Miracle-dz/UniFAR-FTUs huggingface dataset:
Humic Acid-Oxidizing, Nitrate-Reducing Bacteria in Agricultural Soils

ABSTRACT This study demonstrates the prevalence, phylogenetic diversity, and physiology of nitrate-reducing microorganisms capable of utilizing reduced humic acids (HA) as electron donors in agricultural soils. Most probable number (MPN) enumeration of agricultural soils revealed large populations (104 to 106 cells g−1 soil) of microorganisms capable of reducing nitrate while oxidizing the reduced HA analog 2,6-anthrahydroquinone disulfonate (AH2DS) to its corresponding quinone. Nitrate-dependent HA-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups. Subsequent 16S rRNA gene-based high-density oligonucleotide microarray (PhyloChip) indicated that reduced HA columns supported the development of a bacterial community enriched with members of the Acidobacteria, Firmicutes, and Betaproteobacteria relative to the no-donor control and initial inoculum. This study identifies a previously unrecognized role for HA in stimulating denitrification processes in saturated soil systems. Furthermore, this study indicates that reduced humic acids impact soil geochemistry and the indigenous bacterial community composition. IMPORTANCE This study identifies a new metabolic capacity in soil microbial communities that may be responsible for the mediation of significant nitrogen losses from soil systems. Nitrate-dependent humic acid (HA)-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups. This study identifies a new metabolic capacity in soil microbial communities that may be responsible for the mediation of significant nitrogen losses from soil systems. Nitrate-dependent humic acid (HA)-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups.
Vacuolar H+-ATPase Protects Saccharomyces cerevisiae Cells against Ethanol-Induced Oxidative and Cell Wall Stresses

ABSTRACT During fermentation, increased ethanol concentration is a major stress for yeast cells. Vacuolar H+-ATPase (V-ATPase), which plays an important role in the maintenance of intracellular pH homeostasis through vacuolar acidification, has been shown to be required for tolerance to straight-chain alcohols, including ethanol. Since ethanol is known to increase membrane permeability to protons, which then promotes intracellular acidification, it is possible that the V-ATPase is required for recovery from alcohol-induced intracellular acidification. In this study, we show that the effects of straight-chain alcohols on membrane permeabilization and acidification of the cytosol and vacuole are strongly dependent on their lipophilicity. These findings suggest that the membrane-permeabilizing effect of straight-chain alcohols induces cytosolic and vacuolar acidification in a lipophilicity-dependent manner. Surprisingly, after ethanol challenge, the cytosolic pH in Δvma2 and Δvma3 mutants lacking V-ATPase activity was similar to that of the wild-type strain. It is therefore unlikely that the ethanol-sensitive phenotype of vma mutants resulted from severe cytosolic acidification. Interestingly, the vma mutants exposed to ethanol exhibited a delay in cell wall remodeling and a significant increase in intracellular reactive oxygen species (ROS). These findings suggest a role for V-ATPase in the regulation of the cell wall stress response and the prevention of endogenous oxidative stress in response to ethanol. IMPORTANCE The yeast Saccharomyces cerevisiae has been widely used in the alcoholic fermentation industry. Among the environmental stresses that yeast cells encounter during the process of alcoholic fermentation, ethanol is a major stress factor that inhibits yeast growth and viability, eventually leading to fermentation arrest. This study provides evidence for the molecular mechanisms of ethanol tolerance, which is a desirable characteristic for yeast strains used in alcoholic fermentation. The results revealed that straight-chain alcohols induced cytosolic and vacuolar acidification through their membrane-permeabilizing effects. Contrary to expectations, a role for V-ATPase in the regulation of the cell wall stress response and the prevention of endogenous oxidative stress, but not in the maintenance of intracellular pH, seems to be important for protecting yeast cells against ethanol stress. These findings will expand our understanding of the mechanisms of ethanol tolerance and provide promising clues for the development of ethanol-tolerant yeast strains.
CD4+ T Cell Recovery and Hepatitis B Virus Coinfection in HIV-Infected Patients from Côte d'Ivoire Initiating Antiretroviral Therapy.

