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https://www.readbyqxmd.com/read/28339747/deep-learning-for-pharmacovigilance-recurrent-neural-network-architectures-for-labeling-adverse-drug-reactions-in-twitter-posts
#1
Anne Cocos, Alexander G Fiks, Aaron J Masino
Objective: Social media is an important pharmacovigilance data source for adverse drug reaction (ADR) identification. Human review of social media data is infeasible due to data quantity, thus natural language processing techniques are necessary. Social media includes informal vocabulary and irregular grammar, which challenge natural language processing methods. Our objective is to develop a scalable, deep-learning approach that exceeds state-of-the-art ADR detection performance in social media...
February 22, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28335964/highly-sensitive-colorimetric-immunosensor-for-influenza-virus-h5n1-based-on-enzyme-encapsulated-liposome
#2
Cuiying Lin, Yajuan Guo, Mengmeng Zhao, Mi Sun, Fang Luo, Longhua Guo, Bin Qiu, Zhenyu Lin, Guonan Chen
Development of simple but sensitive biosensor for influenza detection is highly important in immediate and effective clinical treatment. In this study, a sensitive colorimetric immunosensor which combines the advantages of high selectivity of immunoassay and simplicity of colorimetric detection has been developed to detect influenza virus H5N1 based on enzyme-encapsulated liposome. Biotin-tagged liposome encapsulated with large amount of horseradish peroxidase (HRP) was firstly synthesized. In the presence of H5N1, H5N1 co-bound with the capture antibody and the biotinylated detection antibody to form sandwich immunocomplex...
April 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28331958/nucleic-acid-sensing-with-enzyme-dna-binding-protein-conjugates-cascade-and-simple-dna-nanostructures
#3
Gülsen Betül Aktas, Vasso Skouridou, Lluis Masip
A versatile and universal DNA sensing platform is presented based on enzyme-DNA binding protein tags conjugates and simple DNA nanostructures. Two enzyme conjugates were thus prepared, with horseradish peroxidase linked to the dimeric single-chain bacteriophage Cro repressor protein (HRP-scCro) and glucose oxidase linked to the dimeric headpiece domain of Escherichia coli LacI repressor protein (GOx-dHP), and used in conjunction with a hybrid ssDNA-dsDNA detection probe. This probe served as a simple DNA nanostructure allowing first for target recognition through its target-complementary single-stranded DNA (ssDNA) part and then for signal generation after conjugate binding on the double-stranded DNA (dsDNA) containing the specific binding sites for the dHP and scCro DNA binding proteins...
March 22, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28325051/bioavailability-of-immobilized-epidermal-growth-factor-covalent-versus-noncovalent-grafting
#4
Nesrine Riahi, Frederic Murschel, Sophie Lerouge, Yves Durocher, Olivier Henry, Gregory De Crescenzo
In an effort to rationalize and optimize an antiapoptotic coating combining chondroitin sulfate (CS) and epidermal growth factor (EGF) for vascular applications, the authors here report the comparison of two grafting strategies aiming to display EGF in an oriented fashion on CS. For that purpose, the authors produced, purified, and characterized a chimeric protein corresponding to EGF that was N-terminally fused to a cysteine and a coil peptide. The chimera was covalently immobilized via its free thiol group or captured via coiled-coil interactions at the surface of a biosensor or on a chondroitin sulfate coating in multiwell plates, mimicking the coating that was previously developed by them for stent-graft surfaces...
