Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymorphism analysis of miR182 and CDKN2B genes in Greek patients with primary open angle glaucoma

Glaucoma is a progressive optic neuropathy resulting from retinal ganglion cells death; it represents one of the leading causes of irreversible blindness worldwide. Although, primary open angle glaucoma (POAG) is the most common type of the disease, the pathogenesis of POAG and the genetic factors contributing to disease development remain poorly understood. The aim of this study was to investigate whether the polymorphisms rs76481776 in miR182 gene and rs3217992 in cyclin-dependent kinase inhibitor-2B (CDKN2B) gene are risk factors for POAG in a series of patients of Greek origin. A case-control study was conducted including 120 patients with POAG and 113 unaffected healthy controls of Greek origin, surveyed for polymorphisms with potential correlation to POAG. DNA from each individual was tested for the miR182 rs76481776 and CDKN2B rs3217992 polymorphisms. Regarding the miR182 rs76481776 polymorphism, the T allele occurred with significantly higher frequency in POAG patients compared to controls (OR: 2.62, 95% CI: 1.56–4.39; p = 0.0002). The CDKN2B rs3217992 A allele frequency was found significantly increased in POAG patients compared to healthy individuals (OR: 1.72, 95% CI: 1.18–2.49; p = 0.005). Therefore, both rs76481776 polymorphism in miR182 gene and rs3217992 polymorphism in CDKN2B gene seem to be associated with the development of POAG in a Greek population. The carriers of the T allele of rs76481776 in miR182 and the carriers of the A allele of rs3217992 in CDKN2B have an increased risk of developing POAG.
Effect of inulin and oligofructose on caecal pH during various thiamine doses administration in rats.

A 15-day experiment was performed on male Wistar rats allocated into three blocks diversified by a daily thiamine dose: 0, 20, 40 μg/day/rat. In each block the rats were divided into five groups depending on the type of diet: control group (FF) - fructan-free diet; experimental groups (1-5,1-10, OF-5, OF-10) - diets containing: 5%, 10% of inulin, as well as 5%, 10% of oligofructose respectively. Thiamine-free experimental diets were prepared according to AIN-93M recommendations, where inulin and oligofructose were added instead of wheat starch. The thiamine was administered per os as a water solution. Compared to the initial value, caecal pH decreased in all groups of rats. The daily thiamine dose as well as the kind of fructan influenced caecal pH. There could be observed the synergistic action of inulin and thiamine in decreasing pH. Inulin and oligofructose, due to prebiotic properties, can cause fluctuations in the caecum pH but the direction of changes is closely dependent on the presence of dietary thiamine. The most suitable pH values for endogenous thiamine uptake are reported during dietary deficit of this vitamin, independently on the type and dose of fructan.
Auditory receptor organs in the forelegs of Gampsocleis gratiosa (Tettigoniidae): Morphology and function of the organs in comparison to the frequency parameters of the conspecific song

The morphology and the physiology of the auditory receptor organs in the forelegs of the tettigoniid species Gampsocleis gratiosa were investigated in detail. According to the tonotopic organization of the receptor cells of the crista acoustica in bushcrickets the threshold curves of all receptors found in the organs were correlated with the morphology of the auditory receptor cells. This was done by arranging them in relation to their frequency tuning with the receptors along the chain of cells in both organs starting proximally with the extreme low frequency cell up to the highest ultrasonic cells at the distal end of the crista acoustica. This investigation reveals that the auditory receptor organs of Gampsocleis gratiosa possess a broard banded hearing threshold curve including very low frequency parts. Also the conspecific stridulatory song is very broard banded with extraordinarily low frequency components. Therefore the sender and the receiver of this species-specific communication system seem to be well adapted to each other. © 1993 wiley-Liss, Inc.
Effect of P‐body component Mov10 on HCV virus production and infectivity

