Miracle-dz/UniFAR-FTUs huggingface dataset:
Leptospirosis diagnosis among patients suspected of dengue fever in Brazil

Abstract Background: The early symptoms of leptospirosis and dengue fever are difficult to distinguish and can cause diagnostic confusion. Due to the large dengue epidemics that has occurred in Brazil in recent years, it is possible that cases of leptospirosis were unreported. Therefore, we performed a retrospective study to detect leptospirosis in patients who were tested for dengue, but whose laboratory diagnoses were negative. Methods: Sera samples from 2,017 patients from 48 cities located in the central region of São Paulo state, Brazil, were studied. All samples were subjected to the microscopic agglutination test (MAT), 305 of which were taken from patients five days or less since the onset of symptoms, and were additionally subjected to real-time polymerase chain reaction (PCR). Results: The overall prevalence of leptospirosis cases was 21 (1.04%), with 20 through MAT (18 for Icterohaemorrhagiae and two for the Cynopteri serogroup) and one through PCR (amplicon sequencing compatible with Leptospira interrogans). According to previously established criteria, eight cases of leptospirosis were classified as “confirmed” and 13 as “probable”. The Brazilian notification system for health surveillance had no records for 16 patients positive for leptospirosis and, thus, they were considered unreported cases. Statistical analyses revealed that the prevalence of leptospirosis was higher in men (1.56%) than in women (0.56%), and the mean age was higher in positive patients (43.7 years) than in negative ones (32.3 years). Conclusion: The results indicated that patients suspected of dengue fever had evidence of leptospirosis or Leptospira infection, and most of these cases were unreported in the Brazilian notification system. The high burden of dengue may contribute to the misdiagnosis of leptospirosis, and health professionals should increase their awareness of leptospirosis as an important differential diagnosis of patients with suspicion of dengue.
Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.
Evaluation of prognostic variables in chronic lymphocytic leukemia and association with disease stage

The aim of the present study was to investigate different biological prognostic markers to identify high-risk patients with chronic lymphocytic leukemia (CLL) with a higher tumor burden, in order to ensure appropriate management. A total of 81 Egyptian patients with CLL were enrolled in the present study, with 75 healthy subjects serving as the control group. The expression of CD49d, CD38 and ZAP-70 in CLL cells was assessed using flow cytometry. The fluorescence in situ hybridization technique was employed to evaluate TP53 (del17p), ataxia-telangiectasia (del11q) and 13q14 (del13q14) genes and the presence of trisomy 12. The serological markers β2 microglobulin (B2M) and sCD23 were measured by ELISA. The CD49d gene was highly expressed in 25.9% and cytogenetic aberrations were observed in 66.6% of all recruited CLL patients. The patients were categorized according to the Binet staging system and a significant increase in the expression of sCD23, CD49d and ZAP-70 was detected in group C (P=0.008, 0.034 and 0.017, respectively) when compared to groups A and B. CD49d+ patients exhibited significantly higher expression of CD38 (P=0.002) and trisomy 12 (P=0.015) and lower expression of del13q14 (P=0.001). Patients who were CD49d+ with B2M>3.5 µg/ml exhibited higher total leukocyte count (P=0.048), higher absolute lymphocyte count (P=0.036), higher expression of CD38 (P=0.002) and trisomy 12 (P=0.034) and lower expression of del13q14 (P=0.002). Therefore, sCD23, CD49d and ZAP-70 may be considered as an optimal prognostic marker combination to be evaluated in the early stages of CLL and throughout disease management. Integrating both serological markers and CD49d expression by flow cytometry may add to the prognostic value of each marker alone and help identify high-risk patients with a higher tumor burden.
Experimental research in rats on the reactivity of new corneal blood vessels to adrenaline

