Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors associated with hospital admission and critical illness among 5279 people with coronavirus disease 2019 in New York City: prospective cohort study

Abstract Objective To describe outcomes of people admitted to hospital with coronavirus disease 2019 (covid-19) in the United States, and the clinical and laboratory characteristics associated with severity of illness. Design Prospective cohort study. Setting Single academic medical center in New York City and Long Island. Participants 5279 patients with laboratory confirmed severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) infection between 1 March 2020 and 8 April 2020. The final date of follow up was 5 May 2020. Main outcome measures Outcomes were admission to hospital, critical illness (intensive care, mechanical ventilation, discharge to hospice care, or death), and discharge to hospice care or death. Predictors included patient characteristics, medical history, vital signs, and laboratory results. Multivariable logistic regression was conducted to identify risk factors for adverse outcomes, and competing risk survival analysis for mortality. Results Of 11 544 people tested for SARS-Cov-2, 5566 (48.2%) were positive. After exclusions, 5279 were included. 2741 of these 5279 (51.9%) were admitted to hospital, of whom 1904 (69.5%) were discharged alive without hospice care and 665 (24.3%) were discharged to hospice care or died. Of 647 (23.6%) patients requiring mechanical ventilation, 391 (60.4%) died and 170 (26.2%) were extubated or discharged. The strongest risk for hospital admission was associated with age, with an odds ratio of >2 for all age groups older than 44 years and 37.9 (95% confidence interval 26.1 to 56.0) for ages 75 years and older. Other risks were heart failure (4.4, 2.6 to 8.0), male sex (2.8, 2.4 to 3.2), chronic kidney disease (2.6, 1.9 to 3.6), and any increase in body mass index (BMI) (eg, for BMI >40: 2.5, 1.8 to 3.4). The strongest risks for critical illness besides age were associated with heart failure (1.9, 1.4 to 2.5), BMI >40 (1.5, 1.0 to 2.2), and male sex (1.5, 1.3 to 1.8). Admission oxygen saturation of <88% (3.7, 2.8 to 4.8), troponin level >1 (4.8, 2.1 to 10.9), C reactive protein level >200 (5.1, 2.8 to 9.2), and D-dimer level >2500 (3.9, 2.6 to 6.0) were, however, more strongly associated with critical illness than age or comorbidities. Risk of critical illness decreased significantly over the study period. Similar associations were found for mortality alone. Conclusions Age and comorbidities were found to be strong predictors of hospital admission and to a lesser extent of critical illness and mortality in people with covid-19; however, impairment of oxygen on admission and markers of inflammation were most strongly associated with critical illness and mortality. Outcomes seem to be improving over time, potentially suggesting improvements in care.
Delayed Release of Intracellular Microcystin Following Partial Oxidation of Cultured and Naturally Occurring Cyanobacteria

Oxidation processes can provide an effective barrier to eliminate cyanotoxins by damaging cyanobacteria cell membranes, releasing intracellular cyanotoxins, and subsequently oxidizing these toxins (now in extracellular form) based on published reaction kinetics. In this work, cyanobacteria cells from two natural blooms (from the United States and Canada) and a laboratory-cultured Microcystis aeruginosa strain were treated with chlorine, monochloramine, chlorine dioxide, ozone, and potassium permanganate. The release of microcystin was measured immediately after oxidation (t ≤ 20 min), and following oxidant residual quenching (stagnation times = 96 or 168 h). Oxidant exposures (CT) were determined resulting in complete release of intracellular microcystin following chlorine (21 mg-min/L), chloramine (72 mg-min/L), chlorine dioxide (58 mg-min/L), ozone (4.1 mg-min/L), and permanganate (391 mg-min/L). Required oxidant exposures using indigenous cells were greater than lab-cultured Microcystis. Following partial oxidation of cells (oxidant exposures ≤ CT values cited above), additional intracellular microcystin and dissolved organic carbon (DOC) were released while the samples remained stagnant in the absence of an oxidant (>96 h after quenching). The delayed release of microcystin from partially oxidized cells has implications for drinking water treatment as these cells may be retained on a filter surface or in solids and continue to slowly release cyanotoxins and other metabolites into the finished water.
Glial A2B Adenosine Receptors Modulate Abnormal Tachykininergic Responses and Prevent Enteric Inflammation Associated with High Fat Diet-Induced Obesity

