Dissection of the insulin signaling pathway via quantitative phosphoproteomics

DEFF Research Database (Denmark)

Krüger, Marcus; Kratchmarova, Irina; Blagoev, Blagoy

2008-01-01

spectrum of the tyrosine phosphorylation cascade, we have defined the tyrosine-phosphoproteome of the insulin signaling pathway, using high resolution mass spectrometry in combination with phosphotyrosine immunoprecipitation and stable isotope labeling by amino acids in cell culture (SILAC......The insulin signaling pathway is of pivotal importance in metabolic diseases, such as diabetes, and in cellular processes, such as aging. Insulin activates a tyrosine phosphorylation cascade that branches to create a complex network affecting multiple biological processes. To understand the full...

The Arabidopsis thaliana Cyclic-Nucleotide-Dependent Response – a Quantitative Proteomic and Phosphoproteomic Analysis

KAUST Repository

Alqurashi, May M.

2013-11-01

Protein phosphorylation governs many regulatory pathways and an increasing number of kinases, proteins that transfer phosphate groups, are in turn activated by cyclic nucleotides. One of the cyclic nucleotides, cyclic adenosine monophosphate (cAMP), has been shown to be a second messenger in abiotic and biotic stress responses. However, little is known about the precise role of cAMP in plants and in the down-stream activation of kinases, and hence cAMP-dependent phosphorylation. To increase our understanding of the role of cAMP, proteomic and phosphoproteomic profiles of Arabidopsis thaliana suspension culture cells were analyzed before and after treatment of cells with two different concentrations of 8-Bromo-cAMP (1 µM and 100 nM) and over a time-course of one hour. A comparative quantitative analysis was undertaken using two- dimensional gel electrophoresis and the Delta 2D software (DECODON) followed by protein spot identification by tandem mass spectrometry combined with Mascot and Scaffold. Differentially expressed proteins and regulated phosphoproteins were categorized according to their biological function using bioinformatics tools. The results revealed that the treatment with 1 µM and 100 nM 8-Bromo-cAMP was sufficient to induce specific concentration- and time-dependent changes at the proteome and phosphoproteome levels. In particular, different phosphorylation patterns were observed overtime preferentially affecting proteins in a number of functional categories, notably phosphatases, proteins that remove phosphate groups. This suggests that cAMP both transiently activates and deactivates proteins through specific phosphorylation events and provides new insight into biological mechanisms and functions at the systems level.

Identification of novel protein functions and signaling mechanisms by genetics and quantitative phosphoproteomics in Caenorhabditis elegans

DEFF Research Database (Denmark)

Fredens, Julius; Engholm-Keller, Kasper; Møller-Jensen, Jakob

2014-01-01

knockdown by feeding the nematode on pre-labeled lysine auxotroph Escherichia coli. In this chapter, we describe in details the generation of the E. coli strain, incorporation of heavy isotope-labeled lysine in C. elegans, and the procedure for a comprehensive global phosphoproteomic experiment.......Stable isotope labeling by amino acids combined with mass spectrometry is a widely used methodology for measuring relative changes in protein and phosphorylation levels at a global level. We have applied this method to the model organism Caenorhabditis elegans in combination with RNAi-mediated gene...

Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (PhosphoProteomic Profiling

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Ilyas Singec

2016-09-01

Full Text Available Controlled differentiation of human embryonic stem cells (hESCs can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs. This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families, phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt.

Enhanced Phosphoproteomic Profiling Workflow For Growth Factor Signaling Analysis

DEFF Research Database (Denmark)

Sylvester, Marc; Burbridge, Mike; Leclerc, Gregory

2010-01-01

Background Our understanding of complex signaling networks is still fragmentary. Isolated processes have been studied extensively but cross-talk is omnipresent and precludes intuitive predictions of signaling outcomes. The need for quantitative data on dynamic systems is apparent especially for our...... understanding of pathological processes. In our study we create and integrate data on phosphorylations that are initiated by several growth factor receptors. We present an approach for quantitative, time-resolved phosphoproteomic profiling that integrates the important contributions by phosphotyrosines. Methods...

Global investigation of interleukin-1β signaling in primary β-cells using quantitative phosphoproteomics

DEFF Research Database (Denmark)

Engholm-Keller, Kasper; Størling, Joachim; Pociot, Flemming

in β-cells by which this cytokine can modulate cell-matrix interactions during inflammation, a regulation shown in other cell types. Further data analysis is currently ongoing, and the collective results of the experiments will hopefully facilitate additional insights into the effect of IL-1β......Novel Aspect: Global phosphoproteomic analysis of cytokine signaling in primary β-cells Introduction The insulin-producing β-cells of the pancreatic islets of Langerhans are targeted by aberrant immune system responses in diabetes mellitus involving cytokines, especially interleukin-1β (IL-1 β......), which initiate apoptosis of the β-cells. As only limited amounts of primary β-cells can be isolated from model organisms like mouse and rat, global phosphoproteomic analysis of these signaling events by mass spectrometry has generally been unfeasible. We have therefore developed a strategy...

Phosphoproteomic analysis of cell-based resistance to BRAF inhibitor therapy in melanoma

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Robert eParker

2015-05-01

Full Text Available The treatment of melanoma by targeted inhibition of the mutated kinase BRAF with small molecules only temporarily suppresses metastatic disease. In the face of chemical inhibition tumor plasticity, both innate and adaptive, promotes survival through the biochemical and genetic reconfiguration of cellular pathways that can engage proliferative and migratory systems. To investigate this process high-resolution mass spectrometry was used to characterize the phosphoproteome of this transition in vitro. A simple and accurate, label-free quantitative method was used to localize and quantitate thousands of phosphorylation events. We also correlated changes in the phosphoproteome with the proteome to more accurately determine changes in the activity of regulatory kinases determined by kinase landscape profiling. The abundance of phosphopeptides with sites that function in cytoskeletal regulation, GTP/GDP exchange, Protein Kinase C, IGF signaling and melanosome maturation were highly divergent after transition to a drug resistant phenotype.

Quantitative proteome and phosphoproteome analyses of Streptomyces coelicolor reveal proteins and phosphoproteins modulating differentiation and secondary metabolism

DEFF Research Database (Denmark)

Rioseras, Beatriz; Sliaha, Pavel V; Gorshkov, Vladimir

2018-01-01

identified and quantified 3461 proteins corresponding to 44.3% of the S. coelicolor proteome across three developmental stages: vegetative hypha (MI); secondary metabolite producing hyphae (MII); and sporulating hyphae. A total of 1350 proteins exhibited more than 2-fold expression changes during....../Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor. We...... the bacterial differentiation process. These proteins include 136 regulators (transcriptional regulators, transducers, Ser/Thr/Tyr kinases, signalling proteins), as well as 542 putative proteins with no clear homology to known proteins which are likely to play a role in differentiation and secondary metabolism...

Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.

Science.gov (United States)

Panizza, Elena; Branca, Rui M M; Oliviusson, Peter; Orre, Lukas M; Lehtiö, Janne

2017-07-03

Protein phosphorylation is involved in the regulation of most eukaryotic cells functions and mass spectrometry-based analysis has made major contributions to our understanding of this regulation. However, low abundance of phosphorylated species presents a major challenge in achieving comprehensive phosphoproteome coverage and robust quantification. In this study, we developed a workflow employing titanium dioxide phospho-enrichment coupled with isobaric labeling by Tandem Mass Tags (TMT) and high-resolution isoelectric focusing (HiRIEF) fractionation to perform in-depth quantitative phosphoproteomics starting with a low sample quantity. To benchmark the workflow, we analyzed HeLa cells upon pervanadate treatment or cell cycle arrest in mitosis. Analyzing 300 µg of peptides per sample, we identified 22,712 phosphorylation sites, of which 19,075 were localized with high confidence and 1,203 are phosphorylated tyrosine residues, representing 6.3% of all detected phospho-sites. HiRIEF fractions with the most acidic isoelectric points are enriched in multiply phosphorylated peptides, which represent 18% of all the phospho-peptides detected in the pH range 2.5-3.7. Cross-referencing with the PhosphoSitePlus database reveals 1,264 phosphorylation sites that have not been previously reported and kinase association analysis suggests that a subset of these may be functional during the mitotic phase.

Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

Science.gov (United States)

Mayya, Viveka; Han, David K

2009-12-01

Phosphorylation of proteins is a predominant, reversible post-translational modification. It is central to a wide variety of physiological responses and signaling mechanisms. Recent advances have allowed the global scope of phosphorylation to be addressed by mass spectrometry using phosphoproteomic approaches. In this perspective, we discuss four aspects of phosphoproteomics: the insights and implications from recently published phosphoproteomic studies and the applications and limitations of current phosphoproteomic strategies. Since approximately 50,000 known phosphorylation sites do not yet have any ascribed function, we present our perspectives on a major function of protein phosphorylation that may be of predictive value in hypothesis-based investigations. Finally, we discuss strategies to measure the stoichiometry of phosphorylation in a proteome-wide manner that is not provided by current phosphoproteomic approaches.

Analytical strategies in mass spectrometry-based phosphoproteomics

DEFF Research Database (Denmark)

Rosenqvist, Heidi; Ye, Juanying; Jensen, Ole N

2011-01-01

then discuss various tandem mass spectrometry approaches for phosphopeptide sequencing and quantification, and we consider aspects of phosphoproteome data analysis and interpretation. Efficient integration of these stages of phosphoproteome analysis is highly important to ensure a successful outcome of large...

Quantitative cardiac phosphoproteomics profiling during ischemia-reperfusion in an immature swine model

Energy Technology Data Exchange (ETDEWEB)

Ledee, Dolena R.; Kang, Min A.; Kajimoto, Masaki; Purvine, Samuel O.; Brewer, Heather M.; Pasa Tolic, Ljiljana; Portman, Michael A.

2017-07-01

Ischemia-reperfusion (I/R) results in altered metabolic and molecular responses, and phosphorylation is one of the most noted regulatory mechanisms mediating signaling mechanisms during physiological stresses. To expand our knowledge of the potential phosphoproteomic changes in the myocardium during I/R, we used Isobaric Tags for Relative and Absolute Quantitation-based analyses in left ventricular samples obtained from porcine hearts under control or I/R conditions. The data are available via ProteomeXchange with identifier PXD006066. We identified 1,896 phosphopeptides within left ventricular control and I/R porcine samples. Significant differential phosphorylation between control and I/R groups was discovered in 111 phosphopeptides from 86 proteins. Analysis of the phosphopeptides using Motif-x identified five motifs: (..R..S..), (..SP..), (..S.S..), (..S…S..), and (..S.T..). Semiquantitative immunoblots confirmed site location and directional changes in phosphorylation for phospholamban and pyruvate dehydrogenase E1, two proteins known to be altered by I/R and identified by this study. Novel phosphorylation sites associated with I/R were also identified. Functional characterization of the phosphopeptides identified by our methodology could expand our understanding of the signaling mechanisms involved during I/R damage in the heart as well as identify new areas to target therapeutic strategies.

Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response.

Science.gov (United States)

Schmidt, Andreas; Trentini, Débora Broch; Spiess, Silvia; Fuhrmann, Jakob; Ammerer, Gustav; Mechtler, Karl; Clausen, Tim

2014-02-01

Arginine phosphorylation is an emerging protein modification implicated in the general stress response of Gram-positive bacteria. The modification is mediated by the arginine kinase McsB, which phosphorylates and inactivates the heat shock repressor CtsR. In this study, we developed a mass spectrometric approach accounting for the peculiar chemical properties of phosphoarginine. The improved methodology was used to analyze the dynamic changes in the Bacillus subtilis arginine phosphoproteome in response to different stress situations. Quantitative analysis showed that a B. subtilis mutant lacking the YwlE arginine phosphatase accumulated a strikingly large number of arginine phosphorylations (217 sites in 134 proteins), however only a minor fraction of these sites was increasingly modified during heat shock or oxidative stress. The main targets of McsB-mediated arginine phosphorylation comprise central factors of the stress response system including the CtsR and HrcA heat shock repressors, as well as major components of the protein quality control system such as the ClpCP protease and the GroEL chaperonine. These findings highlight the impact of arginine phosphorylation in orchestrating the bacterial stress response.

Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.

Science.gov (United States)

Imamura, Haruna; Wagih, Omar; Niinae, Tomoya; Sugiyama, Naoyuki; Beltrao, Pedro; Ishihama, Yasushi

2017-04-07

Protein kinase A (PKA or cAMP-dependent protein kinase) is a serine/threonine kinase that plays essential roles in the regulation of proliferation, differentiation, and apoptosis. To better understand the functions of PKA, it is necessary to elucidate the direct interplay between PKA and their substrates in living human cells. To identify kinase target substrates in a high-throughput manner, we first quantified the change of phosphoproteome in the cells of which PKA activity was perturbed by drug stimulations. LC-MS/MS analyses identified 2755 and 3191 phosphopeptides from experiments with activator or inhibitor of PKA. To exclude potential indirect targets of PKA, we built a computational model to characterize the kinase sequence specificity toward the substrate target site based on known kinase-substrate relationships. Finally, by combining the sequence recognition model with the quantitative changes in phosphorylation measured in the two drug perturbation experiments, we identified 29 reliable candidates of PKA targeting residues in living cells including 8 previously known substrates. Moreover, 18 of these sites were confirmed to be site-specifically phosphorylated in vitro. Altogether this study proposed a confident list of PKA substrate candidates, expanding our knowledge of PKA signaling network.

Phosphoproteome profiling for cold temperature perception.

Science.gov (United States)

Park, Seyeon; Jang, Mi

2011-02-01

Temperature sensation initiates from the activation of cellular receptors when the cell is exposed to a decrease in temperature. Here, we applied a phosphoproteome profiling approach to the human lung epithelial cell line BEAS-2B to elucidate cellular cold-responsive processes. The primary aim of this study was to determine which intracellular changes of phosphorylation are accompanied by cold sensation. Eighteen protein spots that exhibited differentially phosphorylated changes in cells were identified. Most of the proteins that were phosphorylated after 5 or 10 min were returned to control levels after 30 or 60 min. Identified proteins were mainly RNA-related (i.e., they were involved in RNA binding and splicing). Temperature (18 and 10°C) stimuli showed homologies that were detected for time course changes in phosphoproteome. The data indicated a time-shift between two temperatures. The phosphorylation of putative cold responsive markers, such as ribosomal protein large P0 and heterochromatin-associated proteins 1, were verified by Western blotting in cells transfected with TRPM8 or TRPA1. Copyright © 2010 Wiley-Liss, Inc.

Large-Scale Phosphoproteomics Reveals Shp-2 Phosphatase-Dependent Regulators of Pdgf Receptor Signaling

DEFF Research Database (Denmark)

Batth, Tanveer S; Papetti, Moreno; Pfeiffer, Anamarija

2018-01-01

Despite its low cellular abundance, phosphotyrosine (pTyr) regulates numerous cell signaling pathways in health and disease. We applied comprehensive phosphoproteomics to unravel differential regulators of receptor tyrosine kinase (RTK)-initiated signaling networks upon activation by Pdgf-ββ, Fgf-2...... of Pdgfr pTyr signaling. Application of a recently introduced allosteric Shp-2 inhibitor revealed global regulation of the Pdgf-dependent tyrosine phosphoproteome, which significantly impaired cell migration. In addition, we present a list of hundreds of Shp-2-dependent targets and putative substrates...

