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https://www.readbyqxmd.com/read/28109432/targeted-in-depth-quantification-of-signaling-using-label-free-mass-spectrometry
#1
P R Cutillas
Protein phosphorylation encodes information on the activity of kinase-driven signaling pathways that regulate cell biology. This chapter discusses an approach, named TIQUAS (targeted in-depth quantification of signaling), to quantify cell signaling comprehensively and without bias. The workflow-based on mass spectrometry (MS) and computational science-consists of targeting the analysis of phosphopeptides previously identified by shotgun liquid chromatography tandem MS (LC-MS/MS) across the samples that are being compared...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109426/wgcna-application-to-proteomic-and-metabolomic-data-analysis
#2
G Pei, L Chen, W Zhang
Progresses in mass spectrometric instrumentation and bioinformatics identification algorithms made over the past decades allow quantitative measurements of relative or absolute protein/metabolite amounts in cells in a high-throughput manner, which has significantly expedited the exploration into functions and dynamics of complex biological systems. However, interpretation of high-throughput data is often restricted by the limited availability of suitable computational methods and enough statistical power. While many computational methodologies have been developed in the past decades to address the issue, it becomes clear that network-focused rather than individual gene/protein-focused strategies would be more appropriate to obtain a complete picture of cellular responses...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109310/consolidating-drug-data-on-a-global-scale-using-linked-data
#3
Milos Jovanovik, Dimitar Trajanov
BACKGROUND: Drug product data is available on the Web in a distributed fashion. The reasons lie within the regulatory domains, which exist on a national level. As a consequence, the drug data available on the Web are independently curated by national institutions from each country, leaving the data in varying languages, with a varying structure, granularity level and format, on different locations on the Web. Therefore, one of the main challenges in the realm of drug data is the consolidation and integration of large amounts of heterogeneous data into a comprehensive dataspace, for the purpose of developing data-driven applications...
January 21, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28109300/knowledge-attitudes-and-practices-in-tamarind-tamarindus-indica-l-use-and-conservation-in-eastern-uganda
#4
Esther Ebifa-Othieno, Antony Mugisha, Philip Nyeko, John David Kabasa
BACKGROUND: Tamarindus indica L is one of the indigenous fruit tree species that traditionally contributes to food security and ecosystem stability in sub-Saharan Africa. We hypothesized that the indigenous people of Eastern Uganda have used T. indica for generations and developed practices that promote its conservation and therefore we expected that they possess an elaborate indigenous knowledge (IK) system and that most of them have planted the species. The aim of this study was to assess the influence of IK, attitudes and practices on the use and conservation of T...
January 21, 2017: Journal of Ethnobiology and Ethnomedicine
https://www.readbyqxmd.com/read/28109221/charge-and-energy-migration-in-molecular-clusters-a-stochastic-schr%C3%A3-dinger-equation-approach
#5
Thomas Plehn, Volkhard May
The performance of stochastic Schrödinger equations for simulating dynamic phenomena in large scale open quantum systems is studied. Going beyond small system sizes, commonly used master equation approaches become inadequate. In this regime, wave function based methods profit from their inherent scaling benefit and present a promising tool to study, for example, exciton and charge carrier dynamics in huge and complex molecular structures. In the first part of this work, a strict analytic derivation is presented...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28108922/association-between-heavy-metal-and-metalloid-levels-in-topsoil-and-cancer-mortality-in-spain
#6
Olivier Núñez, Pablo Fernández-Navarro, Iván Martín-Méndez, Alejandro Bel-Lan, Juan F Locutura Rupérez, Gonzalo López-Abente
Spatio-temporal cancer mortality studies in Spain have revealed patterns for some tumours which display a distribution that is similar across the sexes and persists over time. Such characteristics would be common to tumours that shared risk factors, including the geochemical composition of the soil. The aim of this study was to assess the possible association between heavy metal and metalloid levels in topsoil (upper soil horizon) and cancer mortality in mainland Spain. Ecological cancer mortality study at a municipal level, covering 861,440 cancer deaths (27 different tumour locations) in 7917 Spanish mainland towns, from 1999 to 2008...
January 20, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28108588/inferring-recent-demography-from-isolation-by-distance-of-long-shared-sequence-blocks
#7
Harald Ringbauer, Graham Coop, Nicholas H Barton
Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes...
