Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of Low-density Inflammatory Neutrophils Correlates with Hypercoagulable State and Disease Severity in COVID-19 Patients

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel viral pathogen that causes a clinical disease called coronavirus disease 2019 (COVID-19). Approximately 20% of infected patients experience a severe manifestation of the disease, causing bilateral pneumonia and acute respiratory distress syndrome. Severe COVID-19 patients also have a pronounced coagulopathy with approximately 30% of patients experiencing thromboembolic complications. However, the etiology driving the coagulopathy remains unknown. Here, we explore whether the prominent neutrophilia seen in severe COVID-19 patients contributes to inflammation-associated coagulation. We found in severe patients the emergence of a CD16IntCD44lowCD11bInt low-density inflammatory band (LDIB) neutrophil population that trends over time with changes in disease status. These cells demonstrated spontaneous neutrophil extracellular trap (NET) formation, phagocytic capacity, enhanced cytokine production, and associated clinically with D-dimer and systemic IL-6 and TNF- levels, particularly for CD40+ LDIBs. We conclude that the LDIB subset contributes to COVID-19-associated coagulopathy (CAC) and could be used as an adjunct clinical marker to monitor disease status and progression. Identifying patients who are trending towards LDIB crisis and implementing early, appropriate treatment could improve all-cause mortality rates for severe COVID-19 patients.
Risks and etiology of bacterial vaginosis revealed by species dominance network analysis

BV (bacterial vaginosis) influences 20-40% of women but its etiology is still poorly understood. An open question about the BV is which of the hundreds of bacteria found in the human vaginal microbiome (HVM) are the causal pathogens of BV? Existing attempts to identify them have failed for at least two reasons: (i) a focus on species per se that ignores species interactions; (ii) a lack of systems-level understanding of the HVM. Here, we recast the question of microbial causality of BV by asking if there are any reliable 'signatures' of community composition (or poly-microbial 'cults') associated with it? We apply a new framework (species dominance network analysis by Ma & Ellison (2019: Ecological Monographs) to detect critical structures in HVM networks associated with BV risks and etiology. We reanalyzed the metagenomic datasets of a mixed-cohort of 25 BV patients and healthy women. In these datasets, we detected 15 trio-motifs that occurred exclusively in BV patients. We failed to find any of these 15 trio-motifs in three additional cohorts of 1535 healthy women. Most member-species of the 15 trio motifs are BV-associated anaerobic bacteria (BVAB), Ravel's community-state type indicators, or the most dominant species; virtually all species interactions in these trios are high-salience skeletons, suggesting that those trios are strongly connected 'cults'. The presence of trio motifs unique to BV may act as indicators for its personalized diagnosis and could help elucidate a more mechanistic interpretation of its risks and etiology.
Investigating SARS-CoV-2 surface and air contamination in an acute healthcare setting during the peak of the COVID-19 pandemic in London

Objectives: To evaluate SARS-CoV-2 surface and air contamination during the peak of the COVID-19 pandemic in London. Design: Prospective cross-sectional observational study. Setting: An acute NHS healthcare provider. Participants: All inpatient wards were fully occupied by patients with COVID-19 at the time of sampling. Interventions: Air and surface samples were collected from a range of clinical areas and a public area of the hospital. An active air sampler was used to collect three or four 1.0 m3 air samples in each area. Surface samples were collected by swabbing approximately 25 cm2 of items in the immediate vicinity of each air sample. SARS-CoV-2 was detected by RT-qPCR and viral culture using Vero E6 and Caco2 cells; additionally the limit of detection for culturing SARS-CoV-2 dried onto surfaces was determined. Main outcome measures: SARS-CoV-2 detected by PCR or culture. Results: Viral RNA was detected on 114/218 (52.3%) of surface and 14/31 (38.7%) air samples but no virus was cultured. The proportion of surface samples contaminated with viral RNA varied by item sampled and by clinical area. Viral RNA was detected on surfaces and in air in public areas of the hospital but was more likely to be found in areas immediately occupied by COVID-19 patients (67/105 (63.8%) in areas immediately occupied by COVID-19 patients vs. 29/64 (45.3%) in other areas (odds ratio 0.5, 95% confidence interval 0.2-0.9, p=0.025, Fishers exact test). The PCR Ct value for all surface and air samples (>30) indicated a viral load that would not be culturable. Conclusions: Our findings of extensive viral RNA contamination of surfaces and air across a range of acute healthcare settings in the absence of cultured virus underlines the potential risk from surface and air contamination in managing COVID-19, and the need for effective use of PPE, social distancing, and hand/surface hygiene.
Sleep in severe disorders of consciousness: 24-h behavioral and polysomnographic recording