Data set from a comprehensive phosphoproteomic analysis of rice variety IRBB5 in response to bacterial blight

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Yuxuan Hou

2016-03-01

Full Text Available Bacterial blight (BB caused by Xanthomonas oryzae pv. oryzae (Xoo has become one of the most devastating diseases for rice, a major food source for over half of the world populations. To investigate the roles of protein phosphorylation in rice bacterial blight resistance, a quantitative phosphoproteomic study was conducted in rice variety IRBB5 at 0 h and 24 h after Xoo infection. 2367 and 2223 phosphosites on 1334 and 1297 representative proteins were identified in 0 h and 24 h after Xoo infection, respectively, out of which 762 proteins were found to be differentially phosphorylated. In associated with the published article “A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight” in BMC Plant Biology (Hou et al., 2015 [1], this dataset article provided the detailed information of experimental designing, methods, features as well as the raw data of mass spectrometry (MS identification. The MS proteomics data could be fully accessed from the ProteomeXchange Consortium with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002222. Keywords: Rice (Oryza sativa L., Bacterial blight, Phosphoproteome

Quantitative phosphoproteomic analysis reveals shared and specific targets of Arabidopsis MPK3, MPK4 and MPK6

KAUST Repository

Rayapuram, Naganand; Bigeard, Jean; Alhoraibi, Hanna Mohsen Abdulrab; Bonhomme, Ludovic; Hesse, Anne-Marie; Vinh, Joelle; Hirt, Heribert; Pflieger, Delphine

2017-01-01

In Arabidopsis, mitogen-activated protein kinases MPK3, MPK4 and MPK6 constitute essential relays for a variety of functions including cell division, development and innate immunity. While some substrates of MPK3, MPK4 and MPK6 have been identified, the picture is still far from complete. To identify substrates of these MAPKs likely involved in cell division, growth and development we compared the phosphoproteomes of wild-type and mpk3, mpk4 and mpk6. To study the function of these MAPKs in innate immunity, we analyzed their phosphoproteomes following microbe-associated molecular pattern (MAMP) treatment. Partially overlapping substrates were retrieved for all three MAPKs, showing target specificity to one, two or all three MAPKs in different biological processes. More precisely, our results illustrate the fact that the entity to be defined as a specific or a shared substrate for MAPKs is not a phosphoprotein but a particular (S/T)P phosphorylation site in a given protein. As a whole, 152 peptides were identified to be differentially phosphorylated in response to MAMP treatment and/or when compared between genotypes and 70 of them could be classified as putative MAPK targets. Biochemical analysis of a number of putative MAPK substrates by phosphorylation and interaction assays confirmed the global phosphoproteome approach. Our study also expands the set of MAPK substrates to involve other protein kinases, including calcium-dependent (CDPK) and sugar non-fermenting (SnRK) protein kinases.

Quantitative phosphoproteomic analysis reveals shared and specific targets of Arabidopsis MPK3, MPK4 and MPK6

KAUST Repository

Rayapuram, Naganand

2017-11-23

In Arabidopsis, mitogen-activated protein kinases MPK3, MPK4 and MPK6 constitute essential relays for a variety of functions including cell division, development and innate immunity. While some substrates of MPK3, MPK4 and MPK6 have been identified, the picture is still far from complete. To identify substrates of these MAPKs likely involved in cell division, growth and development we compared the phosphoproteomes of wild-type and mpk3, mpk4 and mpk6. To study the function of these MAPKs in innate immunity, we analyzed their phosphoproteomes following microbe-associated molecular pattern (MAMP) treatment. Partially overlapping substrates were retrieved for all three MAPKs, showing target specificity to one, two or all three MAPKs in different biological processes. More precisely, our results illustrate the fact that the entity to be defined as a specific or a shared substrate for MAPKs is not a phosphoprotein but a particular (S/T)P phosphorylation site in a given protein. As a whole, 152 peptides were identified to be differentially phosphorylated in response to MAMP treatment and/or when compared between genotypes and 70 of them could be classified as putative MAPK targets. Biochemical analysis of a number of putative MAPK substrates by phosphorylation and interaction assays confirmed the global phosphoproteome approach. Our study also expands the set of MAPK substrates to involve other protein kinases, including calcium-dependent (CDPK) and sugar non-fermenting (SnRK) protein kinases.

Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation.

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Philipp eSpät

2015-03-01

Full Text Available Cyanobacteria have shaped the earth’s biosphere as the first oxygenic photoautotrophs and still play an important role in many ecosystems. The ability to adapt to changing environmental conditions is an essential characteristic in order to ensure survival. To this end, numerous studies have shown that bacteria use protein post-translational modifications such as Ser/Thr/Tyr phosphorylation in cell signalling, adaptation and regulation. Nevertheless, our knowledge of cyanobacterial phosphoproteomes and their dynamic response to environmental stimuli is relatively limited. In this study, we applied gel-free methods and high accuracy mass spectrometry towards the unbiased detection of Ser/Thr/Tyr phosphorylation events in the model cyanobacterium Synechocystis sp. PCC 6803. We could identify over 300 phosphorylation events in cultures grown on nitrate as exclusive nitrogen source. Chemical dimethylation labelling was applied to investigate proteome and phosphoproteome dynamics during nitrogen starvation. Our dataset describes the most comprehensive (phosphoproteome of Synechocystis to date, identifying 2,382 proteins and 183 phosphorylation events and quantifying 2,111 proteins and 148 phosphorylation events during nitrogen starvation. Global protein phosphorylation levels were increased in response to nitrogen depletion after 24 hours. Among the proteins with increased phosphorylation, the PII signalling protein showed the highest fold-change, serving as positive control. Other proteins with increased phosphorylation levels comprised functions in photosynthesis and in carbon and nitrogen metabolism. This study reveals dynamics of Synechocystis phosphoproteome in response to environmental stimuli and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of homeostatic control in cyanobacteria.

Impact of Phosphoproteomics in the Era of Precision Medicine for Prostate Cancer

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Johnny R. Ramroop

2018-02-01

Full Text Available Prostate cancer is the most common malignancy in men in the United States. While androgen deprivation therapy results in tumor responses initially, there is relapse and progression to metastatic castration-resistant prostate cancer. Currently, all prostate cancer patients receive essentially the same treatment, and there is a need for clinically applicable technologies to provide predictive biomarkers toward personalized therapies. Genomic analyses of tumors are used for clinical applications, but with a paucity of obvious driver mutations in metastatic castration-resistant prostate cancer, other applications, such as phosphoproteomics, may complement this approach. Immunohistochemistry and reverse phase protein arrays are limited by the availability of reliable antibodies and evaluates a preselected number of targets. Mass spectrometry-based phosphoproteomics has been used to profile tumors consisting of thousands of phosphopeptides from individual patients after surgical resection or at autopsy. However, this approach is time consuming, and while a large number of candidate phosphopeptides are obtained for evaluation, limitations are reduced reproducibility, sensitivity, and precision. Targeted mass spectrometry can help eliminate these limitations and is more cost effective and less time consuming making it a practical platform for future clinical testing. In this review, we discuss the use of phosphoproteomics in prostate cancer and other clinical cancer tissues for target identification, hypothesis testing, and possible patient stratification. We highlight the majority of studies that have used phosphoproteomics in prostate cancer tissues and cell lines and propose ways forward to apply this approach in basic and clinical research. Overall, the implementation of phosphoproteomics via targeted mass spectrometry has tremendous potential to aid in the development of more rational, personalized therapies that will result in increased survival

Analytical strategies for phosphoproteomics

DEFF Research Database (Denmark)

Thingholm, Tine E; Jensen, Ole N; Larsen, Martin R

2009-01-01

sensitive and specific strategies. Today, most phosphoproteomic studies are conducted by mass spectrometric strategies in combination with phospho-specific enrichment methods. This review presents an overview of different analytical strategies for the characterization of phosphoproteins. Emphasis...

Identification of Putative Mek1 Substrates during Meiosis in Saccharomyces cerevisiae Using Quantitative Phosphoproteomics.

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Raymond T Suhandynata

Full Text Available Meiotic recombination plays a key role in sexual reproduction as it generates crossovers that, in combination with sister chromatid cohesion, physically connect homologous chromosomes, thereby promoting their proper segregation at the first meiotic division. Meiotic recombination is initiated by programmed double strand breaks (DSBs catalyzed by the evolutionarily conserved, topoisomerase-like protein Spo11. Repair of these DSBs is highly regulated to create crossovers between homologs that are distributed throughout the genome. This repair requires the presence of the mitotic recombinase, Rad51, as well as the strand exchange activity of the meiosis-specific recombinase, Dmc1. A key regulator of meiotic DSB repair in Saccharomyces cerevisiae is the meiosis-specific kinase Mek1, which promotes interhomolog strand invasion and is required for the meiotic recombination checkpoint and the crossover/noncrossover decision. Understanding how Mek1 regulates meiotic recombination requires the identification of its substrates. Towards that end, an unbiased phosphoproteomic approach utilizing Stable Isotope Labeling by Amino Acids in Cells (SILAC was utilized to generate a list of potential Mek1 substrates, as well as proteins containing consensus phosphorylation sites for cyclin-dependent kinase, the checkpoint kinases, Mec1/Tel1, and the polo-like kinase, Cdc5. These experiments represent the first global phosphoproteomic dataset for proteins in meiotic budding yeast.

Recent findings and technological advances in phosphoproteomics for cells and tissues

DEFF Research Database (Denmark)

von Stechow, Louise; Francavilla, Chiara; Olsen, Jesper V

2015-01-01

in different diseases, including cancer. Large-scale studies of phosphoproteins - termed phosphoproteomics - strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many...... technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed...

Enrichment techniques employed in phosphoproteomics

Czech Academy of Sciences Publication Activity Database

Fíla, Jan; Honys, David

2012-01-01

Roč. 43, č. 3 (2012), s. 1025-1047 ISSN 0939-4451 R&D Projects: GA ČR(CZ) GAP501/11/1462; GA ČR GA522/09/0858; GA ČR GA525/09/0994; GA MŠk OC08011 Institutional research plan: CEZ:AV0Z50380511 Keywords : Phosphoproteomics * Enrichment * IMAC Subject RIV: ED - Physiology Impact factor: 3.914, year: 2012

Benchmarking common quantification strategies for large-scale phosphoproteomics

DEFF Research Database (Denmark)

Hogrebe, Alexander; von Stechow, Louise; Bekker-Jensen, Dorte B

2018-01-01

Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free...

Quantitative Phosphoproteomic Analysis Provides Insight into the Response to Short-Term Drought Stress in Ammopiptanthus mongolicus Roots

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Huigai Sun

2017-10-01

Full Text Available Drought is one of the major abiotic stresses that negatively affects plant growth and development. Ammopiptanthus mongolicus is an ecologically important shrub in the mid-Asia desert region and used as a model for abiotic tolerance research in trees. Protein phosphorylation participates in the regulation of various biological processes, however, phosphorylation events associated with drought stress signaling and response in plants is still limited. Here, we conducted a quantitative phosphoproteomic analysis of the response of A. mongolicus roots to short-term drought stress. Data are available via the iProx database with project ID IPX0000971000. In total, 7841 phosphorylation sites were found from the 2019 identified phosphopeptides, corresponding to 1060 phosphoproteins. Drought stress results in significant changes in the abundance of 103 phosphopeptides, corresponding to 90 differentially-phosphorylated phosphoproteins (DPPs. Motif-x analysis identified two motifs, including [pSP] and [RXXpS], from these DPPs. Functional enrichment and protein-protein interaction analysis showed that the DPPs were mainly involved in signal transduction and transcriptional regulation, osmotic adjustment, stress response and defense, RNA splicing and transport, protein synthesis, folding and degradation, and epigenetic regulation. These drought-corresponsive phosphoproteins, and the related signaling and metabolic pathways probably play important roles in drought stress signaling and response in A. mongolicus roots. Our results provide new information for understanding the molecular mechanism of the abiotic stress response in plants at the posttranslational level.

IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data.

Science.gov (United States)

Mischnik, Marcel; Sacco, Francesca; Cox, Jürgen; Schneider, Hans-Christoph; Schäfer, Matthias; Hendlich, Manfred; Crowther, Daniel; Mann, Matthias; Klabunde, Thomas

2016-02-01

Phosphoproteomics measurements are widely applied in cellular biology to detect changes in signalling dynamics. However, due to the inherent complexity of phosphorylation patterns and the lack of knowledge on how phosphorylations are related to functions, it is often not possible to directly deduce protein activities from those measurements. Here, we present a heuristic machine learning algorithm that infers the activities of kinases from Phosphoproteomics data using kinase-target information from the PhosphoSitePlus database. By comparing the estimated kinase activity profiles to the measured phosphosite profiles, it is furthermore possible to derive the kinases that are most likely to phosphorylate the respective phosphosite. We apply our approach to published datasets of the human cell cycle generated from HeLaS3 cells, and insulin signalling dynamics in mouse hepatocytes. In the first case, we estimate the activities of 118 at six cell cycle stages and derive 94 new kinase-phosphosite links that can be validated through either database or motif information. In the second case, the activities of 143 kinases at eight time points are estimated and 49 new kinase-target links are derived. The algorithm is implemented in Matlab and be downloaded from github. It makes use of the Optimization and Statistics toolboxes. https://github.com/marcel-mischnik/IKAP.git. marcel.mischnik@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

DEFF Research Database (Denmark)

Batth, Tanveer S; Francavilla, Chiara; Olsen, Jesper V

2014-01-01

thousands of phosphorylation sites. However, in-depth phosphoproteomics often require off-line enrichment and fractionation techniques. In this study, we provide a detailed analysis of the physicochemical characteristics of phosphopeptides, which have been fractionated by off-line high-pH chromatography (Hp...... phosphorylated peptides over that with SCX. Further optimizations in the pooling and concatenation strategy increased the total number of multiphosphorylated peptides detected after HpH fractionation. In conclusion, we provide a basic framework and resource for performing in-depth phosphoproteome studies...

The phosphoproteome of toll-like receptor-activated macrophages

DEFF Research Database (Denmark)

Weintz, Gabriele; Olsen, Jesper Velgaard; Frühauf, Katja

2010-01-01

other signalling modules (e.g. mTOR, ATM/ATR kinases) and the cytoskeleton as hotspots of LPS-regulated phosphorylation. Finally, weaving together phosphoproteome and nascent transcriptome data by in silico promoter analysis, we implicated several phosphorylated TFs in primary LPS-controlled gene...

Phosphoproteomic fingerprinting of epidermal growth factor signaling and anticancer drug action in human tumor cells.

Science.gov (United States)

Lim, Yoon-Pin; Diong, Lang-Shi; Qi, Robert; Druker, Brian J; Epstein, Richard J

2003-12-01

Many proteins regulating cancer cell growth are tyrosine phosphorylated. Using antiphosphotyrosine affinity chromatography, thiourea protein solubilization, two-dimensional PAGE, and mass spectrometry, we report here the characterization of the epidermal growth factor (EGF)-induced phosphoproteome in A431 human epidermoid carcinoma cells. Using this approach, more than 50 distinct tyrosine phosphoproteins are identifiable within five main clusters-cytoskeletal proteins, signaling enzymes, SH2-containing adaptors, chaperones, and focal adhesion proteins. Comparison of the phosphoproteomes induced in vitro by transforming growth factor-alpha and platelet-derived growth factor demonstrates the pathway- and cell-specific nature of the phosphoproteomes induced. Elimination of both basal and ligand-dependent phosphoproteins by cell exposure to the EGF receptor catalytic inhibitor gefitinib (Iressa, ZD1839) suggests either an autocrine growth loop or the presence of a second inhibited kinase in A431 cells. By identifying distinct patterns of phosphorylation involving novel signaling substrates, and by clarifying the mechanism of action of anticancer drugs, these findings illustrate the potential of immunoaffinity-based phosphoproteomics for guiding the discovery of new drug targets and the rational utilization of pathway-specific chemotherapies.