Mov10 is a processing body (P‐body) protein and an interferon‐stimulated gene that can affect replication of retroviruses, hepatitis B virus, and hepatitis C virus (HCV). The mechanism of HCV inhibition by Mov10 is unknown. Here, we investigate the effect of Mov10 on HCV infection and determine the virus life cycle steps affected by changes in Mov10 overexpression. Mov10 overexpression suppresses HCV RNA in both infectious virus and subgenomic replicon systems. Additionally, Mov10 overexpression decreases the infectivity of released virus, unlike control P‐body protein DCP1a that has no effect on HCV RNA production or infectivity of progeny virus. Confocal imaging of uninfected cells shows endogenous Mov10 localized at P‐bodies. However, in HCV‐infected cells, Mov10 localizes in circular structures surrounding cytoplasmic lipid droplets with NS5A and core protein. Mutagenesis experiments show that the RNA binding activity of Mov10 is required for HCV inhibition, while its P‐body localization, helicase, and ATP‐binding functions are not required. Unexpectedly, endogenous Mov10 promotes HCV replication, as CRISPR‐Cas9‐based Mov10 depletion decreases HCV replication and infection levels. Our data reveal an important and complex role for Mov10 in HCV replication, which can be perturbed by excess or insufficient Mov10.
Role of the pyruvate metabolic network on carbohydrate metabolism and virulence in Streptococcus pneumoniae

Streptococcus pneumoniae is a major human pathogen that must adapt to unique nutritional environments in several host niches. The pneumococcus can metabolize a range of carbohydrates that feed into glycolysis ending in pyruvate, which is catabolized by several enzymes. We investigated how the pneumococcus utilizes these enzymes to metabolize different carbohydrates and how this impacts survival in the host. Loss of ldh decreased bacterial burden in the nasopharynx and enhanced bacteremia in mice. Loss of spxB, pdhC or pfl2 decreased bacteremia and increased host survival. In glucose or galactose, loss of ldh increased capsule production, whereas loss of spxB and pdhC reduced capsule production. The pfl2 mutant exhibited reduced capsule production only in galactose. In glucose, pyruvate was metabolized primarily by LDH to generate lactate and NAD+ and by SpxB and PDHc to generate acetyl‐CoA. In galactose, pyruvate metabolism was shunted toward acetyl‐CoA production. The majority of acetyl‐CoA generated by PFL was used to regenerate NAD+ with a subset used in capsule production, while the acetyl‐CoA generated by SpxB and PDHc was utilized primarily for capsule biosynthesis. These data suggest that the pneumococcus can alter flux of pyruvate metabolism dependent on the carbohydrate present to succeed in distinct host niches.
Influence of postharvest handling practices and dip treatments on development of black root rot on fresh market carrots

Standard postharvest handling practices for fresh market carrots (Daucus carora) grown in organic soils in the Fraser Valley of British Columbia were monitored during 1990-1992 at two grading and packaging operations. Root samples were obtained from 29 loads over the harvest season (July to November) at various stages after carrots were washed, sized, graded, and packaged; and the samples were assessed for the development of black root rot, caused by Chalara elegans (Thielaviapsis basicola). Disease was not detected on carrots harvested by hand from fields infested with the pathogen, and was less than 5% on carrots sampled from the truck following mechanized harvesting
A Randomized Trial of Hydroxychloroquine as Postexposure Prophylaxis for Covid-19

Abstract Background Coronavirus disease 2019 (Covid-19) occurs after exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For persons who are exposed, the standard of care is observation and quarantine. Whether hydroxychloroquine can prevent symptomatic infection after SARS-CoV-2 exposure is unknown. Methods We conducted a randomized, double-blind, placebo-controlled trial across the United States and parts of Canada testing hydroxychloroquine as postexposure prophylaxis. We enrolled adults who had household or occupational exposure to someone with confirmed Covid-19 at a distance of less than 6 ft for more than 10 minutes while wearing neither a face mask nor an eye shield (high-risk exposure) or while wearing a face mask but no eye shield (moderate-risk exposure). Within 4 days after exposure, we randomly assigned participants to receive either placebo or hydroxychloroquine (800 mg once, followed by 600 mg in 6 to 8 hours, then 600 mg daily for 4 additional days). The primary outcome was the incidence of either laboratory-confirmed Covid-19 or illness compatible with Covid-19 within 14 days. Results We enrolled 821 asymptomatic participants. Overall, 87.6% of the participants (719 of 821) reported a high-risk exposure to a confirmed Covid-19 contact. The incidence of new illness compatible with Covid-19 did not differ significantly between participants receiving hydroxychloroquine (49 of 414 [11.8%]) and those receiving placebo (58 of 407 [14.3%]); the absolute difference was −2.4 percentage points (95% confidence interval, −7.0 to 2.2; P=0.35). Side effects were more common with hydroxychloroquine than with placebo (40.1% vs. 16.8%), but no serious adverse reactions were reported. Conclusions After high-risk or moderate-risk exposure to Covid-19, hydroxychloroquine did not prevent illness compatible with Covid-19 or confirmed infection when used as postexposure prophylaxis within 4 days after exposure. (Funded by David Baszucki and Jan Ellison Baszucki and others; ClinicalTrials.gov number, NCT04308668.)
Assessment of IgE- and cell-mediated immunity in pediatric patients with eosinophilic esophagitis.

