Miracle-dz/UniFAR-FTUs huggingface dataset:
Caffeine, alcohol, khat, and tobacco use during pregnancy in Butajira, South Central Ethiopia

Background The use of excessive caffeine and consumption of alcohol, cigarette, and khat during pregnancy can result in adverse health effects on the fetus. The World Health Organization (WHO) recommends a daily caffeine intake not exceeding 300 mg. Likewise, pregnant women are recommended to avoid alcohol, khat and tobacco use. However, the prevalence’s of the use of substances among pregnant women were not well studied in developing countries such as Ethiopia. Therefore, the study aimed to estimate the prevalence of caffeine and alcohol consumption, khat chewing, and tobacco use during pregnancy and identify key factors associated with excess caffeine consumption. Methods We conducted a community based cross-sectional study and used a random sampling technique to recruit 352 pregnant women. We adapted a questionnaire from Caffeine Consumption Questionnaire-Revised (CCQ-R), Alcohol Use Disorder Identification Test (AUDIT), Global Adult Tobacco Survey (GATS), and Ethiopian Demographic Health Survey 2016 for caffeine, alcohol consumption, tobacco use, and khat chewing assessment, respectively. We conducted non-consecutive two days 24-hour recall to determine the habitual intake of caffeine from caffeinated beverages and foods. Prevalence with 95% confidence interval was estimated for excess caffeine intake per day, alcohol consumption, khat chewing, and passive tobacco smoking. We ran a multivariable binary logistic regression model to identify factors associated with excess caffeine intake. Results Almost all pregnant women (98.2%) consumed caffeine as estimated using the 2 days 24-hour average. The median daily caffeine intake was 170.5 mg and ranged from 0.00 mg to 549.8 mg per day. In addition, 17.6% (95% CI: 13.9%, 22.0%) of them had a daily caffeine consumption of 300 mg and above exceeding the WHO recommended daily caffeine intake during pregnancy. The prevalence of alcohol consumption and Khat chewing were 10.0% (95% CI: 7.2%, 13.7%) and 35.8% (95% CI: 30.8, 41.0%) respectively. None of the pregnant women were active tobacco smokers. However, 23.2% (95% CI: 19.0, 28.0%) were passive tobacco smokers. We found that pregnant women in the richest wealth quintile (AOR = 3.66; 95% CI: 1.13, 11.88), and the first trimester of pregnancy (AOR = 4.04; 95% CI: 1.26, 13.05) had higher odds of consuming excessive caffeine. Conclusions The study showed a considerable magnitude of substance use among pregnant women in the study area. Given this findings, we recommend, programs and services focusing on pregnant women to consider addressing substance use.
Clinical Characteristics of and Medical Interventions for COVID-19 in Hemodialysis Patients in Wuhan, China.

BACKGROUND Reports indicate that those most vulnerable to developing severe coronavirus disease 2019 (COVID-19) are older adults and those with underlying illnesses, such as diabetes mellitus, hypertension, or cardiovascular disease, which are common comorbidities among patients undergoing maintenance hemodialysis. However, there is limited information about the clinical characteristics of hemodialysis patients with COVID-19 or about interventions to control COVID-19 in hemodialysis centers. METHODS We collected data retrospectively through an online registration system that includes all patients receiving maintenance hemodialysis at 65 centers in Wuhan, China. We reviewed epidemiologic and clinical data of patients with laboratory-confirmed COVID-19 between January 1, 2020 and March 10, 2020. RESULTS Of 7154 patients undergoing hemodialysis, 154 had laboratory-confirmed COVID-19. The mean age of the 131 patients in our analysis was 63.2 years; 57.3% were men. Many had underlying comorbidities, with cardiovascular disease (including hypertension) being the most common (68.7%). Only 51.9% of patients manifested fever; 21.4% of infected patients were asymptomatic. The most common finding on chest computed tomography (CT) was ground-grass or patchy opacity (82.1%). After initiating comprehensive interventions-including entrance screening of body temperature and symptoms, universal chest CT and blood tests, and other measures-new patients presenting with COVID-19 peaked at 10 per day on January 30, decreasing to 4 per day on February 11. No new cases occurred between February 26 and March 10, 2020. CONCLUSIONS We found that patients receiving maintenance hemodialysis were susceptible to COVID-19 and that hemodialysis centers were high-risk settings during the epidemic. Increasing prevention efforts, instituting universal screening, and isolating patients with COVID-19 and directing them to designated hemodialysis centers were effective in preventing the spread of COVID-19 in hemodialysis centers.
Deglycosylation of the Isoflavone C-Glucoside Puerarin by a Combination of Two Recombinant Bacterial Enzymes and 3-Oxo-Glucose