Technologies and challenges in large-scale phosphoproteomics

DEFF Research Database (Denmark)

Engholm-Keller, Kasper; Larsen, Martin Røssel

2013-01-01

become the main technique for discovery and characterization of phosphoproteins in a nonhypothesis driven fashion. In this review, we describe methods for state-of-the-art MS-based analysis of protein phosphorylation as well as the strategies employed in large-scale phosphoproteomic experiments...... with focus on the various challenges and limitations this field currently faces....

Phosphoproteomics Analysis of Endometrium in Women with or without Endometriosis

Directory of Open Access Journals (Sweden)

Hong-Mei Xu

2015-01-01

Conclusions: That large-scale phosphoproteome quantification has been successfully identified in endometrium tissues of women with or without endometriosis will provide new insights to understand the molecular mechanisms of the development of endometriosis.

Quantitative Phosphoproteomics Reveals Wee1 Kinase as a Therapeutic Target in a Model of Proneural Glioblastoma.

Science.gov (United States)

Lescarbeau, Rebecca S; Lei, Liang; Bakken, Katrina K; Sims, Peter A; Sarkaria, Jann N; Canoll, Peter; White, Forest M

2016-06-01

Glioblastoma (GBM) is the most common malignant primary brain cancer. With a median survival of about a year, new approaches to treating this disease are necessary. To identify signaling molecules regulating GBM progression in a genetically engineered murine model of proneural GBM, we quantified phosphotyrosine-mediated signaling using mass spectrometry. Oncogenic signals, including phosphorylated ERK MAPK, PI3K, and PDGFR, were found to be increased in the murine tumors relative to brain. Phosphorylation of CDK1 pY15, associated with the G2 arrest checkpoint, was identified as the most differentially phosphorylated site, with a 14-fold increase in phosphorylation in the tumors. To assess the role of this checkpoint as a potential therapeutic target, syngeneic primary cell lines derived from these tumors were treated with MK-1775, an inhibitor of Wee1, the kinase responsible for CDK1 Y15 phosphorylation. MK-1775 treatment led to mitotic catastrophe, as defined by increased DNA damage and cell death by apoptosis. To assess the extensibility of targeting Wee1/CDK1 in GBM, patient-derived xenograft (PDX) cell lines were also treated with MK-1775. Although the response was more heterogeneous, on-target Wee1 inhibition led to decreased CDK1 Y15 phosphorylation and increased DNA damage and apoptosis in each line. These results were also validated in vivo, where single-agent MK-1775 demonstrated an antitumor effect on a flank PDX tumor model, increasing mouse survival by 1.74-fold. This study highlights the ability of unbiased quantitative phosphoproteomics to reveal therapeutic targets in tumor models, and the potential for Wee1 inhibition as a treatment approach in preclinical models of GBM. Mol Cancer Ther; 15(6); 1332-43. ©2016 AACR. ©2016 American Association for Cancer Research.

Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia.

Science.gov (United States)

Hernandez-Valladares, Maria; Aasebø, Elise; Selheim, Frode; Berven, Frode S; Bruserud, Øystein

2016-08-22

Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.

Science.gov (United States)

Melas, Ioannis N; Mitsos, Alexander; Messinis, Dimitris E; Weiss, Thomas S; Rodriguez, Julio-Saez; Alexopoulos, Leonidas G

2012-04-01

Construction of large and cell-specific signaling pathways is essential to understand information processing under normal and pathological conditions. On this front, gene-based approaches offer the advantage of large pathway exploration whereas phosphoproteomic approaches offer a more reliable view of pathway activities but are applicable to small pathway sizes. In this paper, we demonstrate an experimentally adaptive approach to construct large signaling pathways from phosphoproteomic data within a 3-day time frame. Our approach--taking advantage of the fast turnaround time of the xMAP technology--is carried out in four steps: (i) screen optimal pathway inducers, (ii) select the responsive ones, (iii) combine them in a combinatorial fashion to construct a phosphoproteomic dataset, and (iv) optimize a reduced generic pathway via an Integer Linear Programming formulation. As a case study, we uncover novel players and their corresponding pathways in primary human hepatocytes by interrogating the signal transduction downstream of 81 receptors of interest and constructing a detailed model for the responsive part of the network comprising 177 species (of which 14 are measured) and 365 interactions.

Quantitative Phospho-proteomic Analysis of TNFα/NFκB Signaling Reveals a Role for RIPK1 Phosphorylation in Suppressing Necrotic Cell Death.

Science.gov (United States)

Mohideen, Firaz; Paulo, Joao A; Ordureau, Alban; Gygi, Steve P; Harper, J Wade

2017-07-01

TNFα is a potent inducer of inflammation due to its ability to promote gene expression, in part via the NFκB pathway. Moreover, in some contexts, TNFα promotes Caspase-dependent apoptosis or RIPK1/RIPK3/MLKL-dependent necrosis. Engagement of the TNF Receptor Signaling Complex (TNF-RSC), which contains multiple kinase activities, promotes phosphorylation of several downstream components, including TAK1, IKKα/IKKβ, IκBα, and NFκB. However, immediate downstream phosphorylation events occurring in response to TNFα signaling are poorly understood at a proteome-wide level. Here we use Tandem Mass Tagging-based proteomics to quantitatively characterize acute TNFα-mediated alterations in the proteome and phosphoproteome with or without inhibition of the cIAP-dependent survival arm of the pathway with a SMAC mimetic. We identify and quantify over 8,000 phosphorylated peptides, among which are numerous known sites in the TNF-RSC, NFκB, and MAP kinase signaling systems, as well as numerous previously unrecognized phosphorylation events. Functional analysis of S320 phosphorylation in RIPK1 demonstrates a role for this event in suppressing its kinase activity, association with CASPASE-8 and FADD proteins, and subsequent necrotic cell death during inflammatory TNFα stimulation. This study provides a resource for further elucidation of TNFα-dependent signaling pathways. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia

Directory of Open Access Journals (Sweden)

Maria Hernandez-Valladares

2016-08-01

Full Text Available Global mass spectrometry (MS-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC or metal oxide affinity chromatography (MOAC. We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.

Identification and quantitation of signal molecule-dependent protein phosphorylation

KAUST Repository

Groen, Arnoud J.

2013-09-03

Phosphoproteomics is a fast-growing field that aims at characterizing phosphorylated proteins in a cell or a tissue at a given time. Phosphorylation of proteins is an important regulatory mechanism in many cellular processes. Gel-free phosphoproteome technique involving enrichment of phosphopeptide coupled with mass spectrometry has proven to be invaluable to detect and characterize phosphorylated proteins. In this chapter, a gel-free quantitative approach involving 15N metabolic labelling in combination with phosphopeptide enrichment by titanium dioxide (TiO2) and their identification by MS is described. This workflow can be used to gain insights into the role of signalling molecules such as cyclic nucleotides on regulatory networks through the identification and quantification of responsive phospho(proteins). © Springer Science+Business Media New York 2013.

Phosphoproteomic analysis of chromoplasts from sweet orange during fruit ripening.

Science.gov (United States)

Zeng, Yunliu; Pan, Zhiyong; Wang, Lun; Ding, Yuduan; Xu, Qiang; Xiao, Shunyuan; Deng, Xiuxin

2014-02-01

Like other types of plastids, chromoplasts have essential biosynthetic and metabolic activities which may be regulated via post-translational modifications, such as phosphorylation, of their resident proteins. We here report a proteome-wide mapping of in vivo phosphorylation sites in chromoplast-enriched samples prepared from sweet orange [Citrus sinensis (L.) Osbeck] at different ripening stages by titanium dioxide-based affinity chromatography for phosphoprotein enrichment with LC-MS/MS. A total of 109 plastid-localized phosphoprotein candidates were identified that correspond to 179 unique phosphorylation sites in 135 phosphopeptides. On the basis of Motif-X analysis, two distinct types of phosphorylation sites, one as proline-directed phosphorylation motif and the other as casein kinase II motif, can be generalized from these identified phosphopeptides. While most identified phosphoproteins show high homology to those already identified in plastids, approximately 22% of them are novel based on BLAST search using the public databases PhosPhAt and P(3) DB. A close comparative analysis showed that approximately 50% of the phosphoproteins identified in citrus chromoplasts find obvious counterparts in the chloroplast phosphoproteome, suggesting a rather high-level of conservation in basic metabolic activities in these two types of plastids. Not surprisingly, the phosphoproteome of citrus chromoplasts is also characterized by the lack of phosphoproteins involved in photosynthesis and by the presence of more phosphoproteins implicated in stress/redox responses. This study presents the first comprehensive phosphoproteomic analysis of chromoplasts and may help to understand how phosphorylation regulates differentiation of citrus chromoplasts during fruit ripening. © 2013 Scandinavian Plant Physiology Society.

Battle through signaling between wheat and the fungal pathogen Septoria tritici revealed by proteomics and phosphoproteomics.

Science.gov (United States)

Yang, Fen; Melo-Braga, Marcella N; Larsen, Martin R; Jørgensen, Hans J L; Palmisano, Giuseppe

2013-09-01

The fungus Septoria tritici causes the disease septoria tritici blotch in wheat, one of the most economically devastating foliar diseases in this crop. To investigate signaling events and defense responses in the wheat-S. tritici interaction, we performed a time-course study of S. tritici infection in resistant and susceptible wheat using quantitative proteomics and phosphoproteomics, with special emphasis on the initial biotrophic phase of interactions. Our study revealed an accumulation of defense and stress-related proteins, suppression of photosynthesis, and changes in sugar metabolism during compatible and incompatible interactions. However, differential regulation of the phosphorylation status of signaling proteins, transcription and translation regulators, and membrane-associated proteins was observed between two interactions. The proteomic data were correlated with a more rapid or stronger accumulation of signal molecules, including calcium, H2O2, NO, and sugars, in the resistant than in the susceptible cultivar in response to the infection. Additionally, 31 proteins and 5 phosphoproteins from the pathogen were identified, including metabolic proteins and signaling proteins such as GTP-binding proteins, 14-3-3 proteins, and calcium-binding proteins. Quantitative PCR analysis showed the expression of fungal signaling genes and genes encoding a superoxide dismutase and cell-wall degrading enzymes. These results indicate roles of signaling, antioxidative stress mechanisms, and nutrient acquisition in facilitating the initial symptomless growth. Taken in its entirety, our dataset suggests interplay between the plant and S. tritici through complex signaling networks and downstream molecular events. Resistance is likely related to several rapidly and intensively triggered signal transduction cascades resulting in a multiple-level activation of transcription and translation processes of defense responses. Our sensitive approaches and model provide a comprehensive

Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity

DEFF Research Database (Denmark)

Jersie-Christensen, Rosa R.; Sultan, Abida; Olsen, Jesper V

2016-01-01

The traditional sample preparation workflow for mass spectrometry (MS)-based phosphoproteomics is time consuming and usually requires multiple steps, e.g., lysis, protein precipitation, reduction, alkylation, digestion, fractionation, and phosphopeptide enrichment. Each step can introduce chemical...... artifacts, in vitro protein and peptide modifications, and contaminations. Those often result in sample loss and affect the sensitivity, dynamic range and accuracy of the mass spectrometric analysis. Here we describe a simple and reproducible phosphoproteomics protocol, where lysis, denaturation, reduction......, and alkylation are performed in a single step, thus reducing sample loss and increasing reproducibility. Moreover, unlike standard cell lysis procedures the cell harvesting is performed at high temperatures (99 °C) and without detergents and subsequent need for protein precipitation. Phosphopeptides are enriched...

Phosphoproteomic biomarkers predicting histologic nonalcoholic steatohepatitis and fibrosis.

Science.gov (United States)

Younossi, Zobair M; Baranova, Ancha; Stepanova, Maria; Page, Sandra; Calvert, Valerie S; Afendy, Arian; Goodman, Zachary; Chandhoke, Vikas; Liotta, Lance; Petricoin, Emanuel

2010-06-04

The progression of nonalcoholic fatty liver disease (NAFLD) has been linked to deregulated exchange of the endocrine signaling between adipose and liver tissue. Proteomic assays for the phosphorylation events that characterize the activated or deactivated state of the kinase-driven signaling cascades in visceral adipose tissue (VAT) could shed light on the pathogenesis of nonalcoholic steatohepatitis (NASH) and related fibrosis. Reverse-phase protein microarrays (RPMA) were used to develop biomarkers for NASH and fibrosis using VAT collected from 167 NAFLD patients (training cohort, N = 117; testing cohort, N = 50). Three types of models were developed for NASH and advanced fibrosis: clinical models, proteomics models, and combination models. NASH was predicted by a model that included measurements of two components of the insulin signaling pathway: AKT kinase and insulin receptor substrate 1 (IRS1). The models for fibrosis were less reliable when predictions were based on phosphoproteomic, clinical, or the combination data. The best performing model relied on levels of the phosphorylation of GSK3 as well as on two subunits of cyclic AMP regulated protein kinase A (PKA). Phosphoproteomics technology could potentially be used to provide pathogenic information about NASH and NASH-related fibrosis. This information can lead to a clinically relevant diagnostic/prognostic biomarker for NASH.

The proteome and phosphoproteome of maize pollen uncovers fertility candidate proteins.

Science.gov (United States)

Chao, Qing; Gao, Zhi-Fang; Wang, Yue-Feng; Li, Zhe; Huang, Xia-He; Wang, Ying-Chun; Mei, Ying-Chang; Zhao, Biligen-Gaowa; Li, Liang; Jiang, Yu-Bo; Wang, Bai-Chen

2016-06-01

Maize is unique since it is both monoecious and diclinous (separate male and female flowers on the same plant). We investigated the proteome and phosphoproteome of maize pollen containing modified proteins and here we provide a comprehensive pollen proteome and phosphoproteome which contain 100,990 peptides from 6750 proteins and 5292 phosphorylated sites corresponding to 2257 maize phosphoproteins, respectively. Interestingly, among the total 27 overrepresented phosphosite motifs we identified here, 11 were novel motifs, which suggested different modification mechanisms in plants compared to those of animals. Enrichment analysis of pollen phosphoproteins showed that pathways including DNA synthesis/chromatin structure, regulation of RNA transcription, protein modification, cell organization, signal transduction, cell cycle, vesicle transport, transport of ions and metabolisms, which were involved in pollen development, the following germination and pollen tube growth, were regulated by phosphorylation. In this study, we also found 430 kinases and 105 phosphatases in the maize pollen phosphoproteome, among which calcium dependent protein kinases (CDPKs), leucine rich repeat kinase, SNF1 related protein kinases and MAPK family proteins were heavily enriched and further analyzed. From our research, we also uncovered hundreds of male sterility-associated proteins and phosphoproteins that might influence maize productivity and serve as targets for hybrid maize seed production. At last, a putative complex signaling pathway involving CDPKs, MAPKs, ubiquitin ligases and multiple fertility proteins was constructed. Overall, our data provides new insight for further investigation of protein phosphorylation status in mature maize pollen and construction of maize male sterile mutants in the future.

In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis

NARCIS (Netherlands)

Zanivan, S.; Meves, A.; Behrendt, K.; Schoof, E.M.; Neilson, L.J.; Cox, J.; Tang, H.R.; Kalna, G.; Ree, J.H. van; Deursen, J.M.A. van; Trempus, C.S.; Machesky, L.M.; Linding, R.; Wickstrom, S.A.; Fassler, R.; Mann, M.

