Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybridization and Phylogeny of the Pine Wood Nematode (b uRsaphelenchus Spp.)

Reciprocal crosses were made between the following four strains of the pine wood nematode (Bursaphelenchus spp.) : i) a strain of B. xylophilus (rounded tail or "R" form); ii) a strain of B. mucronatus (mucronate tail or "M" form), both from Japan; iii) a French strain morphobiometrically identical to B. mucronatus and found in declining Pinus pinaster in the Landes forest; iv) a strain isolated from Abies balsamea in Minnesota (U.S.A.), also resembling B. mucronatus but shown by Wingfield et al. (1983) to hybridize with B. xylophilus and not with B. mucronatus. The results confirm the reproductive isolation of B. mucronatus and B. xylophilus. The French strain gives fertile hybrids with both B. mucronatus and with B. xylophilus; it also gives fertile hybrids with the strain from Minnesota when the parents are left with the F1, but not when they are separated from it. The hypothesis is forwarded that the Japanese and American strains of the pine wood nematodes have derived from a common stock from Western Europe, with existing populations now forming a "circle of species" (Ticehurst, 1938) which has been closed by the introduction of the American strain in Japan. A Supraspecies is proposed to include the existing populations of the pine wood nematode.
Weibull and percentile models for lidar-based estimation of basal area distribution

Abstract The aim of this study was to assess the accuracy of basal area distributions of sample plots in coniferous forest derived from small-footprint airborne laser scanner data, and to compare the accuracy of two methods for derivation of such distributions based on: (1) two percentiles of a two-parameter Weibull and parameter recovery, and (2) a system of 10 percentiles defined across the range of observed diameters. The 12 percentiles were derived from the empirical basal area distributions of 141 plots with size 300–400 m2. Regression analysis was used to relate the percentiles to various canopy height and canopy density metrics derived from the laser data. On average, the distance between transmitted laser pulses was 0.9 m on the ground. The plots were divided into three strata according to age class and site quality. The stratum-specific regressions explained 7–91% of the variability. Total plot volume predicted from the estimated distributions was used to assess the accuracy of the regressions. Cross-validation of the regressions revealed a bias of −1.2 to 2.1% between predicted and ground-truth values of plot volume. The standard deviations of the differences between predicted and ground-truth values of plot volume were 15.1–16.4%. Neither bias nor standard deviation differed significantly between the two validated methods.
Effects of Corn Oil and Broccoli on Instrumental Texture and Color Properties of Bologna-Type Sausage

The effects of substitution of sheep tail fat with corn oil (50%) and the addition of broccoli (0, 5, or 10%) on the instrumental texture and color properties of bologna-type sausage were investigated during chilled storage (90 days at 4°C). Thiobarbituric acid-reactive substances and pH analysis were also carried out in fresh and storaged samples. The substitution of sheep tail fat by corn oil had very significant (P < 0.01) effects on the color scores (L*, a*, and b*) and textural properties of samples. The use of broccoli affected significantly (P < 0.01) color scores and hardness, gumminess, and chewiness values. Storage time had significant effects (P < 0.01) on hardness, springiness and cohesiveness, and color scores. The use of corn oil in bologna-type sausage decreased thiobarbituric acid-reactive substances value. However, at the end of storage this value was not over 15 μmol MDA/kg in sausage with animal fat. The pH values were not below 6.1 at the end of the storage.
Modelling the impact of reducing control measures on the COVID-19 pandemic in a low transmission setting

Aims: We assessed COVID-19 epidemic risks associated with relaxing a set of physical distancing restrictions in the state of Victoria, Australia - a setting with low community transmission - in line with a national framework that aims to balance sequential policy relaxations with longer-term public health and economic need. Methods: An agent-based model, Covasim, was calibrated to the local COVID-19 epidemiological and policy environment. Contact networks were modelled to capture transmission risks in households, schools and workplaces, and a variety of community spaces (e.g. public transport, parks, bars, cafes/restaurants) and activities (e.g. community or professional sports, large events). Policy changes that could prevent or reduce transmission in specific locations (e.g. opening/closing businesses) were modelled in the context of interventions that included testing, contact tracing (including via a smartphone app), and quarantine. Results: Policy changes leading to the gathering of large, unstructured groups with unknown individuals (e.g. bars opening, increased public transport use) posed the greatest risk, while policy changes leading to smaller, structured gatherings with known individuals (e.g. small social gatherings) posed least risk. In the model, epidemic impact following some policy changes took more than two months to occur. Model outcomes support continuation of working from home policies to reduce public transport use, and risk mitigation strategies in the context of social venues opening, such as >30% population-uptake of a contact-tracing app, physical distancing policies within venues reducing transmissibility by >40%, or patron identification records being kept to enable >60% contact tracing. Conclusions: In a low transmission setting, care should be taken to avoid lifting sequential COVID-19 policy restrictions within short time periods, as it could take more than two months to detect the consequences of any changes. These findings have implications for other settings with low community transmission where governments are beginning to lift restrictions.
Comorbidity and Sociodemographic determinants in COVID-19 Mortality in an US Urban Healthcare System

