Miracle-dz/UniFAR-FTUs huggingface dataset:
Helicobacter pylori causes delayed gastric emptying by decreasing interstitial cells of Cajal

Helicobacter pylori (HP) infection is one of the most frequent bacterial infections in humans and is associated with the pathogenesis of gastric motility disorders such as delayed gastric emptying (DGE). Although HP infection is considered to delay gastric emptying, there has been little research on the underlying mechanism. Gastric motility involves interactions among gastrointestinal hormones, smooth muscle, enteric and extrinsic autonomic nerves and interstitial cells of Cajal (ICCs), and ICCs play an important role in gastrointestinal motility. Mutation or loss of stem cell factor (SCF) expression is known to reduce the number of ICCs or alter the integrity of the ICC network, contributing to gastrointestinal dysmotility. The aim of the present study was to investigate whether a reduction in ICCs contributes to the DGE caused by HP. A mouse model of HP infection was established and gastric emptying was compared between HP-infected and uninfected mice using the bead method. In addition, ICC counts and SCF expression levels in gastric tissue were evaluated using immunohistochemistry and western blotting, respectively. The results revealed that gastric emptying was significantly slower, the number of ICCs in gastric tissue was significantly reduced and the protein level of SCF in gastric tissue was significantly decreased in HP-infected mice compared with uninfected mice. Therefore, it may be concluded that HP reduced the number of ICCs by decreasing the expression of SCF protein in gastric tissue, thereby causing DGE.
The impact of iodine on biochemical blood parameters in laying hens.

In the areas, where the biosphere is deficient in iodine, the feed for domestic animals and laying hens should be supplemented with larger than the recommended doses of the trace element iodine. That would enable to concentrate the reserves of this element in the production, thus enriching human nutrition with iodine. The goal of the trial was to investigate the changes in the amount of the thyroid hormones, proteins and fats in the blood and blood serum of laying hens by using a stable concentrated preparation “Jodis” instead of the usual potassium iodide in the feed. For the trial, three equal groups of laying hens were randomly formed, each containing 40 hens from 30 to 47 weeks of age. The laying hens of Group 1 (control group) were fed with the standard diet supplemented with a recommended daily dose iodine i. e. 1 mg I/kg feed in the form of potassium iodide. The laying hens of Groups 2 and 3 (experimental groups) were fed with the standard diet where potassium iodide was replaced by a dry stable iodine supplement "Jodis". The amount of iodine in the diet given to laying hens in Group 2 was 1 mg I/ 1 kg feed, and in Group 3 − 4 mg I/ 1 kg feed, respectively. There were significantly increased levels of thyroglobulin and free thyroxine, and decreased levels of free triiodothyronine in blood, and triglicerides in blood serum of experimental laying hens (Groups 2 and 3) compared to controls (Group 1). The HDL and LDL cholesterol level in blood serum of experimental hens was lower than in controls, but the difference was not statistically significant.
BEZ235 Increases the Sensitivity of Hepatocellular Carcinoma to Sorafenib by Inhibiting PI3K/AKT/mTOR and Inducing Autophagy

Acquired resistance of hepatocellular carcinoma (HCC) to sorafenib (SFB) is the main reason for the failure of SFB treatment of the cancer. Abnormal activation of the PI3K/AKT/mTOR pathway is important in the acquired resistance of SFB. Therefore, we investigated whether BEZ235 (BEZ) could reverse acquired sorafenib resistance by targeting the PI3K/mTOR pathway. A sorafenib-resistant HCC cell line Huh7R was established. MTT assay, clone formation assay, flow cytometry, and immunofluorescence were used to analyze the effects of BEZ235 alone or combined with sorafenib on cell proliferation, cell cycle, apoptosis, and autophagy of Huh7 and Huh7R cells. The antitumor effect was evaluated in animal models of Huh7R xenografts in vivo. Western blot was used to detect protein levels of the PI3K/AKT/mTOR pathway and related effector molecules. In vitro results showed that the Huh7R had a stronger proliferation ability and antiapoptosis effect than did Huh7, and sorafenib had no inhibitory effect on Huh7R. SFB + BEZ inhibited the activation of the PI3K/AKT/mTOR pathway caused by sorafenib. Moreover, SFB + BEZ inhibited the proliferation and cloning ability, blocked the cell cycle in the G0/G1 phase, and promoted apoptosis in the two cell lines. The autophagy level in Huh7R cells was higher than in Huh7 cells, and BEZ or SFB + BEZ further promoted autophagy in the two cell lines. In vivo, SFB + BEZ inhibited tumor growth by inducing apoptosis and autophagy. We concluded that BEZ235 enhanced the sensitivity of sorafenib through suppressing the PI3K/AKT/mTOR pathway and inducing autophagy. These observations may provide the experimental basis for sorafenib combined with BEZ235 in trial treatment of HCC.
Association between gonadal hormones and osteoporosis in schizophrenia patients undergoing risperidone monotherapy: a cross-sectional study

