Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Hydrogen Sulfide on the Microbiome: From Toxicity to Therapy

Significance: Hydrogen sulfide (H2S), an important regulator of physiology and health, helps resolve inflammation and promotes tissue repair in the gastrointestinal tract. Recent Advances: Gut microbiota live as a multispecies biofilm in close interaction with the upper mucus layer lining the epithelium. The relative abundance, spatial organization, and function of these microorganisms affect a broad range of health outcomes. This article provides a state-of-the-art review of our understanding of the cross talk between H2S, the gut microbiota, and health. H2S can have toxic or therapeutic effects, depending on its concentration and source. When produced at excessive concentrations by local microbiota, H2S may cause mucus disruption and inflammation and contribute to development of cancer. In contrast, low levels of endogenous or exogenous H2S directly stabilize mucus layers, prevent fragmentation and adherence of the microbiota biofilm to the epithelium, inhibit the release of invasive pathobionts, and help resolve inflammation and tissue injury. Although scarce, research findings suggest that dietary H2S obtained from plants or ingestion of the H2S precursor, L-cysteine, may also modulate the abundance and function of microbiota. Critical Issues: A critical issue is the lack of understanding of the metagenomic, transcriptomic, and proteomic alterations that characterize the interactions between H2S and gut microbiota to shape health outcomes. Future Directions: The ambivalent roles of H2S in the gut offer a fertile ground for research on such critical issues. The findings will improve our understanding of how H2S modulates the microbiota to affect body function and will help identify novel therapeutic strategies. Antioxid. Redox Signal. 36, 211–219.
Genitourinary syndrome of menopause in Chinese perimenopausal and postmenopausal women

Abstract Objective The aim of this study was to investigate genitourinary syndrome of menopause (GSM) in a large cohort, analyzing the dependency on age and menopausal status and possible differences between non-hysterectomized and hysterectomized women. Methods Data were assessed by validated questionnaires, collected over 2 years for all eligible women attending our ‘Menopause Clinic’ from 31 Chinese provinces. Simple and unconditional logistic regression analysis was used with adjustments by all analyzed factors. Results A total of 4063 women (mean age 50.53 ± 6.57 years), 2107 perimenopausal and 1956 postmenopausal, were included. Almost all GSM symptoms were more frequent and severe in postmenopausal women. GSM was more frequent in hysterectomized women compared to non-hysterectomized women. Independent of menopausal status, low sexual interest (92.78%), urinary incontinence (91.65%) and vaginal dryness (91.60%) were the top three GSM symptoms. Most severe were low sexual interest (21.01%), vaginal pain (20.10%) and decreased sexual pleasure (17.13%). Prevalence and severity of GSM were not related to age, but were related to menopausal status and increased with time since menopause. Conclusions Within 2 years, more than 4000 women with GSM traveled from all over China to our specialized clinic, indicating the great importance of GSM. Hysterectomy can increase the risk of GSM, and GSM symptoms increase from perimenopause to postmenopause and with an increase of time since menopause, pointing to the dependency on the loss of ovarian function.
Interrelations between factors related to physical activity in inactive adults with knee pain

Abstract Purpose The purpose was to explore interrelations between factors related to engagement in physical activity in inactive adults with knee pain. Method Inactive adults with knee pain (n = 35) participated in six focus groups designed to inquire about barriers and facilitators related with engagement in physical activity. Directed content analysis and inductive thematic analysis were used to identify factors related to physical activity and associated interrelations respectively. As an exploratory analysis, sex differences in barriers and facilitators to physical activity were assessed. Results In this cohort (age = 60.9 ± 8.6 years; 22 females), self-reported physical activity was 26.3 ± 46.8 min/week. Factors related to physical activity were grouped into domains of physical status, psychological status, environment, knowledge, and resources. It was seen that the interrelations between a person and their environment, as well as, between impairments and everyday responsibilities influenced engagement in physical activity. Females were more likely to identify physical and psychological status, social expectations, and lack of knowledge as barriers. Males indicated a preference for using mobile technologies to overcome barriers. Conclusion Interplay of various barriers and facilitators is related to engagement in physical activity in inactive older adults with knee pain. Interventions to promote physical activity should address these interrelations and sex differences. Implications for rehabilitation Interrelations between individual factors related to engagement in physical activity and sex differences in these factors are present in inactive adults with knee pain. Interventions to improve physical activity should be implemented by addressing factors and interrelations between factors related to physical activity in inactive adults with knee pain. Interventions to address low levels of physical activity in adults with knee pain should take into account sex differences.
Factors determining nurses' knowledge of evidence-based pressure ulcer prevention practices in Finland: a correlational cross-sectional study.