The role played by adenosine A2B receptors (A2BRs) in the regulation of enteric glial cell (EGC) functions remains unclear. This study was aimed at investigating the involvement of A2BRs in the control of EGC functions in a model of obesity. C57BL/6 mice were fed with standard diet (SD) or high fat diet (HFD) for eight weeks. Colonic tachykininergic contractions were recorded in the presence of BAY60-6583 (A2BRs agonist), MRS1754 (A2BRs antagonist), and the gliotoxin fluorocitrate. Immunofluorescence distribution of HuC/D, S100β, and A2BRs was assessed in whole mount preparations of colonic myenteric plexus. To mimic HFD, EGCs were incubated in vitro with palmitate (PA) and lipopolysaccharide (LPS), in the absence or in the presence of A2BR ligands. Toll-like receptor 4 (TLR4) expression was assessed by Western blot analysis. Interleukin-1β (IL-1β), substance P (SP), and glial cell derived neurotrophic factor (GDNF) release were determined by enzyme-linked immunosorbent assay (ELISA) assays. MRS1754 enhanced electrically evoked tachykininergic contractions of colonic preparations from HFD mice. BAY60-6583 decreased the evoked tachykininergic contractions, with higher efficacy in HFD mice. Such effects were blunted upon incubation with fluorocitrate. In in vitro experiments on EGCs, PA and LPS increased TLR4 expression as well as IL-1β, GDNF, and SP release. Incubation with BAY60-6583 reduced TLR4 expression as well as IL-1β, GDNF, and SP release. Such effects were blunted by MRS1754. The present results suggest that A2BRs, expressed on EGCs, participate in the modulation of enteric inflammation and altered tachykininergic responses associated with obesity, thus representing a potential therapeutic target.
Spatial and Temporal Distribution of Proopiomelanotropin and Proopiocortin mRNA during the Life Cycle of the Sea Lamprey: A Qualitative and Quantitativein SituHybridization Study

Two POMC-like pituitary prohormones proopiocortin (POC) and proopiomelanotropin (POM) have been characterized from adult sea lampreys (Petromyzon marinus). POC encodes a nasohypophysial factor (NHF), ACTH, an MSH, and beta-END; and POM encodes MSH-A, MSH-B, and beta-END. Two radiolabeled riboprobes, one encoding a unique portion of POC mRNA and the other encoding the MSH-B domain unique to POM mRNA, were generated in order to examine the expression of POC and POM during the life cycle of the sea lamprey by in situ hybridization. POC expression appears evenly distributed throughout most cells of the rostral pars distalis (RPD) during the entire life cycle. POC expression also occurs in scattered cells of the caudal (proximal) pars distalis (CPD) at stage 5 of metamorphosis. By the prespawner period, POC expression is mainly distributed in the dorsal aspect of this region. POM expression was completely confined to most cells of the pars intermedia (PI) at all periods examined. Quantitative, computer-assisted, image analysis of POM expression revealed high signal densities in all larvae which decreased by early metamorphosis, steadily increased and reached high levels by late metamorphosis (stages 6 and 7), and attained even higher levels in prespawners. Volumetric analysis revealed that the net volume of POM expressing cells is at its lowest in larvae and increases during subsequent development. Analysis of signal density and volumetric measurements of POC expression revealed that POC expression in the RPD is low in larvae and steadily increases during subsequent intervals of the life cycle reaching very high levels by the prespawning period. POC expression in the CPD, first visible at stage 5, increases steadily throughout the remainder of metamorphosis and reaches the highest levels of expression in prespawning animals. These results would implicate the role of POM and POC in some developmental processes but not in the initiation of metamorphosis. The very high levels of POM and POC expression in prespawner animals suggest that the two genes may have important roles at this time in the life cycle of lampreys.
Potential Plasticity of the Mannoprotein Repertoire Associated to Mycobacterium tuberculosis Virulence Unveiled by Mass Spectrometry-Based Glycoproteomics

