Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduced antibiotic use after initial treatment of acute respiratory infections with phytopharmaceuticals- a retrospective cohort study

ABSTRACT Objectives: We examined the relationship between the initial treatment of acute lower and upper tract respiratory infections with phytopharmaceuticals and the duration of the disease as well as between the initial treatment and the use of antibiotics in the further course of the disease. Method: Outpatients from the IMS® Disease Analyzer database with diagnoses of acute respiratory infections between January 2015 and March 2019 were observed for 30 days. Patients who had been prescribed phytopharmaceuticals on the day of their diagnosis were matched with controls who had not received such prescriptions by treating practice, diagnosis, age, sex, insurance status, index year, and Charlson comorbidity score. Patients antibiotic precriptions on the day of diagnosis were excluded. Logistic regression was used to investigate the relationship between phytopharmaceutical prescription, antibiotic prescription in the further course of the disease, and duration of sick leave. Results: A total of 117,182 patients who had been prescribed phytopharmaceuticals and an equal number of controls were available for analysis. Phytotherapeutics were associated with fewer antibiotic prescriptions. Extract of Pelargonium sidoides root (odds ratio (OR) 0.49 [0.43–0.57]) and thyme extract (OR 0.62 [0.49–0.76]) exhibited the strongest effect among patients treated by general practitioners, while Pelargonium sidoides root extract (OR 0.57 [0.38–0.84]), thyme and ivy extract (OR 0.66 [0.60–0.73]), and thyme and primrose root extract (OR 0.67 [0.47–0.96]) proved most effective in pediatric patients. Patients receiving phytopharmaceuticals had a significantly lower risk of prolonged periods of sick leave. The risk of sick leave durations of >7 days was most markedly reduced in patients taking cineole (OR 0.74 [0.63–0.86]) and Pelargonium root extract (OR 0.79 [0.54–0.96]). Conclusion: The use of selected phytopharmaceuticals for acute respiratory infections is associated with a significantly reduced need for antibiotic prescriptions in the further course of the disease, as well as significantly shorter sick leaves.
Impairment of endothelial progenitor cells function in patient with mustard gas intoxication

Abstract Background: Sulfur mustard (SM), also known as mustard gas, was first widely used in the Iraq–Iran. After SM exposure, the most prominent clinical signs are the development of extensive non-healing skin wounds and pulmonary signs, persisting over long time. Since the most frequent complications in SM-intoxicated patients are respiratory and dermatologic lesions, and with respect to the important role of endothelial progenitor cells (EPCs) in the pathophysiology of these lesion, we conducted this study to recognize the potential effects of SM on biological features of EPCs in patients exposed with this gas. Methods: In this study, 30 patients with the history of SM exposure during the Iran–Iraq war (1984–1988), 27 patients with pulmonary signs with no history of SM exposure and 20 healthy participants were included. Cell population and function of EPCs were assessed 4 years post-exposure. For this purpose, circulating EPCs (cEPCs) were harvested and cultivated, then the biological features of these cells, including migratory, proliferative, and tubulogenic activities were analyzed. We also measured serum antioxidants levels and mRNA levels of some proangiogenic factors in EPCs from SM-intoxicated patients. Results: Our results showed lesser number of cEPCs in patients exposed with SM, which was associated with decreased proliferative, migratory, and tubulogenic activity of these cells. Also, we found the lesser serum activity of SOD, GPX and MDA in the SM group than in the healthy control group. Conclusions: SM exposure resulted in decreased proliferation and migration of EPCs, which was associated with decreased tubule formation and angiogenic factors.
Mathematical modelling of T cell homeostasis

T cell homeostasis describes the process through which the immune system regulates cell survival, proliferation, differentiation and death to maintain T cell numbers and diversity in a range of different conditions. The aim of this thesis is to better understand how this process leads to the development of the naive CD4+ T cell compartment during childhood. Mathematical modelling is used in combination with experimental observations to estimate naive T cell kinetics over the lifetime of an individual. The analysis described here shows that post-thymic proliferation contributes more than double the number of cells entering the pool each day from the thymus. This ratio is preserved from birth to age 20 years; as the thymus involutes, the average time between naive T-cell divisions in the periphery lengthens with age and the naive population is maintained by improved naive cell survival. Thymic output is quantified from birth to age 60 years by combining models to interpret naive T cell TRECs and Ki67 expression data. Three distinct phases of thymic T cell output are identified: (i) increasing production from birth to age 1 year; (ii) steep decline to age 8 years; (iii) slow decline from age 8 years onwards. Finally, the role of inter-cellular variation in T cell residency times is explored. It is able to explain the persistence of PTK7+ naive CD4+ T cells in thymectomised individuals. Importantly, the model predicts the accumulation of veteran PTK7+ T cells in older individuals and suggests that the residual population in thymectomised individuals will also consist predominantly of veteran PTK7+ T cells. The model has implications for the use of PTK7 as a marker of recent thymic emigration and also naturally explains improved T cell survival in older individuals.
The effect of Brahman genes on body temperature plasticity of heifers on pasture under heat stress.

