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https://www.readbyqxmd.com/read/28087515/h-blast-a-fast-protein-sequence-alignment-toolkit-on-heterogeneous-computers-with-gpus
#1
Weicai Ye, Ying Chen, Yongdong Zhang, Yuesheng Xu
MOTIVATION: The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved. RESULTS: We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST...
January 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28060926/comparison-of-tst-and-igra-in-diagnosis-of-latent-tuberculosis-infection-in-a-high-tb-burden-setting
#2
Surendra K Sharma, Richa Vashishtha, L S Chauhan, V Sreenivas, Divya Seth
BACKGROUND: There are currently two tests for diagnosing latent tuberculosis infection (LTBI); TST and IGRA. However, it is still unclear that which one of these tests performs better in high TB-burden settings. METHODS: 1511 household contacts of pulmonary TB patients were enrolled to compare the performance of TST and IGRA for LTBI. At baseline all participant underwent testing for IGRA [QuantiFERON-TB® Gold In-tube (QFT-GIT) assay] and TST [2 tuberculin unit (TU), purified protein derivative (PPD), RT23, Staten Serum Institute (SSI), Copenhagen, Denmark]...
2017: PloS One
https://www.readbyqxmd.com/read/28043588/characterization-of-the-cd4-and-cd8-t-cell-response-in-the-quantiferon-tb-gold-plus-kit
#3
Elisa Petruccioli, Teresa Chiacchio, Ilaria Pepponi, Valentina Vanini, Rocco Urso, Gilda Cuzzi, Lucia Barcellini, Fabrizio Palmieri, Daniela M Cirillo, Giuseppe Ippolito, Delia Goletti
OBJECTIVE/BACKGROUND: QuantiFERON-TB Gold In-Tube (QFT-GIT, Qiagen, Hilden, Germany) is an interferon-γ (IFN-γ) release assay designed to detect latent tuberculosis infection (LTBI). Although QFT-GIT has several advantages (mainly that it is not affected by the Bacille Calmette-Guérin vaccination), it has a poor sensitivity in immune-compromised individuals as it involves an immune response-based detection. Recently, QuantiFERON-TB Gold Plus (QFT-Plus) assay has been proposed as a new generation of QFT-GIT...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27994031/flexible-model-based-clustering-of-mixed-binary-and-continuous-data-application-to-genetic-regulation-and-cancer
#4
Fatin N Zainul Abidin, David R Westhead
Clustering is used widely in 'omics' studies and is often tackled with standard methods, e.g. hierarchical clustering. However, the increasing need for integration of multiple data sets leads to a requirement for clustering methods applicable to mixed data types, where the straightforward application of standard methods is not necessarily the best approach. A particularly common problem involves clustering entities characterized by a mixture of binary data (e.g. presence/absence of mutations, binding, motifs and epigenetic marks) and continuous data (e...
December 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27979220/controlling-the-potential-gastrointestinal-fate-of-%C3%AE-carotene-emulsions-using-interfacial-engineering-impact-of-coating-lipid-droplets-with-polyphenol-protein-carbohydrate-conjugate
#5
Fuguo Liu, Cuicui Ma, Ruojie Zhang, Yanxiang Gao, David Julian McClements
The impact of interfacial coatings comprised of polyphenol-protein-carbohydrate conjugates on the properties of nutraceutical-fortified lipid droplets during digestion was investigated. Surface-active chlorogenic acid-lactoferrin-polydextrose (CA-LF-PD) conjugate was synthesized as emulsifier to stabilize lipid droplets in β-carotene-enriched oil-in-water emulsions. Changes in droplet size, charge, and microstructure were monitored as β-carotene emulsions were passed through a simulated gastrointestinal tract model (mouth, stomach, small intestine)...