March 21, 2017: Biointerphases
https://www.readbyqxmd.com/read/28297945/multifractality-in-individual-honeybee-behavior-hints-at-colony-specific-social-cascades-reanalysis-of-radio-frequency-identification-data-from-five-different-colonies
#5
Nicole S Carver, Damian G Kelty-Stephen
Honeybees (Apis mellifera) exhibit complex coordination and interaction across multiple behaviors such as swarming. This coordination among honeybees in the same colony is remarkably similar to the concept of informational cascades. The multifractal geometry of cascades suggests that multifractal measures of individual honeybee activity might carry signatures of these colony-wide coordinations. The present work reanalyzes time stamps of entrances to and exits from the hive captured by radio-frequency identification (RFID) sensors reading RFID tags on individual bees...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28285199/nanosphere-based-one-step-strategy-for-efficient-and-nondestructive-detection-of-circulating-tumor-cells
#6
Ling-Ling Wu, Cong-Ying Wen, Jiao Hu, Man Tang, Chu-Bo Qi, Na Li, Cui Liu, Lan Chen, Dai-Wen Pang, Zhi-Ling Zhang
Detecting viable circulating tumor cells (CTCs) without disruption to their functions for in vitro culture and functional study could unravel the biology of metastasis and promote the development of personalized anti-tumor therapies. However, existing CTC detection approaches commonly include CTC isolation and subsequent destructive identification, which damages CTC viability and functions and generates substantial CTC loss. To address the challenge of efficiently detecting viable CTCs for functional study, we develop a nanosphere-based cell-friendly one-step strategy...
March 7, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28282148/alterations-in-the-salivary-proteome-and-n-glycome-of-sj%C3%A3-gren-s-syndrome-patients
#7
Steven C Hall, Maria E Hassis, Katherine E Williams, Matthew E Albertolle, Akraporn Prakobphol, Andrew B Dykstra, Megan Laurance, Katherine Ona, Richard K Niles, Namrata Prasad, Matthew Gormley, Caroline Shiboski, Lindsey A Criswell, H Ewa Witkowska, Susan J Fisher
We used isobaric mass tagging (iTRAQ) and lectin affinity capture mass spectrometry (MS)-based workflows for global analyses of parotid saliva (PS) and whole saliva (WS) samples obtained from patients diagnosed with primary Sjögren's Syndrome (pSS) who were enrolled in the Sjögren's International Collaborative Clinical Alliance (SICCA) as compared with two control groups. The iTRAQ analyses revealed up- and down-regulation of numerous proteins that could be involved in the disease process (e.g., histones) or attempts to mitigate the ensuing damage (e...
March 24, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28267323/a-dna-templated-aptamer-probe-for-identification-of-target-proteins
#8
Wenjing Bi, Xue Bai, Fan Gao, Congcong Lu, Ye Wang, Guijin Zhai, Shanshan Tian, Enguo Fan, YuKui Zhang, Kai Zhang
Using aptamers as molecular probes for biomarker discovery has attracted a great deal of attention in recent years. However, it is still a big challenge to accurately identify those protein markers that are targeted by aptamers under physiological conditions due to weak and non-covalent aptamer-protein interactions. Herein, we developed an aptamer based dual-probe using DNA-templated chemistry and photo-crosslinking technique for the identification of target proteins that are recognized by aptamers. In this system, the aptamer was modified by a single strand DNA as binding probe (BP), and another comple-mentary DNA with a photo-active group and reporter group was modified as capture probe (CP)...
March 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28261350/identifying-dcn-and-hspd1-as-potential-biomarkers-in-colon-cancer-using-2d-lc-ms-ms-combined-with-itraq-technology
#9
Guoqing Li, Maoyu Li, Xujun Liang, Zhefeng Xiao, Pengfei Zhang, Meiying Shao, Fang Peng, Yongheng Chen, Yuanyuan Li, Zhuchu Chen
Colon cancer is one of the most common types of gastrointestinal cancers and the fourth cause of cancer death worldwide. To discover novel diagnostic biomarkers for colon cancer and investigate potential mechanisms of oncogenesis, quantitative proteomic approach using iTRAQ-tagging and 2D-LC-MS/MS was performed to characterize proteins alterations in colon cancer and non-neoplastic colonic mucosa (NNCM) using laser capture microdissection-harvested from the two types of tissues, respectively. As a result, 188 DEPs were identified, and the differential expression of two DEPs (DCN and HSPD1) was further verified by Western blotting and immunohistochemistry...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28256722/discovering-protein-protein-interactions-using-nucleic-acid-programmable-protein-arrays
#10
Yanyang Tang, Ji Qiu, Matthias Machner, Joshua LaBaer
We have developed a protocol enabling the study of protein-protein interactions (PPIs) at the proteome level using in vitro-synthesized proteins. Assay preparation requires molecular cloning of the query gene into a vector that supports in vitro transcription/translation (IVTT) and appends a HaloTag to the query protein of interest. In parallel, protein microarrays are prepared by printing plasmids encoding glutathione S-transferase (GST)-tagged target proteins onto a carrier matrix/glass slide coated with antibody directed against GST...
