k-space undersampling factors. Tracking was achieved using two different auto-segmentation algorithms: a deformable image registration B-spline similar to that implemented on the MR-linac and a convolutional neural network approach known as U-Net. RESULTS Radial imaging allows for increased temporal resolution with reliable tumor tracking, although tracking robustness decreases as temporal resolution increases. Additional acquisition-based artifacts can be avoided by reducing the angle increment using tiny golden angles. The U-net algorithm was found to have superior auto-segmentation metrics compared to B-spline. U-net was able to track two well defined tumors, imaged with just 30 spokes per image (10.6 frames per second), with an average Dice coefficient ≥ 83 %, Hausdorff distance ≤ 1.4 pixel, and mean contour distance ≤ 0.5 pixel. CONCLUSIONS Radial acquisitions are commonplace in dynamic imaging; however, in MR-guided radiotherapy robust tumor tracking is also required. This study demonstrates the in vivo feasibility of tumor tracking from radially acquired images on a low-field MR-linac. Radial imaging allows for decreased image acquisition times while maintaining robust tracking. The U-net algorithm can track a tumor with higher accuracy in images with undersampling artifacts than a conventional deformable B-spline algorithm and is a promising tool for tracking in MR-guided radiation therapy.
Cardiometabolic evaluation of small for gestational age children: protective effect of breast milk.

INTRODUCTION human growth is the result of an interaction between genetic, hormonal, nutritional, and environmental factors. It is not yet fully understood what is predominant and decisive in determining an individual's weight and height. OBJECTIVE the aim of this study was to evaluate the cardiometabolic profile of exclusively breastfed children born small for gestational age (SGA). METHODS this is a prospective cohort study of children born at term who were classified as SGA, and as appropiate for gestational age (AGA), who were followed up to pre-school age. Anthropometric measures and body composition parameters were obtained. Breastfeeding duration was calculated in days, and achievement of catch up of weight was considered an increase in Z-score ≥ 0.67. The cardiometabolic profile was evaluated in the first month of life and repeated at pre-school age. At pre-school age, fasting blood glucose, insulin, HOMA-IR, and blood pressure were measured. RESULTS twenty SGA and 12 AGA children were studied. The mean duration of exclusive breastfeeding (EBF) was 180 days in both groups. Of SGA children, 85 % had recovery anthropometric parameters for age within the first six months, with a speed of weight gain significantly higher than the that of AGAs (p < 0.001). SGAs continued to be thinner and smaller than AGAs at pre-school age. There was no diagnosis of overweight or obesity in the studied sample, and no differences were foun between groups in laboratory tests. CONCLUSION these findings suggest that EBF may confer protection until pre-school age in children born SGA, who are considered at higher risk for chronic non-communicable diseases.
Lipid and Protein Oxidation Marker Compounds in Horse Meat Determined by MIR Spectroscopy

This work broadens the study of lipid and protein oxidation marker compounds in foal meat, employing the technology of Attenuated Total Reflectance-Fourier Transform Mid-Infrared Spectroscopy (ATR-FT/MIR, shortened in the following as MIR). As a main objective, marker compounds from 23 foals were extracted and their absorbance spectra were measured to establish prediction models (calibration and validation) between them and classical quantification analysis of the compounds. Another objective was to ascertain whether a previous extraction of the marker compounds before executing their MIR analysis is preferable compared to direct MIR measurements on the raw meat samples. In this context, marker compound results (TBARS between 0.4387 and 2.1040, and carbonyls between 4.07 and 4.68) showed more consistent predictive models than the ones achieved using quantitative analysis of the spectra obtained from the raw meat. Lipid oxidation compounds predictive models obtained in this work offered an R2cv of 63.18% and protein oxidation R2cv obtained in this project showed a value of 54.24%. Thus, MIR technology arises as a promising tool to identify and quantify products derived from lipid and protein oxidation in fresh foal meat.
mTOR inhibition in COVID‐19: A commentary and review of efficacy in RNA viruses

In this commentary, we shed light on the role of the mammalian target of rapamycin (mTOR) pathway in viral infections. The mTOR pathway has been demonstrated to be modulated in numerous RNA viruses. Frequently, inhibiting mTOR results in suppression of virus growth and replication. Recent evidence points towards modulation of mTOR in severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. We discuss the current literature on mTOR in SARS‐CoV‐2 and highlight evidence in support of a role for mTOR inhibitors in the treatment of coronavirus disease 2019.
De Novo Protein Design Using the Blueprint Builder in Rosetta

While native proteins cover diverse structural spaces and achieve various biological events, not many of them can directly serve human needs. One reason is that the native proteins usually contain idiosyncrasies evolved for their native functions but disfavoring engineering requirements. To overcome this issue, one strategy is to create de novo proteins which are designed to possess improved stability, high environmental tolerance, and enhanced engineering potential. Compared to other protein engineering strategies, in silico design of de novo proteins has significantly expanded the protein structural and sequence spaces, reduced wet lab workload, and incorporated engineered features in a guided and efficient manner. In the Baker laboratory we have been applying a design pipeline that uses the blueprint builder to design different folds of de novo proteins, and have successfully obtained libraries of de novo proteins with improved stability and engineering potential. In this article, we will use the design of de novo β‐barrel proteins as an example to describe the principles and basic procedures of the blueprint builder−based design pipeline. © 2020 Wiley Periodicals LLC.