Background: New York City is the US epicenter of the coronavirus disease 2019 (COVID-19) pandemic. Early international data indicated that comorbidity contributes significantly to poor prognosis and fatality in patients infected with SARS-CoV-2. It is not known to what degree medical comorbidity and sociodemographic determinants impact COVID-19 mortality in the US. Methods: Evaluation of de-identified electronic health records of 7,592 COVID-19 patients confirmed by SARS-CoV-2 lab tests in New York City. Medical comorbidites and outcome of mortality, and other covariates, including clinical, sociodemographic, and medication measures were assessed by bivariate and multivariate logistic regression models. Results: Of common comorbid conditions (hypertension, chronic kidney disease, chronic obstructive pulmonary disease, asthma, obesity, diabetes, HIV, cancer), when adjusted for covariates, chronic kidney disease remained significantly associated with increased odds of mortality. Patients who had more than one comorbidities, former smokers, treated with Azithromycin without Hydroxychloroquine, reside within the boroughs of Brooklyn and Queens Higher had higher odds of death. Conclusions: Increasing numbers of comorbid factors increase COVID-19 mortality, but several clinical and sociodemographic factors can mitigate risk. Continued evaluation of COVID-19 in large diverse populations is important to characterize individuals at risk and improve clinical outcomes.
Plasma levels of soluble ACE2 are associated with sex, Metabolic Syndrome, and its biomarkers in a large cohort, pointing to a possible mechanism for increased severity in COVID-19

We examined the associations between plasma concentrations of soluble ACE2 and biomarkers of Metabolic Syndrome in a large (N=2,051) sample of individuals who participated in a commercial wellness program and who underwent deep molecular phenotyping. sACE2 levels were significantly higher in men, compared to women, and in individuals with Metabolic Syndrome, compared to controls. sACE2 levels showed reliable associations with all individuals components of Metabolic Syndrome, including obesity, hypertension, insulin resistance, hyperlipidemia, and as well as markers of liver damage. This profile of associations was statistically significantly stronger in men, compared to women, and suggests that preexisting cardiometabolic conditions might confer increased severity of symptoms in some COVID-19 patients through increased expression of ACE2 in the liver.
PROGNOSTIC VALUE OF COMORMIDITY FOR SEVERITY OF COVID-19: A SYSTEMATIC REVIEW AND META-ANALYSIS STUDY

Abstract: Background and Aim: With the increase in the number of COVID-19 infections, global health is facing insufficient sources; this study aimed to provide additional data regarding the clinical characteristics of patients diagnosed with COVID-19 and in particular to analyze the factors associated with disease severity, unimprovement and mortality. Methods: 82 studies were included in the present meta-analysis that all of them have been published before May 1, 2020 and were found by searching through the databases Scopus and MEDLINE. The selected papers were studied and analyzed by employing the version 14 of stata software. It should be noted that, we employed I2 statistics for testing and verifying heterogeneity. Results: 82 papers were finally chosen for this meta- analysis, including 74855 infected patients (35673 men, 31140 women). The mean age of the patients was 56.49. The results indicate the prevalence of fever 79.84 (95% CI: 75.22-84.13), cough 59.53 (95% CI: 55.35-63.65), fatigue or myalgia 33.46 (95% CI: 28.68-38.40), dyspnea 31.48 (95% CI: 25.75-37.49) and diarrhea 10.71 (95% CI: 8.20-13.49). The prevalence of the most common comorbidities were hypertension 25.10 (95% CI: 19.91-30.64), diabetes 13.48 (95% CI: 10.61-16.62), cardiovascular diseases 8.94 (95% CI: 6.99-11.10), and chronic kidney disease 3.27 (95% CI: 2.22-4.47). Conclusion: The results of this study are seriously needed to effectively monitor the health of people with comorbidities (hypertension, diabetes, cardiovascular and cerebrovascular disease, coronary heart disease, and chronic kidney disease) to prevent the development of COVID-19 infection.
On the increasing role of older adolescents and younger adults during the SARS-CoV-2 epidemic in Mexico