Objective Patients with schizophrenia are at increased risk of osteoporosis. This study first determined the osteoporosis rate in patients with schizophrenia and then then explored the association between serum gonadal hormone levels and osteoporosis among these patients. Methods A total of 250 patients with schizophrenia and 288 healthy controls were recruited. Osteoporosis was defined by decreased bone mineral density (BMD) of the calcaneus. Serum fasting levels of gonadal hormones (prolactin, estradiol, testosterone, progesterone, follicle-stimulating hormone, luteinizing hormone) were determined. The relationship between osteoporosis and hormone levels was statistically analyzed by binary logistic regression analysis. Results Our results showed that patients with schizophrenia had a markedly higher rate of osteoporosis (24.4% vs. 10.1%) than healthy controls (P < 0.001). Patients with osteoporosis were older, had a longer disease course, and had a lower body mass index (BMI) than patients without osteoporosis (all P < 0.05). Regarding gonadal hormones, we found significantly higher prolactin, but lower estradiol, levels in patients with osteoporosis than in those without osteoporosis (both P < 0.05). The regression analysis revealed that PRL (OR = 1.1, 95% CI [1.08–1.15], P < 0.001) and E2 level (OR = 0.9, 95%CI [0.96–0.99], P = 0.011) were significantly associated with osteoporosis in patients with schizophrenia. Conclusion Our results indicate that patients with schizophrenia who are being treated with risperidone have a high rate of osteoporosis. Increased prolactin and reduced estradiol levels are significantly associated with osteoporosis.
Nutrient solution and substrates for ‘cedro doce’ (Pochota fendleri) seedling production

Solução nutritiva e substratos para produção de mudas de cedro doce (Pochota fendleri) R E S U M O Objetivou-se, neste trabalho, verificar o efeito da adição de solução nutritiva em diferentes substratos na produção de mudas de Pochota fendleri, e seu efeito nos teores de macro e micronutrientes e de clorofilas a e b nas folhas. O delineamento experimental utilizado foi inteiramente casualizado em esquema fatorial 3 x 2, com quatro repetições. Os fatores foram três substratos e adição ou não de solução nutritiva, compondo seis tratamentos: (T1) = areia; (T2) = solo; (T3) = solo + areia (1:1); (T4) = areia + solução nutritiva; (T5) = solo + solução nutritiva; (T6) = solo + areia + solução nutritiva. Foram avaliadas características de crescimento (altura, diâmetro do colo e massa seca da parte aérea e radicular, relação raiz/ parte aérea e massa seca total), além dos teores de macro e micronutrientes e de clorofilas a e b. A utilização de solução nutritiva reduz o tempo para obtenção de mudas de Pochota fendleri e é importante para o crescimento e qualidade das mudas. A sequência de exigência nutricional das mudas nos três substratos com adição de solução nutritiva segue em ordem decrescente: macronutrientes (N > Ca > K > Mg > P > S ) e micronutrientes (Fe > Mn > B > Zn > Cu).
Development of a Gas Chromatography - Tandem Mass Spectrometry Procedure for Determination of Pesticide Residues in Honey and Honeybee Samples

A new analytical procedure of determination of multiresidue of pesticides based on application of the modified QuEChERS approach at the step of sample preparation and technique GC-MS/MS has been developed and applied for studies the real honey and honeybee samples. Samples were collected from northern Poland (Pomerania). The proposed procedure enables for the determination of 34 and 30 pesticide residues respectively in honey and honeybee samples. The recovery of analytes was between 70 and 120% with relative standard deviation ≤ 20%. The limits of quantification were in the range of 2.3-27 ng/g and 2.2-29 ng/g respectively for honey and honeybee samples. The proposed procedure was proven to be a powerful, highly sensitive, and environmentally friendly analytical tool that requires minimal sample preparation.
Endogenous level of abscisic acid down-regulated by brassinosteroids signaling via BZR1 to control the growth of Arabidopsis thaliana