One important role of the gut microbiota is to metabolize dietary nutrients and supplements such as flavonoid glycosides. Ingested glycosides are metabolized by intestinal bacteria to more-absorbable aglycones and further degradation products that show beneficial effects in humans. Although numerous glycoside hydrolases that catalyze O-deglycosylation have been reported, enzymes responsible for C-deglycosylation are still limited. In this study, we characterized enzymes involved in the C-deglycosylation of puerarin from a human intestinal bacterium, PUE. Here, we report the purification and characterization of a recombinant oxidoreductase involved in C-glucoside degradation. This study provides new insights for the elucidation of mechanisms of enzymatic C-deglycosylation. ABSTRACT A human intestinal bacterium strain related to Dorea species, PUE, can metabolize the isoflavone C-glucoside puerarin (daidzein 8-C-glucoside) to daidzein and glucose. We reported previously that 3″-oxo-puerarin is an essential reaction intermediate in enzymatic puerarin degradation, and we characterized a bacterial enzyme, the DgpB-DgpC complex, that cleaved the C-glycosidic bond in 3″-oxo-puerarin. However, the exact enzyme catalyzing the oxidation of the C-3″ hydroxyl in puerarin has not been identified. In this study, we demonstrated that recombinant DgpA, a Gfo/Idh/MocA family oxidoreductase, catalyzed puerarin oxidation in the presence of 3-oxo-glucose as the hydride acceptor. In the redox reaction, NAD(H) functioned as the cofactor, which bound tightly but noncovalently to DgpA. Kinetics analysis of DgpA revealed that the reaction proceeded via a ping-pong mechanism. Enzymatic C-deglycosylation of puerarin was achieved by a combination of recombinant DgpA, the DgpB-DgpC complex, and 3-oxo-glucose. In addition, the metabolite derived from the sugar moiety in the 3″-oxo-puerarin-cleaving reaction catalyzed by the DgpB-DgpC complex was characterized as 1,5-anhydro-d-erythro-hex-1-en-3-ulose, suggesting that the C-glycosidic linkage is cleaved through a β-elimination-like mechanism. IMPORTANCE One important role of the gut microbiota is to metabolize dietary nutrients and supplements such as flavonoid glycosides. Ingested glycosides are metabolized by intestinal bacteria to more-absorbable aglycones and further degradation products that show beneficial effects in humans. Although numerous glycoside hydrolases that catalyze O-deglycosylation have been reported, enzymes responsible for C-deglycosylation are still limited. In this study, we characterized enzymes involved in the C-deglycosylation of puerarin from a human intestinal bacterium, PUE. Here, we report the purification and characterization of a recombinant oxidoreductase involved in C-glucoside degradation. This study provides new insights for the elucidation of mechanisms of enzymatic C-deglycosylation.
Tailoring Uptake Efficacy of HSV-1 gD Tailoring Uptake Efficacy of Hsv-1 GD Derived Carrier Peptides