Background: The SARSCoV2 epidemic in Mexico is growing, and there is uncertainty regarding the role that different age groups play in propagating the epidemic. Methods: We used data on hospitalizations with confirmed SARSCoV2 infection from the Mexican Ministry of Health in ten 5-year age groups: 10 to 14 through 55 to 59 years. For each age group g, we computed the proportion E(g) of individuals in that age group among all hospitalized cases aged 10-59 years during the early period (between April 20 to May 3, 2020), the corresponding proportion L(g) during the later periods (May 11 to 24), as well as the relative risk RR(g)= L(g)/E(g). For each pair of age groups g1,g2, RR(g1)>RR(g2) is interpreted as a relative increase in SARSCoV2 infections in the age group g1 compared with g2 for the later vs. early period. Results: The highest RR estimates belong to persons aged 15 to 19 years (RR=1.93(95% CI (1.19,3.12)) and 20 to 24 years (RR=1.40(1.07,1.83)). The RR estimates in persons aged over 30 years were significantly lower compared to persons aged 15-24 years. Conclusions: Our results suggest a temporal increase in the incidence of SARSCoV2 infection in older adolescents and younger adults compared to other age groups. Targeted interventions, particularly public health messaging at those age groups to increase knowledge and risk awareness may be considered.
Diagnostic Accuracy of the 4AT for delirium detection: systematic review and meta-analysis.

Objective: Detection of delirium in hospitalised older adults is recommended in national and international guidelines. The 4 'A's Test (4AT) is a short (<2 min) instrument for delirium detection that is used internationally as a standard tool in clinical practice. We performed a systematic review and meta-analysis of diagnostic test accuracy of the 4AT for delirium detection. Methods: We searched MEDLINE, EMBASE, PsycINFO, CINAHL, clinicaltrials.gov and the Cochrane Central Register of Controlled Trials, from 2011 (year of 4AT release on the website www.the4AT.com) until 21 December 2019. Inclusion criteria were: older adults ([≥]65y); diagnostic accuracy study of the 4AT index test when compared to delirium reference standard (standard diagnostic criteria or validated tool). Methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. Pooled estimates of sensitivity and specificity were generated from a bivariate random effects model. Results: 17 studies (3721 observations) were included. Settings were acute medicine, surgery, a care home, and the emergency department. Three studies assessed performance of the 4AT in stroke. The overall prevalence of delirium was 24.2% (95% CI 17.8-32%; range 10.5-61.9%). The pooled sensitivity was 0.88 (95% CI 0.80-0.93) and the pooled specificity was 0.88 (95% CI 0.82-0.92). Excluding the stroke studies, the pooled sensitivity was 0.86 (95% CI 0.77-0.92) and the pooled specificity was 0.89 (95% CI 0.83-0.93). The methodological quality of studies varied but was moderate to good. Conclusions: The 4AT shows good diagnostic test accuracy for delirium in the 17 available studies. These findings support its use in routine clinical practice in delirium detection.
Timing COVID-19 - Synchronization of longitudinal patient data to the underlying disease progression using CRP as a temporal marker

Advances in medical technology and IT infrastructure have led to increased availability of continuous patient data that allows to investigate the longitudinal progression of novel and known diseases in unprecedented detail. However, to accurately describe any underlying pathophysiology with longitudinal data, the individual patient trajectories have to be synchronized based on temporal markers. In this study, we use longitudinal data from 28 critically ill ICU COVID-19 patients to compare the commonly used alignment markers "onset of symptoms", "hospital admission" and "ICU admission" with a novel objective method based on the peak value of inflammatory marker C-reactive protein (CRP). By applying our CRP-based method to align the progression of neutrophils and lymphocytes, we were able to define a pathophysiological window that allowed further mortality risk stratification in our COVID-19 patient cohort. Our data highlights that proper synchronization of patient data to the underlying pathophysiology is crucial to differentiate severity subgroups and to allow reliable interpatient comparisons.
First Clinical Use of Lenzilumab to Neutralize GM-CSF in Patients with Severe and Critical COVID-19 Pneumonia