2013-01-01

Cancer progresses through distinct stages, and mouse models recapitulating traits of this progression are frequently used to explore genetic, morphological, and pharmacological aspects of tumor development. To complement genomic investigations of this process, we here quantify phosphoproteomic

Analysis of T4SS-induced signaling by H. pylori using quantitative phosphoproteomics

Directory of Open Access Journals (Sweden)

Frithjof eGlowinski

2014-07-01

Full Text Available Helicobacter pylori is a Gram-negative bacterial pathogen colonizing the human stomach. Infection with H. pylori causes chronic inflammation of the gastric mucosa and may lead to peptic ulceration and/or gastric cancer. A major virulence determinant of H. pylori is the type IV secretion system (T4SS, which is used to inject the virulence factor CagA into the host cell, triggering a wide range of cellular signaling events. Here, we used a phosphoproteomic approach to investigate tyrosine signaling in response to host-pathogen interaction, using stable isotope labeling in cell culture (SILAC of AGS cells to obtain a differential picture between multiple infection conditions. Cells were infected with wild type H. pylori P12, a P12ΔCagA deletion mutant, and a P12ΔT4SS deletion mutant to compare signaling changes over time and in the absence of CagA or the T4SS. Tryptic peptides were enriched for tyrosine (Tyr phosphopeptides and analysed by nano-LC-Orbitrap MS. In total, 58 different phosphosites were found to be regulated following infection. The majority of phosphosites identified were kinases of the MAPK familiy. CagA and the T4SS were found to be key regulators of Tyr phosphosites. Our findings indicate that CagA primarily induces activation of ERK1 and integrin linked factors, whereas the T4SS primarily modulates JNK and p38 activation.

Battle through signaling between wheat and the fungal pathogen Septoria tritici revealed by proteomics and phosphoproteomics

DEFF Research Database (Denmark)

Yang, Fen; Braga, Marcella Nunes de Melo; Larsen, Martin Røssel

2013-01-01

The fungus Septoria tritici causes the disease septoria tritici blotch in wheat, one of the most economically devastating foliar diseases in this crop. To investigate signaling events and defense responses in the wheat-S. tritici interaction, we performed a time-course study of S. tritici infection...... in resistant and susceptible wheat using quantitative proteomics and phosphoproteomics, with special emphasis on the initial biotrophic phase of interactions. Our study revealed an accumulation of defense and stress-related proteins, suppression of photosynthesis, and changes in sugar metabolism during...... compatible and incompatible interactions. However, differential regulation of the phosphorylation status of signaling proteins, transcription and translation regulators, and membrane-associated proteins was observed between two interactions. The proteomic data were correlated with a more rapid or stronger...

Resources on Quantitative/Statistical Research for Applied Linguists

Science.gov (United States)

Brown, James Dean

2004-01-01

The purpose of this review article is to survey and evaluate existing books on quantitative/statistical research in applied linguistics. The article begins by explaining the types of texts that will not be reviewed, then it briefly describes nine books that address how to do quantitative/statistical applied linguistics research. The review then…

Dataset of the Botrytis cinerea phosphoproteome induced by different plant-based elicitors.

Science.gov (United States)

Liñeiro, Eva; Chiva, Cristina; Cantoral, Jesús M; Sabido, Eduard; Fernández-Acero, Francisco Javier

2016-06-01

Phosphorylation is one of the main post-translational modification (PTM) involved in signaling network in the ascomycete Botrytis cinerea , one of the most relevant phytopathogenic fungus. The data presented in this article provided a differential mass spectrometry-based analysis of the phosphoproteome of B. cinerea under two different phenotypical conditions induced by the use of two different elicitors: glucose and deproteinized Tomate Cell Walls (TCW). A total 1138 and 733 phosphoproteins were identified for glucose and TCW culture conditions respectively. Raw data are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier (PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD003099). Further interpretation and discussion of these data are provided in our research article entitled "Phosphoproteome analysis of B.cinerea in response to different plant-based elicitors" (Liñeiro et al., 2016) [1].

System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

DEFF Research Database (Denmark)

Rigbolt, Kristoffer T.G.; Prokhorova, Tatyana; Akimov, Vyacheslav

2011-01-01

by feeder cells. We profiled 6521 proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic changes in phosphorylation status during 24 hours of differentiation. These data are a resource for studies of the events associated with the maintenance of hESC pluripotency and those...... of the matching sequence motif. In addition to identifying previously unknown phosphorylation sites on factors associated with differentiation, such as kinases and transcription factors, we observed dynamic phosphorylation of DNA methyltransferases (DNMTs). We found a specific interaction of DNMTs during early......To elucidate cellular events underlying the pluripotency of human embryonic stem cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic analyses of hESCs during differentiation initiated by a diacylglycerol analog or transfer to media that had not been conditioned...

Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer

Directory of Open Access Journals (Sweden)

Chiara Francavilla

2017-03-01

Full Text Available Our understanding of the molecular determinants of cancer is still inadequate because of cancer heterogeneity. Here, using epithelial ovarian cancer (EOC as a model system, we analyzed a minute amount of patient-derived epithelial cells from either healthy or cancerous tissues by single-shot mass-spectrometry-based phosphoproteomics. Using a multi-disciplinary approach, we demonstrated that primary cells recapitulate tissue complexity and represent a valuable source of differentially expressed proteins and phosphorylation sites that discriminate cancer from healthy cells. Furthermore, we uncovered kinase signatures associated with EOC. In particular, CDK7 targets were characterized in both EOC primary cells and ovarian cancer cell lines. We showed that CDK7 controls cell proliferation and that pharmacological inhibition of CDK7 selectively represses EOC cell proliferation. Our approach defines the molecular landscape of EOC, paving the way for efficient therapeutic approaches for patients. Finally, we highlight the potential of phosphoproteomics to identify clinically relevant and druggable pathways in cancer.

Recent findings and technological advances in phosphoproteomics for cells and tissues.

Science.gov (United States)

von Stechow, Louise; Francavilla, Chiara; Olsen, Jesper V

2015-01-01

Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins - termed phosphoproteomics - strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed.

A Primer on Disseminating Applied Quantitative Research

Science.gov (United States)

Bell, Bethany A.; DiStefano, Christine; Morgan, Grant B.

2010-01-01

Transparency and replication are essential features of scientific inquiry, yet scientific communications of applied quantitative research are often lacking in much-needed procedural information. In an effort to promote researchers dissemination of their quantitative studies in a cohesive, detailed, and informative manner, the authors delineate…

Resources on quantitative/statistical research for applied linguists

OpenAIRE

Brown , James Dean

2004-01-01

Abstract The purpose of this review article is to survey and evaluate existing books on quantitative/statistical research in applied linguistics. The article begins by explaining the types of texts that will not be reviewed, then it briefly describes nine books that address how to do quantitative/statistical applied linguistics research. The review then compares (in prose and tables) the general characteris...

Dataset of the Botrytis cinerea phosphoproteome induced by different plant-based elicitors

Directory of Open Access Journals (Sweden)

Eva Liñeiro

2016-06-01

Full Text Available Phosphorylation is one of the main post-translational modification (PTM involved in signaling network in the ascomycete Botrytis cinerea, one of the most relevant phytopathogenic fungus. The data presented in this article provided a differential mass spectrometry-based analysis of the phosphoproteome of B. cinerea under two different phenotypical conditions induced by the use of two different elicitors: glucose and deproteinized Tomate Cell Walls (TCW. A total 1138 and 733 phosphoproteins were identified for glucose and TCW culture conditions respectively. Raw data are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier (PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD003099. Further interpretation and discussion of these data are provided in our research article entitled “Phosphoproteome analysis of B.cinerea in response to different plant-based elicitors” (Liñeiro et al., 2016 [1].

Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection.

Science.gov (United States)

Labots, Mariette; van der Mijn, Johannes C; Beekhof, Robin; Piersma, Sander R; de Goeij-de Haas, Richard R; Pham, Thang V; Knol, Jaco C; Dekker, Henk; van Grieken, Nicole C T; Verheul, Henk M W; Jiménez, Connie R

2017-06-06

Mass spectrometry-based phosphoproteomics of cancer cell and tissue lysates provides insight in aberrantly activated signaling pathways and potential drug targets. For improved understanding of individual patient's tumor biology and to allow selection of tyrosine kinase inhibitors in individual patients, phosphoproteomics of small clinical samples should be feasible and reproducible. We aimed to scale down a pTyr-phosphopeptide enrichment protocol to biopsy-level protein input and assess reproducibility and applicability to tumor needle biopsies. To this end, phosphopeptide immunoprecipitation using anti-phosphotyrosine beads was performed using 10, 5 and 1mg protein input from lysates of colorectal cancer (CRC) cell line HCT116. Multiple needle biopsies from 7 human CRC resection specimens were analyzed at the 1mg-level. The total number of phosphopeptides captured and detected by LC-MS/MS ranged from 681 at 10mg input to 471 at 1mg HCT116 protein. ID-reproducibility ranged from 60.5% at 10mg to 43.9% at 1mg. Per 1mg-level biopsy sample, >200 phosphopeptides were identified with 57% ID-reproducibility between paired tumor biopsies. Unsupervised analysis clustered biopsies from individual patients together and revealed known and potential therapeutic targets. This study demonstrates the feasibility of label-free pTyr-phosphoproteomics at the tumor biopsy level based on reproducible analyses using 1mg of protein input. The considerable number of identified phosphopeptides at this level is attributed to an effective down-scaled immuno-affinity protocol as well as to the application of ID propagation in the data processing and analysis steps. Unsupervised cluster analysis reveals patient-specific profiles. Together, these findings pave the way for clinical trials in which pTyr-phosphoproteomics will be performed on pre- and on-treatment biopsies. Such studies will improve our understanding of individual tumor biology and may enable future pTyr-phosphoproteomics

Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer.

Science.gov (United States)

Francavilla, Chiara; Lupia, Michela; Tsafou, Kalliopi; Villa, Alessandra; Kowalczyk, Katarzyna; Rakownikow Jersie-Christensen, Rosa; Bertalot, Giovanni; Confalonieri, Stefano; Brunak, Søren; Jensen, Lars J; Cavallaro, Ugo; Olsen, Jesper V

2017-03-28

Our understanding of the molecular determinants of cancer is still inadequate because of cancer heterogeneity. Here, using epithelial ovarian cancer (EOC) as a model system, we analyzed a minute amount of patient-derived epithelial cells from either healthy or cancerous tissues by single-shot mass-spectrometry-based phosphoproteomics. Using a multi-disciplinary approach, we demonstrated that primary cells recapitulate tissue complexity and represent a valuable source of differentially expressed proteins and phosphorylation sites that discriminate cancer from healthy cells. Furthermore, we uncovered kinase signatures associated with EOC. In particular, CDK7 targets were characterized in both EOC primary cells and ovarian cancer cell lines. We showed that CDK7 controls cell proliferation and that pharmacological inhibition of CDK7 selectively represses EOC cell proliferation. Our approach defines the molecular landscape of EOC, paving the way for efficient therapeutic approaches for patients. Finally, we highlight the potential of phosphoproteomics to identify clinically relevant and druggable pathways in cancer. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana

KAUST Repository

Bigeard, Jean

2014-07-10

The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.

Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana

KAUST Repository

Bigeard, Jean; Rayapuram, Naganand; Bonhomme, Ludovic; Hirt, Heribert; Pflieger, Delphine

2014-01-01

The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.

Improving the Phosphoproteome Coverage for Limited Sample Amounts Using TiOsub>2sub>-SIMAC-HILIC (TiSH) Phosphopeptide Enrichment and Fractionation

DEFF Research Database (Denmark)

Engholm-Keller, Kasper; Larsen, Martin R

2016-01-01

spectrometry (LC-MS/MS) analysis. Due to the sample loss resulting from fractionation, this procedure is mainly performed when large quantities of sample are available. To make large-scale phosphoproteomics applicable to smaller amounts of protein we have recently combined highly specific TiO2-based...... protocol we describe the procedure step by step to allow for comprehensive coverage of the phosphoproteome utilizing only a few hundred micrograms of protein....

Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation

DEFF Research Database (Denmark)

Nagaraj, Nagarjuna; D'Souza, Rochelle C J; Cox, Juergen

2010-01-01

Mass spectrometry (MS)-based proteomics now enables the analysis of thousands of phosphorylation sites in single projects. Among a wide range of analytical approaches, the combination of high resolution MS scans in an Orbitrap analyzer with low resolution MS/MS scans in a linear ion trap has proven......-scale phosphoproteome analysis alongside collisional induced dissociation, (CID) and electron capture/transfer dissociation (ECD/ETD)....

Comparative Phosphoproteomics Reveals an Important Role of MKK2 in Banana (Musa spp.) Cold Signal Network

Science.gov (United States)

Gao, Jie; Zhang, Sheng; He, Wei-Di; Shao, Xiu-Hong; Li, Chun-Yu; Wei, Yue-Rong; Deng, Gui-Ming; Kuang, Rui-Bin; Hu, Chun-Hua; Yi, Gan-Jun; Yang, Qiao-Song

2017-01-01

Low temperature is one of the key environmental stresses, which greatly affects global banana production. However, little is known about the global phosphoproteomes in Musa spp. and their regulatory roles in response to cold stress. In this study, we conducted a comparative phosphoproteomic profiling of cold-sensitive Cavendish Banana and relatively cold tolerant Dajiao under cold stress. Phosphopeptide abundances of five phosphoproteins involved in MKK2 interaction network, including MKK2, HY5, CaSR, STN7 and kinesin-like protein, show a remarkable difference between Cavendish Banana and Dajiao in response to cold stress. Western blotting of MKK2 protein and its T31 phosphorylated peptide verified the phosphoproteomic results of increased T31 phosphopeptide abundance with decreased MKK2 abundance in Daojiao for a time course of cold stress. Meanwhile increased expression of MKK2 with no detectable T31 phosphorylation was found in Cavendish Banana. These results suggest that the MKK2 pathway in Dajiao, along with other cold-specific phosphoproteins, appears to be associated with the molecular mechanisms of high tolerance to cold stress in Dajiao. The results also provide new evidence that the signaling pathway of cellular MKK2 phosphorylation plays an important role in abiotic stress tolerance that likely serves as a universal plant cold tolerance mechanism. PMID:28106078

Salinity-Induced Palmella Formation Mechanism in Halotolerant Algae Dunaliella salina Revealed by Quantitative Proteomics and Phosphoproteomics

Directory of Open Access Journals (Sweden)

Sijia Wei

2017-05-01

Full Text Available Palmella stage is critical for some unicellular algae to survive in extreme environments. The halotolerant algae Dunaliella salina is a good single-cell model for studying plant adaptation to high salinity. To investigate the molecular adaptation mechanism in salinity shock-induced palmella formation, we performed a comprehensive physiological, proteomics and phosphoproteomics study upon palmella formation of D. salina using dimethyl labeling and Ti4+-immobilized metal ion affinity chromatography (IMAC proteomic approaches. We found that 151 salinity-responsive proteins and 35 salinity-responsive phosphoproteins were involved in multiple signaling and metabolic pathways upon palmella formation. Taken together with photosynthetic parameters and enzyme activity analyses, the patterns of protein accumulation and phosphorylation level exhibited the mechanisms upon palmella formation, including dynamics of cytoskeleton and cell membrane curvature, accumulation and transport of exopolysaccharides, photosynthesis and energy supplying (i.e., photosystem II stability and activity, cyclic electron transport, and C4 pathway, nuclear/chloroplastic gene expression regulation and protein processing, reactive oxygen species homeostasis, and salt signaling transduction. The salinity-responsive protein–protein interaction (PPI networks implied that signaling and protein synthesis and fate are crucial for modulation of these processes. Importantly, the 3D structure of phosphoprotein clearly indicated that the phosphorylation sites of eight proteins were localized in the region of function domain.