January 20, 2017: Genetics
https://www.readbyqxmd.com/read/28108448/arnapipe-a-balanced-efficient-and-distributed-pipeline-for-processing-rna-seq-data-in-high-performance-computing-environments
#8
Arnald Alonso, Brittany N Lasseigne, Kelly Williams, Josh Nielsen, Ryne C Ramaker, Andrew A Hardigan, Bobbi Johnston, Brian S Roberts, Sara J Cooper, Sara Marsal, Richard M Myers
The wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing, and sequence variant calling...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28107994/application-of-passive-sampling-devices-based-on-multi-walled-carbon-nanotubes-for-the-isolation-of-selected-pharmaceuticals-and-phenolic-compounds-in-water-samples-possibilities-and-limitations
#9
Aleksandra Jakubus, Magdalena Tyma, Piotr Stepnowski, Monika Paszkiewicz
Nowadays, carbon nanotubes, as commercially available materials, have attracted great attention because of their unique physicochemical properties, especially their strong adsorption abilities. This paper deals with the possibilities and limitations of the application of multi-walled carbon nanotubes as an alternative sorbent in passive sampling devices for the isolation of selected pharmaceuticals and phenolic compounds directly in water samples. Compounds with different properties, including sulfapyridine, sulfamethoxazole, carbamazepine, p-nitrophenol, 17-β-estradiol, 3,5-dichlorophenol and diclofenac were selected as model compounds...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107983/characterization-of-inclusion-complexes-of-organic-ions-with-hydrophilic-hosts-by-ion-transfer-voltammetry-with-solvent-polymeric-membranes
#10
José Manuel Olmos, Eduardo Laborda, Joaquín Ángel Ortuño, Ángela Molina
The quantitative characterization of inclusion complexes formed in aqueous phase between organic ions and hydrophilic hosts by ion-transfer voltammetry with solvent polymeric membrane ion sensors is studied, both in a theoretical and experimental way. Simple analytical solutions are presented for the determination of the binding constant of the complex from the variation with the host concentration of the electrochemical signal. These solutions are valid for any voltammetric technique and for solvent polymeric membrane ion sensors comprising one polarisable interface (1PI) and also, for the first time, two polarisable interfaces (2PIs)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107965/loopback-rolling-circle-amplification-for-ultrasensitive-detection-of-kras-gene
#11
Huo Xu, Dong Wu, Yifan Jiang, Rongbo Zhang, Qingzheng Wu, Yiyun Liu, Feng Li, Zai-Sheng Wu
Mutations in Kras gene may be used as a diagnostic marker and a target for treatment of the broad spectrum of human cancers. In this study, we developed a new class of amplification assay, double-hairpin molecular beacon (DHMB)-based cascade rolling circle amplification (RCA), for ultrasensitive and selective detection of Kras gene in a homogenous solution. Specifically, target DNA can hybridize with DHMB and activate cyclical target strand-displacement polymerization (CTDP) and nicking-mediated strand-displacement polymerization (NMDP)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107961/new-approach-of-a-transient-icp-ms-measurement-method-for-samples-with-high-salinity
#12
Christina Hein, Jonas Michael Sander, Ralf Kautenburger
In the near future it is necessary to establish a disposal for high level nuclear waste (HLW) in deep and stable geological formations. In Germany typical host rocks are salt or claystone. Suitable clay formations exist in the south and in the north of Germany. The geochemical conditions of these clay formations show a strong difference. In the northern ionic strengths of the pore water up to 5M are observed. The determination of parameters like Kd values during sorption experiments of metal ions like uranium or europium as homologues for trivalent actinides onto clay stones are very important for long term safety analysis...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107908/evaluation-and-reduction-of-the-analytical-uncertainties-in-gc-ms-analysis-using-a-boundary-regression-model
#13
Miao Yu, Xingwang Hou, Qian Liu, Yawei Wang, Jiyan Liu, Guibin Jiang
The uncertainties in analysis of trace environmental pollutants may come from sample matrix and sample pretreatment process. In this study, a boundary model was developed based on the visualized data of mass spectrometry to evaluate the influences from sample matrix and pretreatment process. The factors affecting the pretreatment procedures, such as the solvents, the extraction sorbents and the extraction process had limited influences compared with matrix effects. Using such boundary model, we found that selecting suitable qualitative and quantitative ions for MS detector is more important for reducing the matrix effect in GC-MS analysis than the traditionally used methods of optimizing the pretreatment process since some clean up sorbents might be useless to reduce the matrix effects...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107906/development-of-data-independent-acquisition-workflows-for-metabolomic-analysis-on-a-quadrupole-orbitrap-platform
#14
Juntuo Zhou, Yuhua Li, Xi Chen, Lijun Zhong, Yuxin Yin
Untargeted metabolomic profiling has been widely used in recent years. However, the low reproducibility of the data-dependent acquisition (DDA) strategy presents a major bottleneck that considerably limits the reliability of metabolomic studies in biological and clinical research. The data-independent acquisition (DIA) strategy is proposed to solve the above-mentioned problem, and it is gaining popularity. This paper presents a novel approach for performing metabolomic analysis using an untargeted, liquid chromatography-data independent-mass spectrometry (LC-DIA-MS) strategy on a quadrupole-Orbitrap platform...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107831/high-throughput-untargeted-screening-of-veterinary-drug-residues-and-metabolites-in-tilapia-using-high-resolution-orbitrap-mass-spectrometry
#15
Wei Jia, Xiaogang Chu, James Chang, Perry G Wang, Ying Chen, Feng Zhang
An analytical method was developed and validated for simultaneous analysis of one hundred and thirty-seven veterinary drug residues and metabolites from sixteen different classes in tilapia utilizing an improved fully non-targeted way of data acquisition with fragmentation. The automated on-line extraction procedure was achieved in a simple disposable pipet extraction. Ultrahigh-performance liquid chromatography and electrospray ionization quadrupole Orbitrap high-resolution mass spectrometry (UHPLC Q-Orbitrap) was used for the separation and detection of all the analytes...