Immunorecovery could be attenuated in HIV-hepatitis B virus (HBV) coinfection versus HIV monoinfection during antiretroviral therapy (ART), yet, whether it also occurs in individuals from sub-Saharan Africa without severe comorbidities is unknown. In this study, 808 HIV-infected patients in Côte d'Ivoire initiating continuous ART were included. Six-month CD4+ count trajectories and the proportion reaching CD4+ T cell counts >350/mm3, HIV-RNA <300 copies/mL, still alive and not lost to follow-up within 18 months ("optimal immunorecovery") were compared between coinfected groups. At inclusion, 80 (9.9%) patients were HIV-HBV coinfected, 40 (50.0%) of whom had high HBV-DNA viral load (VL) (>104 copies/mL). Coinfected patients with high HBV-DNA replication initiated ART with significantly lower median CD4+ T cell counts [216/mm3, interquartile range (IQR) = 150-286] compared to coinfection with low HBV-DNA replication (268/mm3, IQR = 178-375) or HIV monoinfection (257/mm3, IQR = 194-329) (p = .003). These patients had significantly faster rates of CD4+ cell count increase from baseline after adjusting for baseline age, World Health Organization stage III/IV, and CD4+ cell counts (p = .04), yet, were not more likely to exhibit optimal immunorecovery (82.5% vs. 80.0% and 77.9%, respectively) (p = .8). In conclusion, change in CD4+ cell counts after ART-initiation was accelerated in coinfected patients with high HBV DNA VLs, but this did not lead to increased rates of optimal immunorecovery.
Quality of Fresh Cut Zucchini as Affected by Cultivar, Maturity at Processing and Packaging

Appropriate plant material at processing and film packaging selection has a strong influence on product quality preservation. This is the first report studying the feasibility for minimal processing of four zucchini cultivars at two maturity stages, immature (MS1) and mature, stored at 6 °C during 10 days under different packaging conditions. The treatments consisted a 4 × 2 × 2 × 3 factorial combination of variety, maturity at processing, film packaging and storage time, including correlation studies between quality parameters. Negative effect on final quality after processing at MS1 was observed as a result of a higher respiration rate (between 15.91 and 20.12% than at mature), CO2 production and soluble solid consumption contributing to loss of firmness, slice discolouration and less overall quality. After 10 days under 25 µm film, cv. ‘Cronos’ showed the highest values in total chlorophylls (9.03 mg/100 g FW), while slices at MS1 suffered a noticeable oxidative stress increasing the total phenolic content (cv. ‘Parador’ > ‘Amalthée’ > ‘Cronos’ > ‘Cassiope’). At the end of storage, the highest vitamin C content was observed in trays sealed with 25 µm film (more evident in cv. ‘Cronos’ at MS1). In conclusion, processing more mature zucchini and 25 µm film packaging were the most effective combination for preserving quality. Copyright © 2016 John Wiley & Sons, Ltd.
Structural and Functional Characterization of Cargo-Binding Sites on the μ4-Subunit of Adaptor Protein Complex 4

Adaptor protein (AP) complexes facilitate protein trafficking by playing key roles in the selection of cargo molecules to be sorted in post-Golgi compartments. Four AP complexes (AP-1 to AP-4) contain a medium-sized subunit (μ1-μ4) that recognizes YXXØ-sequences (Ø is a bulky hydrophobic residue), which are sorting signals in transmembrane proteins. A conserved, canonical region in μ subunits mediates recognition of YXXØ-signals by means of a critical aspartic acid. Recently we found that a non-canonical YXXØ-signal on the cytosolic tail of the Alzheimer's disease amyloid precursor protein (APP) binds to a distinct region of the μ4 subunit of the AP-4 complex. In this study we aimed to determine the functionality of both binding sites of μ4 on the recognition of the non-canonical YXXØ-signal of APP. We found that substitutions in either binding site abrogated the interaction with the APP-tail in yeast-two hybrid experiments. Further characterization by isothermal titration calorimetry showed instead loss of binding to the APP signal with only the substitution R283D at the non-canonical site, in contrast to a decrease in binding affinity with the substitution D190A at the canonical site. We solved the crystal structure of the C-terminal domain of the D190A mutant bound to this non-canonical YXXØ-signal. This structure showed no significant difference compared to that of wild-type μ4. Both differential scanning fluorimetry and limited proteolysis analyses demonstrated that the D190A substitution rendered μ4 less stable, suggesting an explanation for its lower binding affinity to the APP signal. Finally, in contrast to overexpression of the D190A mutant, and acting in a dominant-negative manner, overexpression of μ4 with either a F255A or a R283D substitution at the non-canonical site halted APP transport at the Golgi apparatus. Together, our analyses support that the functional recognition of the non-canonical YXXØ-signal of APP is limited to the non-canonical site of μ4.
How should CT coronary angiography be integrated into the management of patients with chest pain and how does this affect outcomes?