Aim: The purpose of this experimental study was to evaluate the existence of adrenergic receptors in ketamine-induced corneal blood vessels in rat pups. Methods: The study of corneal neovascularization motricity was performed on 45-day-old Wistar rats in which, starting from the 15th day of life, corneal blood vessels were obtained by injecting intraperitoneal ketamine at a dose of 150 mg/ kg body weight, a total of 5 successive doses. The examination of the neovascularization was done with the help of a Nikon stereomicroscope connected to a video camera and a computer, the total magnification being 400X. The reactivity of the new corneal blood vessels to the administration in conjunctival instillations of a 1.5 mmol/L adrenaline solution was tested. The parameters followed were represented by variations in the caliber of corneal blood vessels. The data were analyzed using Microsoft Office Excel. Results: Administration of distilled water did not produce statistically significant changes in corneal blood vessels, while adrenaline produced a statistically significant constriction of vascular diameter (p=0.01 at T9, p=0.004 at T10, p=0.019 at time T11 of examinations). Conclusions: The results showed that adrenaline produces vasoconstriction in the new corneal blood vessels, which allows us to assume that they contain α-adrenergic receptors. However, we cannot say that corneal pathological vessels do not contain β2-type adrenergic receptors, because the effect of adrenaline may be an algebraic sum between vasoconstriction produced by stimulating α-adrenergic receptors and vasodilation produced by stimulating β2-adrenergic receptors, but in which the vasodilating effect may be masked by the vasoconstrictor effect given by a higher density of α-adrenergic receptors. Abbreviations: A= adrenaline, DNM = non-measurable diameter, NA= noradrenaline, Std.Er. = Standard error
Food Supply Chains and Covid‐19: Impacts and Policy Lessons

Summary Covid‐19 placed unprecedented stresses on food supply chains. Farms faced bottlenecks for some inputs, notably seasonal labour. Processing was disrupted by labour shortages and shutdowns, especially in meat processing. Air freight, important for fruits and vegetables, was severely disrupted. Demand from restaurants and food service collapsed, while retail food demand surged. Yet supply chains in the developed world have been remarkably resilient to date. Store shelves were replenished as stockpiling behaviour subsided and as supply chain actors expanded operating hours, increased staff, simplified the product range and found alternative suppliers. This rapid recovery was facilitated by policy decisions to reduce border waiting times, to streamline certification procedures and to relax regulations on trade in food. Importantly, policymakers have so far mostly avoided a repeat of the mistakes of the 2007–2008 food price crisis, which was greatly exacerbated by export bans. Some bottlenecks remain, and there may be new supply risks as Covid‐19 spreads in Latin America. Overall, the biggest risk to food security is not food availability, but consumers’ loss of income. Safety nets and food assistance are essential to avoid an increase in hunger, especially in developing countries.
High Blood Eosinophil and YKL-40 Levels, as Well as Low CXCL9 Levels, are Associated with Increased Readmission in Patients with Acute Exacerbation of Chronic Obstructive Pulmonary Disease

Background Readmission after hospital discharge is common among patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Predictive biomarkers of readmission would facilitate stratification strategies and individualized prognosis. Therefore, this study aimed to investigate the utility of type 2 biomarkers (eosinophils, periostin, and YKL-40) and a type 1 biomarker (CXCL9) in predicting readmission events in patients with AECOPD. Methods This is a prospective observational study design. Blood levels of eosinophils, periostin, YKL-40, and CXCL9 were measured at admission. The clinical outcomes were 12-month COPD-related readmission, time to COPD-related readmission, and number of 12-month COPD-related readmissions. These outcomes were analyzed using logistic and Cox regression models and Spearman’s rank test. Results A total of 123 patients were included, of whom 51 had experienced at least one readmission for AECOPD. High levels of eosinophils (≥200 cells/μL or 2% of the total white blood cell count, adjusted odds ratio [aOR] =3.138, P=0.009) and YKL-40 (≥14.5 ng/mL, aOR =2.840, P=0.015), as well as low CXCL9 levels (≤30.1 ng/mL, aOR =2.551, P=0.028), were associated with an increased COPD-related readmission. The highest relative readmission rate was observed in patients with both high eosinophil and YKL-40 levels. Moreover, high eosinophil and YKL-40 levels were associated with a shorter time to first COPD-related readmission and an increased number of 12-month COPD-related readmissions. Conclusion High blood eosinophil and YKL-40 levels, as well as low CXCL9 levels, have predictive utility for the 12-month COPD-related readmission rate. Using eosinophils and YKL-40 together allows more precise identification of patients at high risk of COPD-related readmission.
The mitochondrial genome of an Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea

Abstract The mitochondrial genome of the Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea is determined and characterized in detail. It is 15,737 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one control region. It has a base composition of 31.23% for A, 16.29% for G, 17.84% for C, and 34.64% for T. The phylogenetic trees reconstructed based on the maximum-likelihood (ML) method and Bayesian inference (BI) confirmed that K. nodifila belongs to the Semisulcospiridae clade in the monophyletic caeonogastropod superfamily Cerithioidea.
Low Use of Outpatient Parenteral Antimicrobial Therapy for Drug Use-Associated Infective Endocarditis in an Urban Hospital System

Abstract Background The opioid crisis in the United States has led to increasing hospitalizations for drug use-associated infective endocarditis (DUA-IE). Outpatient parenteral antimicrobial therapy (OPAT), the preferred modality for intravenous antibiotics for infective endocarditis, has demonstrated similar outcomes among patients with DUA-IE versus non-DUA-IE, but current studies suffer selection bias. The utilization of OPAT for DUA-IE more generally is not well studied. Methods This retrospective cohort study compared OPAT use for DUA-IE versus non-DUA-IE in adults hospitalized between January 1, 2015 and September 1, 2019 at 3 urban hospitals. We used multivariable regression analysis to assess the association between DUA-IE and discharge with OPAT, adjusting for clinically significant covariables. Results The cohort included 518 patients (126 DUA-IE, 392 non-DUA-IE). Compared to those with non-DUA-IE, DUA-IE patients were younger (53.0 vs 68.2 years, P < .001) and more commonly undomiciled (9.5% vs 0.3%, P < .01). Patients with DUA-IE had a significantly lower odds of discharge with OPAT than non-DUA-IE patients (adjusted odds ratio [aOR] = 0.20; 95% confidence interval [CI], 0.10–0.39). Odds of discharge with OPAT remained lower for patients with DUA-IE after excluding undomiciled patients (aOR = 0.22; 95% CI, 0.11–0.43) and those with patient-directed discharges (aOR = 0.27; 95% CI, 0.14–0.52). Conclusions Significantly fewer patients with DUA-IE were discharged with OPAT compared to those with non-DUA-IE, and undomiciled patients or patient-directed discharges did not fully account for this difference. Efforts to increase OPAT utilization among patients with DUA-IE could have important benefits for patients and the healthcare system.
MOISTURE ADSORPTION ISOTHERMS OF ASSAM GREEN TEA POWDER

Moisture adsorption isotherms of Assam green tea powder were determined at 25, 35 and 45C. A water activity analyzer (Novasina ® model LabMaster-aw) was used to detecting the equilibrium over the relative humidity range of 30-70%. The sorption isotherms of Assam green tea powder were typical type III sigmoid curves, according to BET classification. The equilibrium moisture content data were fitted to six mathematical models. From the estimated parameters of different models, it was indicated that the Peleg model gives the best fit to the experimental data and it is the most suitable model for describing the relationships between equilibrium moisture content (EMC) and equilibrium relative humidity (ERH) of Assam green tea powder over the entire range of temperature. The net isosteric heat of sorption was determined by the Clausius-Clapeyron equation and was found to be between 45.2 and 45.6 kJ/mol at moisture levels ranged 0.05-0.25 g/g dry matter.
Germinal center reactions in tertiary lymphoid structures associate with neoantigen burden, humoral immunity and long-term survivorship in pancreatic cancer

ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) has traditionally been thought of as an immunologically quiescent tumor type presumably because of a relatively low tumor mutational burden (TMB) and poor responses to checkpoint blockade therapy. However, many PDAC tumors exhibit T cell inflamed phenotypes. The presence of tertiary lymphoid structures (TLS) has recently been shown to be predictive of checkpoint blockade response in melanomas and sarcomas, and are prognostic for survival in PDAC. In order to more comprehensively understand tumor immunity in PDAC patients with TLS, we performed RNA-seq, single and multiplex IHC, flow cytometry and predictive genomic analysis on treatment naïve, PDAC surgical specimens. Forty-six percent of tumors contained distinct T and B cell aggregates reflective of “early-stage TLS” (ES-TLS), which correlated with longer overall and progression-free survival. These tumors had greater CD8+ T cell infiltration but were not defined by previously published TLS gene-expression signatures. ES-TLS+ tumors were enriched for IgG1 class-switched memory B cells and memory CD4+ T cells, suggesting durable immunological memory persisted in these patients. We also observed the presence of active germinal centers (mature-TLS) in 31% of tumors with lymphocyte clusters, whose patients had long-term survival (median 56 months). M-TLS-positive tumors had equivalent overall T cell infiltration to ES-TLS, but were enriched for activated CD4+ memory cells, naive B cells and NK cells. Finally, using a TCGA-PDAC dataset, ES-TLS+ tumors harbored a decreased TMB, but M-TLS with germinal centers expressed significantly more MHCI-restricted neoantigens as determined by an in silico neoantigen prediction method. Interestingly, M-TLS+ tumors also had evidence of increased rates of B cell somatic hypermutation, suggesting that germinal centers form in the presence of high-quality tumor neoantigens leading to increased humoral immunity that confers improved survival for PDAC patients. AbbreviationsTLS: tertiary lymphoid structures; GC: germinal center(s); PDAC: pancreatic ductal adenocarcinoma; RNA-seq: RNA sequencing; BCRseq: B cell receptor sequencing; HEV: high endothelial venule; PNAd: peripheral node addressin; TMB: tumor mutational burden; TCGA: the cancer genome atlas; PAAD: pancreatic adenocarcinoma; FFPE: formalin fixed paraffin embedded; TIME: tumor immune microenvironment.
Outcome of the Public Consultation on the draft statement of the PPR Panel on a framework for conducting the environmental exposure and risk assessment for transition metals when used as active substances in plant protection products (PPP)

EFSA performed a public consultation of the draft statement of the PPR Panel on a framework for conducting the environmental exposure and risk assessment for transition metals when used as active substances in plant protection products (PPP) from 3 August to 21 September 2020. EFSA was asked by the European Commission to prepare a public consultation on the draft statement. The statement provides a framework for conducting the environmental exposure, hazard characterisation and risk assessment for transition metals when used as active substances in plant protection products according to Regulation (EC) No 1107/2009 of the European Parliament and the Council. This report presents statistics on the comments received and answers to them. These comments were taken into account when finalising the statement. © European Food Safety Authority, 2021
Electronic Structure and Optical Properties of Non-Metals (N, F, P, Cl, S)-Doped Cubic NaTaO3 by Density Functional Theory

Electronic structure and optical properties of non-metals (N, S, F, P, Cl) -doped cubic NaTaO3 were investigated systematically by density functional theory (DFT). The results showed that the substitution of (N, S, P, Cl) for O in NaTaO3 was effective in narrowing the band-gap relative to the F-doped NaTaO3. The larger red shift of the absorption edge and the higher visible light absorption at about 520 nm were found for the (N and P)-doped NaTaO3. The excitation from the impurity states to the conduction band may account for the red shift of the absorption edge in an electron-deficiency non-metal doped NaTaO3. The obvious absorption in the visible light region for (N and P)-doped NaTaO3 provides an important guidance for the design and preparation of the visible light photoactive materials.
Glimpsing the raging seas that stop swans: A qualitative look at living with multimorbidity and pain in patients from a tertiary care service