April 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/27976713/genetically-manipulated-phages-with-improved-ph-resistance-for-oral-administration-in-veterinary-medicine
#6
Franklin L Nobrega, Ana Rita Costa, José F Santos, Melvin F Siliakus, Jan W M van Lent, Servé W M Kengen, Joana Azeredo, Leon D Kluskens
Orally administered phages to control zoonotic pathogens face important challenges, mainly related to the hostile conditions found in the gastrointestinal tract (GIT). These include temperature, salinity and primarily pH, which is exceptionally low in certain compartments. Phage survival under these conditions can be jeopardized and undermine treatment. Strategies like encapsulation have been attempted with relative success, but are typically complex and require several optimization steps. Here we report a simple and efficient alternative, consisting in the genetic engineering of phages to display lipids on their surfaces...
December 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852671/highly-multiplexed-proteomic-analysis-of-quantiferon-supernatants-to-identify-biomarkers-of-latent-tuberculosis-infection
#7
Mary Ann De Groote, Michael Higgins, Thomas Hraha, Kirsten Wall, Michael L Wilson, David G Sterling, Nebojsa Janjic, Randall Reves, Urs A Ochsner, Robert Belknap
The tests for diagnosing latent tuberculosis infection (LTBI) are limited by poor predictive value for identifying people at highest risk for progression to active TB, and have varying sensitivity and specificity in different populations. The identification of a more robust signature for LTBI is important for TB prevention and elimination. A pilot study was conducted with samples from immigrants to the U.S. that were screened for LTBI by the three commercially approved tests: Tuberculin Skin Test (TST), QuantiFERON-TB Gold In-Tube (QFT-GIT), and T-SPOT...
November 16, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27847276/polyelectrolyte-complexes-as-prospective-carriers-for-the-oral-delivery-of-protein-therapeutics
#8
REVIEW
Vassilis Bourganis, Theodora Karamanidou, Olga Kammona, Costas Kiparissides
The oral administration of protein therapeutics is hindered by the multitude of barriers confronted by these molecules along the gastrointestinal tract (i.e., acidic environment, proteolytic degradation, mucosal barrier, etc.). Their unique properties (e.g., high molecular weight, hydrophilicity, charge, etc.) and labile structure are mainly responsible for their instability in the harsh conditions along the gastrointestinal tract (GIT) and dictate the employment of alternative routes for their administration (e...
November 12, 2016: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/27829344/identifying-drug-target-interactions-with-decision-template
#9
Xiao-Ying Yan, Shao-Wu Zhang
During the development process of new drugs, identification of the drug-target interactions wins primary concerns. However, the chemical or biological experiments bear the limitation in coverage as well as the huge cost of both time and money. Based on drug similarity and target similarity, chemogenomic methods can be able to predict potential drug-target interactions (DTIs) on a large scale and have no luxurious need about target structures or ligand entries. Nevertheless, existing methods of drug chemical structure-based similarity and target sequence-based similarity may not reflect the cases that the drugs having variant structures interact with common targets and the targets having dissimilar sequences interact with same drugs...
November 7, 2016: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/27816629/hdm-pampa-to-predict-gastrointestinal-absorption-binding-percentage-equilibrium-and-kinetics-constants-with-human-serum-albumin-and-using-2-end-point-measurements
#10
Alban Bujard, Charlotte Petit, Pierre-Alain Carrupt, Serge Rudaz, Julie Schappler
The parallel artificial membrane permeability assay (PAMPA) is a high-throughput screening (HTS) technique developed to predict passive permeability through numerous different biological membranes, such as the gastrointestinal tract (GIT), the blood brain barrier (BBB), and the dermal layer. PAMPA is based on an artificial membrane, such as hexadecane (HDM), which separates two compartments (i.e., a donor and an acceptor compartment). In the present study, an HDM-PAMPA method was developed with human serum albumin (HSA) under iso-pH and gradient-pH conditions to predict the percentage of binding, dissociation/association constants (Kd and Ka, respectively) and dissociation/association kinetic rates (koff and kon, respectively) between a given drug and HSA...
January 15, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27760159/variations-of-phosphorous-accessibility-causing-changes-in-microbiome-functions-in-the-gastrointestinal-tract-of-chickens
#11
Bruno Tilocca, Maren Witzig, Markus Rodehutscord, Jana Seifert
The chicken gastrointestinal tract (GIT) harbours a complex microbial community, involved in several physiological processes such as host immunomodulation and feed digestion. For the first time, the present study analysed dietary effects on the protein inventory of the microbiome in crop and ceca of broilers. We performed quantitative label-free metaproteomics by using 1-D-gel electrophoresis coupled with LC-MS/MS to identify the structural and functional changes triggered by diets supplied with varying amount of mineral phosphorous (P) and microbial phytase (MP)...