BACKGROUND Pressure ulcers cause economic burden, human suffering, pain and decreased health-related quality of life in patients. Pressure ulcers are preventable in most cases, and nursing staff knowledge is a key factor in successful pressure ulcer prevention. Further evidence is needed to better tailor pressure ulcer prevention training programmes to the nursing staff. AIM To evaluate the level of nursing staff knowledge about evidence-based pressure ulcer prevention practices in both primary and specialised care, and to identify what factors determine nurses' knowledge levels. METHODS A correlational, cross-sectional study was conducted from 2018 to 2019 in two hospital districts in Finland. The Pressure Ulcer Prevention Knowledge test was used to collect data, and the Attitude towards Pressure ulcer Prevention (APuP) instrument was used as a background variable. The data were statistically analysed with Wilcoxon and Kruskal-Wallis tests, Spearman correlations and multiple linear regression. RESULTS The pressure ulcer prevention knowledge of the participating registered nurses, practical nurses and ward managers (N = 554) was on average 24.40 (max. 35.00). There was no difference in the participants' knowledge based on the type of unit in which they were working (primary or specialised care). The participants' attitudes (p < 0.0001), current position (p = 0.0042), frequency of taking care of patients with pressure ulcers (p = 0.0001) and self-evaluated training needs (p < 0.0001) independently explained the variation in the knowledge scores. CONCLUSIONS Special attention needs to be paid to the knowledge of those nurses working in positions that require lower levels of education and those who rarely take care of patients with pressure ulcers. Supporting nurses' positive attitudes towards pressure ulcer prevention should be an essential part of pressure ulcer prevention training. Nurses' self-evaluations of their training needs can be used to target training. The limitations of the study should be considered when generalising the results.
Randomized Trial of Ruxolitinib in Antiretroviral-Treated Adults with HIV.

BACKGROUND Inflammation is associated with end-organ disease and mortality for people with HIV (PWH). Ruxolitinib, a Jak 1/2 inhibitor, reduces systemic inflammation for individuals without HIV and HIV reservoir markers ex vivo. The goal of this trial was to determine safety and efficacy of ruxolitinib for PWH on antiretroviral therapy (ART). METHODS ACTG A5336 was an open-label, multi-site, randomized-controlled trial (RCT). Participants were randomly assigned (2:1) using centralized software to ruxolitinib (10mg twice-daily) plus stable ART for five weeks versus ART alone, stratified by efavirenz-use. Eligible participants were suppressed on ART for ≥2 years, without comorbidities, and had >350 CD4+ T-cells/µL. Primary endpoints were premature discontinuation, safety events, and change in plasma IL-6. Secondary endpoints included other measures of inflammation/immune activation and HIV reservoir. RESULTS Sixty participants enrolled from May 16, 2016 to January 10, 2018. Primary safety events occurred in 2.5% (one participant) for ruxolitinib and 0% for controls, (p=0.67). Three participants (7.5%) prematurely discontinued ruxolitinib. By week five, differences in IL-6 (mean Fold Change (FC) 0.93 vs 1.10, p=0.18) and sCD14 levels (mean FC 0.96 vs 1.08, relative FC=0.96 (90%CI: 0.90,1.02)) for ruxolitinib versus controls was observed. Ruxolitinib reduced CD4+ T-cells expressing HLADR/CD38 (difference in means -0.34%, 90%CI: -0.66,-0.12)) and Bcl-2 (-3.30%, 90%CI: (-4.72,-1.87)). CONCLUSIONS In this RCT of healthy, virologically-suppressed PWH on ART, ruxolitinib was well-tolerated. Baseline IL-6 levels were normal, and showed no significant reduction. Ruxolitinib significantly decreased markers of immune activation and cell survival. Future studies of Jak inhibitors should target PWH with residual inflammation despite suppressive ART.
Implications of an improved model of the TSH receptor transmembrane domain (TSHR-TMD -TRIO).