Multimorbidity requires complex and ongoing care. Understanding the subjective illness experience is critical to effective care. Literature isn’t clear about illness perception in patients with multimorbidity followed in services of high complexity. This study aims to investigate the illness experience based on narratives about daily living and symptoms of patients with multimorbidity and pain in a tertiary health care service. Methods: Qualitative narrative inquiry design with framework analysis from semi-structured interviews at a tertiary internal medicine outpatient clinic. Patients with Elixhauser comorbidity index ≧3 or and pain during the last week were included. Framework analysis was performed using 3 main patterns of illness experience from a previous study: “Gliding swan” (Resilience); “Stormy Seas” (Vulnerability); and “Stuck adrift” (Disruption); and identifying subthemes. One case study was selected from each main category. 43 patients, 14 classified as “gliding swan,” 12 as “stormy seas” and 17 as “stuck adrift. ” Within the “gliding swan” group, positive examples of how to navigate through physical and emotional factors to sustain their wellbeing based on comprehension; In the “stormy seas” group, themes revolved around vulnerability, burden and ambiguity in relation to the health team. In the “stuck adrift” group the main content was about overwhelmed feelings and limitations. Conclusion(s): Narratives brought the content about lacking personalized understanding of diseases, with great emotional repercussion. Some meaningful anchors were highlighted. This study reinforces multimorbidity and pain interact and that healthcare professional should be aware of the turbulences that can disturb navigation in the raging seas of long-term multimorbid conditions.
Health workforce surge capacity during the COVID‐19 pandemic and other global respiratory disease outbreaks: A systematic review of health system requirements and responses

Abstract Health system decision‐makers need comprehensive evidence to mitigate surges in the demand for human resources for health (HRH) during infectious disease outbreaks. This study aimed to assess the state of the evidence on policy and planning responses to HRH surge capacity during the coronavirus disease (COVID‐19) pandemic and other viral respiratory disease outbreaks of global significance in the 21st century. We systematically searched eight bibliographic databases to extract primary research articles published between January 2000 and June 2020 capturing temporal changes in health workforce requirements and responses surrounding respiratory virus pandemics. Following the Preferred Reporting Items for Systematic Reviews and Meta‐analyses standard, 16 studies met our inclusion criteria. Five focused on COVID‐19, three on H1N1, and eight modelled a hypothetical pandemic. Investigations of different training, mobilization, and redeployment options to address pandemic‐time health system capacity were reviewed; however, few scenarios drew on observational HRH data, and heterogeneity of study approaches and outcomes generally precluded comparability across contexts. Notable evidence gaps included occupational and psychosocial factors affecting healthcare workers' absenteeism and risk of burnout, gendered considerations of HRH capacity, evaluations in low‐ and lower‐middle income countries, and policy‐actionable assessments to inform post‐pandemic recovery and sustainability of services for noncommunicable disease management.
Extraction of Essential Oils from Some Types of Umbelifera Family using Microwave-Assisted Water Distillation

Microwave oven has been modified to essential oil distiller. Essential oils were extracted from seeds of caraway, cumin, aniseed and fennel by using microwave-assisted water distillation (MAWD) and traditional water distillation (TWD). Extraction temperature, oil yield (%), consumed power (kWh) and physical characteristics have been investigated. Mathematical modeling was used to predict of oil yield values. The results showed that the extraction temperature of essential oils by microwave-assisted water distillation was higher than traditional water distillation. Oil yield extracted from caraway, cumin, aniseed and fennel by using MAWD was significantly higher than TWD. The consumed power by MAWD was significantly less than TWD. A theoretical data from mathematical modeling was closed to practical data, moreover the determination coefficient ranged between 0.93-0.99. Essential oils extracted by MAWD and TWD have a high effect on the inactivation of Bactria. The results showed that the activity of linoleic acid antioxidants of extracted essential oils by MAHD and THD were convergent. Keywords: essential oil, microwave, water distillation, Umbelifera