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https://www.readbyqxmd.com/read/28636592/quantifiable-predictive-features-define-epitope-specific-t-cell-receptor-repertoires
#1
Pradyot Dash, Andrew J Fiore-Gartland, Tomer Hertz, George C Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, E Bridie Clemens, Thi H O Nguyen, Katherine Kedzierska, Nicole L La Gruta, Philip Bradley, Paul G Thomas
T cells are defined by a heterodimeric surface receptor, the T cell receptor (TCR), that mediates recognition of pathogen-associated epitopes through interactions with peptide and major histocompatibility complexes (pMHCs). TCRs are generated by genomic rearrangement of the germline TCR locus, a process termed V(D)J recombination, that has the potential to generate marked diversity of TCRs (estimated to range from 10(15) (ref. 1) to as high as 10(61) (ref. 2) possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28636590/host-and-viral-traits-predict-zoonotic-spillover-from-mammals
#2
Kevin J Olival, Parviez R Hosseini, Carlos Zambrana-Torrelio, Noam Ross, Tiffany L Bogich, Peter Daszak
The majority of human emerging infectious diseases are zoonotic, with viruses that originate in wild mammals of particular concern (for example, HIV, Ebola and SARS). Understanding patterns of viral diversity in wildlife and determinants of successful cross-species transmission, or spillover, are therefore key goals for pandemic surveillance programs. However, few analytical tools exist to identify which host species are likely to harbour the next human virus, or which viruses can cross species boundaries. Here we conduct a comprehensive analysis of mammalian host-virus relationships and show that both the total number of viruses that infect a given species and the proportion likely to be zoonotic are predictable...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28635172/doxorubicin-kinetics-and-effects-on-lung-cancer-cell-lines-using-in-vitro-raman-micro-spectroscopy-binding-signatures-drug-resistance-and-dna-repair
#3
Zeineb Farhane, Franck Bonnier, Orla Howe, Alan Casey, Hugh J Byrne
Raman micro-spectroscopy is a non-invasive analytical tool, whose potential in cellular analysis and monitoring drug mechanisms of action has already been demonstrated, and which can potentially be used in pre-clinical and clinical applications for the prediction of chemotherapeutic efficacy. To further investigate such potential clinical application, it is important to demonstrate its capability to differentiate drug mechanisms of action and cellular resistances. Using the example of Doxorubicin (DOX), in this study, it was used to probe the cellular uptake, signatures of chemical binding and subsequent cellular responses, of the chemotherapeutic drug in two lung cancer cell lines, A549 and Calu-1...
June 21, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28634780/echocardiographic-inferior-vena-cava-measurement-as-an-alternative-to-central-venous-pressure-measurement-in-neonates
#4
Muzamil Mustafa Mugloo, Seema Malik, Rubeena Akhtar
OBJECTIVES: To evaluate the correlation between echocardiographic inferior vena cava (IVC) measurements and central venous pressure (CVP) in neonates. Also, to evaluate the correlation between IVC measurements and gestational age (GA) and body weight (BW). METHODS: This cross sectional analytical study was conducted from June 2014 through June 2016 in a level III NICU. All neonates requiring intensive hemodynamic monitoring and having umbilical venous catheter (UVC) in place for clinical indications were enrolled in the study...