The TSH receptor is a GPCR Group A family member with seven transmembrane helices. We generated three new models of its entire transmembrane region using a 600 ns molecular simulation. The simulation started from our previously published model which we have now revised by also modeling the intracellular loops and the C-terminal tail, adding internal waters and embedding it into a lipid bilayer with a water layer and with ions added to complete the system. We have named this model TSHR-TMD - TRIO since three representative dominant structures were then extracted from the simulation trajectory and compared with the original model. These structures each showed small but significant changes in the relative positions of the helices. The three models were also used as targets to dock a set of small molecules that are known active compounds including a new TSHR antagonist (BT362), which confirmed the appropriateness of the model with some small molecules showing significant preference for one or other of the structures.
Chain orientation and defects in lamellar single crystals of syndiotactic polypropylene fractions

Sectorization is frequently observed in elongated rectangular single crystals of syndiotactic polypropylene (s-PP) grown from the melt in thin films. The crystals are bound laterally by {100} and {010} growth planes. The constituent sectors are readily observed because of a difference in thicknesses; specifically, the sectors bound by the {100} planes [the (100) growth sectors] are thicker than those bounded by the {010} planes [the (010) growth sectors]. Dark field (DF) transmission electron microscopy (TEM) was utilized to examine the chain orientation and lattice defects in the different growth sectors of s-PP single crystals. The (020) DF images exhibited pairs of bright streaks that are more or less perpendicular to the (100) planes and cross over the whole width of the (100) sectors. In the (200) DF images, the (100) sectors also exhibited similar but dimmer streaks than those in the (020) DF images. This suggests that the crystal c-axis orientation in the (100) crystal sectors undergoes a periodic .
A mechanistic overview of taste bud maintenance and impairment in cancer therapies.

Since the early 20 th century, progress in cancer therapies has significantly improved disease prognosis. Nonetheless, cancer treatments are often associated with side effects that can negatively affect patient wellbeing and disrupt the course of treatment. Among the main side effects, taste impairment is associated with depression, malnutrition and morbid weight loss. Although relatively common, taste disruption associated with cancer therapies remains poorly understood. Here, we review the current knowledge related to the molecular mechanisms underlying taste maintenance and disruption in the context of cancer therapies.
Accurate prediction of inter-protein residue–residue contacts for homo-oligomeric protein complexes

Abstract Protein–protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein–protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein–protein interactions. Recently, deep learning has led to a breakthrough in intra-protein contact prediction, achieving an unusual high accuracy in recent Critical Assessment of protein Structure Prediction (CASP) structure prediction challenges. However, due to the limited number of known homologous protein–protein interactions and the challenge to generate joint multiple sequence alignments of two interacting proteins, the advances in inter-protein contact prediction remain limited. Here, we have proposed a deep learning model to predict inter-protein residue–residue contacts across homo-oligomeric protein interfaces, named as DeepHomo. Unlike previous deep learning approaches, we integrated intra-protein distance map and inter-protein docking pattern, in addition to evolutionary coupling, sequence conservation, and physico-chemical information of monomers. DeepHomo was extensively tested on both experimentally determined structures and realistic CASP-Critical Assessment of Predicted Interaction (CAPRI) targets. It was shown that DeepHomo achieved a high precision of >60% for the top predicted contact and outperformed state-of-the-art direct-coupling analysis and machine learning-based approaches. Integrating predicted inter-chain contacts into protein–protein docking significantly improved the docking accuracy on the benchmark dataset of realistic homo-dimeric targets from CASP-CAPRI experiments. DeepHomo is available at http://huanglab.phys.hust.edu. cn/DeepHomo/
Synthesis Gas from Methane by Using a Plasma-Assisted Gliding Arc Catalytic Partial Oxidation Reactor