Bos taurus indicus cattle have superior ability for regulation of body temperature during heat stress due to a number of physiological and cellular level adaptive traits. The objectives of this study were to quantify the change in body temperature in heifers with various proportions of Brahman genes per unit increase in heat stress as measured by THI and to assess how different breed groups responded to varying intensity and duration of heat stress. A total of 299 two-year old heifers from six breed groups ranging from 100% Angus to 100% Brahman were evaluated under hot and humid conditions during 2017 and 2018 summer days. Two strategies were used to estimate the plasticity in body temperature of breed groups in response to environmental challenges: (1) a random regression mixed model was used to estimate reaction norm parameters for each breed group in response to a specified environmental heat stress, and (2) a repeated measures mixed model was used to evaluate the response to different environmental heat loads. The reaction norm model estimated an intercept and slope measuring the change in body temperature per unit increase in THI environmental heat stress for different breed groups of animals and allows the identification of genotypes which are robust, with low slope values indicative of animals that are able to maintain normal body temperature across a range of environments. The repeated measures mixed model showed that Brahman cattle have an advantage under moderate or high heat stress conditions but both Angus and Brahman breed groups are greatly affected when heat stress is severe. A critical factor appears to be the opportunity to cool down during the night hours more than the number of hours with extreme THI. With heat stress conditions predicted to intensify and expand into currently temperate zones, developing effective strategies to ensure sustainable beef production systems are imperative. Effective strategies will require the identification of the genes conferring the superior thermotolerance in Brahman cattle.
Blocking Angiopoietin-2 Promotes Vascular Damage and Growth Inhibition in Mouse Tumors Treated with Small Doses of Radiation

These findings offer a preclinical rationale for further testing of the use of radiation in combination with Ang2-blocking antibodies to improve the overall outcome of cancer treatment. Abnormal vasculature in tumors leads to poor tissue perfusion and cytostatic drug delivery. Although drugs inducing vascular normalization, for example, angiopoietin-2 (Ang2)-blocking antibodies, have shown promising results in preclinical tumor models, clinical studies have so far shown only little efficacy. Because Ang2 is known to play a protective role in stressed endothelial cells, we tested here whether Ang2 blocking could enhance radiation-induced tumor vascular damage. Tumor-bearing mice were treated with anti-Ang2 antibodies every 3 or 4 days starting 3 days before 3 × 2 Gy or 4 × 0.5 Gy whole-body or tumor-focused radiation. Combination treatment with anti-Ang2 and radiation improved tumor growth inhibition and extended the survival of mice with melanoma or colorectal tumors. Single-cell RNA-sequencing revealed that Ang2 blocking rescued radiation-induced decreases in T cells and cells of the monocyte/macrophage lineage. In addition, anti-Ang2 enhanced radiation-induced apoptosis in cultured endothelial cells. In vivo, combination treatment decreased tumor vasculature and increased tumor necrosis in comparison with tumors treated with monotherapies. These results suggest that a combination of Ang2-blocking antibodies with radiation increases tumor growth inhibition and extends the survival of tumor-bearing mice. Significance: These findings offer a preclinical rationale for further testing of the use of radiation in combination with Ang2-blocking antibodies to improve the overall outcome of cancer treatment.
Elevation and latitude drives structure and tree species composition in Andean forests: Results from a large-scale plot network

Our knowledge about the structure and function of Andean forests at regional scales remains limited. Current initiatives to study forests over continental or global scales still have important geographical gaps, particularly in regions such as the tropical and subtropical Andes. In this study, we assessed patterns of structure and tree species diversity along ~ 4000 km of latitude and ~ 4000 m of elevation range in Andean forests. We used the Andean Forest Network (Red de Bosques Andinos, https://redbosques.condesan.org/) database which, at present, includes 491 forest plots (totaling 156.3 ha, ranging from 0.01 to 6 ha) representing a total of 86,964 identified tree stems ≥ 10 cm diameter at breast height belonging to 2341 identified species, 584 genera and 133 botanical families. Tree stem density and basal area increases with elevation while species richness decreases. Stem density and species richness both decrease with latitude. Subtropical forests have distinct tree species composition compared to those in the tropical region. In addition, floristic similarity of subtropical plots is between 13 to 16% while similarity between tropical forest plots is between 3% to 9%. Overall, plots ~ 0.5-ha or larger may be preferred for describing patterns at regional scales in order to avoid plot size effects. We highlight the need to promote collaboration and capacity building among researchers in the Andean region (i.e., South-South cooperation) in order to generate and synthesize information at regional scale.
Optimizing the deployment of ultra-low volume and targeted indoor residual spraying for dengue outbreak response