ABSTRACT The increased level of endogenous abscisic acid (ABA) in brassinosteroid (BR)-deficient mutants, such as det2 and cyp85a1 × cyp85a2, suggests that ABA synthesis is inhibited by endogenous BRs in Arabidopsis thaliana. Expression of the ABA biosynthesis gene ABA-deficient 2 (ABA2) was negatively regulated by exogenously applied BR but up-regulated by the application of brassinazole and in det2 and cyp85a1 × cyp85a2. In addition, ABA2 expression decreased in bzr1-1D, showing that ABA biosynthesis is inhibited by BR signaling via BZR1, intermediated by ABA2, in Arabidopsis. Four cis-element sequences (E-boxes 1–4) in the putative promoter region of ABA2 were identified as BZR1 binding sites. The electrophoretic mobility shift assay and chromatin immune precipitation analysis demonstrated that BZR1 directly binds to overlapped E-boxes (E-box 3/4) in the promoter region of ABA2. The level of endogenous ABA was decreased in bzr1-1D compared to wild-type, indicating that binding of BZR1 to the ABA2 promoter inhibits ABA synthesis in Arabidopsis. Compared to wild-type, aba2-1 exhibited severely reduced growth and development. The abnormalities in aba2-1 were rescued by the application of ABA, suggesting that ABA2 expression and ABA synthesis are necessary for the normal growth and development of A. thaliana. Finally, bzr1-KO × aba2-1 exhibited inhibitory growth of primary roots compared to bzr1-KO, verifying that ABA2 is a downstream target of BZR1 in the plant. Taken together, the level of endogenous ABA is down-regulated by BR signaling via BZR1, controlling the growth of A. thaliana.
DeepBSP - a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures

In recent years, machine-learning-based scoring functions have significantly improved the scoring power. However, many of these methods do not perform well in distinguishing the native structure from docked decoy poses due to the lack of decoy structural information in their training data. Here, we developed a machine-learning model, named DeepBSP, that can directly predict the root mean square deviation (rmsd) of a ligand docking pose with reference to its native binding pose. Unlike the binding affinity, the rmsd between the docking poses with reference to their native structures can be straightforwardly determined. By training on a generated data set with 11,925 native complexes and more than 165,000 docked poses, our model shows excellent docking power on our test set and also on the CASF-2016 docking decoy set compared to other major scoring functions. Thus, by combining molecular dockings that generate many poses with the application of DeepBSP, one can more accurately predict the best binding pose that is closest to the native complex structure. This DeepBSP model shall be very useful in picking out poses close to their natives from many poses generated from a dock application.
Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery

Abstract Motivation High throughput and high content screening are extensively used to determine the effect of small molecule compounds and other potential therapeutics upon particular targets as part of the early drug development process. However, screening is typically used to find compounds that have a desired effect but not to identify potential undesirable side effects. This is because the size of the search space precludes measuring the potential effect of all compounds on all targets. Active machine learning has been proposed as a solution to this problem. Results In this article, we describe an improved imputation method, Impute by Committee, for completion of matrices containing categorical values. We compare this method to existing approaches in the context of modeling the effects of many compounds on many targets using latent similarities between compounds and conditions. We also compare these methods for the task of driving active learning in well-characterized settings for synthetic and real datasets. Our new approach performed the best overall both in the accuracy of matrix completion itself and in the number of experiments needed to train an accurate predictive model compared to random selection of experiments. We further improved upon the performance of our new method by developing an adaptive switching strategy for active learning that iteratively chooses between different matrix completion methods. Availability and implementation A Reproducible Research Archive containing all data and code is available at http://murphylab.cbd. cmu.edu/software. Supplementary information Supplementary data are available at Bioinformatics online.
Quantitative and qualitative lipid improvement with chronic hepatitis C virus eradication using direct‐acting antivirals