Abstract When examining the role of a diagnostic test in clinical practice, consideration must be placed not only on the accuracy of the result, but also its impact on patient care and outcomes. Proving a direct effect on outcomes may be difficult because the impact of the diagnostic test largely depends on the clinician's interpretation and consequent actions as well as the patient's response to changes in their diagnosis, investigations, and treatment. Recent major clinical trials of symptomatic patients with suspected coronary heart disease (CHD) have shown that computed tomography coronary angiography (CTCA) can markedly clarify the diagnosis and lead to major changes in patient investigation and management including the use of invasive angiography, preventative therapies, and coronary revascularization. Thus, when added to our existing clinical tools, such as exercise electrocardiography, CTCA represents a powerful method of identifying and excluding CHD. Furthermore, it can identify patients with prognostically relevant non-obstructive CHD and, with recent technological advances, will be able to assess the functional impact of anatomically detected coronary artery stenoses. Overall, the routine integration of CTCA into the investigation of patients with chest pain improves clinical diagnostic certainty that has led to better targeting of investigations and evidence-based treatments that have ultimately translated into improved clinical outcomes.
Exploring the Impact of Information Seeking Behaviors of Online Health Consumers in the Arab World

In the Arab world, increasing numbers of people are seeking online health related information for diagnoses, medicine, fitness, pharmaceutical drugs, and smoking cessation programs, among others. Studies exploring the impact of social media channels on health seeking behavior among Arabic users are limited. This study has two goals: (1) describe the prevalence of online health information-seeking behavior in the Arab world, and (2) study the impacts of social media based platforms in helping promote healthy living in the Arab world. In order to gather primary data, a web-based cross-sectional survey with a total of 7013 self-administered questionnaires was sent via SMS messages (n=1278), to Twitter followers of an Arab women's health social media account (n=3630 followers), and WhatsApp messages (n=2105) to participants above 16 years of age representing different socioeconomic groups and within the Arabic speaking world. The findings of this study show high interest among the participants (84.9%) in seeking online health information. Furthermore, reporting online information had an impact on participant health behaviors. Social media can play an important role in strengthening the health care system to provide valuable information, educational programs and interventions to promote healthy life styles among the Arabic people.
The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

ABSTRACT The development and continuous improvement of high-throughput sequencing platforms have stimulated interest in the study of complex microbial communities. Currently, the most popular sequencing approach to study microbial community composition and dynamics is targeted 16S rRNA gene metabarcoding. To prepare samples for sequencing, there are a variety of processing steps, each with the potential to introduce bias at the data analysis stage. In this short review, key information from the literature pertaining to each processing step is described, and consequently, general recommendations for future 16S rRNA gene metabarcoding experiments are made.
Seed size plasticity in response to embryonic lethality conferred by ectopic CYCD activation is dependent on plant architecture

ABSTRACT The size of seeds is the result of cell proliferation and growth in the three seed compartments: the embryo, endosperm and integuments. Targeting expression of the D-type cyclin CYCD7;1 to the central cell and early endosperm (FWA:CYCD7;1) triggered nuclear divisions and partial ovule abortion, reducing seed number in each silique and leading to increased seed size. A similar effect on seed size was observed with other segregating embryo lethal mutations, suggesting caution is needed in interpreting apparent seed size phenotypes. Here, we show that the positive effect of FWA:CYCD7;1 on Arabidopsis seed size is modulated by the architecture of the mother plant. Larger seeds were produced in FWA:CYCD7;1 lines with unmodified inflorescences, and also upon removal of side branches and axillary stems. This phenotype was absent from inflorescences with increased axillary floral stems produced by pruning of the main stem. Given this apparent confounding influence of resource allocation on transgenes effect, we conclude that plant architecture is a further important factor to consider in appraising seed phenotypes.
A Systematic Review of the Effect of Rotavirus Vaccination on Diarrhea Outcomes Among Children Younger Than 5 Years