Recent years have seen rising incidence of dengue and large outbreaks of Zika and chikungunya, which are all caused by viruses transmitted by Aedes aegypti mosquitoes. In most settings, the primary intervention against Aedes-transmitted viruses is vector control, such as indoor, ultra-low volume (ULV) spraying. Targeted indoor residual spraying (TIRS) has the potential to more effectively impact Aedes-borne diseases, but its implementation requires careful planning and evaluation. The optimal time to deploy these interventions and their relative epidemiological effects are, however, not well understood. We used an agent-based model of dengue virus transmission calibrated to data from Iquitos, Peru to assess the epidemiological effects of these interventions under differing strategies for deploying them. Specifically, we compared strategies where spray application was initiated when incidence rose above a threshold based on incidence in recent years to strategies where spraying occurred at the same time(s) each year. In the absence of spraying, the model predicted 361,000 infections [inter-quartile range (IQR): 347,000–383,000] in the period 2000–2010. The ULV strategy with the fewest median infections was spraying twice yearly, in March and October, which led to a median of 172,000 infections [IQR: 158,000–183,000], a 52% reduction from baseline. Compared to spraying once yearly in September, the best threshold-based strategy utilizing ULV had fewer median infections (254,000 vs. 261,000), but required more spraying (351 vs. 274 days). For TIRS, the best strategy was threshold-based, which led to the fewest infections of all strategies tested (9,900; [IQR: 8,720–11,400], a 94% reduction), and required fewer days spraying than the equivalent ULV strategy (280). Although spraying twice each year is likely to avert the most infections, our results indicate that a threshold-based strategy can become an alternative to better balance the translation of spraying effort into impact, particularly if used with a residual insecticide.
Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish

Water sampling and filtration of environmental DNA (eDNA) analysis have been performed by several different methods, and each method may yield a different species composition or eDNA concentration. Here, we investigated the eDNA of seawater samples directly collected by SCUBA to compare two widely used filtration methods: open filtration with a glass filter (GF/F) and enclosed filtration (Sterivex). We referred to biomass based on visual observation data collected simultaneously to clarify the difference between organism groups. Water samples were collected at two points in the Sea of Japan in May, September and December 2018. The respective samples were filtered through GF/F and Sterivex for eDNA extraction. We quantified the eDNA concentration of five fish and two cnidarian species by quantitative polymerase chain reaction (qPCR) using species-specific primers/probe sets. A strong correlation of eDNA concentration was obtained between GF/F and Sterivex; the intercepts and slopes of the linear regression lines were slightly different in fish and jellyfish. The amount of eDNA detected using the GF/F filtration method was higher than that detected using Sterivex when the eDNA concentration was high; the opposite trend was observed when the eDNA concentration was relatively low. The concentration of eDNA correlated with visually estimated biomass; eDNA concentration per biomass in jellyfish was approximately 700 times greater than that in fish. We conclude that GF/F provides an advantage in collecting a large amount of eDNA, whereas Sterivex offers superior eDNA sensitivity. Both filtration methods are effective in estimating the spatiotemporal biomass size of target marine species.
Specific IgG and IgA Antibody Reactivities in Sera of Children by Enzyme-Linked Immunoassay and Comparison With Giardia duodenalis Diagnosis in Feces

Background Giardia duodenalis is conventionally diagnosed in fecal samples using parasitological methods. However, sensitivity is poor when only a single sample is analyzed, due to intermittent excretion of cysts in feces. Alternatively, the serum antibodies to G. duodenalis can be used for parasite diagnosis and epidemiological studies to determine previous exposure. We compared the rate of G. duodenalis infection between serum anti-Giardia IgG and IgA antibodies and fecal examination in Brazilian children. Methods Fecal and serum samples were tested from 287 children at a clinical laboratory and from 187 children at daycare centers. Fecal samples were processed using conventional parasitological methods and coproantigen detection for Giardia diagnosis. Serum samples were tested using an in-house ELISA for detection of anti-Giardia IgG and IgA. Results G. duodenalis was found in 8.2% (N=39) of the 474 children analyzed. The sensitivity and specificity of ELISA were 80.0% and 90.0% for IgG and 80.0% and 83.3% for IgA, respectively. The total positivity rate of anti-Giardia IgG and IgA in the sera was 13.9% (N=66) and 23.6% (N=112). The agreement between the positivity of specific antibodies and the detection of G. duodenalis in feces was moderate for ELISA-IgG, kappa index (95% CI)=0.543 (0.422–0.664), and mild for ELISA-IgA, kappa index (95% CI)=0.283 (0.162–0.404). Among the children infected with other enteroparasites, 11.6% (N=10) and 24.4% (N=21) showed reactivity to anti-Giardia IgG and to IgA, respectively. This cross-reactivity was more frequent in samples from children infected with Endolimax nana and Entamoeba coli. Conclusions The higher frequency of specific antibody reactivity compared with G. duodenalis diagnosis in feces could reflect continuous exposure of children to G. duodenalis infection, resulting in long-lasting immunological memory and/or cross-reactivity with other intestinal amoebas.
Twig Growth of Eight Species of Shade Trees Following Transplanting