June 21, 2017: Indian Journal of Pediatrics
https://www.readbyqxmd.com/read/28633816/a-derivation-of-the-stable-cavitation-threshold-accounting-for-bubble-bubble-interactions
#5
Matthieu Guédra, Corentin Cornu, Claude Inserra
The subharmonic emission of sound coming from the nonlinear response of a bubble population is the most used indicator for stable cavitation. When driven at twice their resonance frequency, bubbles can exhibit subharmonic spherical oscillations if the acoustic pressure amplitude exceeds a threshold value. Although various theoretical derivations exist for the subharmonic emission by free or coated bubbles, they all rest on the single bubble model. In this paper, we propose an analytical expression of the subharmonic threshold for interacting bubbles in a homogeneous, monodisperse cloud...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633409/the-effect-of-pd-l1-testing-on-the-cost-effectiveness-and-economic-impact-of-immune-checkpoint-inhibitors-for-the-second-line-treatment-of-nsclc
#6
P N Aguiar, L Perry, J Penny-Dimr, H Babiker, H Tadokoro, R A de Mello, G L Lopes
Background: Immune checkpoint inhibitors improve outcomes compared to chemotherapy in lung cancer. Tumor PD-L1 receptor expression is being studied as a predictive biomarker. The objective of this study was to assess the cost-effectiveness and economic impact of second-line treatment with nivolumab, pembrolizumab, and atezolizumab with and without the use of PD-L1 testing for patient selection. Design: We developed a decision-analytic model to determine the cost-effectiveness of PD-L1 assessment and second-line immunotherapy versus docetaxel...
June 15, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28633385/timiner-ngs-data-mining-pipeline-for-cancer-immunology-and-immunotherapy
#7
Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski
Summary: Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing (NGS) data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from NGS data. TIminer enables integrative immunogenomic analyses, including: human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates, and quantification of tumor immunogenicity...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28631236/use-of-ctx-i-and-pinp-as-bone-turnover-markers-national-bone-health-alliance-recommendations-to-standardize-sample-handling-and-patient-preparation-to-reduce-pre-analytical-variability
#8
P Szulc, K Naylor, N R Hoyle, R Eastell, E T Leary
N-terminal propeptide of type I procollagen and C-terminal telopeptide of type I collagen are the reference standards for bone turnover markers for monitoring osteoporosis treatment. We provide recommendations for standardized sample handling and encompassing aspects of preanalytical variability to improve the reproductibility of their measurements, their reliability, and clinical interpretation. The International Osteoporosis Foundation and International Federation of Clinical Chemistry bone turnover marker standards working group have identified N-terminal propeptide of type I procollagen (PINP) and C-terminal telopeptide of type I collagen (CTX-I) in the blood to be the international reference standards for bone turnover markers for the prediction of fracture risk and monitoring of osteoporosis treatment...
June 19, 2017: Osteoporosis International
https://www.readbyqxmd.com/read/28631226/introduction-of-a-simple-second-tier-screening-test-for-c5-isobars-in-dried-blood-spots-reducing-the-false-positive-rate-for-isovaleric-acidaemia-in-expanded-newborn-screening
#9
R S Carling, D Burden, I Hutton, R Randle, K John, J R Bonham
In 2015 the English Newborn Screening programme expanded to include Isovaleric Acidaemia (IVA). Screening is performed by flow injection analysis tandem mass spectrometry of isovalerylcarnitine. Isovalerylcarnitine is isobaric with pivaloylcarnitine which can be present in blood due to the use of pivalic ester pro-drugs or pivalic acid derivatives used as emollients in some nipple creams; the potential for false positives (FP) is well documented. A pilot study in England screened 438,164 babies, 18 had presumptive positive results but only 4 were confirmed as true positives (TP)...
June 20, 2017: JIMD Reports
https://www.readbyqxmd.com/read/28630712/quantifying-drivers-of-wild-pig-movement-across-multiple-spatial-and-temporal-scales
#10
Shannon L Kay, Justin W Fischer, Andrew J Monaghan, James C Beasley, Raoul Boughton, Tyler A Campbell, Susan M Cooper, Stephen S Ditchkoff, Steve B Hartley, John C Kilgo, Samantha M Wisely, A Christy Wyckoff, Kurt C VerCauteren, Kim M Pepin
BACKGROUND: The movement behavior of an animal is determined by extrinsic and intrinsic factors that operate at multiple spatio-temporal scales, yet much of our knowledge of animal movement comes from studies that examine only one or two scales concurrently. Understanding the drivers of animal movement across multiple scales is crucial for understanding the fundamentals of movement ecology, predicting changes in distribution, describing disease dynamics, and identifying efficient methods of wildlife conservation and management...