2016: PloS One
https://www.readbyqxmd.com/read/27684040/development-of-an-antigen-driven-colitis-model-to-study-presentation-of-antigens-by-antigen-presenting-cells-to-t-cells
#12
Valerio Rossini, Katarina Radulovic, Christian U Riedel, Jan Hendrik Niess
Inflammatory bowel disease (IBD) is a chronic inflammation which affects the gastrointestinal tract (GIT). One of the best ways to study the immunological mechanisms involved during the disease is the T cell transfer model of colitis. In this model, immunodeficient mice (RAG(-/-) recipients) are reconstituted with naive CD4(+) T cells from healthy wild type hosts. This model allows examination of the earliest immunological events leading to disease and chronic inflammation, when the gut inflammation perpetuates but does not depend on a defined antigen...
2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27649239/food-matrix-effects-of-polyphenol-bioaccessibility-from-almond-skin-during-simulated-human-digestion
#13
Giuseppina Mandalari, Maria Vardakou, Richard Faulks, Carlo Bisignano, Maria Martorana, Antonella Smeriglio, Domenico Trombetta
The goal of the present study was to quantify the rate and extent of polyphenols released in the gastrointestinal tract (GIT) from natural (NS) and blanched (BS) almond skins. A dynamic gastric model of digestion which provides a realistic simulation of the human stomach was used. In order to establish the effect of a food matrix on polyphenols bioaccessibility, NS and BS were either digested in water (WT) or incorporated into home-made biscuits (HB), crisp-bread (CB) and full-fat milk (FM). Phenolic acids were the most bioaccessible class (68...
September 15, 2016: Nutrients
https://www.readbyqxmd.com/read/27621205/abundance-of-drug-transporters-in-the-human-kidney-cortex-as-quantified-by-quantitative-targeted-proteomics
#14
Bhagwat Prasad, Katherine Johnson, Sarah Billington, Caroline Lee, Git W Chung, Colin D A Brown, Edward J Kelly, Jonathan Himmelfarb, Jashvant D Unadkat
Protein expression of renal uptake and efflux transporters was quantified by quantitative targeted proteomics using the surrogate peptide approach. Renal uptake transporters assessed in this study included organic anion transporters (OAT1-OAT4), organic cation transporter 2 (OCT2), organic/carnitine cation transporters (OCTN1 and OCTN2), and sodium-glucose transporter 2 (SGLT2); efflux transporters included P-glycoprotein, breast cancer resistance protein, multidrug resistance proteins (MRP2 and MRP4), and multidrug and toxin extrusion proteins (MATE1 and MATE2-K)...
December 2016: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/27587723/temporal-distribution-of-encapsulated-bacteriophages-during-passage-through-the-chick-gastrointestinal-tract
#15
Yin-Hing Ma, Golam S Islam, Ying Wu, Parviz M Sabour, James R Chambers, Qi Wang, Shirley X Y Wu, Mansel W Griffiths
Encapsulation of bacteriophages ("phage") protects phage against environmental deactivation and provides a product that is easy to handle for storage and application with animal feed as an antibiotic alternative. The objective of this study was to evaluate an orally administered, encapsulated phage for efficient phage release in the gastrointestinal tract (GIT) of young chicks receiving feed. An optimized formulation that consisted of 0.8% low molecular weight (MW) alginate, 2% ultra-low molecular weight alginate and 3% whey protein completely released the encapsulated phage within 60 min under simulated intestinal conditions...