Regions of the Herpes simplex virus-1 (HSV-1) glycoprotein D (gD) were chosen to design carrier peptides based on the known tertiary structure of the virus entry receptor complexes. These complexes consist of the following: HSV-1 gD–nectin-1 and HSV-1 gD–herpesvirus entry mediator (HVEM). Three sets of peptides were synthesised with sequences covering the (i) N-terminal HVEM- and nectin-1 binding region -5–42, (ii) the 181–216 medium region containing nectin-1 binding sequences and (iii) the C-terminal nectin-1 binding region 214–255. The carrier candidates were prepared with acetylated and 5(6)-carboxyfluorescein labelled N-termini. The peptides were chemically characterised and their conformational features in solution were also determined. In vitro internalisation profile and intracellular localisation were evaluated on SH-SY5Y neuroblastoma cells. Peptide originated from the C-terminal region 224–247 of the HSV-1 gD showed remarkable internalisation compared to the other peptides with low to moderate entry. Electronic circular dichroism secondary structure studies of the peptides revealed that the most effectively internalised peptides exhibit high helical propensity at increasing TFE concentrations. We proved that oligopeptides derived from the nectin-1 binding region are promising candidates—with possibility of Lys237Arg and/or Trp241Phe substitutions—for side-reaction free conjugation of bioactive compounds—drugs or gene therapy agents—as cargos.
A Comprehensive Survey of Indoor Localization Methods Based on Computer Vision

Computer vision based indoor localization methods use either an infrastructure of static cameras to track mobile entities (e.g., people, robots) or cameras attached to the mobile entities. Methods in the first category employ object tracking, while the others map images from mobile cameras with images acquired during a configuration stage or extracted from 3D reconstructed models of the space. This paper offers an overview of the computer vision based indoor localization domain, presenting application areas, commercial tools, existing benchmarks, and other reviews. It provides a survey of indoor localization research solutions, proposing a new classification based on the configuration stage (use of known environment data), sensing devices, type of detected elements, and localization method. It groups 70 of the most recent and relevant image based indoor localization methods according to the proposed classification and discusses their advantages and drawbacks. It highlights localization methods that also offer orientation information, as this is required by an increasing number of applications of indoor localization (e.g., augmented reality).
Flavonoids are indispensable for complete male fertility in rice.

Flavonoids are essential for male fertility in some but not all plant species. In rice, the chalcone synthase mutant oschs1 produces flavonoid-depleted pollens and is male sterile. The mutant pollens are viable with normal structure but they displayed reduced germination rate and pollen tube length. Analysis of pollens of oschs1/+ heterozygous lines showed that pollen flavonoid deposition is a paternal effect and fertility is independent from the haploid genotypes (OsCHS1 or oschs1). To understand which classes of flavonoids are involved in male fertility, we further analyzed rice mutants for branch-point enzymes of the downstream flavonoid pathways, including flavanone 3-hydroxylase (OsF3H; flavonol pathway entry enzyme), flavone synthase II (CYP93G1; flavone pathway entry enzyme) and flavanone 2-hydroxylase (CYP93G2; flavone C-glycoside pathway entry enzyme). Rice osf3h and cyp93g1 cyp93g2 CRISPR/Cas9 mutants, and cyp93g1 and cyp93g2 T-DNA insertional mutants showed altered flavonoid profiles in anthers but only osf3h and cyp93g1 cyp93g2 mutants displayed reduction in seed yield. Our findings indicated that flavonoids are essential for complete male fertility in rice and a combination of different classes (flavanones, flavonols, flavones, and flavone C-glycosides) are likely to be important, as opposed to the essential role played primarily by flavonols as reported previously in several plant species.
Benefits of a Three-Day Bamboo Forest Therapy Session on the Physiological Responses of University Students