Objectives: To quantify, on a reliable evaluation basis, the distribution of behavioral and neurophysiological sleep patterns in Disorders of Consciousness (DOC) over a 24h period while controlling for environmental factors (by recruiting a group of conscious tetraplegic patients who resided in the same hospital). Methods: We evaluated the distribution of sleep and wakefulness by means of polysomnography (EEG, EOG, EMG) and video recordings in 32 DOC patients (16 Unresponsive Wakefulness Syndrome [UWS], 16 Minimally Conscious State [MCS]) and 10 clinical control patients with severe tetraplegia (CC). Three independent raters scored the patients' polysomnographic recordings. Results: All but one patient (UWS) showed behavioral and electrophysiological signs of sleep. CC and MCS patients spent significantly more time in sleep during the night than during daytime, a pattern that was not evident in UWS. DOC patients (particularly UWS) exhibited less REM sleep than control patients. 44% of UWS patients and 12% of MCS patients did not have any REM sleep, while all control patients (100%) showed signs of all sleep stages and sleep spindles. Furthermore, no sleep spindles were found in 62% of UWS patients and 21% of MCS patients. In the remaining DOC patients who had spindles, their number and amplitude were significantly lower than in controls. Interpretation: The distribution of sleep signs in DOC over 24 hours differs significantly from the normal sleep-wakefulness pattern. These abnormalities of sleep in DOC are independent of external factors such as severe immobility and hospital environment.
Computational Methods for Continuous Eye-Tracking Perimetry Based on Spatio-Temporal Integration and a Deep Recurrent Neural Network

The measurement of retinal sensitivity at different visual field locations–perimetry–is a fundamental procedure in ophthalmology. The most common technique for this scope, the Standard Automated Perimetry, suffers from several issues that make it less suitable to test specific clinical populations: it can be tedious, it requires motor manual feedback, and requires from the patient high levels of compliance. Previous studies attempted to create user-friendlier alternatives to Standard Automated Perimetry by employing eye movements reaction times as a substitute for manual responses while keeping the fixed-grid stimuli presentation typical of Standard Automated Perimetry. This approach, however, does not take advantage of the high spatial and temporal resolution enabled by the use of eye-tracking. In this study, we introduce a novel eye-tracking method to perform high-resolution perimetry. This method is based on the continuous gaze-tracking of a stimulus moving along a pseudo-random walk interleaved with saccadic jumps. We then propose two computational methods to obtain visual field maps from the continuous gaze-tracking data: the first is based on the spatio-temporal integration of ocular positional deviations using the threshold free cluster enhancement (TFCE) algorithm; the second is based on using simulated visual field defects to train a deep recurrent neural network (RNN). These two methods have complementary qualities: the TFCE is neurophysiologically plausible and its output significantly correlates with Standard Automated Perimetry performed with the Humphrey Field Analyzer, while the RNN accuracy significantly outperformed the TFCE in reconstructing the simulated scotomas but did not translate as well to the clinical data from glaucoma patients. While both of these methods require further optimization, they show the potential for a more patient-friendly alternative to Standard Automated Perimetry.
The fate of SARS-CoV-2 in wastewater treatment plants points out the sludge line as a suitable spot for incidence monitoring