TiO2-Based Phosphoproteomic Analysis of the Plasma Membrane and the Effects of Phosphatase Inhibitor Treatment

DEFF Research Database (Denmark)

Thingholm, Tine; Larsen, Martin Røssel; Ingrell, Christian

2008-01-01

Phosphorylation of plasma membrane proteins frequently initiates signal transduction pathways or attenuate plasma membrane transport processes. Because of the low abundance and hydrophobic features of many plasma membrane proteins and the low stoichiometry of protein phosphorylation, studies...... of the plasma membrane phosphoproteome are challenging. We present an optimized analytical strategy for plasma membrane phosphoproteomics that combines efficient plasma membrane protein preparation with TiO 2-based phosphopeptide enrichment and high-performance mass spectrometry for phosphopeptide sequencing....... We used sucrose centrifugation in combination with sodium carbonate extraction to achieve efficient and reproducible purification of low microgram levels of plasma membrane proteins from human mesenchymal stem cells (hMSCs, 10 (7) cells), achieving more than 70% yield of membrane proteins...

Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome.

Science.gov (United States)

Licona-Cassani, Cuauhtemoc; Lim, Sooa; Marcellin, Esteban; Nielsen, Lars K

2014-05-01

Actinomycetes undergo a dramatic reorganization of metabolic and cellular machinery during a brief period of growth arrest ("metabolic switch") preceding mycelia differentiation and the onset of secondary metabolite biosynthesis. This study explores the role of phosphorylation in coordinating the metabolic switch in the industrial actinomycete Saccharopolyspora erythraea. A total of 109 phosphopeptides from 88 proteins were detected across a 150-h fermentation using open-profile two-dimensional LC-MS proteomics and TiO(2) enrichment. Quantitative analysis of the phosphopeptides and their unphosphorylated cognates was possible for 20 pairs that also displayed constant total protein expression. Enzymes from central carbon metabolism such as putative acetyl-coenzyme A carboxylase, isocitrate lyase, and 2-oxoglutarate dehydrogenase changed dramatically in the degree of phosphorylation during the stationary phase, suggesting metabolic rearrangement for the reutilization of substrates and the production of polyketide precursors. In addition, an enzyme involved in cellular response to environmental stress, trypsin-like serine protease (SACE_6340/NC_009142_6216), decreased in phosphorylation during the growth arrest stage. More important, enzymes related to the regulation of protein synthesis underwent rapid phosphorylation changes during this stage. Whereas the degree of phosphorylation of ribonuclease Rne/Rng (SACE_1406/NC_009142_1388) increased during the metabolic switch, that of two ribosomal proteins, S6 (SACE_7351/NC_009142_7233) and S32 (SACE_6101/NC_009142_5981), dramatically decreased during this stage of the fermentation, supporting the hypothesis that ribosome subpopulations differentially regulate translation before and after the metabolic switch. Overall, we show the great potential of phosphoproteomic studies to explain microbial physiology and specifically provide evidence of dynamic protein phosphorylation events across the developmental cycle of

Temporal Dynamics of the Saccharopolyspora erythraea Phosphoproteome*

Science.gov (United States)

Licona-Cassani, Cuauhtemoc; Lim, SooA; Marcellin, Esteban; Nielsen, Lars K.

2014-01-01

Actinomycetes undergo a dramatic reorganization of metabolic and cellular machinery during a brief period of growth arrest (“metabolic switch”) preceding mycelia differentiation and the onset of secondary metabolite biosynthesis. This study explores the role of phosphorylation in coordinating the metabolic switch in the industrial actinomycete Saccharopolyspora erythraea. A total of 109 phosphopeptides from 88 proteins were detected across a 150-h fermentation using open-profile two-dimensional LC-MS proteomics and TiO2 enrichment. Quantitative analysis of the phosphopeptides and their unphosphorylated cognates was possible for 20 pairs that also displayed constant total protein expression. Enzymes from central carbon metabolism such as putative acetyl-coenzyme A carboxylase, isocitrate lyase, and 2-oxoglutarate dehydrogenase changed dramatically in the degree of phosphorylation during the stationary phase, suggesting metabolic rearrangement for the reutilization of substrates and the production of polyketide precursors. In addition, an enzyme involved in cellular response to environmental stress, trypsin-like serine protease (SACE_6340/NC_009142_6216), decreased in phosphorylation during the growth arrest stage. More important, enzymes related to the regulation of protein synthesis underwent rapid phosphorylation changes during this stage. Whereas the degree of phosphorylation of ribonuclease Rne/Rng (SACE_1406/NC_009142_1388) increased during the metabolic switch, that of two ribosomal proteins, S6 (SACE_7351/NC_009142_7233) and S32 (SACE_6101/NC_009142_5981), dramatically decreased during this stage of the fermentation, supporting the hypothesis that ribosome subpopulations differentially regulate translation before and after the metabolic switch. Overall, we show the great potential of phosphoproteomic studies to explain microbial physiology and specifically provide evidence of dynamic protein phosphorylation events across the developmental cycle of

ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen

DEFF Research Database (Denmark)

Kozlov, Sergei V; Waardenberg, Ashley J; Engholm-Keller, Kasper

2016-01-01

ATM (ataxia-telangiectasia, mutated) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signalling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle checkpoi......ATM (ataxia-telangiectasia, mutated) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signalling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle...... checkpoints, initiating DNA repair and regulating gene expression. ATM kinase can be activated by a variety of stimuli, including oxidative stress. Here we confirmed activation of cytoplasmic ATM by autophosphorylation at multiple sites. Then we employed a global quantitative phosphoproteomics approach...... to identify cytoplasmic proteins altered in their phosphorylation state in control and A-T (ataxia-telangiectasia) cells in response to oxidative damage. We demonstrated that ATM was activated by oxidative damage in the cytoplasm as well as in the nucleus and identified a total of 9,833 phosphorylation sites...

Activation of Human Peripheral Blood Eosinophils by Cytokines in a Comparative Time-Course Proteomic/Phosphoproteomic Study.

Science.gov (United States)

Soman, Kizhake V; Stafford, Susan J; Pazdrak, Konrad; Wu, Zheng; Luo, Xuemei; White, Wendy I; Wiktorowicz, John E; Calhoun, William J; Kurosky, Alexander

2017-08-04

Activated eosinophils contribute to airway dysfunction and tissue remodeling in asthma and thus are considered to be important factors in asthma pathology. We report here comparative proteomic and phosphoproteomic changes upon activation of eosinophils using eight cytokines individually and in selected cytokine combinations in time-course reactions. Differential protein and phosphoprotein expressions were determined by mass spectrometry after 2-dimensional gel electrophoresis (2DGE) and by LC-MS/MS. We found that each cytokine-stimulation produced significantly different changes in the eosinophil proteome and phosphoproteome, with phosphoproteomic changes being more pronounced and having an earlier onset. Furthermore, we observed that IL-5, GM-CSF, and IL-3 showed the greatest change in protein expression and phosphorylation, and this expression differed markedly from those of the other five cytokines evaluated. Comprehensive univariate and multivariate statistical analyses were employed to evaluate the comparative results. We also monitored eosinophil activation using flow cytometry (FC) analysis of CD69. In agreement with our proteomic studies, FC indicated that IL-5, GM-CSF, and IL-3 were more effective than the other five cytokines studied in stimulating a cell surface CD69 increase indicative of eosinophil activation. Moreover, selected combinations of cytokines revealed proteomic patterns with many proteins in common with single cytokine expression patterns but also showed a greater effect of the two cytokines employed, indicating a more complex signaling pathway that was reflective of a more typical inflammatory pathology.

Systems Analysis for Interpretation of Phosphoproteomics Data

DEFF Research Database (Denmark)

Munk, Stephanie; Refsgaard, Jan C; Olsen, Jesper V

2016-01-01

Global phosphoproteomics investigations yield overwhelming datasets with up to tens of thousands of quantified phosphosites. The main challenge after acquiring such large-scale data is to extract the biological meaning and relate this to the experimental question at hand. Systems level analysis...... provides the best means for extracting functional insights from such types of datasets, and this has primed a rapid development of bioinformatics tools and resources over the last decade. Many of these tools are specialized databases that can be mined for annotation and pathway enrichment, whereas others...... provide a platform to generate functional protein networks and explore the relations between proteins of interest. The use of these tools requires careful consideration with regard to the input data, and the interpretation demands a critical approach. This chapter provides a summary of the most...

Phosphoproteomics Reveals Regulatory T Cell-Mediated DEF6 Dephosphorylation That Affects Cytokine Expression in Human Conventional T Cells

KAUST Repository

Joshi, Rubin N.; Binai, Nadine A.; Marabita, Francesco; Sui, Zhenhua; Altman, Amnon; Heck, Albert J. R.; Tegner, Jesper; Schmidt, Angelika

2017-01-01

(Tcons) independently of IP levels, consequently inhibiting NFAT signaling and effector cytokine expression. Here, we study Treg suppression mechanisms through unbiased phosphoproteomics of primary human Tcons upon TCR stimulation and Treg

Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals extensive phosphorylation of inner membrane protein complexes and enzymes

DEFF Research Database (Denmark)

Zhao, Xiaolu; Leon, Ileana R; Bak, Steffen

2011-01-01

. In skeletal muscle, mitochondrial dysfunction is linked to insulin resistance in humans with obesity and type 2 diabetes. We performed a phosphoproteomic study of functional mitochondria isolated from human muscle biopsies with the aim to obtain a comprehensive overview of mitochondrial phosphoproteins...... in insulin resistance. We also assigned phosphorylation sites in mitochondrial proteins involved in amino acid degradation, importers and transporters, calcium homeostasis, and apoptosis. Bioinformatics analysis of kinase motifs revealed that many of these mitochondrial phosphoproteins are substrates....... Future comparative phosphoproteome analysis of mitochondria from healthy and diseased individuals will provide insights into the role of abnormal phosphorylation in pathologies, such as type 2 diabetes....

Quantitative EEG Applying the Statistical Recognition Pattern Method

DEFF Research Database (Denmark)

Engedal, Knut; Snaedal, Jon; Hoegh, Peter

2015-01-01

BACKGROUND/AIM: The aim of this study was to examine the discriminatory power of quantitative EEG (qEEG) applying the statistical pattern recognition (SPR) method to separate Alzheimer's disease (AD) patients from elderly individuals without dementia and from other dementia patients. METHODS...

Offline High pH Reversed-Phase Peptide Fractionation for Deep Phosphoproteome Coverage

DEFF Research Database (Denmark)

Batth, Tanveer S; Olsen, Jesper V

2016-01-01

Protein phosphorylation, a process in which kinases modify serines, threonines, and tyrosines with phosphoryl groups is of major importance in eukaryotic biology. Protein phosphorylation events are key initiators of signaling responses which determine cellular outcomes after environmental...... and metabolic stimuli, and are thus highly regulated. Therefore, studying the mechanism of regulation by phosphorylation, and pinpointing the exact site of phosphorylation on proteins is of high importance. This protocol describes in detail a phosphoproteomics workflow for ultra-deep coverage by fractionating...

Hippocampal phosphoproteomics of F344 rats exposed to 1-bromopropane

International Nuclear Information System (INIS)

Huang, Zhenlie; Ichihara, Sahoko; Oikawa, Shinji; Chang, Jie; Zhang, Lingyi; Hu, Shijie; Huang, Hanlin; Ichihara, Gaku

2015-01-01

1-Bromopropane (1-BP) is neurotoxic in both experimental animals and human. To identify phosphorylated modification on the unrecognized post-translational modifications of proteins and investigate their role in 1-BP-induced neurotoxicity, changes in hippocampal phosphoprotein expression levels were analyzed quantitatively in male F344 rats exposed to 1-BP inhalation at 0, 400, or 1000 ppm for 8 h/day for 1 or 4 weeks. Hippocampal protein extracts were analyzed qualitatively and quantitatively by Pro-Q Diamond gel staining and SYPRO Ruby staining coupled with two-dimensional difference in gel electrophoresis (2D-DIGE), respectively, as well as by matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to identify phosphoproteins. Changes in selected proteins were further confirmed by Manganese II (Mn 2+ )-Phos-tag SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Bax and cytochrome c protein levels were determined by western blotting. Pro-Q Diamond gel staining combined with 2D-DIGE identified 26 phosphoprotein spots (p < 0.05), and MALDI-TOF/MS identified 18 up-regulated proteins and 8 down-regulated proteins. These proteins are involved in the biological process of response to stimuli, metabolic processes, and apoptosis signaling. Changes in the expression of phosphorylated 14-3-3 θ were further confirmed by Mn 2+ -Phos-tag SDS-PAGE. Western blotting showed overexpression of Bax protein in the mitochondria with down-regulation in the cytoplasm, whereas cytochrome c expression was high in the cytoplasm but low in the mitochondria after 1-BP exposure. Our results suggest that the pathogenesis of 1-BP-induced hippocampal damage involves inhibition of antiapoptosis process. Phosphoproteins identified in this study can potentially serve as biomarkers for 1-BP-induced neurotoxicity. - Highlights: • 1-BP modified hippocampal phosphoproteome in rat and 23 altered proteins were identified. • 1-BP changed phosphorylation of GRP78

Hippocampal phosphoproteomics of F344 rats exposed to 1-bromopropane

Energy Technology Data Exchange (ETDEWEB)

Huang, Zhenlie [Guangdong Provincial Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou 510-300 (China); Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466-8550 (Japan); Ichihara, Sahoko [Graduate School of Regional Innovation Studies, Mie University, Tsu 514-8507 (Japan); Oikawa, Shinji [Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie 514-8507 (Japan); Chang, Jie [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466-8550 (Japan); Graduate School of Regional Innovation Studies, Mie University, Tsu 514-8507 (Japan); Zhang, Lingyi [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466-8550 (Japan); Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510 (Japan); Hu, Shijie [Guangdong Provincial Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou 510-300 (China); Huang, Hanlin, E-mail: huanghl@gdoh.org [Guangdong Provincial Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou 510-300 (China); Ichihara, Gaku, E-mail: gak@rs.tus.ac.jp [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466-8550 (Japan); Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510 (Japan)

2015-01-15

1-Bromopropane (1-BP) is neurotoxic in both experimental animals and human. To identify phosphorylated modification on the unrecognized post-translational modifications of proteins and investigate their role in 1-BP-induced neurotoxicity, changes in hippocampal phosphoprotein expression levels were analyzed quantitatively in male F344 rats exposed to 1-BP inhalation at 0, 400, or 1000 ppm for 8 h/day for 1 or 4 weeks. Hippocampal protein extracts were analyzed qualitatively and quantitatively by Pro-Q Diamond gel staining and SYPRO Ruby staining coupled with two-dimensional difference in gel electrophoresis (2D-DIGE), respectively, as well as by matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to identify phosphoproteins. Changes in selected proteins were further confirmed by Manganese II (Mn{sup 2+})-Phos-tag SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Bax and cytochrome c protein levels were determined by western blotting. Pro-Q Diamond gel staining combined with 2D-DIGE identified 26 phosphoprotein spots (p < 0.05), and MALDI-TOF/MS identified 18 up-regulated proteins and 8 down-regulated proteins. These proteins are involved in the biological process of response to stimuli, metabolic processes, and apoptosis signaling. Changes in the expression of phosphorylated 14-3-3 θ were further confirmed by Mn{sup 2+}-Phos-tag SDS-PAGE. Western blotting showed overexpression of Bax protein in the mitochondria with down-regulation in the cytoplasm, whereas cytochrome c expression was high in the cytoplasm but low in the mitochondria after 1-BP exposure. Our results suggest that the pathogenesis of 1-BP-induced hippocampal damage involves inhibition of antiapoptosis process. Phosphoproteins identified in this study can potentially serve as biomarkers for 1-BP-induced neurotoxicity. - Highlights: • 1-BP modified hippocampal phosphoproteome in rat and 23 altered proteins were identified. • 1-BP changed phosphorylation

Reactive Oxygen Species (ROS)-Activated ATM-Dependent Phosphorylation of Cytoplasmic Substrates Identified by Large-Scale Phosphoproteomics Screen*

Science.gov (United States)