To date, Mycobacterium tuberculosis (Mtb) remains the world’s greatest infectious killer. The rise of multidrug-resistant strains stresses the need to identify new therapeutic targets to fight the epidemic. We previously demonstrated that bacterial protein-O-mannosylation is crucial for Mtb infectiousness, renewing the interest of the bacterial-secreted mannoproteins as potential drug-targetable virulence factors. The difficulty of inventorying the mannoprotein repertoire expressed by Mtb led us to design a stringent multi-step workflow for the reliable identification of glycosylated peptides by large-scale mass spectrometry-based proteomics. Applied to the differential analyses of glycoproteins secreted by the wild-type Mtb strain—and by its derived mutant invalidated for the protein-O-mannosylating enzyme PMTub—this approach led to the identification of not only most already known mannoproteins, but also of yet-unknown mannosylated proteins. In addition, analysis of the glycoproteome expressed by the isogenic recombinant Mtb strain overexpressing the PMTub gene revealed an unexpected mannosylation of proteins, with predicted or demonstrated functions in Mtb growth and interaction with the host cell. Since in parallel, a transient increased expression of the PMTub gene has been observed in the wild-type bacilli when infecting macrophages, our results strongly suggest that the Mtb mannoproteome may undergo adaptive regulation during infection of the host cells. Overall, our results provide deeper insights into the complexity of the repertoire of mannosylated proteins expressed by Mtb, and open the way to novel opportunities to search for still-unexploited potential therapeutic targets.
Psychiatry teaching amongst medical undergraduates: stories that matter and mediators of better learning outcome

ABSTRACT Objectives Psychotic disorders can exact a toll on both patients and caregivers. Whilst the desired teaching goals include gaining an understanding of the manifestations, neurobiology and treatment of these conditions, such concepts may appear abstract to medical undergraduates new to psychiatry before their clinical rotation. This study aimed to examine the use of patient narratives in teaching. Based on self-determination and Kolb’s learning theories, it was hypothesized that intermediate processes (such as engagement, motivation, reflection) mediate narratives’ effectiveness as a pedagogical tool. Methods Narratives in the form of stories of prominent individuals with psychotic disorders (such as John Nash) were incorporated in undergraduate teaching. Overall, 1014 out of 1500 (67.6%) medical undergraduates provided feedback over 2014–2018 through an anonymized questionnaire after the teaching session. Relationships between the use of narratives, intermediate processes, and overall effectiveness of session were assessed using correlation, regression, and structural equation modeling analyses. Results Most learners (97.2%) found that use of narratives helped them better appreciate the topic. Use of narratives correlated with better engagement, motivation, feeling equipped, reflection about the topic, and effectiveness as a pedagogical medium. The use of narratives was significantly predictive of ratings on these intermediate processes (all p < 0.001), which in turn mediated the relationship between narratives and overall session ratings. Conclusion Consistent with adult learning theories, the use of narratives can improve appreciation of psychotic spectrum disorders via better engagement, motivation, and reflection within learners. Appropriate narratives can be incorporated into other topics to enhance undergraduate psychiatry education.
The Impact of Sampling Method on Maximum Entropy Species Distribution Modeling for Bats

As species distribution modeling (SDM) becomes more commonly incorporated into ecological studies, there is a need to address how the use of different sampling techniques for assessing the presence of a species can impact the final models produced. Over a four-year period, we sampled for the presence of bats throughout North Dakota via mist netting (physical capture) and ultrasonic acoustic monitoring. We used maximum-entropy modeling to develop habitat suitability maps for each study species using physical capture data, acoustic data and both detection techniques combined. We evaluated the amount of niche overlap between maps to determine how sampling technique impacted the final SDMs and which technique was best for modeling SDMs for each species. We found variation among species in the amount of overlap between SDMs, ranging from pronounced differences (33.9% overlap; Myotis septentrionalis) to highly similar models (80.4% overlap; Myotis lucifugus). Our findings show that acoustic detection results in better SDMs for Myotis spp. while physical capture was best for modeling Eptesicus fuscus and Lasionycteris noctivagans. Although both methods produce highly reliable SDMs, care must be taken when using maximum-entropy modeling for species in which presence data can be gathered in multiple ways. We emphasize that researchers should consider the ecology and behavioral characteristics of their focal species to address any biases associated with sampling technique.
An observational study of the lung clearance index throughout childhood in cystic fibrosis: early years matter