In this work, the potential for the catalytic partial oxidation (CPOX) of methane (CH4) to produce synthesis gas (H2 and CO) was studied both experimentally and thermodynamically at a fixed pressure (1 bar) and electric power (0.3 kW). The investigations were performed in a partially adiabatic plasma-assisted (nonthermal) Gliding Arc (GlidArc) reactor, using a Ni-based catalyst. Two cases were studied: in the first, normal air (molar ratio of O2/N2 = 21/79) was used, whereas enriched air (O2/N2 = 40/60) was utilized in the second. The individual effect of the O2/CH4 molar ratio, gas hour space velocity (GHSV), and bed exiting temperature (Texit) was studied for both cases. The main trends of the CH4 conversion, the synthesis gas yield, and the thermal efficiency of the reactor based on the LHV (lower heating value) were analyzed and compared, and any deviations from equilibrium could be explained by temperature gradients and an irregular gas flow. In the findings from the studies, the results revealed tha.
Toxicological evaluation of milk from lactating dairy cows following consumption of newsprint

One of the uses that has been suggested for the extremely large waste stream of newspapers is for cattle bedding. Cows, however, are inclined to consume newspaper, which may contain a number of potentially toxic compounds including dioxins in the paper and benzidines in the inks used in the printing process. Conceivably, these compounds, many of which are lipophilic, could bioaccumulate in the milk of cows and thus enter the human food chain. In this study milk was collected from lactating cows before and after consuming a diet containing 10% newspaper for 2 weeks. The presence of mutagens was evaluated in the paper, diet, inks, and milk, and the concentration of dioxins was measured in the paper. Mutagens were found in newsprint, in the inks, and in two samples of milk. The concentration of the most toxic dioxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin, in the paper was below the level of detection (0.5 ppt) but the concentration of hepta- and octachlorodibenzo-p-dioxin and heptachlorodibenzofurans ranged from 5.4 to 350 ppt. Although the results of this study suggest that the risk to human health from drinking milk from cows that consumed newsprint is less than that from drinking coffee or tea, caution is urged in the use of newsprint as cattle bedding material because of the variability and lack of regulation of constituents in newspaper and associated shredded waste.
Fibrinolysis vs. primary percutaneous coronary intervention for ST‐segment elevation myocardial infarction cardiogenic shock

There are limited contemporary data on the use of initial fibrinolysis in ST‐segment elevation myocardial infarction cardiogenic shock (STEMI‐CS). This study sought to compare the outcomes of STEMI‐CS receiving initial fibrinolysis vs. primary percutaneous coronary intervention (PPCI).
Neighborhoods with Greater Prevalence of Minority Residents Have Lower CPAP Adherence.

RATIONALE Limited data suggest racial disparities in continuous positive airway pressure (CPAP) adherence exist. OBJECTIVES To assess if CPAP adherence varies by neighborhood racial composition at a national scale. METHODS Telemonitoring data from a CPAP manufacturer database were used to assess adherence in adult patients initiating CPAP therapy between November 2015 and October 2018. Mapping zip code to zip code tabulation areas (ZCTAs), age- and gender- adjusted CPAP adherence data at a neighborhood level was computed as a function of neighborhood racial composition. Secondary analyses adjusted for neighborhood education and poverty. MEASUREMENTS AND MAIN RESULTS Among 787,236 patients living in 26,180 ZCTAs, the prevalence of CPAP adherence was 1.3% (95% CI 1.0-1.6%) lower in neighborhoods with high (≥25%) versus low (<1%) percentage of Black residents and 1.2% (95% CI 0.9-1.5%) lower in neighborhoods with high versus low percentage of Hispanic residents (p<0.001 for both) even after adjusting for neighborhood differences in poverty and education. Mean CPAP usage was similar across neighborhoods over the first 2-days, but by 90-days, differences in CPAP usage increased to 22 min (95% CI 18-27 min) between neighborhoods with high versus low percentage of Black residents and 22 min (95% CI 17-27 min) between neighborhoods with high versus low percentage of Hispanic residents (p<0.001 for both). CONCLUSIONS CPAP adherence is lower in neighborhoods with greater proportions of Black and Hispanic residents independent of education or poverty. These differences lead to a lower likelihood of meeting insurance coverage requirements for CPAP therapy, potentially exacerbating sleep health disparities.
Associations of Total Legume, Pulse, and Soy Consumption with Incident Type 2 Diabetes: Federated Meta-Analysis of 27 Studies from Diverse World Regions