Kozlov, Sergei V.; Waardenberg, Ashley J.; Engholm-Keller, Kasper; Arthur, Jonathan W.; Graham, Mark E.; Lavin, Martin

2016-01-01

Ataxia-telangiectasia, mutated (ATM) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signaling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle checkpoints, initiating DNA repair, and regulating gene expression. ATM kinase can be activated by a variety of stimuli, including oxidative stress. Here, we confirmed activation of cytoplasmic ATM by autophosphorylation at multiple sites. Then we employed a global quantitative phosphoproteomics approach to identify cytoplasmic proteins altered in their phosphorylation state in control and ataxia-telangiectasia (A-T) cells in response to oxidative damage. We demonstrated that ATM was activated by oxidative damage in the cytoplasm as well as in the nucleus and identified a total of 9,833 phosphorylation sites, including 6,686 high-confidence sites mapping to 2,536 unique proteins. A total of 62 differentially phosphorylated peptides were identified; of these, 43 were phosphorylated in control but not in A-T cells, and 19 varied in their level of phosphorylation. Motif enrichment analysis of phosphopeptides revealed that consensus ATM serine glutamine sites were overrepresented. When considering phosphorylation events, only observed in control cells (not observed in A-T cells), with predicted ATM sites phosphoSerine/phosphoThreonine glutamine, we narrowed this list to 11 candidate ATM-dependent cytoplasmic proteins. Two of these 11 were previously described as ATM substrates (HMGA1 and UIMCI/RAP80), another five were identified in a whole cell extract phosphoproteomic screens, and the remaining four proteins had not been identified previously in DNA damage response screens. We validated the phosphorylation of three of these proteins (oxidative stress responsive 1 (OSR1), HDGF, and ccdc82) as ATM dependent after H2O2 exposure, and another protein (S100A11) demonstrated ATM

Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58

Directory of Open Access Journals (Sweden)

Agnieszka Hareza

2018-04-01

Full Text Available Many kinases are still ‘orphans,’ which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum and to influence trafficking via the secretory pathway. Subsequently, DIA1 is subjected to phosphoproteomics analysis to cast light on its signalling pathways. A liquid chromatography–tandem mass spectrometry proteomic approach with phosphopeptide enrichment is applied to membrane fractions of DIA1-overexpressing and control HEK293T cells, and phosphosites dependent on the presence of DIA1 are elucidated. Most of these phosphosites belonged to CK2- and proline-directed kinase types. In parallel, the proteomics of proteins immunoprecipitated with DIA1 reported its probable interactors. This pilot study provides the basis for deeper studies of DIA1 signalling.

Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58.

Science.gov (United States)

Hareza, Agnieszka; Bakun, Magda; Świderska, Bianka; Dudkiewicz, Małgorzata; Koscielny, Alicja; Bajur, Anna; Jaworski, Jacek; Dadlez, Michał; Pawłowski, Krzysztof

2018-01-01

Many kinases are still 'orphans,' which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum and to influence trafficking via the secretory pathway. Subsequently, DIA1 is subjected to phosphoproteomics analysis to cast light on its signalling pathways. A liquid chromatography-tandem mass spectrometry proteomic approach with phosphopeptide enrichment is applied to membrane fractions of DIA1-overexpressing and control HEK293T cells, and phosphosites dependent on the presence of DIA1 are elucidated. Most of these phosphosites belonged to CK2- and proline-directed kinase types. In parallel, the proteomics of proteins immunoprecipitated with DIA1 reported its probable interactors. This pilot study provides the basis for deeper studies of DIA1 signalling.

Phosphoproteomics Reveals Regulatory T Cell-Mediated DEF6 Dephosphorylation That Affects Cytokine Expression in Human Conventional T Cells

KAUST Repository

Joshi, Rubin N.

2017-09-25

Regulatory T cells (Tregs) control key events of immune tolerance, primarily by suppression of effector T cells. We previously revealed that Tregs rapidly suppress T cell receptor (TCR)-induced calcium store depletion in conventional CD4CD25 T cells (Tcons) independently of IP levels, consequently inhibiting NFAT signaling and effector cytokine expression. Here, we study Treg suppression mechanisms through unbiased phosphoproteomics of primary human Tcons upon TCR stimulation and Treg-mediated suppression, respectively. Tregs induced a state of overall decreased phosphorylation as opposed to TCR stimulation. We discovered novel phosphosites (T595_S597) in the DEF6 (SLAT) protein that were phosphorylated upon TCR stimulation and conversely dephosphorylated upon coculture with Tregs. Mutation of these DEF6 phosphosites abrogated interaction of DEF6 with the IP receptor and affected NFAT activation and cytokine transcription in primary Tcons. This novel mechanism and phosphoproteomics data resource may aid in modifying sensitivity of Tcons to Treg-mediated suppression in autoimmune disease or cancer.

Parallel reaction monitoring on a Q Exactive mass spectrometer increases reproducibility of phosphopeptide detection in bacterial phosphoproteomics measurements.

Science.gov (United States)

Taumer, Christoph; Griesbaum, Lena; Kovacevic, Alen; Soufi, Boumediene; Nalpas, Nicolas C; Macek, Boris

2018-03-29

Increasing number of studies report the relevance of protein Ser/Thr/Tyr phosphorylation in bacterial physiology, yet the analysis of this type of modification in bacteria still presents a considerable challenge. Unlike in eukaryotes, where tens of thousands of phosphorylation events likely occupy more than two thirds of the proteome, the abundance of protein phosphorylation is much lower in bacteria. Even the state-of-the-art phosphopeptide enrichment protocols fail to remove the high background of abundant unmodified peptides, leading to low signal intensity and undersampling of phosphopeptide precursor ions in consecutive data-dependent MS runs. Consequently, large-scale bacterial phosphoproteomic datasets often suffer from poor reproducibility and a high number of missing values. Here we explore the application of parallel reaction monitoring (PRM) on a Q Exactive mass spectrometer in bacterial phosphoproteome analysis, focusing especially on run-to-run sampling reproducibility. In multiple measurements of identical phosphopeptide-enriched samples, we show that PRM outperforms data-dependent acquisition (DDA) in terms of detection frequency, reaching almost complete sampling efficiency, compared to 20% in DDA. We observe a similar trend over multiple heterogeneous phosphopeptide-enriched samples and conclude that PRM shows a great promise in bacterial phosphoproteomics analyses where reproducible detection and quantification of a relatively small set of phosphopeptides is desired. Bacterial phosphorylated peptides occur in low abundance compared to their unmodified counterparts, and are therefore rarely reproducibly detected in shotgun (DDA) proteomics measurements. Here we show that parallel reaction monitoring complements DDA analyses and makes detection of known, targeted phosphopeptides more reproducible. This will be of significance in replicated MS measurements that have a goal to reproducibly detect and quantify phosphopeptides of interest. Copyright �

Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri.

Science.gov (United States)

Le Bihan, Thierry; Hindle, Matthew; Martin, Sarah F; Barrios-Llerena, Martin E; Krahmer, Johanna; Kis, Katalin; Millar, Andrew J; van Ooijen, Gerben

2015-12-01

Casein kinase 2 (CK2) is a protein kinase that phosphorylates a plethora of cellular target proteins involved in processes including DNA repair, cell cycle control, and circadian timekeeping. CK2 is functionally conserved across eukaryotes, although the substrate proteins identified in a range of complex tissues are often different. The marine alga Ostreococcus tauri is a unicellular eukaryotic model organism ideally suited to efficiently study generic roles of CK2 in the cellular circadian clock. Overexpression of CK2 leads to a slow circadian rhythm, verifying functional conservation of CK2 in timekeeping. The proteome was analysed in wild-type and CK2-overexpressing algae at dawn and dusk, revealing that differential abundance of the global proteome across the day is largely unaffected by overexpression. However, CK2 activity contributed more strongly to timekeeping at dusk than at dawn. The phosphoproteome of a CK2 overexpression line and cells treated with CK2 inhibitor was therefore analysed and compared to control cells at dusk. We report an extensive catalogue of 447 unique CK2-responsive differential phosphopeptide motifs to inform future studies into CK2 activity in the circadian clock of more complex tissues. All MS data have been deposited in the ProteomeXchange with identifier PXD000975 (http://proteomecentral.proteomexchange.org/dataset/PXD000975). © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

SIMAC - A phosphoproteomic strategy for the rapid separation of mono-phosphorylated from multiply phosphorylated peptides

DEFF Research Database (Denmark)

Thingholm, Tine E; Jensen, Ole N; Robinson, Phillip J

2008-01-01

spectrometric analysis, such as immobilized metal affinity chromatography or titanium dioxide the coverage of the phosphoproteome of a given sample is limited. Here we report a simple and rapid strategy - SIMAC - for sequential separation of mono-phosphorylated peptides and multiply phosphorylated peptides from...... and an optimized titanium dioxide chromatographic method. More than double the total number of identified phosphorylation sites was obtained with SIMAC, primarily from a three-fold increase in recovery of multiply phosphorylated peptides....

Applied quantitative finance

CERN Document Server

Chen, Cathy; Overbeck, Ludger

2017-01-01

This volume provides practical solutions and introduces recent theoretical developments in risk management, pricing of credit derivatives, quantification of volatility and copula modeling. This third edition is devoted to modern risk analysis based on quantitative methods and textual analytics to meet the current challenges in banking and finance. It includes 14 new contributions and presents a comprehensive, state-of-the-art treatment of cutting-edge methods and topics, such as collateralized debt obligations, the high-frequency analysis of market liquidity, and realized volatility. The book is divided into three parts: Part 1 revisits important market risk issues, while Part 2 introduces novel concepts in credit risk and its management along with updated quantitative methods. The third part discusses the dynamics of risk management and includes risk analysis of energy markets and for cryptocurrencies. Digital assets, such as blockchain-based currencies, have become popular b ut are theoretically challenging...

Phosphoproteomic investigation of a solvent producing bacterium Clostridium acetobutylicum.

Science.gov (United States)

Bai, Xue; Ji, Zhihong

2012-07-01

In this study, we employed TiO₂ enrichment and high accuracy liquid chromatography-mass spectrometry-mass spectrometry to identify the phosphoproteome of Clostridium acetobutyicum ATCC824 in acidogenesis and solventogenesis. As many as 82 phosphopeptides in 61 proteins, with 107 phosphorylated sites on serine, threonine, or tyrosine, were identified with high confidence. We detected 52 phosphopeptides from 44 proteins in acidogenesis and 70 phosphopeptides from 51 proteins in solventogenesis, respectively. Bioinformatic analysis revealed most of the phosphoproteins located in cytoplasm and participated in carbon metabolism. Based on comparison between the two stages, we found 27 stage-specific phosphorylated proteins (10 in acidogenesis and 17 in solventogenesis), some of which were solvent production-related enzymes and metabolic regulators, showed significantly different phosphorylated status. Further analysis indicated that protein phosphorylation could be involved in the shift of stages or in solvent production pathway directly. Comparison against several other organisms revealed the evolutionary diversity among them on phosphorylation level in spite of their high homology on protein sequence level.

Effects of poly-ether B on proteome and phosphoproteome expression in biofouling Balanus amphitrite cyprids

KAUST Repository

Dash, Swagatika

2012-04-01

Biofouling is ubiquitous in marine environments, and the barnacle Balanus amphitrite is one of the most recalcitrant and aggressive biofoulers in tropical waters. Several natural antifoulants that were claimed to be non-toxic have been isolated in recent years, although the mechanism by which they inhibit fouling is yet to be investigated. Poly-ether B has shown promise in the non-toxic inhibition of larval barnacle attachment. Hence, in this study, multiplex two-dimensional electrophoresis (2-DE) was applied in conjunction with mass spectrometry to investigate the effects of poly-ether B on barnacle larvae at the molecular level. The cyprid proteome response to poly-ether B treatment was analyzed at the total proteome and phosphoproteome levels, with 65 protein and 19 phosphoprotein spots found to be up- or down-regulated. The proteins were found to be related to energy-metabolism, oxidative stress, and molecular chaperones, thus indicating that poly-ether B may interfere with the redox-regulatory mechanisms governing the settlement of barnacle larvae. The results of this study demonstrate the usefulness of the proteomic technique in revealing the working mechanisms of antifouling compounds. © 2012 Copyright Taylor and Francis Group, LLC.

Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome.

Science.gov (United States)

Solari, Fiorella A; Mattheij, Nadine J A; Burkhart, Julia M; Swieringa, Frauke; Collins, Peter W; Cosemans, Judith M E M; Sickmann, Albert; Heemskerk, Johan W M; Zahedi, René P

2016-10-01

The Scott syndrome is a very rare and likely underdiagnosed bleeding disorder associated with mutations in the gene encoding anoctamin-6. Platelets from Scott patients are impaired in various Ca 2+ -dependent responses, including phosphatidylserine exposure, integrin closure, intracellular protein cleavage, and cytoskeleton-dependent morphological changes. Given the central role of anoctamin-6 in the platelet procoagulant response, we used quantitative proteomics to understand the underlying molecular mechanisms and the complex phenotypic changes in Scott platelets compared with control platelets. Therefore, we applied an iTRAQ-based multi-pronged strategy to quantify changes in (1) the global proteome, (2) the phosphoproteome, and (3) proteolytic events between resting and stimulated Scott and control platelets. Our data indicate a limited number of proteins with decreased (70) or increased (64) expression in Scott platelets, among those we confirmed the absence of anoctamin-6 and the strong up-regulation of aquaporin-1 by parallel reaction monitoring. The quantification of 1566 phosphopeptides revealed major differences between Scott and control platelets after stimulation with thrombin/convulxin or ionomycin. In Scott platelets, phosphorylation levels of proteins regulating cytoskeletal or signaling events were increased. Finally, we quantified 1596 N-terminal peptides in activated Scott and control platelets, 180 of which we identified as calpain-regulated, whereas a distinct set of 23 neo-N termini was caspase-regulated. In Scott platelets, calpain-induced cleavage of cytoskeleton-linked and signaling proteins was downregulated, in accordance with an increased phosphorylation state. Thus, multipronged proteomic profiling of Scott platelets provides detailed insight into their protection against detrimental Ca 2+ -dependent changes that are normally associated with phosphatidylserine exposure. © 2016 by The American Society for Biochemistry and Molecular

Investigating temporal changes in the yeast phosphoproteome upon fatty acid starvation

DEFF Research Database (Denmark)

Pultz, Dennis; Bennetzen, Martin; Andersen, Jens S.

2011-01-01

under nutrition but not malnutrition extends the life span of multiple species, ranging from single-celled organisms like yeast to mammals. This increase in longevity by dietary restriction (DR) is coupled to profound beneficial effects on age-related pathology. Despite the number of studies on DR......Investigating stemporal changes in the yeast phosphoproteome upon fatty acid starvation Dennis Pultz*, Martin Bennetzen*, Jens S. Andersen and Nils J.Færgeman. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, 5230 Reducing food intake to induce...... and the physiological changes DR induces, only little is known about the genetics and signalling networks which regulate the DR response. We have recently shown that inhibition of fatty acid synthesis in Saccharomyces cerevisiae results in a dependency on autophagy in maintaining normal life span. We further believe...

Kinomic and phospho-proteomic analysis of breast cancer stem-like cells

DEFF Research Database (Denmark)

Leth-Larsen, Rikke; Christensen, Anne Geske Lindhard; Ehmsen, Sidse

Kinomic and phospho-proteomic analysis of breast cancer stem-like cells Rikke Leth-Larsen1, Anne G Christensen1, Sidse Ehmsen1, Mark Møller1, Giuseppe Palmisano2, Martin R Larsen2, Henrik J Ditzel1,3 1Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark 2Institute...... of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark 3Dept. of Oncology, Odense University Hospital, Odense, Denmark Cancer stem cells are thought to be responsible for tumorigenic potential and to possess resistance mechanisms against chemotherapy- and radiation-induced cancer...... cell death, while the bulk of a tumor lacks these capacities. The resistance mechanisms may cause these cells to survive and become the source of later tumor recurrence, highlighting the need for therapeutic strategies that specifically target pathways central to these cancer stem cells. The CD44hi...

Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.

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Matthew A Schechter

Full Text Available The molecular differences between ischemic (IF and non-ischemic (NIF heart failure are poorly defined. A better understanding of the molecular differences between these two heart failure etiologies may lead to the development of more effective heart failure therapeutics. In this study extensive proteomic and phosphoproteomic profiles of myocardial tissue from patients diagnosed with IF or NIF were assembled and compared. Proteins extracted from left ventricular sections were proteolyzed and phosphopeptides were enriched using titanium dioxide resin. Gel- and label-free nanoscale capillary liquid chromatography coupled to high resolution accuracy mass tandem mass spectrometry allowed for the quantification of 4,436 peptides (corresponding to 450 proteins and 823 phosphopeptides (corresponding to 400 proteins from the unenriched and phospho-enriched fractions, respectively. Protein abundance did not distinguish NIF from IF. In contrast, 37 peptides (corresponding to 26 proteins exhibited a ≥ 2-fold alteration in phosphorylation state (p<0.05 when comparing IF and NIF. The degree of protein phosphorylation at these 37 sites was specifically dependent upon the heart failure etiology examined. Proteins exhibiting phosphorylation alterations were grouped into functional categories: transcriptional activation/RNA processing; cytoskeleton structure/function; molecular chaperones; cell adhesion/signaling; apoptosis; and energetic/metabolism. Phosphoproteomic analysis demonstrated profound post-translational differences in proteins that are involved in multiple cellular processes between different heart failure phenotypes. Understanding the roles these phosphorylation alterations play in the development of NIF and IF has the potential to generate etiology-specific heart failure therapeutics, which could be more effective than current therapeutics in addressing the growing concern of heart failure.

Highly Efficient Single-Step Enrichment of Low Abundance Phosphopeptides from Plant Membrane Preparations

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Xu Na Wu

2017-09-01

Full Text Available Mass spectrometry (MS-based large scale phosphoproteomics has facilitated the investigation of plant phosphorylation dynamics on a system-wide scale. However, generating large scale data sets for membrane phosphoproteins usually requires fractionation of samples and extended hands-on laboratory time. To overcome these limitations, we developed “ShortPhos,” an efficient and simple phosphoproteomics protocol optimized for research on plant membrane proteins. The optimized workflow allows fast and efficient identification and quantification of phosphopeptides, even from small amounts of starting plant materials. “ShortPhos” can produce label-free datasets with a high quantitative reproducibility. In addition, the “ShortPhos” protocol recovered more phosphorylation sites from membrane proteins, especially plasma membrane and vacuolar proteins, when compared to our previous workflow and other membrane-based data in the PhosPhAt 4.0 database. We applied “ShortPhos” to study kinase-substrate relationships within a nitrate-induction experiment on Arabidopsis roots. The “ShortPhos” identified significantly more known kinase-substrate relationships compared to previous phosphoproteomics workflows, producing new insights into nitrate-induced signaling pathways.

The beginnings of crop phosphoproteomics: exploring early warning systems of stress.

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Christof eRampitsch

2012-07-01

Full Text Available This review examines why a knowledge of plant protein phosphorylation events is important in devising strategies to protect crops from both biotic and abiotic stresses, and why proteomics should be included when studying stress pathways. Most of the achievements in elucidating phospho-signalling pathways in biotic and abiotic stress are reported from model systems: while these are discussed, this review attempts mainly to focus on work done with crops, with examples of achievements reported from rice, maize, wheat, grape, Brassica, tomato and soy bean after cold acclimation, hormonal and oxidative H2O2 treatment, salt stress, mechanical wounding or pathogen challenge. The challenges that remain to transfer this information into a format that can be used to protect crops against biotic and abiotic stresses are enormous. The tremendous increase in the speed and ease of DNA sequencing is poised to reveal the whole genomes of many crop species in the near future, which will facilitate phosphoproteomics and phosphogenomics research.

Celiac anti-type 2 transglutaminase antibodies induce phosphoproteome modification in intestinal epithelial Caco-2 cells.

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Gaetana Paolella

Full Text Available BACKGROUND: Celiac disease is an inflammatory condition of the small intestine that affects genetically predisposed individuals after dietary wheat gliadin ingestion. Type 2-transglutaminase (TG2 activity seems to be responsible for a strong autoimmune response in celiac disease, TG2 being the main autoantigen. Several studies support the concept that celiac anti-TG2 antibodies may contribute to disease pathogenesis. Our recent findings on the ability of anti-TG2 antibodies to induce a rapid intracellular mobilization of calcium ions, as well as extracellular signal-regulated kinase phosphorylation, suggest that they potentially act as signaling molecules. In line with this concept, we have investigated whether anti-TG2 antibodies can induce phosphoproteome modification in an intestinal epithelial cell line. METHODS AND PRINCIPAL FINDINGS: We studied phosphoproteome modification in Caco-2 cells treated with recombinant celiac anti-TG2 antibodies. We performed a two-dimensional electrophoresis followed by specific staining of phosphoproteins and mass spectrometry analysis of differentially phosphorylated proteins. Of 14 identified proteins (excluding two uncharacterized proteins, three were hypophosphorylated and nine were hyperphosphorylated. Bioinformatics analyses confirmed the presence of phosphorylation sites in all the identified proteins and highlighted their involvement in several fundamental biological processes, such as cell cycle progression, cell stress response, cytoskeletal organization and apoptosis. CONCLUSIONS: Identification of differentially phosphorylated proteins downstream of TG2-antibody stimulation suggests that in Caco-2 cells these antibodies perturb cell homeostasis by behaving as signaling molecules. We hypothesize that anti-TG2 autoantibodies may destabilize the integrity of the intestinal mucosa in celiac individuals, thus contributing to celiac disease establishment and progression. Since several proteins here

In vivo phosphoproteome characterization reveals key starch granule-binding phosphoproteins involved in wheat water-deficit response.

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Chen, Guan-Xing; Zhen, Shou-Min; Liu, Yan-Lin; Yan, Xing; Zhang, Ming; Yan, Yue-Ming

2017-10-23

Drought stress during grain development causes significant yield loss in cereal production. The phosphorylated modification of starch granule-binding proteins (SGBPs) is an important mechanism regulating wheat starch biosynthesis. In this study, we performed the first proteomics and phosphoproteomics analyses of SGBPs in elite Chinese bread wheat (Triticum aestivum L.) cultivar Jingdong 17 under well-watered and water-stress conditions. Water stress treatment caused significant reductions in spike grain numbers and weight, total starch and amylopectin content, and grain yield. Two-dimensional gel electrophoresis revealed that the quantity of SGBPs was reduced significantly by water-deficit treatment. Phosphoproteome characterization of SGBPs under water-deficit treatment demonstrated a reduced level of phosphorylation of main starch synthesis enzymes, particularly for granule-bound starch synthase (GBSS I), starch synthase II-a (SS II-a), and starch synthase III (SS III). Specifically, the Ser34 site of the GBSSI protein, the Tyr358 site of SS II-a, and the Ser837 site of SS III-a exhibited significant less phosphorylation under water-deficit treatment than well-watered treatment. Furthermore, the expression levels of several key genes related with starch biosynthesis detected by qRT-PCR were decreased significantly at 15 days post-anthesis under water-deficit treatment. Immunolocalization showed a clear movement of GBSS I from the periphery to the interior of starch granules during grain development, under both water-deficit and well-watered conditions. Our results demonstrated that the reduction in gene expression or transcription level, protein expression and phosphorylation levels of starch biosynthesis related enzymes under water-deficit conditions is responsible for the significant decrease in total starch content and grain yield.

Pinpointing Phosphorylation Sites: Quantitative Filtering and a Novel Site-specific x-Ion Fragment

DEFF Research Database (Denmark)

Kelstrup, Christian D; Hekmat, Omid; Francavilla, Chiara

2011-01-01

Phosphoproteomics deals with the identification and quantification of thousands of phosphopeptides. Localizing the phosphorylation site is however much more difficult than establishing the identity of a phosphorylated peptide. Further, recent findings have raised doubts of the validity of the site......-phase phosphate rearrangement reactions during collision-induced dissociation (CID) and used these spectra to devise a quantitative filter that by comparing signal intensities of putative phosphorylated fragment ions with their nonphosphorylated counterparts allowed us to accurately pinpoint which fragment ions...... contain a phosphorylated residue and which ones do not. We also evaluated higher-energy collisional dissociation (HCD) and found this to be an accurate method for correct phosphorylation site localization with no gas-phase rearrangements observed above noise level. Analyzing a large set of HCD spectra...

Phosphoproteomics analysis of postmortem porcine muscle with pH decline rate and time difference

DEFF Research Database (Denmark)

Huang, Honggang; Larsen, Martin R; Karlsson, Anders H

2012-01-01

The aim of this study was to characterize the protein phosphorylation in postmortem (PM) muscle and reveal the change during meat quality development. The gel-based phosphoproteomic analysis of PM porcine muscle was performed in three pig groups with different pH decline rates from PM 1h to 24 h....... The sarcoplasmic and myofibrillar fractions were analyzed using gel electrophoresis in combination with a phosphoprotein specific staining. Globally, the group with fast pH decline rate had the highest phosphorylation level at PM 1 h, but lowest at PM 24 h, whereas the group with slow pH decline rate showed...... the reverse case. The phosphorylation level of 12 bands in sarcoplasmic fraction and 3 bands in myofibrillar fraction were significantly affected by the synergy effects of pH and time (p

R as a Lingua Franca: Advantages of Using R for Quantitative Research in Applied Linguistics

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Mizumoto, Atsushi; Plonsky, Luke

2016-01-01

In this article, we suggest that using R, a statistical software environment, is advantageous for quantitative researchers in applied linguistics. We first provide a brief overview of the reasons why R is popular among researchers in other fields and why we recommend its use for analyses in applied linguistics. In order to illustrate these…

Global analysis of the yeast osmotic stress response by quantitative proteomics

DEFF Research Database (Denmark)

Soufi, Boumediene; Kelstrup, C.D.; Stoehr, G.

2009-01-01

a comprehensive, quantitative, and time-resolved analysis using high-resolution mass spectrometry of phospho-proteome and proteome changes in response to osmotic stress in yeast. We identified 5534 unique phosphopeptide variants and 3383 yeast proteins. More than 15% of the detected phosphorylation site status...... changed more than two-fold within 5 minutes of treatment. Many of the corresponding phosphoproteins are involved in the early response to environmental stress. Surprisingly, we find that 158 regulated phosphorylation sites are potential substrates of basophilic kinases as opposed to the classical proline......-directed MAP kinase network implicated in stress response mechanisms such as p38 and HOG pathways. Proteome changes reveal an increase in abundance of more than one hundred proteins after 20 min of salt stress. Many of these are involved in the cellular response to increased osmolarity, which include proteins...

Phosphoproteomics and new onco-bio technologies in the study of the pathogenesis and therapy of malignant gliomas

International Nuclear Information System (INIS)

De Maria, R.

2009-01-01

Characterization and crio-conservation and of glioblastoma stem cells. Phosphoproteomic analysis of tumor stem cells and their progeny. The possibility to use in research stem cells isolated from glioblastoma (GSCs) is an indispensable tool for the development of new and more effective therapeutic strategies for this type of cancer, whose prognosis is still poor. The research conducted for the attainment of the first objective has led to isolation of 18 stem cells lines from cancer patients with glioblastoma who have undergone surgery at the Institute of Neurosurgery of the Catholic University of Rome. The resulting cell lines were phenotypically characterized for the expression of stem cell markers and differentiation capabilities

Quantitative Phosphoproteomic Study Reveals that Protein Kinase A Regulates Neural Stem Cell Differentiation Through Phosphorylation of Catenin Beta-1 and Glycogen Synthase Kinase 3β.

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Wang, Shuxin; Li, Zheyi; Shen, Hongyan; Zhang, Zhong; Yin, Yuxin; Wang, Qingsong; Zhao, Xuyang; Ji, Jianguo

2016-08-01

Protein phosphorylation is central to the understanding of multiple cellular signaling pathways responsible for regulating the self-renewal and differentiation of neural stem cells (NSCs). Here we performed a large-scale phosphoproteomic analysis of rat fetal NSCs using strong cation exchange chromatography prefractionation and citric acid-assisted two-step enrichment with TiO2 strategy followed by nanoLC-MS/MS analysis. Totally we identified 32,546 phosphosites on 5,091 phosphoproteins, among which 23,945 were class I phosphosites, and quantified 16,000 sites during NSC differentiation. More than 65% of class I phosphosites were novel when compared with PhosphoSitePlus database. Quantification results showed that the early and late stage of NSC differentiation differ greatly. We mapped 69 changed phosphosites on 20 proteins involved in Wnt signaling pathway, including S552 on catenin beta-1 (Ctnnb1) and S9 on glycogen synthase kinase 3β (Gsk3β). Western blotting and real-time PCR results proved that Wnt signaling pathway plays critical roles in NSC fate determination. Furthermore, inhibition and activation of PKA dramatically affected the phosphorylation state of Ctnnb1 and Gsk3β, which regulates the differentiation of NSCs. Our data provides a valuable resource for studying the self-renewal and differentiation of NSCs. Stem Cells 2016;34:2090-2101. © 2016 AlphaMed Press.

Phosphoproteomic Analysis Identifies Signaling Pathways Regulated by Curcumin in Human Colon Cancer Cells.

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Sato, Tatsuhiro; Higuchi, Yutaka; Shibagaki, Yoshio; Hattori, Seisuke

2017-09-01

Curcumin, a major polyphenol of the spice turmeric, acts as a potent chemopreventive and chemotherapeutic agent in several cancer types, including colon cancer. Although various proteins have been shown to be affected by curcumin, how curcumin exerts its anticancer activity is not fully understood. Phosphoproteomic analyses were performed using SW480 and SW620 human colon cancer cells to identify curcumin-affected signaling pathways. Curcumin inhibited the growth of the two cell lines in a dose-dependent manner. Thirty-nine curcumin-regulated phosphoproteins were identified, five of which are involved in cancer signaling pathways. Detailed analyses revealed that the mTORC1 and p53 signaling pathways are main targets of curcumin. Our results provide insight into the molecular mechanisms of the anticancer activities of curcumin and future molecular targets for its clinical application. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing

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Shinde, Mansi Y.; Sidoli, Simone; Kulej, Katarzyna; Mallory, Michael J.; Radens, Caleb M.; Reicherter, Amanda L.; Myers, Rebecca L.; Barash, Yoseph; Lynch, Kristen W.; Garcia, Benjamin A.; Klein, Peter S.