The London Cystic Fibrosis Collaboration (LCFC) has prospectively followed a clinically diagnosed cohort of infants with cystic fibrosis (CF) born in South East England since 1999 [1–4]. Over the past 20 years, the LCFC has obtained comprehensive measures of lung function and structure, including measures of ventilation inhomogeneity (lung clearance index (LCI)) and high-resolution computed tomography (HRCT) scans. By pre-school age, 73% of this cohort had LCI above the limits of normal, compared with 7% with abnormal forced expiratory volume in 0.5 seconds (FEV0.5) [1]. Children with elevated LCI during pre-school years also had worse lung function at early school age [2]. The aim of this study was to investigate how LCI changes across childhood to better understand to what extent LCI results at pre-school age are an indicator of lung disease severity in adolescence. Lung clearance index (LCI) in the early years was associated with LCI during adolescence in children with cystic fibrosis. Pre-school LCI may help to identify children in whom treatment could be intensified. https://bit.ly/2yKyMbM
Microstructural Contributions of Different Polyolefins to the Deformation Mechanisms of Their Binary Blends

The mixing of polymers, even structurally similar polyolefins, inevitably leads to blend systems with a phase-separated morphology. Fundamentally understanding the changes in mechanical properties and occurring deformation mechanisms of these immiscible polymer blends, is important with respect to potential mechanical recycling. This work focuses on the behavior of binary blends of linear low-density polyethylene (LLDPE), low-density polyethylene (LDPE), high-density polyethylene (HDPE), and polypropylene (PP) under tensile deformation and their related changes in crystallinity and morphology. All of these polymers plastically deform by shear yielding. When unmixed, the high crystalline polyolefins HDPE and PP both exhibit a progressive necking phenomenon. LDPE initiates a local neck before material failure, while LLDPE is characterized by a uniform deformation as well as clear strain hardening. LLDPE/LDPE and LLDPE/PP combinations both exhibit a clear-cut matrix switchover. Polymer blends LLDPE/LDPE, LDPE/HDPE, and LDPE/PP show transition forms with features of composing materials. Combining PP in an HDPE matrix causes a radical switch to brittle behavior.
EFFECTS OF NITROGEN ON YIELD AND PROTEIN CONTENT OF MANITOU AND PITIC WHEATS GROWN UNDER IRRIGATION

In experiments with two cultivars of spring wheat (Triticum aestivum L.) conducted under irrigation at two locations for 2 years, average grain yields of Pitic 62 were 30% higher than those of Manitou but protein content was 20% lower. Pitic produced 3% more total protein than Manitou. Yield responses to N fertilizer ranged from nil to 2139 kg/ha for Manitou and from 941 to 2778 kg/ha for Pitic. The maximum rate of application of N from which a yield response was obtained by Manitou was 110 kg/ha and by Pitic was 165 kg/ha. In 1 year at one location the protein content of Pitic was lower from the first N increment and that of Manitou from the first two increments than those of wheats from plots that received no N. The maximum rate of N from which protein increases were obtained was 220 kg/ha for both cultivars. It is possible to grow wheat with high protein content on irrigated land.
Prospective Associations Between Working Time Arrangements and Psychiatric Treatment in Denmark: Protocol for a Cohort Study