Direct‐acting antivirals have revolutionized hepatitis C virus (HCV) therapy by providing a high sustained virological response (SVR) rate and subsequent favorable lipid increases. Proprotein convertase subtilisin‐kexin like‐9 (PCSK9) plays an important role in regulating quantitative lipid levels. This study examined the interactions between quantitative PCSK9 and lipid changes, as well as qualitative lipid changes in terms of lectin‐like oxidized low‐density lipoprotein (LDL) receptor‐1 ligand containing apolipoprotein B (LAB) and high‐density lipoprotein (HDL) cholesterol uptake capacity (HDL‐CUC).
Social Support and Functional Decline in the Oldest Old

Objective: Longitudinal studies investigating the link between social support and functional decline are limited among the oldest old. Thus, the aim of this study was to examine whether changes in social support are associated with functional decline among the oldest old longitudinally using panel regression models. Methods: Longitudinal data from 3 waves (waves 7, 8, and 9) of a multicenter prospective cohort study covering primary care patients aged ≥85 years were used. In the analytical sample, n equaled 624 individuals. The validated Lawton and Brody Instrumental Activities of Daily Living (IADL) scale and the well-established Barthel Index (ADL) were used to quantify functional status. The psychometrically sound Lubben Social Network Scale was used to measure social support. Several potential confounders such as age, marital status, cognitive decline, or depressive symptoms were included in the fixed effects (FE) regression models. Results: Linear FE regressions showed that a decrease in social support is associated with functional decline (IADL: β = 0.03, p < 0.05; ADL: β = 0.27, p < 0.05) in men but not in women. With IADL as outcome measure, the interaction term (sex × social support) achieved statistical significance (p < 0.01). With regard to covariates, functional decline (IADL and ADL) was consistently associated with increasing age, an increase in the number of chronic conditions (except for women [ADL]), and cognitive decline (except for men [ADL]). Furthermore, functional decline (ADL) was associated with an increase in depressive symptoms. Discussion: Our findings highlight the meaning of social support for functional status among the oldest old. Finding ways to sustain social support in highest age may be a promising approach in order to postpone functional decline.
GC/MS analysis of volatile constituents and antibacterial activity of the essential oil of the leaves of Eucalyptus globulus in atlas median from Morocco

The chemical compounds of the essential oil obtained from the leaves of Eucalyptus globulus in the Atlas median, mountain region of Morocco was determined by hydro-distillation method, analysed by gas chromatography equipped with flame ionisation detector (GC-FID) and gas chromatography coupled with mass spectrometry (GC-MS). The antimicrobial activities were tested in vitro by in a bioassay on three bacterial against gram-negative: Escherichia coli and gram-positive: Staphylococcus aureus, Staphylococcus intermedius and were evaluated using two different methods; agar disc diffusion and minimum inhibitory concentration (MIC). The results of the study revealed that essential oil yield and the total oil of Eucalyptus globulus were 1.21% and 63.96% respectively. 54 compounds were identified in the essential oil and the main constituents of the essential oil were: 1.8-Cineole (22.35%), Limonene, (7.01%), Solanol (6.05%), β-pinene (5.20%), Transverbenol (4.02%), Terpinen-4-ol (3.10%), Aristolene (2.35%), terpinyl acetate (2.10%), Isosativene (1.85%), sabinene (1.49%), α-myrcene (1.15%) and α-terpineol (1.10%). Essential oil extracted from Eucalyptus globulus showed an excellent activity against Escherichia coil, than that of Staphylococcus aureus and Staphylococcus intermedius, with the strongest inhibition zone 48.15, 13.50 and 10.26mm respectively.
Demographic characteristics, medical needs and utilisation of antenatal care among pregnant undocumented migrants living in Denmark between 2011 and 2017