March 3, 2017: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/28250214/improved-tandem-affinity-purification-tag-and-methods-for-isolation-of-proteins-and-protein-complexes-from-schizosaccharomyces-pombe
#11
Nicola Zilio, Michael N Boddy
The tandem affinity purification (TAP) method uses an epitope that contains two different affinity purification tags separated by a site-specific protease site to isolate a protein rapidly and easily. Proteins purified via the TAP tag are eluted under mild conditions, allowing them to be used for structural and biochemical analyses. The original TAP tag contains a calmodulin-binding peptide and the IgG-binding domain from protein A separated by a tobacco etch virus (TEV) protease cleavage site. After capturing the Protein A epitope on an IgG resin, bound proteins are released by incubation with the TEV protease and then isolated on a calmodulin matrix in the presence of calcium; elution from this resin is achieved by chelating calcium with EGTA...
March 1, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28246329/permeation-of-macromolecules-into-the-renal-glomerular-basement-membrane-and-capture-by-the-tubules
#12
Marlon G Lawrence, Michael K Altenburg, Ryan Sanford, Julian D Willett, Benjamin Bleasdale, Byron Ballou, Jennifer Wilder, Feng Li, Jeffrey H Miner, Ulla B Berg, Oliver Smithies
How the kidney prevents urinary excretion of plasma proteins continues to be debated. Here, using unfixed whole-mount mouse kidneys, we show that fluorescent-tagged proteins and neutral dextrans permeate into the glomerular basement membrane (GBM), in general agreement with Ogston's 1958 equation describing how permeation into gels is related to molecular size. Electron-microscopic analyses of kidneys fixed seconds to hours after injecting gold-tagged albumin, negatively charged gold nanoparticles, and stable oligoclusters of gold nanoparticles show that permeation into the lamina densa of the GBM is size-sensitive...
March 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28220895/resetting-predator-baselines-in-coral-reef-ecosystems
#13
Darcy Bradley, Eric Conklin, Yannis P Papastamatiou, Douglas J McCauley, Kydd Pollock, Amanda Pollock, Bruce E Kendall, Steven D Gaines, Jennifer E Caselle
What did coral reef ecosystems look like before human impacts became pervasive? Early efforts to reconstruct baselines resulted in the controversial suggestion that pristine coral reefs have inverted trophic pyramids, with disproportionally large top predator biomass. The validity of the coral reef inverted trophic pyramid has been questioned, but until now, was not resolved empirically. We use data from an eight-year tag-recapture program with spatially explicit, capture-recapture models to re-examine the population size and density of a key top predator at Palmyra atoll, the same location that inspired the idea of inverted trophic biomass pyramids in coral reef ecosystems...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28208247/quantum-dots-labeling-strategy-for-counting-and-visualization-of-hepg2-cells
#14
Bin Yang, Beibei Chen, Man He, Bin Hu
We report a sensitive, selective, simple, and reliable magnetic immunoassay protocol for detection and imaging of HepG2 cells. After being captured by Cs-doped multicore magnetic nanoparticles (MMNPs), HepG2 cells were labeled by CdSe/ZnS quantum dots (QDs), which could be visualized by fluorescence imaging using the photoluminescence property of QDs, and subsequently, they can be counted by inductively coupled plasma mass spectrometry (ICP-MS) with Cd/Cs as elemental tag. Because of the superior photoluminescence properties and the large quantities of detectable Cd atoms contained in the QDs core, QDs play a dual function role in this assay, making the method easier and more comprehensive than other similar approaches...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193857/mass-spectrometry-based-cross-linking-study-shows-that-the-psb28-protein-binds-to-cytochrome-b559-in-photosystem-ii
#15
Daniel A Weisz, Haijun Liu, Hao Zhang, Sundarapandian Thangapandian, Emad Tajkhorshid, Michael L Gross, Himadri B Pakrasi
Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28187301/the-preparation-of-dual-functional-hybrid-nanoflower-and-its-application-in-the-ultrasensitive-detection-of-disease-related-biomarker
#16
Yucheng Liu, Jinyang Chen, Mingyuan Du, Xinxin Wang, Xinghu Ji, Zhike He
In this work, dual-functional streptavidin (SA)-horseradish peroxidase (HRP) hybrid nanoflowers, integrating the functions of biological recognition and signal amplification, were prepared through facile one-pot green synthesis method. The prepared SA-HRP-Cu3(PO4)2 hybrid nanoflowers loaded abundant HRP and simultaneously exhibited enhanced catalytic activity, stability, and durability compared with free enzyme, which fits greatly well with the requirement of signal tag for bioassay. Besides, due to the general SA-biotin linking interaction, the SA-HRP-Cu3(PO4)2 hybrid nanoflowers possess universal capture ability to the biotinylated antibody...