Background: In COVID-19, high levels of granulocyte macrophage-colony stimulating factor (GM-CSF) and inflammatory myeloid cells correlate with disease severity, cytokine storm, and respiratory failure. With this rationale, we used lenzilumab, an anti-human GM-CSF monoclonal antibody, to treat patients with severe COVID-19 pneumonia. Methods: Hospitalized patients with COVID-19 pneumonia and risk factors for poor outcomes were treated with lenzilumab 600 mg intravenously for three doses through an emergency single-use IND application. Patient characteristics, clinical and laboratory outcomes, and adverse events were recorded. All patients receiving lenzilumab through May 1, 2020 were included in this report. Results: Twelve patients were treated with lenzilumab. Clinical improvement was observed in 11 out of 12 (92%), with a median time to discharge of 5 days. There was a significant improvement in oxygenation: The proportion of patients with SpO2/FiO2 < 315 at the end of observation was 8% vs. compared to 67% at baseline (p=0.00015). A significant improvement in mean CRP and IL-6 values on day 3 following lenzilumab administration was also observed (137.3 mg/L vs 51.2 mg/L, p = 0.040; 26.8 pg/mL vs 16.1 pg/mL, p = 0.035; respectively). Cytokine analysis showed a reduction in inflammatory myeloid cells two days after lenzilumab treatment. There were no treatment-emergent adverse events attributable to lenzilumab, and no mortality in this cohort of patients with severe COVID-19 pneumonia. Conclusions: In high-risk COVID-19 patients with severe pneumonia, GM-CSF neutralization with lenzilumab was safe and associated with improved clinical outcomes, oxygen requirement, and cytokine storm.
Associations between wearing masks, washing hands, and social distancing practices, and risk of COVID-19 infection in public: a cohort-based case-control study in Thailand

Objective. To investigate whether wearing masks, washing hands and social distancing practices are associated with lower risk of COVID-19 infection. Design. A retrospective cohort-based case-control study. All participants were retrospectively interviewed by phone about their preventive measures against COVID-19 infection. Setting. Thailand, using the data from contact tracing of COVID-19 patients associated with nightclub, boxing stadium and state enterprise office clusters from the Surveillance Rapid Response Team, Department of Disease Control, Ministry of Public Health. Contacts were tested for COVID-19 using PCR assays per national contact tracing guidelines. Participants. A cohort of 1,050 asymptomatic contacts of COVID-19 patients between 1 and 31 March 2020. Main outcome measures. Diagnosis of COVID-19 by 21 April 2020. Odds ratios for COVID-19 infection and population attributable fraction were calculated. Exposure. The study team retrospectively asked about wearing masks, washing hands, and social distancing practices during the contact period through telephone interviews. Results. Overall, 211 (20%) were diagnosed with COVID-19 by 21 Apr 2020 (case group) while 839 (80%) were not (control group). Fourteen percent of cases (29/210) and 24% of controls (198/823) reported wearing either non-medical or medical masks all the time during the contact period. Wearing masks all the time (adjusted odds ratio [aOR] 0.23; 95%CI 0.09-0.60) was associated with lower risk of COVID-19 infections compared to not wearing masks, while wearing masks sometimes (aOR 0.87; 95%CI 0.41-1.84) was not. Shortest distance of contact >1 meter (aOR 0.15; 95%CI 0.04-0.63), duration of close contact [≤]15 minutes (aOR 0.24; 95%CI 0.07-0.90) and washing hands often (aOR 0.33; 95%CI 0.13-0.87) were significantly associated with lower risk of infection. Sharing a cigarette (aOR 3.47; 95%CI 1.09-11.02) was associated with higher risk of infection. Type of mask was not independently associated with risk of infection. Those who wore masks all the time were more likely to wash hands and practice social distancing. We estimated that if everyone wore a mask all the time, washed hands often, did not share a dish, cup or cigarette, had shortest distance of contact >1 meter and had duration of close contact [≤]15 minutes, cases would have been reduced by 84%. Conclusions. Our findings support consistently wearing non-medical masks, washing hands, and social distancing in public to prevent COVID-19 infections.
Efeito hipolipemiante da suplementação dietética com a farinha do cubiu (Solanum sessiliflorum Dunal) em ratos hipercolesterolêmicos