Introduction: An estimated 22,900–28,900 individuals live undocumented in Denmark, of whom many are women of reproductive age. Undocumented migrants in Denmark who are pregnant only have legal rights to health care in emergencies, which may lead to under-utilisation of antenatal care, despite the possibility of these women seeking antenatal care through informal networks. This study aimed to describe the demographics, general medical needs and prevalence of induced abortions among pregnant undocumented migrant women. Further, we aimed to investigate if the women received antenatal services as recommended, focusing on the timing of their first entry to antenatal care and the number of antenatal visits. Methods: This was a retrospective cross-sectional study. We used data from medical records at a health clinic managed by non-governmental organisations (NGOs) in Denmark from 1 January 2011 to 31 December 2017. Data regarding 679 pregnant women were included in descriptive and regression analyses. Results: The women had a mean age of 28.7 years, originated from 78 different countries and had diverse migration backgrounds. Among the 679 included women, there were 119 pregnancy-related complications. Regarding the utilisation of antenatal services, 52.6% had a late first attendance to antenatal care, and the likelihood of a late first attendance was highest among 35- to 44-year-olds. The majority (92.6%) of the women did not have the recommended number of antenatal care visits, and this was evident across all regions of origin. Logistic regression showed variation in utilisation of antenatal services according to age and region of origin. Conclusions: A quarter of the study population attended the health clinic requesting pregnancy termination. The pregnant undocumented migrants had few medical complications and predominantly attended the health clinic for antenatal care. However, some did attend the clinic with general or pregnancy-related medical conditions. Almost half of the study population had a late first attendance to antenatal care, and the vast majority did not have the recommended number of antenatal care visits. These results call for consideration as to whether health care for pregnant undocumented migrants should be formally available and free of charge.
Technological advances in elite marathon performance

There is scientific and legal controversy about recent technological advances in performance running shoes that reduce the energetic cost of running and may provide a distinct competitive advantage. To better understand the potential performance-enhancing effects of Nikes pioneering marathon racing shoes, we examined the finishing times and racing shoes of the top 50 male and 50 female runners from the World Marathon Major series in the 2010s - before and after the introduction of new Nike shoe models (4%, NEXT%, Alphafly, and other prototypes; herein referred to as neoteric Nikes). Data for racing shoes were available for 3,886 of the 3,900 performances recorded at the four annual marathons in Boston, London, Chicago, and New York. In full cohort analyses, marathon finishing times were 2.0% or 2.8 min (138.5 +/- 8.1 min vs. 141.3 +/- 7.4 min, P<0.001) faster for male runners wearing neoteric Nikes compared to other shoes. For females, marathon finishing times were 2.6% or 4.3 min (159.1 +/- 10.0 min vs. 163.4 +/- 10.7 min, P<0.001) faster for runners wearing neoteric Nikes. In a subset of within-runner changes in marathon performances (males, n = 138; females, n = 101), marathon finishing times improved by 0.8% or 1.2 min for males wearing neoteric Nikes relative to the most recent marathon in which other shoes were worn, and this performance-enhancing effect was greater among females who demonstrated 1.6% or 3.7 min improvement (P=0.002). Our results demonstrate that marathon performances for world-class athletes are substantially faster wearing neoteric Nikes than other market-leading shoes, particularly among females.
Understanding the Effects of Individual and State-Level Factors on American Public Response to COVID-19

Purpose: To examine multilevel predictors on American public response to COVID-19. Design: Multilevel study. Setting: A national survey was conducted by Qualtrics from August 24 to September 11, 2020. The state-level variables were constructed on data from multiple sources. Subjects: 2,440 respondents 18 years and older from all 50 states and D.C. Measures: The outcome variable is the public response to COVID-19 measured by threat perception, behavioral adjustment, and policy support. The predictors include individual-level sociodemographic factors and state-level indicators about public health conditions, political context, and economic recovery. Analysis: Multilevel structural equation modeling is used for statistical estimation. Results: People from states with more COVID-19 cases (β = 0.020, p < 0.1), mandatory face mask policies (β = 0.069, p < 0.05), and liberal governments (β = 0.002, p < 0.05) are more likely to respond while people from states whose economies have recovered closer to the pre-pandemic level are less likely to do so (β = −0.005, p < 0.05). Regarding individual-level predictors, older people (β = 0.005, p < 0.001) and people with better education (β = 0.029, p < 0.01), leaning toward the Democrat Party (β = 0.066, p < 0.001) and liberal political ideology (β = 0.094, p < 0.001), and have stronger generalized trust (β = 0.033, p < 0.001) are more likely to respond than their counterparts. Conclusion: Differences in the public response to the pandemic stem from variations in individual characteristics and contextual factors of states where people live. These findings contribute to the rapidly growing literature and have implications for public health policies.