Eosinophilic esophagitis (EoE) is a chronic allergen/immune-mediated disease leading to esophageal dysfunction. Food allergens play critical roles in the pathogenesis and treatment of EoE via different mechanisms. This study aimed to present the characteristics and evaluate the ability of skin prick test (SPT), skin prick to prick test (SPP) (IgE-mediated), and atopic patch test (APT) (cell-mediated) individually or simultaneously to diagnose food allergy in patients suffering from EoE. This prospective study was conducted on 58 patients with EoE. Seven patients (12.1%) were positive to only one, 3 (5.2%) were simultaneously positive to two, and 32 (55.2%) were simultaneously positive to three tests. Single and double sensitizations were totally 10.4% in IgE-mediated reactions, while 36.5% in cell-mediated reactions. In contrast, poly sensitization (>2 allergens) was 51.7% in IgE-mediated tests and 20.7% in the cell-mediated test. Multiple sensitization findings showed egg white, milk, yolk, and soy were the most frequent allergens. Our findings indicate that EoE is early onset and associated with multiple food sensitizations, particularly via IgE-mediated mechanisms. These immune-mediated responses encompass both IgE-mediated (SPT and SPP) and cell-mediated (APT) reactions simultaneously not individually. Therefore, employing multiple assays may strengthen the diagnosis of food sensitization.
Prediction of depression cases, incidence, and chronicity in a large occupational cohort using machine learning techniques: an analysis of the ELSA-Brasil study

Abstract Background Depression is highly prevalent and marked by a chronic and recurrent course. Despite being a major cause of disability worldwide, little is known regarding the determinants of its heterogeneous course. Machine learning techniques present an opportunity to develop tools to predict diagnosis and prognosis at an individual level. Methods We examined baseline (2008–2010) and follow-up (2012–2014) data of the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil), a large occupational cohort study. We implemented an elastic net regularization analysis with a 10-fold cross-validation procedure using socioeconomic and clinical factors as predictors to distinguish at follow-up: (1) depressed from non-depressed participants, (2) participants with incident depression from those who did not develop depression, and (3) participants with chronic (persistent or recurrent) depression from those without depression. Results We assessed 15 105 and 13 922 participants at waves 1 and 2, respectively. The elastic net regularization model distinguished outcome levels in the test dataset with an area under the curve of 0.79 (95% CI 0.76–0.82), 0.71 (95% CI 0.66–0.77), 0.90 (95% CI 0.86–0.95) for analyses 1, 2, and 3, respectively. Conclusions Diagnosis and prognosis related to depression can be predicted at an individual subject level by integrating low-cost variables, such as demographic and clinical data. Future studies should assess longer follow-up periods and combine biological predictors, such as genetics and blood biomarkers, to build more accurate tools to predict depression course.
Newly invading species exploiting native host-plants: the case of the African Zaprionus indianus (Gupta) in the Brazilian Cerrado (Diptera, Drosophilidae)

Abstract The African Zaprionus indianus (Diptera, Drosophilidae) was introduced into the Neotropical Region by the end of the 1990’s, and it became abundant in several types of altered and natural environments. In the Cerrado, the second South American biome in extension, it has been found mainly in open vegetation and during the rainy season. In the current work, we showed that Z. indianus utilizes a major native fruit of the Brazilian Cerrado (Solanum lycocarpum) primarily, all over the fructification period and states of fruit’s decay, confirming the adaptative versatility of this invading fly in new environments.
Influence of pumped-storage hydroelectric plant operation on a shallow polymictic lake: Predictions from 3-D hydrodynamic modeling