Studies with fruit and vegetables rich in dietary fiber have shown lowering effects on the blood concentrations of total cholesterol (TC), acting preventively against hypercholesterolemia. The aim of this study was to analyze the chemical composition of cocona and evaluate the effect of the consumption of cocona flour on lipemia of Wistar rats with hypercholesterolemia. Eight animals were used for each treatment, in 7 groups: control; 3 experimental groups with 5%, 25% and 50% of the recommended fiber (AIN-93) from cocona flour; 3 groups per feeding with pectin and cellulose as source of dietary fiber, in the same proportions of the experimental groups. At the end of the assay, we verified that there were not significant variations in the consumption of the animals and the body weight during the experiment. Treatments with cocna flour were responsible for reducing the concentrations of total cholesterol (-21.6%), LDL-c (-56.8%), increasing the excretion of fecal cholesterol (+116%) and lowering the liver cholesterol (-32.1%). None of the treatments significantly altered the triglyceride concentrations. Treatments using pectin and cellulose show results similar to cocona. The observed results can be used in further studies aimed at the biotechnological exploitation of this fruit.
Impact of habitat diversification on arthropod communities: A study in the fields of Chinese cabbage, Brassica chinensis

Abstract Field trials were carried out from June to August in 2004 at Wuyishan (Wuyi Mountains), Fujian province, China, to determine the effects of habitat diversification on arthropod communities. Two Chinese cabbage, Brassica chinensis, field 1 (F1) and field 2 (F2) surrounded by diverse vegetable cultivars were selected, while a monoculture of Chinese cabbage served as the control field (CK). The results showed that: (i) when comparing insect abundance of each order between different habitats, significantly higher numbers of lepidopterous insects (39.76% from the each order) and lower densities of Hymenoptera (19.82%) were found in CK than in F1 and F2; (ii) compared with CK, F1 and F2 had a lower percentage of species richness and an abundance of herbivorous insects, but increased richness, abundance and biodiversity of predatory insects; (iii) no differences were observed in neutral insects’guild between different fields; and (iv) the dominant species for each guild depends on the habitat types and sampling dates. This study suggests that intercropping could conceivably be used in these habitats to increase the population of natural predators, thus achieving desirable and ecologically friendly results in vegetable fields.
Interactions among the α2-, β2-, and β3-adrenergic receptor genes and obesity-related phenotypes in the Quebec Family Study

Abstract The gene-gene interactions between markers in the α2-, β2-, and β3-adrenergic receptor (ADR) genes and obesity-related phenotypes were studied in the Quebec Family Study (QFS) cohort. The prevalence of the Arg allele of the Arg16Gly polymorphism in the β2-ADR gene was higher (49%) in males with a body mass index (BMI) of 35 kg/m 2 or higher versus those with a BMI less than 35 kg/m 2 (33%; P = .010). The β2-ADR gene Arg16Gly and Gln27Glu polymorphisms were associated with plasma total and low-density lipoprotein (LDL) cholesterol concentrations. In addition, the homozygotes for the 6.3-kb allele of Dral polymorphism in the α2-ADR gene had the lowest mean abdominal subcutaneous fat area ( P = .012) and total fat area ( P = .003), as well as insulin area, under the curve during an oral glucose tolerance test ([OGTT] P = .004). Several ADR gene-gene interaction effects on abdominal fat distribution and plasma lipids were detected. First, significant interactions between α2- and β3-ADR genes were observed on total ( P = .015) and subcutaneous ( P = .004) abdominal fat. Second, interaction effects between α2- and β2-ADR gene variants influenced total, high-density lipoprotein (HDL), and LDL cholesterol concentrations. Finally, there were interactions between markers within the β2-ADR gene affecting plasma triglyceride concentrations and subcutaneous abdominal fat. From these results, we conclude that polymorphisms in the ADR genes contribute to body fat and plasma lipid variability in men. Gene-gene interactions among the ADR genes contribute to the phenotypic variability in abdominal obesity and plasma lipid and lipoprotein, but not in visceral fat levels.