Studies have indicated that natural environments have the potential to improve the relationship between a stressful life and psychological well-being and physical health. Forest therapy has recently received widespread attention as a novel solution for stress recovery and health promotion. Bamboo is an important forest type in many countries, especially in East and Southeast Asia and in African countries. Bamboo is widespread throughout southwestern China. Empirical field research on the physiological effects of bamboo forest therapy is currently lacking. To explore the benefits of bamboo forest therapy on the physiological responses of university students, 120 university volunteers between the ages of 19 and 24 participated in this study (60 males and 60 females) and were randomly divided into four groups of equal size (15 males and 15 females in each). Four sites were selected for the experiment, including two natural bamboo forests (YA and YB), a bamboo forest park (DJY), and an urban environment (CS). During the testing period, all participants were asked to view the landscape for 15 min in the morning and then walk in the testing area for 15 min in the afternoon. Blood pressure (BP), heart rate (HR), and peripheral oxygen saturation (SpO2) were measured as the physiological indexes, and the semantic differential method (SDM) questionnaire was completed for the environmental satisfaction evaluation. The SDM for the subjective environmental evaluation differed significantly among the university students; they obtained a better environmental experience, in terms of sensory perception, atmosphere, climate, place, and space, in the bamboo forest sites. The three-day bamboo forest therapy session improved the physiological well-being of university students. First, the blood pressure and heart rate of the university students decreased, and the SpO2 increased, after the three-day viewing and walking activities of the three-day bamboo forest therapy session. The viewing activities had a more pronounced effect on decreased heart rate in university students. Additionally, three-day bamboo forest therapy had a positive impact on decreased systolic blood pressure and heart rate in the university students, and it was significantly decreased in females, while peripheral oxygen saturation (SpO2) remained relatively low. Finally, compared with the urban site (CS), the bamboo forest sites effectively improved the university students’ physiological state of health, decreased their physical pressure, and stabilized their physiological indicators. These findings provide scientific evidence that a three-day bamboo forest therapy session can increase positive physiological responses. The potential for a longer-term effect on human physiological health requires further investigation.
Epistasis, inbreeding depression, and the evolution of self‐fertilization

Inbreeding depression resulting from partially recessive deleterious alleles is thought to be the main genetic factor preventing self‐fertilizing mutants from spreading in outcrossing hermaphroditic populations. However, deleterious alleles may also generate an advantage to selfers in terms of more efficient purging, while the effects of epistasis among those alleles on inbreeding depression and mating system evolution remain little explored. In this article, we use a general model of selection to disentangle the effects of different forms of epistasis (additive‐by‐additive, additive‐by‐dominance, and dominance‐by‐dominance) on inbreeding depression and on the strength of selection for selfing. Models with fixed epistasis across loci, and models of stabilizing selection acting on quantitative traits (generating distributions of epistasis) are considered as special cases. Besides its effects on inbreeding depression, epistasis may increase the purging advantage associated with selfing (when it is negative on average), while the variance in epistasis favors selfing through the generation of linkage disequilibria that increase mean fitness. Approximations for the strengths of these effects are derived, and compared with individual‐based simulation results.
Spatiotemporal regulation of PEDF signaling by type I collagen remodeling

Significance In the extracellular milieu, soluble ligands must be delivered at the right time and place to their target cell surface receptors; however, the extracellular control mechanisms underlying these events remain unclear. We propose that remodeling of type I collagen spatiotemporally regulates pigment epithelium-derived factor (PEDF), a secreted glycoprotein, which promotes either cell survival or death, depending on the context. The crystal structure of PEDF in complex with the heterotrimeric collagen peptide revealed that it recognizes a cryptic site on type I collagen containing a lysyl residue susceptible for intermolecular cross-linking. Therefore, the receptor-binding activity of PEDF is regulated by collagen maturation and cross-linking. This study provides insights that will contribute to understanding the multifaceted nature of PEDF functions. Dynamic remodeling of the extracellular matrix affects many cellular processes, either directly or indirectly, through the regulation of soluble ligands; however, the mechanistic details of this process remain largely unknown. Here we propose that type I collagen remodeling regulates the receptor-binding activity of pigment epithelium-derived factor (PEDF), a widely expressed secreted glycoprotein that has multiple important biological functions in tissue and organ homeostasis. We determined the crystal structure of PEDF in complex with a disulfide cross-linked heterotrimeric collagen peptide, in which the α(I) chain segments—each containing the respective PEDF-binding region (residues 930 to 938)—are assembled with an α2α1α1 staggered configuration. The complex structure revealed that PEDF specifically interacts with a unique amphiphilic sequence, KGHRGFSGL, of the type I collagen α1 chain, with its proposed receptor-binding sites buried extensively. Molecular docking demonstrated that the PEDF-binding surface of type I collagen contains the cross-link–susceptible Lys930 residue of the α1 chain and provides a good foothold for stable docking with the α1(I) N-telopeptide of an adjacent triple helix in the fibril. Therefore, the binding surface is completely inaccessible if intermolecular crosslinking between two crosslink-susceptible lysyl residues, Lys9 in the N-telopeptide and Lys930, is present. These structural analyses demonstrate that PEDF molecules, once sequestered around newly synthesized pericellular collagen fibrils, are gradually liberated as collagen crosslinking increases, making them accessible for interaction with their target cell surface receptors in a spatiotemporally regulated manner.
Pathogen or commensal: a PCR based study of ocular surface bacteria in normal and dry eyes