2017: Movement Ecology
https://www.readbyqxmd.com/read/28628784/identifying-populations-sensitive-to-environmental-chemicals-by-simulating-toxicokinetic-variability
#11
Caroline L Ring, Robert G Pearce, R Woodrow Setzer, Barbara A Wetmore, John F Wambaugh
The thousands of chemicals present in the environment (USGAO, 2013) must be triaged to identify priority chemicals for human health risk research. Most chemicals have little of the toxicokinetic (TK) data that are necessary for relating exposures to tissue concentrations that are believed to be toxic. Ongoing efforts have collected limited, in vitro TK data for a few hundred chemicals. These data have been combined with biomonitoring data to estimate an approximate margin between potential hazard and exposure...
June 16, 2017: Environment International
https://www.readbyqxmd.com/read/28628474/prediction-of-human-iron-bioavailability-using-rapid-c-elisas-for-human-plasma-hepcidin
#12
Nicole U Stoffel, Christophe Zeder, Eloïse Fort, Dorine W Swinkels, Michael B Zimmermann, Diego Moretti
BACKGROUND: Hepcidin is the central systemic regulator of iron metabolism, but its quantification in biological fluids is challenging. Rapid, accurate and user-friendly methods are needed. Our aim was to assess the ability of hepcidin as measured by three different c-ELISA assays to predict iron bioavailability in humans. METHODS: The three assays used were commercially available DRG and Peninsula assays and the c-ELISA method performed at Radboud University Medical Centre, Nijmegen, The Netherlands (Hepcidinanalysis...
June 17, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28626878/should-women-be-advised-to-use-calcium-supplements-during-pregnancy-a-decision-analysis
#13
Linda J E Meertens, Hubertina C J Scheepers, Jessica P M M Willemse, Marc E A Spaanderman, Luc J M Smits
Adequate calcium intake during pregnancy is important in the prevention of pre-eclampsia. A substantial proportion of pregnant women do not meet the recommended daily calcium intake, even in developed countries. Nonetheless, calcium supplementation is not routinely advised to pregnant women in most countries. We aimed to predict the impact of advising pregnant women to use calcium supplements (1,000 mg/day) on the number of cases of pre-eclampsia prevented and related health care costs. By use of a decision-analytic model, we assessed the expected impact of advising calcium supplementation to either (1) all pregnant women, (2) women at high risk of developing pre-eclampsia, or (3) women with a low dietary calcium intake compared with current care...
June 18, 2017: Maternal & Child Nutrition
https://www.readbyqxmd.com/read/28625992/flow-cytometry-a-powerful-novel-tool-to-assess-viability-of-fungal-conidia-in-metal-working-fluids
#14
D Vanhauteghem, K Demeyere, N Callaert, A Boelaert, G Haesaert, K Audenaert, E Meyer
Fungal contamination of metal working fluids (MWF) is a dual problem in automatized processing plants because resulting fungal biofilms obstruct cutting, drilling and polishing machines. Moreover, some fungal species of MWF comprise pathogens such as Fusarium solani Therefore, the development of an accurate analytical tool to evaluate conidia viability in MWF is important. We developed a flow cytometric method to measure fungal viability in MWF using F. solani as model organism. To validate this method, viable and dead conidia were mixed in several proportions and flow cytometrically analyzed...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28625048/moisture-influence-reducing-method-for-heavy-metals-detection-in-plant-materials-using-laser-induced-breakdown-spectroscopy-a-case-study-for-chromium-content-detection-in-rice-leaves
#15
Jiyu Peng, Yong He, Lanhan Ye, Tingting Shen, Fei Liu, Wenwen Kong, Xiaodan Liu, Yun Zhao
Fast detection of heavy metals in plant materials is crucial for environmental remediation and ensuring food safety. However, most plant materials contain high moisture content, the influence of which cannot be simply ignored. Hence, we proposed moisture influence reducing method for fast detection of heavy metals using laser-induced breakdown spectroscopy (LIBS). Firstly, we investigated the effect of moisture content on signal intensity, stability and plasma parameters (temperature and electron density), and determined main influence factors (experimental parameters F and the change of analyte concentration...