Background The burden of mental ill health in working-age populations has prompted research on possible links between work-related factors and mental ill health. Long working hours and night shift work are some of the factors that have been studied in relation to the risk of developing mental ill health. Yet, previous studies have not generated conclusive evidence, and further studies of high quality are needed. Objective This study aims to investigate the prospective association between working time arrangements and mental health in terms of psychotropic drug usage or psychiatric hospital treatment in the general working population of Denmark. Methods Data on total weekly working hours in any job and night shift work from the Danish Labor Force Survey 2000–2013 will be linked to data from the Psychiatric Central Research Register (expected 2400 cases during 700,000 person years at risk) and National Prescription Registry (expected 17,400 cases during 600,000 person years at risk). Participants will be followed for up to 5 years. We will use Poisson regression to separately analyze incidence rates of redeemed prescriptions for psychotropic medicine and incidence rates of psychiatric hospital treatment due to mood disorders, anxiety disorders, or stress-related disorders as a function of weekly working hours and night shift work. The analyses will be controlled for sex, age, calendar time of the interview, and socioeconomic status. Results This is a study protocol. Power calculations indicate that the study has sufficient statistical power to detect relatively small differences in risks and minor interactions (eg, ~90% power to detect a rate ratio of 1.1 for psychoactive medication use). We expect the analyses to be completed by the end of 2020 and the results to be published in 2021. Conclusions In this study protocol, all hypotheses and statistical models of the project have been completely defined before we link the exposure data to the outcome data. The results of the project will indicate to what extent and in what direction the national burden of mental ill health in Denmark has been influenced by long working hours and night shift work. International Registered Report Identifier (IRRID) DERR1-10.2196/18236
Purification and Characterization of an X-Prolyl Dipeptidyl Aminopeptidase from Lactobacillus delbrueckii ssp. bulgaricus LBU-147

Abstract An X-prolyl dipeptidyl aminopeptidase that hydrolyzed L-glycyl-L-prolyl- p -nitroanilide was purified from cells of Lactobacillus delbrueckii ssp. bulgaricus LBU-147 and characterized. The purified enzyme was homogeneous in electrophoresis analysis and appeared to be a trimer because the molecular weight was 270,000 by gel filtration and 90,000 by SDS-PAGE. The optimal pH and temperature for activity were 6.5 and 50°C, respectively. The enzyme was strongly inhibited by metal ions and chemical reagents such as Hg 2+ , Cu 2+ , Fe 3+ Fe 2+ , diisopropyl fluorophosphate, and p -chloromercuribenzoic acid, but it was weakly activated by sulfhydryl-group protective reagents such as 2-mercaptoethanol, dithiothreitol, and cysteine. These results indicated that this enzyme is a serine protease having its active site near a sulfhydryl group.
Demographic and Clinical Characteristics of the Severe Covid-19 Infections: First Report from Mashhad University of Medical Sciences, Iran

Purpose. To report a comparison between fatalities and recovery of the severe Covid-19 infected patients based on demographic and clinical characteristics. Methods. Between 5 March and 12 May 2020, of 4,000 patients, 1,278 were laboratory confirmed to be Covid-19 infection in Mashhad, Iran. Finally, 334 deceased and 733 recovered cases were assessed in terms of demography, exposure history, health outcomes and clinical symptoms. Results. Mean (SD) age for confirmed patients, for deceased cases and for recovered cases. Mean (SD) age for all confirmed-patients was 56.9 (18.74), for the fatalities 67.26 (15.77) and for those recovered 52.82 (17.91) years. The rise of the mortality rate in relation to seniority was statistically significant. Despite a high frequency of Covid-19 infections accrued in the age groups of 30-39 and 40-49 years, most of these cases (88.2 and 85.8%, respectively) recovered. The median (IQR) duration of hospitalization was 9.0 (9) days. The most prevalent co-morbidities were cardiovascular disorders (21%) and diabetes (16.3%). Fever (63.8%), cough (68.1%), and dyspnoea (72.7%) were the most frequent clinical symptoms. 5.2% of infected-cases were healthcare workers that two (3%) of them died. Most patients (48%) received both antiviral and antibiotic therapy. The mortality rate of Kaletra combination prescribed for severe cases was 46.7%. Conclusions. The characteristics of Covid-19 varied from died to survived infected patients. There were a higher number of fatalities in younger patients than in international studies. Diabetes and cardiovascular disorders were most prevalent co-morbidities. The study could not address the case-fatality rate of Covid-19 infection that remains for future studies.