December 1, 2016: Poultry Science
https://www.readbyqxmd.com/read/27537186/elongation-factor-tu-and-heat-shock-protein-70-are-membrane-associated-proteins-from-mycoplasma-ovipneumoniae-capable-of-inducing-strong-immune-response-in-mice
#16
Fei Jiang, Jinyan He, Nalu Navarro-Alvarez, Jian Xu, Xia Li, Peng Li, Wenxue Wu
Chronic non-progressive pneumonia, a disease that has become a worldwide epidemic has caused considerable loss to sheep industry. Mycoplasma ovipneumoniae (M. ovipneumoniae) is the causative agent of interstitial pneumonia in sheep, goat and bighorn. We here have identified by immunogold and immunoblotting that elongation factor Tu (EF-Tu) and heat shock protein 70 (HSP 70) are membrane-associated proteins on M. ovipneumonaiea. We have evaluated the humoral and cellular immune responses in vivo by immunizing BALB/c mice with both purified recombinant proteins rEF-Tu and rHSP70...
2016: PloS One
https://www.readbyqxmd.com/read/27503694/diagnosing-infection-in-patients-undergoing-conversion-of-prior-internal-fixation-to-total-hip-arthroplasty
#17
Daniel J Gittings, Paul M Courtney, Blair S Ashley, Patrick J Hesketh, Derek J Donegan, Neil P Sheth
BACKGROUND: Criteria for diagnosis of infected internal fixation implants at the time of conversion to total hip arthroplasty (THA) are not clear. The purpose of this study is to identify risk factors for infection in patients undergoing conversion to THA. METHODS: We retrospectively reviewed patients at a single institution who underwent conversion to THA from 2009 to 2014. Patients were diagnosed with infection preoperatively using Musculoskeletal Infection Society criteria or postoperatively if they were found to have positive cultures intraoperatively at the time of conversion surgery...
January 2017: Journal of Arthroplasty
https://www.readbyqxmd.com/read/27494637/nutritional-value-of-raw-and-micronised-field-beans-vicia-faba-l-var-minor-with-and-without-enzyme-supplementation-containing-tannase-for-growing-chickens
#18
Jalil Mahmwd Abdulla, Stephen Paul Rose, Alexander Mackay Mackenzie, Sonya Georgieva Ivanova, Genoveva Petrova Staykova, Vasil Radoslavov Pirgozliev
An experiment examined the effects of two field bean cultivar samples with different tannin contents, the effect of heat treatment (micronising) and the effect of dietary supplementation of a proprietary enzyme preparation containing tannase, pectinase, and xylanase activities on metabolisable energy (ME), total tract dry matter digestibility (DMD) and ether extract digestibility (EED), nitrogen retention (NR), tannin degradability, gastrointestinal tract (GIT) development, and endogenous mucin losses excretion in broiler chickens...
October 2016: Archives of Animal Nutrition
https://www.readbyqxmd.com/read/27354691/inheritance-modes-specific-pathogenicity-prioritization-ispp-for-human-protein-coding-genes
#19
Jacob Shujui Hsu, Johnny S H Kwan, Zhicheng Pan, Maria-Mercè Garcia-Barcelo, Pak Chung Sham, Miaoxin Li
MOTIVATION: Exome sequencing studies have facilitated the detection of causal genetic variants in yet-unsolved Mendelian diseases. However, the identification of disease causal genes among a list of candidates in an exome sequencing study is still not fully settled, and it is often difficult to prioritize candidate genes for follow-up studies. The inheritance mode provides crucial information for understanding Mendelian diseases, but none of the existing gene prioritization tools fully utilize this information...
June 26, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27273883/gastrointestinal-transport-of-calcium-and-glucose-in-lactating-ewes
#20
Stefanie Klinger, Bernd Schröder, Anja Gemmer, Julia Reimers, Gerhard Breves, Jens Herrmann, Mirja R Wilkens
During lactation, mineral and nutrient requirements increase dramatically, particularly those for Ca and glucose. In contrast to monogastric species, in ruminants, it is rather unclear to which extend this physiological change due to increased demand for milk production is accompanied by functional adaptations of the gastrointestinal tract (GIT). Therefore, we investigated potential modulations of Ca and glucose transport mechanisms in the GIT of lactating and dried-off sheep. Ussing-chamber technique was applied to determine the ruminal and jejunal Ca flux rates...
June 2016: Physiological Reports
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