June 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28623520/prediction-of-intracranial-hypertension-through-noninvasive-intracranial-pressure-waveform-analysis-in-pediatric-hydrocephalus
#16
Matheus Fernando Manzolli Ballestero, Gustavo Frigieri, Brenno Caetano Troca Cabella, Sergio Mascarenhas de Oliveira, Ricardo Santos de Oliveira
PURPOSE: The purpose of this study is to evaluate a noninvasive device to assess intracranial pressure wave form in children with hydrocephalus. METHODS: A prospective and non-experimental descriptive-analytic study was performed. Fifty-six patients were enrolled in this study. They were divided in four groups: group A, children with clinically compensated hydrocephalus; B, surgically treated hydrocephalus; C, patients with acute intracranial hypertension due to hydrocephalus; and D, children without neurological disease (control)...
June 16, 2017: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28623343/data-driven-nanomechanical-sensing-specific-information-extraction-from-a-complex-system
#17
Kota Shiba, Ryo Tamura, Gaku Imamura, Genki Yoshikawa
Smells are known to be composed of thousands of chemicals with various concentrations, and thus, the extraction of specific information from such a complex system is still challenging. Herein, we report for the first time that the nanomechanical sensing combined with machine learning realizes the specific information extraction, e.g. alcohol content quantification as a proof-of-concept, from the smells of liquors. A newly developed nanomechanical sensor platform, a Membrane-type Surface stress Sensor (MSS), was utilized...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28622607/mammalian-fibroblast-cells-avoid-residual-stress-zone-caused-by-nanosecond-laser-pulses
#18
Candace Colpitts, Amin M Ektesabi, Rachael A Wyatt, Bryan D Crawford, Amirkianoosh Kiani
This study investigates the effects of laser irradiation on crystalline silicon and its application in biomaterials. We used an analytical model to predict the ablation depth and pit size resulting from laser exposure of silicon samples. The temperatures generated are predicted correlate with laser power, and to result in the formation of a residual stress zone bordering the ablated groove. Different crystal orientations found in the substrate confirm that there was crystal distortion, which consequently induces these residual stress zones...
June 9, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28622540/scattering-of-airy-elastic-sheets-by-a-cylindrical-cavity-in-a-solid
#19
F G Mitri
The prediction of the elastic scattering by voids (and cracks) in materials is an important process in structural health monitoring, phononic crystals, metamaterials and non-destructive evaluation/imaging to name a few examples. Earlier analytical theories and numerical computations considered the elastic scattering by voids in plane waves of infinite extent. However, current research suggesting the use of (limited-diffracting, accelerating and self-healing) Airy acoustical-sheet beams for non-destructive evaluation or imaging applications in elastic solids requires the development of an improved analytical formalism to predict the scattering efficiency used as a priori information in quantitative material characterization...
June 8, 2017: Ultrasonics
https://www.readbyqxmd.com/read/28622073/neighborhood-poverty-and-9-1-1-ambulance-contacts
#20
Josh Seim, Joshua English, Karl Sporer
BACKGROUND: Neighborhood poverty is positively associated with frequency of 9-1-1 ambulance utilization, but it is unclear whether this association remains significant when accounting for variations in the severities and types of ambulance contacts. METHODS: We merged EMS ambulance contact records in a single California county (n = 88,027) with data from the American Community Survey at the census tract level (n = 300). Using tract as a proxy for neighborhood and negative binomial regression as an analytical tool, we predicted 16 outcomes: any ambulance contacts, ambulance contacts stratified by three intervention severities, and ambulance contacts varied by 12 primary impression categories...
June 16, 2017: Prehospital Emergency Care
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