June 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28174098/effects-of-organophosphates-on-the-regulation-of-mesenchymal-stem-cell-proliferation-and-differentiation
#17
Amber M Prugh, Stephanie D Cole, Trevor Glaros, Daniel J Angelini
Mesenchymal stem cells (MSCs) are multipotent cells located within various adult tissues. Recent literature has reported that human bone marrow-derived MSCs express active acetylcholinesterase (AChE) and that disruption of AChE activity by organophosphate (OP) chemicals decreases the ability of MSCs to differentiate into osteoblasts. The potential role of AChE in regulating MSC proliferation and differentiation is currently unknown. In the present study, we demonstrate that MSCs exposed to OPs have both decreased AChE activity and abundance...
March 25, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28155874/itraq-based-quantitative-proteomic-analysis-of-the-global-response-to-17%C3%AE-estradiol-in-estrogen-degradation-strain-pseudomonas-putida-sjte-1
#18
Jing Xu, Lei Zhang, Jingli Hou, Xiuli Wang, Huan Liu, Daning Zheng, Rubing Liang
Microorganism degradation is efficient to remove the steroid hormones like 17β-estradiol (E2); but their degradation mechanism and metabolic network to these chemicals are still not very clear. Here the global responses of the estrogen-degradation strain Pseudomonas putida SJTE-1 to 17β-estradiol and glucose were analyzed and compared using the iTRAQ (isobaric tags for relative and absolute quantization) strategy combined with LC-MS/MS (liquid chromatography-tandem mass spectrometry). 78 proteins were identified with significant changes in expression; 45 proteins and 33 proteins were up-regulated and down-regulated, respectively...
February 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28152598/immuno-affinity-capture-followed-by-tmpp-n-terminus-tagging-to-study-catabolism-of-therapeutic-proteins
#19
Majlinda Kullolli, Dan A Rock, Ji Ma
Characterization of in vitro and in vivo catabolism of therapeutic proteins has increasingly become an integral part of discovery and development process for novel proteins. Unambiguous and efficient identification of catabolites can not only facilitate accurate understanding of pharmacokinetic profiles of drug candidates, but also enables follow up protein engineering to generate more catabolically stable molecules with improved properties (pharmacokinetics and pharmacodynamics). Immunoaffinity capture (IC) followed by top-down intact protein analysis using either matrix-assisted laser desorption/ionization or electrospray ionization mass spectrometry analysis have been the primary methods of choice for catabolite identification...
February 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28133395/linking-loggerhead-locations-using-multiple-methods-to-determine-the-origin-of-sea-turtles-in-feeding-grounds
#20
ALan F Rees, Carlos Carreras, Annette C Broderick, Dimitris Margaritoulis, Thomas B Stringell, Brendan J Godley
Many marine megavertebrate taxa, including sea turtles, disperse widely from their hatching or birthing locations but display natal homing as adults. We used flipper tagging, satellite tracking and genetics to identify the origin of loggerhead turtles living in Amvrakikos Gulf, Greece. This location has been identified as hosting regionally important numbers of large-juvenile to adult sized turtles that display long-term residency and/or association to the area, and also presents a male biased sex ratio for adults...
2017: Marine Biology
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