Abstract Pumped-storage hydroelectric plants play important roles in electrical supply grids by providing electricity during periods of peak demand, storing renewable energy and controlling supply frequency. The pumping of water from a lower lake or reservoir to an upper impoundment and the return of that water during power generation can strongly affect the properties of pumped-storage reservoirs, however. For example, plant operation has been found to delay, weaken or eliminate thermal stratification, resuspend bottom sediments and entrain organisms. The aim of this study was to better understand the impacts of a proposed pumped-storage facility on stratification, mixing and sediment resuspension in Lake Elsinore, a shallow, polymictic lake in southern California. Three-dimensional hydrodynamic simulations were conducted using the Environmental Fluid Dynamics Code (EFDC). Model simulations demonstrated regular variations in the lake surface elevation of 0.24–0.5 m associated with pumping and generation, although a large shore-mounted intake structure resulted in quite low velocities near the intake (< 6 cm/s), bottom shear values below the assumed critical threshold for resuspension (< 0.1 N/m2), and limited overall effect on stratification and mixing in the lake. Entrainment of larval fish and other planktonic organisms remains a concern, however.
Common and Uncommon Understory Species Differentially Respond to Restoration Treatments in Ponderosa Pine/Douglas‐Fir Forests, Montana

Restoration treatments have been widely advocated to address declining conditions in Pinus ponderosa forests throughout the western United States. However, few studies have examined treatment effects on individual plant species or whether responses differ for common species and uncommon species (those with low abundance in the community)—information that may be critical in managing for long‐term biodiversity. We investigated understory species responses to restoration treatments in ponderosa pine/Douglas‐fir forests using a randomized block experimental design with three blocks and four treatments (control, burn‐only, thin‐only, and thin‐burn). Understory vegetation was sampled before treatment and for three consecutive years after treatment. We used richness and an index of uniqueness to compare responses of common and uncommon native understory species among treatments, and indicator species analysis to identify individual species that responded to each treatment. Treatments that included thinning had significantly more unique species assemblages than the control. The thin‐only treatment increased common native species richness, whereas all active treatments significantly increased uncommon native species richness over the control, especially the thin‐burn. Generally, life‐forms did not explain the responses of individual species, though in the final sampling year several graminoids were exclusively indicative of treatments that included thinning. Very few species had reduced abundance in the thinning and burning treatments by the final sample year, whereas many uncommon and short‐lived species benefited from active treatments, especially the combined thin‐burn treatment. Active restoration treatments in these forests may foster plant diversity by minimally impacting common species while significantly benefiting disturbance‐dependent native species.
SARS‐CoV‐2: A comprehensive review from pathogenicity of the virus to clinical consequences

Nowadays, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), which caused novel coronavirus disease (COVID‐19) pandemic, is the worldwide challenge. The virus is highly contagious, and clinical consequences were very divers. It is estimated that if no effective action is taken, COVID‐19 could plague 90% of the world's population and kill over 40 million people. So, it is essential to understand the virus pathogenicity and follow the preventive methods to control the high morbidity and mortality rates. Meanwhile our current knowledge of COVID‐19 is still limited, despite hard efforts of scientists and clinicians during last few months. In this review article, we have collected the latest data about characteristics, pathogenesis, clinical manifestations, and diagnostic methods of SARS‐CoV‐2.
Fragment shape and tree species composition in tropical forests: a landscape level investigation