SARS-CoV-2 genetic material is detectable in the faeces of a considerable part of COVID-19 cases and hence, in the urban wastewater. This fact was confirmed early during the spread of the COVID-19 pandemic and prompted several studies that proposed monitoring its incidence by wastewater. This paper studies the fate of SARS-CoV-2 genetic material in wastewater treatment plants using RT-qPCR with a two-fold goal: i) to check the safety of the water effluent and also of the sludge produced and ii) based on the understanding of the virus particles fate, to identify the most suitable spots for detecting the incidence of COVID-19 and monitor its evolution. On the grounds of the affinity of enveloped virus towards biosolids, we hypothesized that the sludge line acts as a concentrator of SARS-CoV-2 genetic material. Sampling several spots in primary, secondary and sludge treatment at the Ourense (Spain) WWTP showed that, in effect, most of SARS-CoV-2 particles cannot be detected in the water effluent as they are retained by the sludge line. We identified the sludge thickener as a suitable spot for detecting SARS-CoV-2 particles thanks to its higher solids concentration (more virus particles) and longer residence time (less sensitive to dilution caused by precipitation). Although more studies will be needed for confirmation, these results contribute to clarify the role of WWTPs in COVID-19 mitigation.
Use of inhibitors of the renin angiotensin system and COVID-19 prognosis: a systematic review and meta-analysis

Background: controversy has arisen in the scientific community on whether the use of renin angiotensin system (RAS) inhibitors in the context of COVID-19 would be of benefit or harmful. A meta-analysis of eligible studies comparing the occurrence of severe and fatal COVID-19 in infected patients who were under treatment with angiotensin converting enzyme inhibitors (ACEI) or angiotensin receptor blockers (ARB) vs no treatment or other antihypertensives was conducted. Methods: PubMed, Google Scholar, the Cochrane Library, MedRxiv and BioRxiv were searched for relevant studies. Fixed-effect models or random-effect models were used depending on the heterogeneity between estimates. Results: a total of fifteen studies with 21,614 patients were included. The use of RAS inhibitors was associated with a non-significant 20% decreased risk of the composite outcome (death, admission to intensive care unit, mechanical ventilation requirement or progression to severe or critical pneumonia): RR 0.81 (95%CI: 0.63-1.04), p=0.10, I2=82%. In a subgroup analysis that included hypertensive subjects only, ACEI/ARB were associated with a 27% significant decrease in the risk of the composite outcome (RR 0.73 (95%CI: 0.56-0.96), p=0.02, I2=65%). Conclusion: the results of this pooled analysis suggest that the use of ACEI/ARB does not worsen the prognosis, and could even be protective in hypertensive subjects. Patients should continue these drugs during their COVID-19 illness.
Student Problem Solving Analysis by Step John Dewey Reviewed from Learning Style

This research aims to describe the student’s mathematical problem solving based on John Dewey’s step viewed by learning style. The subjects are 2 students with a visual learning style, 2 students with auditory learning style, and a student with kinaesthetic learning. The data was collected through a questionnaire of learning style, the test of mathematics problem solving, interview, and documentation. Then it was analyzed used Milles and Huberman model’s data analyzed technique consist of data reduction, data display, and conclusion (verification). This research shows that: (1) the visual subject confronted the problem by reading the question silently in several times, the subject can’t define the problem correctly, can’t found the right solution so that calculating and the answer is not correct, and can’t test consequences (looking back), (2) the auditory subject confronted the problem with reading the question in several times loudly, the subject can define the problem correctly, can found the right solution so that calculating and the answer correctly, and can’t test consequences (looking back), (3) the kinesthetic subject confronted the problem with reading the question in several times, the subject can’t define the problem correctly, can’t found the right solution so that calculating and the answer is not correct, and can’t test consequences (looking back).
Robots, Computers, and the Gender Wage Gap

Abstract We analyze the effects of two automation technologies, industrial robots and computing equipment, on the gender wage gap in US local labor markets between 1990 and 2015. We find distinct impact of robot and computer capital: an increase in robots decreases male wage more than female wage, whereas an increase in computers reduces female wage more than male wage. According to our estimates, one additional unit of robot per thousand workers reduces gender wage gap by 0.3 log points, and by contrast an increase in computer capital by one million dollars per thousand workers increases gender wage gap by 4.1 log points.
In planta Transfer of the Gene (s) for Virulence between Isolates of Pseudomonas syringae pv. atropurpurea