March 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28107709/quantification-of-fatty-acids-in-the-muscle-of-antarctic-fish-trematomus-bernacchii-by-gas-chromatography-mass-spectrometry-optimization-of-the-analytical-methodology
#16
C Truzzi, S Illuminati, A Annibaldi, M Antonucci, G Scarponi
This work presents data on the quantification of fatty acids (FAs, in terms of mass unit per tissue weight) in the muscle of Trematomus bernacchii, a key species in Antarctica, often used as bioindicator for contamination studies. Modifications in fatty acids content should be considered a useful biomarker to study how contaminants affect Antarctic biota. Until now, very few studies quantified fatty acids of muscle of T. bernacchii, and only as percentage of a single fatty acid on total lipids. To perform the quantification of fatty acids, we used an analytical method based on a fast microwave-assisted extraction of lipids from a lyophilized sample, a base-catalyzed trans-esterification of lipid extract to obtain Fatty Acids Methyl Esters (FAMEs), and a separation and identification of FAMEs by gas chromatography-mass spectrometry...
December 31, 2016: Chemosphere
https://www.readbyqxmd.com/read/28107396/mixfit-methodology-for-computing-ancestry-related-genetic-scores-at-the-individual-level-and-its-application-to-the-estonian-and-finnish-population-studies
#17
Toomas Haller, Liis Leitsalu, Krista Fischer, Marja-Liisa Nuotio, Tõnu Esko, Dorothea Irene Boomsma, Kirsten Ohm Kyvik, Tim D Spector, Markus Perola, Andres Metspalu
Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit...
2017: PloS One
https://www.readbyqxmd.com/read/28107295/healthcare-transformation-and-changing-roles-for-nursing
#18
Susan W Salmond, Mercedes Echevarria
Factors driving healthcare transformation include fragmentation, access problems, unsustainable costs, suboptimal outcomes, and disparities. Cost and quality concerns along with changing social and disease-type demographics created the greatest urgency for the need for change. Caring for and paying for medical treatments for patients suffering from chronic health conditions are a significant concern. The Affordable Care Act includes programs now led by the Centers for Medicare & Medicaid Services aiming to improve quality and control cost...
January 2017: Orthopaedic Nursing
https://www.readbyqxmd.com/read/28107264/readmission-and-late-mortality-after-critical-illness-in-childhood
#19
Mary E Hartman, Mohammed J Saeed, Tellen Bennett, Katri Typpo, Renee Matos, Margaret A Olsen
OBJECTIVES: Little is known about the ongoing mortality risk and healthcare utilization among U.S. children after discharge from a hospitalization involving ICU care. We sought to understand risks for hospital readmission and trends in mortality during the year following ICU discharge. DESIGN: Retrospective observational cohort study. SETTING: This study was performed using administrative claims data from 2006-2013 obtained from the Truven Health Analytics MarketScan Database...
January 19, 2017: Pediatric Critical Care Medicine
https://www.readbyqxmd.com/read/28107052/trait-evolution-in-adaptive-radiations-modeling-and-measuring-interspecific-competition-on-phylogenies
#20
Magnus Clarke, Gavin H Thomas, Robert P Freckleton
The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that include interspecific competition among chosen species...
February 2017: American Naturalist
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