Background: Rotavirus is the leading cause of vaccine-preventable diarrhea among children under 5 globally. Rotavirus vaccination has been shown to prevent severe rotavirus infections with varying efficacy and effectiveness by region. Methods: We sought to generate updated region-specific estimates of rotavirus vaccine efficacy and effectiveness. We systematically reviewed published vaccine efficacy and effectiveness studies to assess the region-specific effect of rotavirus vaccination on select diarrheal morbidity and mortality outcomes in children under 5 years of age. We employed meta-analytic methods to generate pooled effect sizes by Millennium Development Goal region. Results: Rotavirus vaccination was both efficacious and effective in preventing rotavirus diarrhea, severe rotavirus diarrhea and rotavirus hospitalizations among children under 5 across all regions represented by the 48 included studies. Efficacy against severe rotavirus diarrhea ranged from 90.6% [95% confidence interval (CI): 82.3–95.0] in the developed region to 88.4% (95% CI: 67.1–95.9) in Eastern/Southeastern Asia, 79.6% (95% CI: 71.3–85.5) in Latin America and the Caribbean, 50.0% (95% CI: 34.4–61.9) in Southern Asia and 46.1% (95% CI: 29.1–59.1) in sub-Saharan Africa. Region-specific effectiveness followed a similar pattern. There was also evidence of vaccine efficacy against severe diarrhea and diarrheal hospitalizations. Conclusion: Our findings confirm the protective efficacy and effectiveness of rotavirus vaccination against rotavirus diarrheal outcomes among children under 5 globally.
Suicidal risk, hopelessness and depression in patients with schizophrenia and internalized stigma.

BACKGROUND Internalized stigma has negative consequences on subjective and objective aspects of the recovery in people diagnosed with mental disorders. Despite its relevance, it has been poorly studied in patients with schizophrenia. METHODS A sample of 71 outpatients with a diagnosis of schizophrenia who attended Psychosocial Rehabilitation Centers of Gran Canaria, Spain, were evaluated. We assessed the prevalence of internalized stigma and its possible association with sociodemographic, clinical, psychological and psychopathological variables, as well as suicidal behaviour and suicidal ideation. RESULTS 21.1% of the patients had internalized stigma. Internalized stigma was associated with higher prevalence of suicidal ideation during the last year, higher number of suicide attempts, higher current suicidal risk, worse self-compassion, higher self-esteem, higher scores on depression, higher prevalence of depression and higher hopelessness. After multivariate analysis, hopelessness and the existence of depression were independently associated with internalized stigma, although depression showed trend towards significance. CONCLUSIONS The association between internalized stigma and higher hopelessness, depression and higher suicidal risk suggests the necessity to systematically assess internalized stigma in patients with schizophrenia, and to intervene to reduce it.
Factors Associated With Hypertension Control in US Adults Using 2017 ACC/AHA Guidelines: National Health and Nutrition Examination Survey 1999–2016