A phytotoxin (coronatine)-producing ability of Pseudomonas syringae pv. atropurpurea NIAES 1309 is associated with 58 Mdal plasmid designated as pCOR1. A conjugative plasmid pBPW 1:: Tn 7 from P. syringae pv. tabaci BR2 was introduced into the strain NIAES 1309. When the strain was mated with avirulent strains derived from NIAES 1309 in Italian ryegrass, pBPW 1:: Tn 7 was transferred to the avirulent strain at a high frequency. Twenty strains out of 894 trans conjugants contained the pCOR1 plasmid co-transferred with pBPW1:: Tn7. All of these strains produced coronatine and induced typical symptoms on Italian ryegrass. That is, in planta trans fer of virulence genes between isolates of phytopathogenic pseudomonad was confirmed. (Received July 9, 1987)
A Study of Febrile Thrombocytopenia

Introduction: Febrile thrombocytopenia is the thrombocytopenia associated with febrile illness. The common causes are dengue, rickettsiae, malaria, typhoid, septicemia and in some cases undifferentiated fever. The present study was intended to know the underlying etiology of febrile thrombocytopenia cases admitted to our hospital, the various presentations and relationship between platelet count and bleeding manifestation and prognosis. Material and methods: The study was conducted on 855 patients aged 18 years and above who presented with fever and thrombocytopenia and were admitted in MVJ Medical College and Research Hospital, Hoskote, Bengaluru rural district from January 2016 to December 2018. Results: A total of 855 patients of febrile thrombocytopenia were admitted to our hospital during study period. Majority of patients were in the age group of 18 to 40 years with male to female ratio of 1.15: 1. Most of the cases presented during the months of July to September. Commonest clinical presentation were fever (100%), myalgia (86.5%) and headache (84.7%). In the majority of patients, thrombocytopenia was transient, present for 2 – 3 days, but bleeding manifestations were seen in 24.3% of patients. Petechiae (14%) was the commonest bleeding manifestation. 691 (80.81%) patients had platelet count between 50000 to 1.5 lakh/mm3 and 164 (19.18%) cases had platelet count less than 50000/mm3 Only 5.6% had need for platelet transfusion. Dengue (51.9%) was the commonest cause of thrombocytopenia followed by rickettsial fever (27.7%). In 15.6% of patients the etiology could not be ascertained. Conclusion: Febrile thrombocytopenia is the most common cause for admission to the hospital which requires extensive evaluation and prompt management.
Behavioral responses of leaves and vascular cambium of Prosopis cineraria (L.) Druce to different regimes of coal-smoke pollution

Abstract The foliar and cambial responses of Prosopis cineraria to five different coal-smoke regimes in Delhi, India, were studied using the monthly collections of leaves and cambial blocks as well as the data on SO2, NO2 and particulate concentrations from each of the five study sites. Coal-smoke inhibited pigment concentration, NR activity and sugar content and promoted stomatal index and the nitrate and sulfur contents. Stomatal conductance was low, leading to a drop in the net photosynthetic rate. Cambial activity started quite late and the annual increment of wood was reduced despite a prolonged active phase, possibly due to a distinctly retarded rate of cambial cell division. Vessel proportion in the wood increased but the size of vessel elements and fibers decreased. Such studies may help in identifying trees suitable for cultivation in the pollution-affected areas.
Mycorrhiza Mutants of Lotus japonicus Define Genetically Independent Steps During Symbiotic Infection

Four nodulation mutants of Lotus japonicus affected in three different genetic loci blocked infection by Glomus intraradices within rhizodermal cells where abnormal deformations of hyphae occurred. Rare successful infections led to the formation of arbuscules. The affected plant genes are therefore essential during the early infection process, but are dispensable for later developmental stages.
Evidence for an increased secretory capacity for dehydroepiandrosterone-sulphate in the pantothenic acid-deficient rat associated with an impaired adrenal cholesterol deposition.