Purpose: To determine the ocular surface bacteria in normal and dry eye subjects and investigate whether there was any association between the bacterial population and goblet cell density (GCD). Methods: Fifty-seven normal and 34 dry eye subjects were recruited. Conventional culture, 16S rDNA PCR and DNA sequencing were used to identify bacteria. The association between reduced GCD and bacterial numbers in a sub-group of 27 subjects was assessed. Conjunctival impression cytology samples were stained with PAS and GCD graded as follows: Grade (1), >30 goblet cells/4 high power fields; (2), 15-30 GC/4HPF; (3), 5-15 GC/4HPF; (4), <5 GC/4HPF. Grades 3 and 4 indicated reduced GCD. Results: The majority of cultured bacteria were coagulase-negative Staphylococci, while molecular methods demonstrated additional atypical bacterial species. Bacterial levels were higher overall in subjects displaying reduced GCD compared to normals. A statistically significant difference (P = 0.005) was noted between mean bacterial counts in IC Grade 4 samples of dry eye subjects (35 cfu/swab) and normals (5 cfu/swab). Conclusions: Molecular analysis revealed a diverse ocular surface bacterial population with identification of potentially pathogenic bacteria presenting a diagnostic dilemma. A trend of increasing bacterial numbers with reduced GCD was observed and studies are ongoing to investigate whether bacterial colonisation of the ocular surface may alter the number and function of goblet cells. The clinical relevance of such results and whether they should prompt intervention with therapy is not yet fully determined. A fuller definition of the normal ocular flora is needed to determine bacteria implicated in ocular surface disease.
Adaptedness and Fitness

Genetic homeostasis is the term used to define the condition of population equilibrium in which phenotypic composition is insensitive to environmental changes. In variable environments, this condition is achieved by superior adaptedness of heterozygous genotypes. I use the term demographic homeostasis to describe the ability of the birth sequence to maintain its stable trajectory when subject to environmental disturbances. This condition is characterized by the variability of the contribution of the different age classes to the stable age-distribution. This is measured by the entropy parameter. A crucial component of fitness is the speed of return of the population to the stable state when perturbed. The suggestion that entropy be used as a measure of fitness is based on two facts. (a) Mean entropy increases under natural selection. (b) Maximum entropy implies maximum stability.
A survey-wide association study to identify youth-specific correlates of major depressive episodes

Background Major depressive disorder is a common disease with high mortality and morbidity worldwide. Though peak onset is during late adolescence, the prevalence of major depressive disorder remains high throughout adulthood. Leveraging an association study design, this study screened a large number of variables in the 2017 National Survey on Drug Use and Health to characterize differences between adult and youth depression across a wide array of phenotypic measurements. Methods All dichotomous variables were manually identified from the survey for association screening. Association between each dichotomous variable and past-year major depressive episode (MDE) occurrence was calculated as an odds ratio for adults (≥18 years) and youth (12–17 years), and tested for significance with Fischer's exact test. Logarithm of the calculated odds ratios were plotted and fitted to a linear model to assess correlation between adult and youth risk factors. Results Many of the screened variables showed similar association between past-year depressive episode occurrence in youth and adults; Lin's concordance correlation coefficient between adult and youth associations was 0.91 (95% CI 0.89–0.92). Differentially associated variables were identified, tracking: female sex, alcohol use, cigarette use, marijuana use, Medicaid/CHIP coverage, cognitive changes due to a mental, physical or emotional condition, and respondents' identification of a single depressive event as the worst experienced. Conclusions While some youth-specific correlates of major depressive episodes were identified through screening, including some novel associations, most examined variables showed similar association with youth and adult depression. Further study of results is warranted, especially concerning the finding of increased association between marijuana use and depressive episodes in youth.