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https://www.readbyqxmd.com/read/29791068/cdpbc-a-software-application-for-estimation-of-concentration-dependent-plasma-binding-capacity-of-small-molecule
#1
Om Prakash, Upendra Nath Dwivedi
Drug-plasma binding (DPB) is an important aspect during pharmacokinetics (PK) studies. DPB of small molecule cannot be evaluated through computational means. Here we present CDPBC; a standalone application for evaluation of small molecule for its capacity (concentration dependent) of binding with plasma proteins. This application is freely available at URL (https://github.com/undwive di/CDPBC.git). The application is enriched with evaluation of five major proteins of plasma. Input for application is a docked complex against the suggested PDBs of plasma proteins...
May 23, 2018: Molecular Informatics
https://www.readbyqxmd.com/read/29790921/mascot-parameter-and-state-inference-under-the-marginal-structured-coalescent-approximation
#2
Nicola F Müller, David Rasmussen, Tanja Stadler
Motivation: The structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many sub-populations, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790546/dietary-fibers-prebiotics-and-exopolysaccharides-produced-by-lactic-acid-bacteria-potential-health-benefits-with-special-regard-to-cholesterol-lowering-effects
#3
REVIEW
E Korcz, Z Kerényi, L Varga
The gastrointestinal (GIT) microbiota, which plays a crucial role in human health, is influenced by a number of factors including diet. Consumption of specific dietary ingredients, such as dietary fibers and prebiotics, is an avenue by which the microbiota can be positively modulated. These substances may also reduce serum cholesterol levels through various mechanisms. Interest has increased in methods of reducing blood cholesterol level, because dyslipidemia is recognized as a contributory risk factor for the development of cardiovascular diseases...
May 23, 2018: Food & Function
https://www.readbyqxmd.com/read/29789721/is-leptin-resistance-the-cause-or-the-consequence-of-diet-induced-obesity
#4
Kathy C G de Git, Céline Peterse, Sanne Beerens, Mieneke C M Luijendijk, Geoffrey van der Plasse, Susanne E la Fleur, Roger A H Adan
BACKGROUND/OBJECTIVES: Obesity is strongly associated with leptin resistance. It is unclear whether leptin resistance results from the (over)consumption of energy-dense diets or if reduced leptin sensitivity is also a pre-existing factor in rodent models of diet-induced obesity (DIO). We here tested whether leptin sensitivity on a chow diet predicts subsequent weight gain and leptin sensitivity on a free choice high-fat high-sucrose (fcHFHS) diet. METHODS: Based upon individual leptin sensitivity on chow diet, rats were grouped in leptin sensitive (LS, n = 22) and leptin resistant (LR, n = 19) rats (P = 0...
May 22, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29779769/seasonal-variation-in-the-performance-of-quantiferon-tb-gold-in-tube-assays-used-for-the-diagnosis-of-tuberculosis-infection
#5
Marc Tebruegge, Nigel Curtis, Vanessa Clifford, Cristina Fernandez-Turienzo, Nigel Klein, Katy Fidler, Salah Mansour, Paul Elkington, Stephen Morris-Jones
This study aimed to determine whether there are seasonal changes in the performance of QuantiFERON-TB Gold In-Tube (QFT-GIT) assays, an interferon-gamma release assay widely used for the diagnosis of tuberculosis infection. Results of 31,932 QFT-GIT assays performed at a large independent, accredited diagnostic service provider in London, UK over a 4.5-year-period were analysed. The proportion of positive results was significantly lower in autumn (14.8%) than in spring (16.0%; p = 0.0366) and summer (17...
May 2018: Tuberculosis
https://www.readbyqxmd.com/read/29777169/difructose-dianhydride-improves-intestinal-calcium-absorption-wound-healing-and-barrier-function
#6
Sang In Lee, In Ho Kim
The gastrointestinal tract (GIT) is critical for nutrient absorption and is an important barrier against harmful pathogens and antigens. Difructose anhydrides (DFA)-IVs are nondigestible disaccharides that enhance calcium and iron absorption by affecting the intestinal epithelial tissue. However, their effects on intestinal functions are not fully understood. In this study, we performed a feeding trial and found that dietary DFA-IVs improved growth performance, relative breast muscle and liver weight, and digestibility and blood calcium and iron concentrations in broilers...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29763614/association-of-oral-helicobacter-pylori-with-gastric-complications
#7
Shazia A Ansar, Mehir Un Nisa Iqbal, Taseer A Khan, Shahana U Kazmi
AIM: This study was aimed to identify the presence of Helicobacter pylori (H. pylori) genes in oral mucosa and find out their relationship between oral H. pylori infection and gastric complications. METHODS: This study is a case control study consists of 567 subjects with periodontal infection (278 gastric complication cases and 289 controls normal gastric intestinal mucosa) with age range of 20-80 years. Oral health status was recorded by calculating oral hygiene index (OHI), probing depths (PD) and clinical attachment loss (CAL)...