Fragmentation of tropical forest alters community composition as a result of changes in forest shape. This paper uses 22 hypotheses to test the effect of fragment shape on tree species composition in Ghana, West Africa, within biological categories of regeneration guild, rarity, phenology and dispersal. For both regenerating and mature trees, relationships between species composition and the shape of forest fragments were complex; almost half were significant but many failed to support the established hypotheses. Irregular shaped fragments had high proportions of regenerating, light-demanding pioneers and mature, animal-dispersed species. Species common to Ghana formed the foundation of communities in fragments of all shapes. Investigation at the landscape level indicated broad patterns of species change. Rigorous hypothesis testing is needed, following extensive demographic work on the ground, before population dynamics within tropical forest fragments can be comprehended fully and applied to conservation management. Resume La fragmentation de la foret tropicale transforme la composition de la communaute suite aux changements dans la forme forestiere. Cette etude se sert de 22 hypotheses afin d’evaluer l’effet de la forme des fragments sur la composition des especes d'arbres au Ghana, en Afrique Occidental - selon des categories biologiques de regeneration, rarete, phenologie et dispersion. Dans le cas des arbres en cours de regeneration et des arbres murs, les correlations entre la composition des especes et la forme des fragments forestiers etaient complexes: tandis que presque la moitie s'averait importante, plusieurs n'ont pas verifie les hypotheses reconnues. Des fragments irreguliers avaient des proportions elevees en matiere d'especes pionnieres regenerantes, exigeant de la lumiere et des especes mures dispersees par des animaux. Des especes particulieres au Ghana ont forme la base des communautes dans les fragments de toutes formes. Au niveau du paysage, l'enquete a indique des changements d'especes de configurations diverses. Des tests rigoureux sur ces hypotheses s'imposent, suivant des travaux considerables sur le terrain, avant que les dynamiques de la population dans les fragments de foret tropicale ne puissent etre parfaitement saisis et appliques a la gestion de la preservation.
Rennin-like milk coagulant enzyme produced by a local isolate of Mucor

Among 20 isolates of Mucor isolated from various environments in Jordan and found to produce a rennin-like acid protease, known as Mucor rennin-like enzyme (MRE), Mucor J20 was found to produce the highest level of MRE. The optimum incubation conditions for enzyme production in a fortified wheat bran mixture using solid-state fermentation were 3-4 days at 30°C. The highest MRE activity (185-200 rennin units or RU) was produced in a medium containing wheat bran and lentil straw (1 : 1 w/w) moistened with whey, and incubated in clay pots at 30 °C for 4 days. A slightly lower activity value (178 RU) was found when using a mineral salt solution or distilled water instead of whey, or when using wheat bran alone with whey. At pH 4, the MRE retained its complete activity (100%) for 6 weeks at 5 °C and 10 °C, and for 3 and 2 weeks at 20°C and 30°C, respectively. After heating at 60°C for 10 min, the enzyme lost its activity at all pH levels used (pH 2-8). The crude extract of MRE was successfully applied in the manufacture of a cheese curd.
Gestational sleep deprivation is associated with higher offspring body mass index and blood pressure

Abstract Study Objectives The objective of this study was to evaluate the association between gestational sleep deprivation and childhood adiposity and cardiometabolic profile. Methods Data were used from two population-based birth cohorts (Rhea study and Amsterdam Born Children and their Development study). A total of 3,608 pregnant women and their children were followed up until the age of 11 years. Gestational sleep deprivation was defined as 6 or fewer hours of sleep per day, reported by questionnaire. The primary outcomes included repeated measures of body mass index (BMI), waist circumference, body fat, serum lipids, systolic and diastolic blood pressure (DBP) levels in childhood. We performed a pooled analysis with adjusted linear mixed effect and Cox proportional hazards models. We tested for mediation by birthweight, gestational age, and gestational diabetes. Results Gestational sleep deprivation was associated with higher BMI (beta; 95% CI: 0.7; 0.4, 1.0 kg/m2) and waist circumference (beta; 95% CI: 0.9; 0.1, 1.6 cm) in childhood, and increased risk for overweight or obesity (HR; 95% CI: 1.4; 1.1, 2.0). Gestational sleep deprivation was also associated with higher offspring DBP (beta; 95% CI: 1.6; 0.5, 2.7 mmHg). The observed associations were modified by sex (all p-values for interaction < 0.05); and were more pronounced in girls. Gestational diabetes and shorter gestational age partly mediated the seen associations. Conclusions This is the first study showing that gestational sleep deprivation may increase offspring’s adiposity and blood pressure, while exploring possible mechanisms. Attention to glucose metabolism and preterm birth might be extra warranted in mothers with gestational sleep deprivation.