Deciduous trees of eight species commonly used in the landscape (Norway maple, green ash, red maple, redbud, sugar maple, pin oak, ginkgo, and little leaf linden), 5-10 cm in diameter, were transplanted on four different dates during the 1979 growing season. The survival rate was excellent for each date. Significant variations in twig growth noted prior to transplanting had no relationship to growth rates after transplanting. For all species, twig growth was significantly reduced during the first 3 years after transplanting. Annual twig growth of all species except Norway maple equaled or exceeded pretransplanting rates by the fifth season after transplanting. Transplanting dates had no consistent effect on total twig growth after 5 years. Many species performed better when transplanted in late spring or summer rather than when transplanted in early spring or fall.
Clonal Distribution of Clindamycin-Resistant Erythromycin-Susceptible (CRES) Streptococcus agalactiae in Korea Based on Whole Genome Sequences

Background The clindamycin-resistant erythromycin-susceptible (CRES) phenotype is rare in Streptococcus agalactiae (group B streptococci). We aimed to determine the molecular characteristics of CRES S. agalactiae using whole genome sequencing (WGS). Methods Sixty-six S. agalactiae isolates obtained from blood (N=26), cerebrospinal fluid (N=10), urine (N=17), and vaginal discharge (N=13) between 2010 and 2017 in Korea were subjected to WGS. Based on the WGS data, we analyzed antimicrobial resistance (AMR) determinants, sequence types (STs), capsular polysaccharide (CPS) genotypes, and virulence gene profiles, and constructed a phylogenetic tree. We included the clindamycin-susceptible erythromycin-resistant (CSER) phenotype for comparison. Results We identified seven CRES S. agalactiae isolates from urine (N=5) and vaginal discharge (N=2) collected between 2010 and 2011. All CRES isolates harbored AMR determinants of lnu(B), lsa(E), and aac(6′)-aph(2″), revealed ST19 and CPS genotype III, and had a virulence gene profile of rib-lmb-cylE. Phylogenetic tree analysis revealed that all CRES isolates belonged to the same cluster, suggesting a clonal distribution. In contrast, seven CSER isolates showed a diverse distribution and clustered separately from the CRES isolates. Conclusions CRES isolates collected between 2010 and 2011 showed a unique cluster with ST19 and CPS genotype III in Korea. This is the first report on WGS-based characteristics of S. agalactiae in Korea.
Open abdomen treatment for complicated intra-abdominal infection patients with gastrointestinal fistula can reduce the mortality

Abstract To evaluate the effect of the open abdomen (OA) and closed abdomen (CA) approaches for treating intestinal fistula with complicated intra-abdominal infection (IFWCIAI), and analyze the risk factors in OA treatment. IFWCIAI is associated with high mortality rates and healthcare costs, as well as longer postoperative hospital stay. However, OA treatment has also been linked with increased mortality and development of secondary intestinal fistula. A total of 195 IFWCIAI patients who were operated over a period of 7 years at our hospital were retrospectively analyzed. These patients were divided into the OA group (n = 112) and CA group (n = 83) accordingly, and the mortality rates, hospital costs, and hospital stay duration of both groups were compared. In addition, the risk factors in OA treatment were also analyzed. OA resulted in significantly lower mortality rates (9.8% vs 30.1%, P < .001) and hospital costs ($11721.40 ± $9368.86 vs $20365.36 ± $21789.06, P < .001) compared with the CA group. No incidences of secondary intestinal fistula was recorded and the duration of hospital stay was similar for both groups (P = .151). Delayed OA was an independent risk factor of death following OA treatment (hazard ratio [HR] = 1.316; 95% confidence interval [CI] = 1.068–1.623, P = .010), whereas early enteral nutrition (EN) exceeding 666.67 mL was a protective factor (HR = 0.996; 95% CI = 0.993–0.999, P = .018). In addition, Acinetobacter baumannii, Pseudomonas aeruginosa, and Candida albicans were the main pathogens responsible for the death of patients after OA treatment. OA decreased mortality rates and hospital costs of IFWCIAI patients, and did not lead to any secondary fistulas. Early OA and EN also reduced mortality rates.