May 12, 2018: Life Sciences
https://www.readbyqxmd.com/read/29758278/prevalence-of-and-risk-factors-associated-with-latent-tuberculosis-in-singapore-a-cross-sectional-survey
#8
Peiling Yap, Kristin Hui Xian Tan, Wei Yen Lim, Timothy Barkham, Linda Wei Lin Tan, Mark Chen I-Cheng, Yee Tang Wang, Cynthia Bin Eng Chee
OBJECTIVES: We performed the first LTBI cross-sectional survey in Singapore, utilizing the QuantiFERON Gold In-tube (QFT-GIT) assay to collect data on the prevalence of LTBI and identify potential risk factors associated with it. METHODS: Nation-wide household addresses were randomly selected for enumeration, where Singaporeans or Permanent Residents (PRs), aged 18-79 years, were identified. One eligible member per household was selected using the Kish grid. Each participant answered a questionnaire, assessing medical history (including TB), socio-economic factors and lifestyle and provided a blood specimen for the QFT-GIT assay...
May 11, 2018: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/29757353/development-and-evaluation-of-a-deep-learning-model-for-protein-ligand-binding-affinity-prediction
#9
Marta M Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki
Motivation: Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has recently gained considerable attention as it allows the model to "learn" to extract features that are relevant for the task at hand. Results: We have developed a novel deep neural network estimating the binding affinity of ligand-receptor complexes...
May 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29755779/immune-checkpoint-inhibitors-in-gastrointestinal-malignancies
#10
REVIEW
Vishal Jindal
Gastrointestinal (GIT) tumors are extremely fatal and lethal tumors with limited therapeutic options. Antitumor immunity is new line of research in management of solid tumors. Immune check points are negative regulators of immune system and control the immune response. These checkpoints are exploited by cancer cells. Cancer cells causes early activation of checkpoints and suppress the immune response, and therefore have unchecked growth and metastasis of malignant cells. Immune checkpoint inhibitors (ICIs), downregulates these checkpoints and activate the proliferation of cytotoxic T cells which helps in lysis of tumor cells...
April 2018: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/29752607/farseer-nmr-automatic-treatment-analysis-and-plotting-of-large-multi-variable-nmr-data
#11
João M C Teixeira, Simon P Skinner, Miguel Arbesú, Alexander L Breeze, Miquel Pons
We present Farseer-NMR ( https://git.io/vAueU ), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution...
May 11, 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29743310/comparison-of-the-quantiferon-tb-gold-plus-and-quantiferon-tb-gold-in-tube-interferon-%C3%AE-release-assays-in-patients-at-risk-for-tuberculosis-and-in-healthcare-workers
#12
Elitza S Theel, Heather Hilgart, Margaret Breen-Lyles, Kevin McCoy, Rhiannon Flury, Laura E Breeher, John Wilson, Irene G Sia, Jennifer A Whitaker, Jeremy Clain, Timothy R Aksamit, Patricio Escalante
The QuantiFERON-TB Gold Plus (QFT-Plus; Qiagen, Germantown, MD) interferon-gamma release assay (IGRA) received FDA-clearance in 2017 and will replace the prior version of the assay, the QFT-Gold In Tube (QFT-GIT). Here, we compared performance of the QFT-Plus assay to the QFT-GIT version in a diverse patient population, including patients undergoing evaluation for or follow-up of latent tuberculosis infection (LTBI; n=39) or active TB (n=3), and in healthcare workers (HCWs; n=119) at Mayo Clinic (Rochester, MN)...
May 9, 2018: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29741131/on-the-distribution-and-metabolism-of-fusarium-toxins-along-the-gastrointestinal-tract-of-endotoxaemic-pigs
#13
Erik Bannert, Tanja Tesch, Jeannette Kluess, Janine Winkler, Jana Frahm, Susanne Kersten, Stefan Kahlert, Lydia Renner, Hermann-Josef Rothkötter, Sven Dänicke
The aim of this study was to investigate the potential modulatory effect of E. coli lipopolysaccharides (LPS) on residues of deoxynivalenol (DON), de-epoxy-deoxynivalenol (DOM-1), zearalenone (ZEN) and its metabolites α-zearalenol (α-ZEL), β-zearalenol (β-ZEL), zearalanone (ZAN), α-zearalanol (α-ZAL) and β-zearalanol (β-ZAL) after pre- or post-hepatic administration along the gastrointestinal axis. Fifteen barrows were exposed to a naturally mycotoxin contaminated diet (4.59 mg DON/kg feed and 0.22 mg ZEN/kg feed) and equipped with jugular (ju) and portal (po) catheters...