ABSTRACT Background The consumption of legumes is promoted as part of a healthy diet in many countries but associations of total and types of legume consumption with type 2 diabetes (T2D) are not well established. Analyses across diverse populations are lacking despite the availability of unpublished legume consumption data in prospective cohort studies. Objective To examine the prospective associations of total and types of legume intake with the risk of incident T2D. Methods Meta-analyses of associations between total legume, pulse, and soy consumption and T2D were conducted using a federated approach without physical data-pooling. Prospective cohorts were included if legume exposure and T2D outcome data were available and the cohort investigators agreed to participate. We estimated incidence rate ratios (IRRs) and CIs of associations using individual participant data including ≤42,473 incident cases among 807,785 adults without diabetes in 27 cohorts across the Americas, Eastern Mediterranean, Europe, and Western Pacific. Random-effects meta-analysis was used to combine effect estimates and estimate heterogeneity. Results Median total legume intake ranged from 0–140 g/d across cohorts. We observed a weak positive association between total legume consumption and T2D (IRR = 1.02, 95% CI: 1.01 to 1.04) per 20 g/d higher intake, with moderately high heterogeneity (I2 = 74%). Analysis by region showed no evidence of associations in the Americas, Eastern Mediterranean, and Western Pacific. The positive association in Europe (IRR = 1.05, 95% CI: 1.01 to 1.10, I2 = 82%) was mainly driven by studies from Germany, UK, and Sweden. No evidence of associations was observed for the consumption of pulses or soy. Conclusions These findings suggest no evidence of an association of legume intakes with T2D in several world regions. The positive association observed in some European studies warrants further investigation relating to overall dietary contexts in which legumes are consumed, including accompanying foods which may be positively associated with T2D.
Enhancing the Microbiological Stability of Malt and Beer — A Review

While beer provides a very stable microbiological environment, a few niche microorganisms are capable of growth in malt, wort and beer. Growth of mycotoxin-producing fungi during malting, production of off-flavours and development of turbidity in the packaged product due to the growth and metabolic activity of wild yeasts, certain lactic acid bacteria (LAB) and anaerobic Gram negative bacteria, impact negatively on beer quality. It follows that any means by which microbial contamination can be reduced or controlled would be of great economic interest to the brewing industry and would serve the public interest. There has been an increasing effort to develop novel approaches to minimal processing, such as the exploitation of inhibitory components natural to raw materials, to enhance the microbiological stability of beer. LAB species, which occur as part of the natural barley microbiota, persist during malting and mashing, and can play a positive role in the beer-manufacturing process by their contribution to wort bioacidification or the elimination of undesirable microorganisms. Other naturally occurring components of beer that have been valued for their preservative properties are hop compounds. It may be possible to enhance the antimicrobial activities of these compounds during brewing. Some yeast strains produce and excrete extracellular toxins called zymocins, which are lethal to sensitive yeast strains. Yeast strains resistant to zymocins have been constructed. Imparting zymocinogenic activity to brewing yeast would offer a defence against wild yeasts in the brewery. Thus, the antimicrobial properties of naturally occurring components of raw materials can be exploited to enhance the microbial stability of beer.
Denitrification in anaerobic digesters: Possibilities and influence of wastewater COD/N‐NOX ratio

Abstract Laboratory‐scale completely‐stirred anaerobic digesters were fed with synthetic wastewaters containing nitrate and nitrite and with glucose as the only source of organic carbon in order to investigate and compare the denitrification potentials of anaerobic digesters in the presence of nitrate and nitrite. Varying the input nitrate and nitrite concentration at fixed COD and HRT, methane production without denitrification occurred at COD/N‐NOX > 53; denitrification and methane production at 8.86 ≤ COD/N‐NOX ≤ 53 and only denitrification at COD/N‐NOX 53, ammonification appeared to be the main nitrate and nitrite reduction pathway. The successful competition of ammonia formers over the true denitrifiers at high ratios was attributed to the low initial nitrate and nitrite concentrations.