BACKGROUND Factors and trends associated with hypertension control (BP < 130/80 mm Hg) and mean blood pressure (BP) among hypertensive adults (BP ≥1 30/80 mm Hg or medicated for hypertension). METHOD Data on 22,911 hypertensive US adults from the 1999-2016 National Health and Nutrition Examination Survey. RESULTS For men, hypertension control prevalence increased from 8.6% in 1999-2000 to 16.2% in 2003-2004 (P < 0.001), and continued the increasing trend afterwards to 23.2% in 2011-2012 (P < 0.001) and then plateaued. For women, hypertension control prevalence increased from 1999-2000 to 2009-2010 (10.8-26.3%, P < 0.001) and then plateaued. For men with hypertension, systolic BP decreased from 1999-2000 to 2011-2012 (135.7-132.8 mm Hg, P < 0.001) and then increased to 135.3 mm Hg in 2015-2016 (P < 0.001). For women with hypertension, systolic BP decreased from 1999-2000 to 2009-2010 (139.7-131.9 mm Hg; P < 0.001) and then increased to 134.4 mm Hg in 2015-2016 (P = 0.003). Diastolic BP decreased from 1999-2000 to 2015-2016 (men: 79.1-75.5 mm Hg and women: 76.4-73.7 mm Hg, P < 0.001 for both). In 2011-2016, hypertension control was 22.0% for men and 25.2% for women. The adjusted prevalence ratio (PR) of hypertension control were lower for non-Hispanic black men and women (PR = 0.72, 95% confidence interval (CI) = 0.61-0.86; PR = 0.83, 95% CI = 0.70-0.99, respectively; non-Hispanic white (NHW) as reference), Hispanic and non-Hispanic Asian men (PR = 0.70, 95% CI = 0.54-0.92; PR = 0.59, 95% CI = 0.39-0.86; respectively; NHW as reference). CONCLUSION Hypertension control significantly increased from 1999-2000 to 2011-2012 (men) and 2009-2010 (women) and then plateaued. About a quarter of US adults with hypertension were controlled in 2011-2016.
RabGAP22 Is Required for Defense to the Vascular Pathogen Verticillium longisporum and Contributes to Stomata Immunity

Verticillium longisporum is a soil-borne pathogen with a preference for plants within the family Brassicaceae. Following invasion of the roots, the fungus proliferates in the plant vascular system leading to stunted plant growth, chlorosis and premature senescence. RabGTPases have been demonstrated to play a crucial role in regulating multiple responses in plants. Here, we report on the identification and characterization of the Rab GTPase-activating protein RabGAP22 gene from Arabidopsis, as an activator of multiple components in the immune responses to V. longisporum. RabGAP22Pro:GUS transgenic lines showed GUS expression predominantly in root meristems, vascular tissues and stomata, whereas the RabGAP22 protein localized in the nucleus. Reduced RabGAP22 transcript levels in mutants of the brassinolide (BL) signaling gene BRI1-ASSOCIATED RECEPTOR KINASE 1, together with a reduction of fungal proliferation following BL pretreatment, suggested RabGAP22 to be involved in BL-mediated responses. Pull-down assays revealed SERINE:GLYOXYLATE AMINOTRANSFERASE (AGT1) as an interacting partner during V. longisporum infection and bimolecular fluorescence complementation (BiFC) showed the RabGAP22-AGT1 protein complex to be localized in the peroxisomes. Further, fungal-induced RabGAP22 expression was found to be associated with elevated endogenous levels of the plant hormones jasmonic acid (JA) and abscisic acid (ABA). An inadequate ABA response in rabgap22-1 mutants, coupled with a stomata-localized expression of RabGAP22 and impairment of guard cell closure in response to V. longisporum and Pseudomonas syringae, suggest that RabGAP22 has multiple roles in innate immunity.
Light rhythmic exercise with dietary milk fat globule membrane improves physical fitness in an elderly Japanese population: a double-blind randomized placebo-controlled trial

Abstract This study aimed to investigate the efficacy of home-based, light gymnastic exercise plus dietary milk fat globule membrane (MFGM) intake on physical fitness of an elderly Japanese sample in a pilot, double-blind, randomized, placebo-controlled trial. Seventy-one subjects (male, n = 13; female, n = 58) were randomly assigned into two groups: placebo (n = 35 [male, n = 6; female, n = 29]) and MFGM group (n = 36 [male, n = 7; female, n = 29]). The intervention was eight weeks. Subjects ingested either MFGM (1 g/day) or placebo tablets daily and engaged in an exercise program daily. Physical function tests were performed at baseline and after four and eight weeks. Foot tapping and open–close stepping scores significantly increased from baseline to eight weeks in the MFGM group. Study results suggest daily MFGM ingestion might further enhance the effects of light-intensity exercise in healthy elderly people. Combination of MFGM intake and light rhythmic gymnastic exercise improved agility in the healthy elderly people. *A significant difference was noted between the two groups in the results of the unpaired t-test (P < 0.05).