June 2018: Archives of Animal Nutrition
https://www.readbyqxmd.com/read/29738475/identifying-cancer-specific-driver-modules-using-a-network-based-method
#14
Feng Li, Lin Gao, Peizhuo Wang, Yuxuan Hu
Detecting driver modules is a key challenge for understanding the mechanisms of carcinogenesis at the pathway level. Identifying cancer specific driver modules is helpful for interpreting the different principles of different cancer types. However, most methods are proposed to identify driver modules in one cancer, but few methods are introduced to detect cancer specific driver modules. We propose a network-based method to detect cancer specific driver modules (CSDM) in a certain cancer type to other cancer types...
May 8, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29726908/varexp-estimating-variance-explained-by-genome-wide-gxe-summary-statistics
#15
Vincent Laville, Amy R Bentley, Florian Privé, Xiaofeng Zhu, Jim Gauderman, Thomas W Winkler, Mike Province, D C Rao, Hugues Aschard
Summary: Many genome-wide association studies (GWAS) and genome-wide screening for gene-environment interactions have been performed to elucidate the underlying mechanisms of human traits and diseases. When the analyzed outcome is quantitative, the overall contribution of identified genetic variants to the outcome is often expressed as the percentage of phenotypic variance explained. This is commonly done using individual-level genotype data but it is challenging when results are derived through meta-analyses...
May 3, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29722882/modeling-one-thousand-intron-length-distributions-with-fitild
#16
Osamu Gotoh
Motivation: Intron length distribution (ILD) is a specific feature of a genome that exhibits extensive species-specific variation. Whereas ILD contributes to up to 30% of the total information content for intron recognition in some species, rendering it an important component of computational gene prediction, very few studies have been conducted to quantitatively characterize ILDs of various species. Results: We developed a set of computer programs (fitild, compild, etc) to build statistical models of ILDs and compare them with one another...
May 2, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29718592/epinephrine-augments-posttetanic-potentiation-in-mouse-skeletal-muscle-with-and-without-myosin-phosphorylation
#17
Stephen Roy Morris, William Gittings, Rene Vandenboom
Sympathetic tone may influence force potentiation, that is, the stimulation-induced increase in skeletal muscle mechanical function associated with myosin phosphorylation, although the mechanism for this effect remains unknown. The purpose of this study was to examine the influence of epinephrine on concentric twitch force potentiation of wild-type and skeletal myosin light-chain kinase devoid mouse muscle (skMLCK-/- ). To this end, concentric twitch force was assessed before and after a potentiating stimulus (PS) to determine the peak and the duration of potentiation in the absence (-EPI) and presence (+EPI) of 1 μmol/L epinephrine in both genotypes...
May 2018: Physiological Reports
https://www.readbyqxmd.com/read/29706851/a-python-library-for-fairer-access-and-deposition-to-the-metabolomics-workbench-data-repository
#18
Andrey Smelter, Hunter N B Moseley
Introduction: The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific 'mwTab' flat file format. Objectives: In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in 'mwTab' formatted files, we implemented a Python library and package...
2018: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/29702236/probiotic-potential-of-bacillus-velezensis-jw-antimicrobial-activity-against-fish-pathogenic-bacteria-and-immune-enhancement-effects-on-carassius-auratus
#19
Yanglei Yi, Zhenhua Zhang, Fan Zhao, Huan Liu, Lijun Yu, Jiwei Zha, Gaoxue Wang
This study evaluated the probiotic potential of B. velezensis JW through experimental and genomic analysis approaches. Strain JW showed antimicrobial activity against a broad range of fish pathogenic bacteria including Aeromonas hydrophila, Aeromonas salmonicida, Lactococcus garvieae, Streptococcus agalactiae, and Vibrio Parahemolyticus. Fish (Carassius auratus) were fed with the diets containing 0 (control), 107 , and 109  cfu/g of B. velezensis JW for 4 weeks. Various immune parameters were examined at 1, 2, 3, and 4 weeks of post-feeding...
April 24, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29700911/alarmins-as-biomarkers-of-gastrointestinal-surgical-injury-a-pilot-study
#20
Jan Maca, Michal Holub, Filip Bursa, Peter Ihnat, Petr Reimer, Zdenek Svagera, Michal Burda, Pavel Sevcik
The dysregulation of inflammatory response to surgical injury affects outcomes. Alarmins, the earliest bioactive substances from damaged cells, play a crucial role in initiating the inflammation. We analyzed serum levels of alarmins (S100A8, S100A12, high mobility group box, and heat shock protein 70) after major abdominal surgery (MAS) in surgical (S) (n = 82) and nonsurgical (NS) groups (n = 35). The main objective was determining a role of selected alarmins in host response to MAS. The secondary objectives were (i) evaluation of the relationship among alarmins and selected biomarkers (C-reactive protein, interleukin-6), (ii) influence of the place of gastrointestinal resection, and (iii) role of alarmins in MAS for cancer...
February 2018: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
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