The adrenal capacity to store cholesterol and to secrete corticosterone, androstenedione, and dehydroepiandrosterone-sulphate (DHEA-S) was investigated following long- and short-term adrenocor-ticotropic hormone (ACTH) stimulation of growing male rats kept on a pantothenic acid-deficient (PAD) diet for about two months. After chronic treatment with ACTH1-24, the pantothenic acid-deficient rats revealed a drastic impairment in adrenal cholesterol storage compared with ad libitum and pair-weight fed control groups. However, corticosteroid plasma responses to short-term as well as to prolonged ACTH stimulation were normal or in the case of DHEA-S, even significantly increased in pantothenic acid deficiency. The elevated secretory capacity for this androgen sulphate was also discernible in an exaggerated renal DHEA-S excretion in PAD rats under ACTH1-24 hyperstimulation. According to the results of a further hormonal study involving metyrapone administration, a PAD-associated increase in specific enzyme activities of the post-pregnenolone pathway of androgen synthesis was excluded as the reason for the DHEA-S hypersecretion. The experimental findings are discussed with regard to a PAD-induced tissue CoA decrease and its consequences for adrenal cholesterol metabolism and steroid hormone secretion. A concept is presented that takes into account the functional differences in the zona fasciculata and the zona reticularis of the adrenal cortex in order to explain the phenomenon of the abnormal capacity of rats to secrete DHEA-S in pantothenic acid deficiency.
Intraguild predation and cannibalism among larvae of detritivorous caddisflies in subalpine wetlands

Comparative data from subalpine wetlands in Colorado indicate that larvae of the limnephilid caddisflies, Asynarchus nigriculus and Limnephilus externus, are recip- rocally abundant among habitats-Limnephilus larvae dominate in permanent waters, whereas Asynarchus larvae dominate in temporary basins. The purpose of this paper is to report on field and laboratory experiments that link this pattern of abundance to biotic interactions among larvae. In the first field experiment, growth and survival were compared in single and mixed species treatments in littoral enclosures. Larvae, which eat mainly vascular plant detritus, grew at similar rates among treatments in both temporary and permanent habitats suggesting that exploitative competition is not important under natural food levels and caddisfly densities. However, the survival of Limnephilus larvae was reduced in the presence of Asynarchus larvae. Subsequent behavioral studies in laboratory arenas revealed that Asynarchus larvae are extremely aggressive predators on Limnephilus larvae. In a second field experiment we manipulated the relative sizes of larvae and found that Limnephilus larvae were preyed on only when Asynarchus larvae had the same size ad- vantage observed in natural populations. Our data suggest that the dominance of Asynarchus larvae in temporary habitats is due to asymmetric intraguild predation (IGP) facilitated by a phenological head start in development. These data do not explain the dominance of Limnephilus larvae in permanent basins, which we show elsewhere to be an indirect effect of salamander predation. Behavioral observations also revealed that Asynarchus larvae are cannibalistic. In con- trast to the IGP on Limnephilus larvae, Asynarchus cannibalism occurs among same-sized larvae and often involves the mobbing of one victim by several conspecifics. In a third field experiment, we found that Asynarchus cannibalism was not density-dependent and occurred even at low larval densities. We hypothesize that Asynarchus IGP and cannibalism provide a dietary supplement to detritus that may be necessary for the timely completion of development in these nutrient-poor, high-elevation wetlands.
Improvement of flock productivity through supply of vitamins for higher laying performance and better egg quality

An adequate supply of all nutrients, including proteins, fats, carbohydrates, vitamins, minerals and water, has to be provided to support maximum productivity of laying hens. Among these nutrients, vitamins are particularly important, since they are essential for optimum health as well as normal physiological functions of the hens. As most vitamins cannot be synthesized by poultry in sufficient amounts to meet physiological demand, they must be obtained from the diet. The absence from feed or impaired absorption or utilization of vitamins can lead to specific deficiency disorders. This review reports on the occurrence and the physiological functions of all vitamins and summarizes research related to the requirements for and the beneficial effects of supplemental vitamins for laying hens. The recommendations for dietary supplementation of vitamins from various organizations are compared and put into perspective of modern poultry genotypes and current husbandry conditions. As there is good evidence that the minimum dietary vitamin levels, required to prevent clinical deficiencies may not support optimum health, performance and welfare of poultry under today's conditions it is recommended to include a safety margin to the vitamin requirements of laying hens.