2017-01-01

Glycogen synthase kinase-3 (GSK-3) is a constitutively active, ubiquitously expressed protein kinase that regulates multiple signaling pathways. In vitro kinase assays and genetic and pharmacological manipulations of GSK-3 have identified more than 100 putative GSK-3 substrates in diverse cell types. Many more have been predicted on the basis of a recurrent GSK-3 consensus motif ((pS/pT)XXX(S/T)), but this prediction has not been tested by analyzing the GSK-3 phosphoproteome. Using stable isotope labeling of amino acids in culture (SILAC) and MS techniques to analyze the repertoire of GSK-3–dependent phosphorylation in mouse embryonic stem cells (ESCs), we found that ∼2.4% of (pS/pT)XXX(S/T) sites are phosphorylated in a GSK-3–dependent manner. A comparison of WT and Gsk3a;Gsk3b knock-out (Gsk3 DKO) ESCs revealed prominent GSK-3–dependent phosphorylation of multiple splicing factors and regulators of RNA biosynthesis as well as proteins that regulate transcription, translation, and cell division. Gsk3 DKO reduced phosphorylation of the splicing factors RBM8A, SRSF9, and PSF as well as the nucleolar proteins NPM1 and PHF6, and recombinant GSK-3β phosphorylated these proteins in vitro. RNA-Seq of WT and Gsk3 DKO ESCs identified ∼190 genes that are alternatively spliced in a GSK-3–dependent manner, supporting a broad role for GSK-3 in regulating alternative splicing. The MS data also identified posttranscriptional regulation of protein abundance by GSK-3, with ∼47 proteins (1.4%) whose levels increased and ∼78 (2.4%) whose levels decreased in the absence of GSK-3. This study provides the first unbiased analysis of the GSK-3 phosphoproteome and strong evidence that GSK-3 broadly regulates alternative splicing. PMID:28916722

Characterization of the human plasma phosphoproteome using linear ion trap mass spectrometry and multiple search engines.

Science.gov (United States)

Carrascal, Montserrat; Gay, Marina; Ovelleiro, David; Casas, Vanessa; Gelpí, Emilio; Abian, Joaquin

2010-02-05

Major plasma protein families play different roles in blood physiology and hemostasis and in immunodefense. Other proteins in plasma can be involved in signaling as chemical messengers or constitute biological markers of the status of distant tissues. In this respect, the plasma phosphoproteome holds potentially relevant information on the mechanisms modulating these processes through the regulation of protein activity. In this work we describe for the first time a collection of phosphopeptides identified in human plasma using immunoaffinity separation of the seven major serum protein families from other plasma proteins, SCX fractionation, and TiO(2) purification prior to LC-MS/MS analysis. One-hundred and twenty-seven phosphosites in 138 phosphopeptides mapping 70 phosphoproteins were identified with FDR search engines.

Nuclear phosphoproteome of developing chickpea seedlings (Cicer arietinum L.) and protein-kinase interaction network.

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Kumar, Rajiv; Kumar, Amit; Subba, Pratigya; Gayali, Saurabh; Barua, Pragya; Chakraborty, Subhra; Chakraborty, Niranjan

2014-06-13

Nucleus, the control centre of eukaryotic cell, houses most of the genetic machineries required for gene expression and their regulation. Post translational modifications of proteins, particularly phosphorylation control a wide variety of cellular processes but its functional connectivity, in plants, is still elusive. This study profiled the nuclear phosphoproteome of a grain legume, chickpea, to gain better understanding of such event. Intact nuclei were isolated from 3-week-old seedlings using two independent methods, and nuclear proteins were resolved by 2-DE. In a separate set of experiments, phosphoproteins were enriched using IMAC method and resolved by 1-DE. The separated proteins were stained with phosphospecific Pro-Q Diamond stain. Proteomic analyses led to the identification of 107 putative phosphoproteins, of which 86 were non-redundant. Multiple sites of phosphorylation were predicted on several key elements, which included both regulatory and functional proteins. The analysis revealed an array of phosphoproteins, presumably involved in a variety of cellular functions, viz., protein folding (24%), signalling and gene regulation (22%), DNA replication, repair and modification (16%), and metabolism (13%), among others. These results represent the first nucleus-specific phosphoproteome map of a non-model legume, which would provide insights into the possible function of protein phosphorylation in plants. Chickpea is grown over 10 million hectares of land worldwide, and global production hovers around 8.5 million metric tons annually. Despite its nutritional merits, it is often referred to as 'orphan' legume and has remained outside the realm of large-scale functional genomics studies. While current chickpea genome initiative has primarily focused on sequence information and functional annotation, proteomics analyses are limited. It is thus important to study the proteome of the cell organelle particularly the nucleus, which harbors most of the genetic

Quantitative phosphoproteomics dissection of seven-transmembrane receptor signaling using full and biased agonists

DEFF Research Database (Denmark)

Christensen, Gitte L; Kelstrup, Christian D; Lyngsø, Christina

2010-01-01

(q)-dependent and -independent AT(1)R signaling. This study provides substantial novel insight into angiotensin II signal transduction and is the first study dissecting the differences between a full agonist and a biased agonist from a 7TMR on a systems-wide scale. Importantly, it reveals a previously unappreciated diversity......Seven-transmembrane receptors (7TMRs) signal through the well described heterotrimeric G proteins but can also activate G protein-independent signaling pathways of which the impact and complexity are less understood. The angiotensin II type 1 receptor (AT(1)R) is a prototypical 7TMR...... and quantity of Galpha(q) protein-independent signaling and uncovers novel signaling pathways. We foresee that the amount and diversity of G protein-independent signaling may be more pronounced than previously recognized for other 7TMRs as well. Quantitative mass spectrometry is a promising tool for evaluation...

Differences in Beef Quality between Angus (Bos taurus taurus) and Nellore (Bos taurus indicus) Cattle through a Proteomic and Phosphoproteomic Approach.

Science.gov (United States)

Rodrigues, Rafael Torres de Souza; Chizzotti, Mario Luiz; Vital, Camilo Elber; Baracat-Pereira, Maria Cristina; Barros, Edvaldo; Busato, Karina Costa; Gomes, Rafael Aparecido; Ladeira, Márcio Machado; Martins, Taiane da Silva

2017-01-01

Proteins are the major constituents of muscle and are key molecules regulating the metabolic changes during conversion of muscle to meat. Brazil is one of the largest exporters of beef and most Brazilian cattle are composed by zebu (Nellore) genotype. Bos indicus beef is generally leaner and tougher than Bos taurus such as Angus. The aim of this study was to compare the muscle proteomic and phosphoproteomic profile of Angus and Nellore. Seven animals of each breed previously subjected the same growth management were confined for 84 days. Proteins were extracted from Longissimus lumborum samples collected immediately after slaughter and separated by two-dimensional electrophoresis. Pro-Q Diamond stain was used in phosphoproteomics. Proteins identification was performed using matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Tropomyosin alpha-1 chain, troponin-T, myosin light chain-1 fragment, cytoplasmic malate dehydrogenase, alpha-enolase and 78 kDa glucose-regulated protein were more abundant in Nellore, while myosin light chain 3, prohibitin, mitochondrial stress-70 protein and heat shock 70 kDa protein 6 were more abundant in Angus (PAngus had greater phosphorylation of phosphoglucomutase-1 and troponin-T (PAngus and Nellore. Furthermore, prohibitin appears to be a potential biomarker of intramuscular fat in cattle. Additionally, differences in phosphorylation of myofilaments and glycolytic enzymes could be involved with differences in muscle contraction force, susceptibility to calpain, apoptosis and postmortem glycolysis, which might also be related to differences in beef quality among Angus and Nellore.

In vivo quantitative phosphoproteomic profiling identifies novel regulators of castration-resistant prostate cancer growth

DEFF Research Database (Denmark)

Jiang, Nan; Hjorth-Jensen, Kim; Hekmat, Omid

2015-01-01

Prostate cancer remains a leading cause of cancer-related mortality worldwide owing to our inability to treat effectively castration-resistant tumors. To understand the signaling mechanisms sustaining castration-resistant growth, we implemented a mass spectrometry-based quantitative proteomic app...

Phosphoproteomic profiling of in vivo signaling in liver by the mammalian target of rapamycin complex 1 (mTORC1.

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Gokhan Demirkan

Full Text Available Our understanding of signal transduction networks in the physiological context of an organism remains limited, partly due to the technical challenge of identifying serine/threonine phosphorylated peptides from complex tissue samples. In the present study, we focused on signaling through the mammalian target of rapamycin (mTOR complex 1 (mTORC1, which is at the center of a nutrient- and growth factor-responsive cell signaling network. Though studied extensively, the mechanisms involved in many mTORC1 biological functions remain poorly understood.We developed a phosphoproteomic strategy to purify, enrich and identify phosphopeptides from rat liver homogenates. Using the anticancer drug rapamycin, the only known target of which is mTORC1, we characterized signaling in liver from rats in which the complex was maximally activated by refeeding following 48 hr of starvation. Using protein and peptide fractionation methods, TiO(2 affinity purification of phosphopeptides and mass spectrometry, we reproducibly identified and quantified over four thousand phosphopeptides. Along with 5 known rapamycin-sensitive phosphorylation events, we identified 62 new rapamycin-responsive candidate phosphorylation sites. Among these were PRAS40, gephyrin, and AMP kinase 2. We observed similar proportions of increased and reduced phosphorylation in response to rapamycin. Gene ontology analysis revealed over-representation of mTOR pathway components among rapamycin-sensitive phosphopeptide candidates.In addition to identifying potential new mTORC1-mediated phosphorylation events, and providing information relevant to the biology of this signaling network, our experimental and analytical approaches indicate the feasibility of large-scale phosphoproteomic profiling of tissue samples to study physiological signaling events in vivo.

Artificial neural networks applied to quantitative elemental analysis of organic material using PIXE

International Nuclear Information System (INIS)

Correa, R.; Chesta, M.A.; Morales, J.R.; Dinator, M.I.; Requena, I.; Vila, I.

2006-01-01

An artificial neural network (ANN) has been trained with real-sample PIXE (particle X-ray induced emission) spectra of organic substances. Following the training stage ANN was applied to a subset of similar samples thus obtaining the elemental concentrations in muscle, liver and gills of Cyprinus carpio. Concentrations obtained with the ANN method are in full agreement with results from one standard analytical procedure, showing the high potentiality of ANN in PIXE quantitative analyses

Artificial neural networks applied to quantitative elemental analysis of organic material using PIXE

Energy Technology Data Exchange (ETDEWEB)

Correa, R. [Universidad Tecnologica Metropolitana, Departamento de Fisica, Av. Jose Pedro Alessandri 1242, Nunoa, Santiago (Chile)]. E-mail: rcorrea@utem.cl; Chesta, M.A. [Universidad Nacional de Cordoba, Facultad de Matematica, Astronomia y Fisica, Medina Allende s/n Ciudad Universitaria, 5000 Cordoba (Argentina)]. E-mail: chesta@famaf.unc.edu.ar; Morales, J.R. [Universidad de Chile, Facultad de Ciencias, Departamento de Fisica, Las Palmeras 3425, Nunoa, Santiago (Chile)]. E-mail: rmorales@uchile.cl; Dinator, M.I. [Universidad de Chile, Facultad de Ciencias, Departamento de Fisica, Las Palmeras 3425, Nunoa, Santiago (Chile)]. E-mail: mdinator@uchile.cl; Requena, I. [Universidad de Granada, Departamento de Ciencias de la Computacion e Inteligencia Artificial, Daniel Saucedo Aranda s/n, 18071 Granada (Spain)]. E-mail: requena@decsai.ugr.es; Vila, I. [Universidad de Chile, Facultad de Ciencias, Departamento de Ecologia, Las Palmeras 3425, Nunoa, Santiago (Chile)]. E-mail: limnolog@uchile.cl

2006-08-15

An artificial neural network (ANN) has been trained with real-sample PIXE (particle X-ray induced emission) spectra of organic substances. Following the training stage ANN was applied to a subset of similar samples thus obtaining the elemental concentrations in muscle, liver and gills of Cyprinus carpio. Concentrations obtained with the ANN method are in full agreement with results from one standard analytical procedure, showing the high potentiality of ANN in PIXE quantitative analyses.

Lost in translation? The hazards of applying social constructionism to quantitative research on sexual orientation development.

Science.gov (United States)

Robboy, Caroline Alex

2002-01-01

This article explores the hazards faced by social constructionists who attempt to conduct quantitative research on sexual orientation development. By critically reviewing two quantitative research studies, this article explores the ways in which the very nature of social constructionist arguments may be incongruous with the methodological requirements of quantitative studies. I suggest this conflict is a result of the differing natures of these two modes of scholarly inquiry. While research requires the acceptance of certain analytical categories, the strength of social constructionism comes from its reflexive scrutiny and problematization of those very categories. Ultimately, social constructionists who try to apply their theories/perspectives must necessarily conform to the methodological constraints of quantitative research. The intent of this article is not to suggest that it is futile or self-contradictory for social constructionists to attempt empirical research, but that these are two distinct modes of scholarly inquiry which can, and should, co-exist in a dialectical relationship to each other.

Inducing autophagy

DEFF Research Database (Denmark)

Harder, Lea M; Bunkenborg, Jakob; Andersen, Jens S.

2014-01-01

catabolism, which has recently been found to induce autophagy in an MTOR independent way and support cancer cell survival. In this study, quantitative phosphoproteomics was applied to investigate the initial signaling events linking ammonia to the induction of autophagy. The MTOR inhibitor rapamycin was used...... as a reference treatment to emphasize the differences between an MTOR-dependent and -independent autophagy-induction. By this means 5901 phosphosites were identified of which 626 were treatment-specific regulated and 175 were coregulated. Investigation of the ammonia-specific regulated sites supported that MTOR...

Comparative Phosphoproteomics Reveals the Role of AmpC β-lactamase Phosphorylation in the Clinical Imipenem-resistant Strain Acinetobacter baumannii SK17*

Science.gov (United States)

Lai, Juo-Hsin; Yang, Jhih-Tian; Chern, Jeffy; Chen, Te-Li; Wu, Wan-Ling; Liao, Jiahn-Haur; Tsai, Shih-Feng; Liang, Suh-Yuen; Chou, Chi-Chi

2016-01-01

Nosocomial infectious outbreaks caused by multidrug-resistant Acinetobacter baumannii have emerged as a serious threat to human health. Phosphoproteomics of pathogenic bacteria has been used to identify the mechanisms of bacterial virulence and antimicrobial resistance. In this study, we used a shotgun strategy combined with high-accuracy mass spectrometry to analyze the phosphoproteomics of the imipenem-susceptible strain SK17-S and -resistant strain SK17-R. We identified 410 phosphosites on 248 unique phosphoproteins in SK17-S and 285 phosphosites on 211 unique phosphoproteins in SK17-R. The distributions of the Ser/Thr/Tyr/Asp/His phosphosites in SK17-S and SK17-R were 47.0%/27.6%/12.4%/8.0%/4.9% versus 41.4%/29.5%/17.5%/6.7%/4.9%, respectively. The Ser-90 phosphosite, located on the catalytic motif S88VS90K of the AmpC β-lactamase, was first identified in SK17-S. Based on site-directed mutagenesis, the nonphosphorylatable mutant S90A was found to be more resistant to imipenem, whereas the phosphorylation-simulated mutant S90D was sensitive to imipenem. Additionally, the S90A mutant protein exhibited higher β-lactamase activity and conferred greater bacterial protection against imipenem in SK17-S compared with the wild-type. In sum, our results revealed that in A. baumannii, Ser-90 phosphorylation of AmpC negatively regulates both β-lactamase activity and the ability to counteract the antibiotic effects of imipenem. These findings highlight the impact of phosphorylation-mediated regulation in antibiotic-resistant bacteria on future drug design and new therapies. PMID:26499836

EBprot: Statistical analysis of labeling-based quantitative proteomics data.

Science.gov (United States)

Koh, Hiromi W L; Swa, Hannah L F; Fermin, Damian; Ler, Siok Ghee; Gunaratne, Jayantha; Choi, Hyungwon

2015-08-01

Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is not incorporated into the differential expression (DE) analysis. Here, we propose a novel probabilistic framework EBprot that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. To illustrate the wide applicability of EBprot in different experimental designs, we applied EBprot to a dataset for lung cancer subtype analysis with biological replicates and another dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells with multiplexed labeling. Through these examples, we show that the peptide-level analysis of EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets. The software suite is freely available on the Sourceforge website http://ebprot.sourceforge.net/. All MS data have been deposited in the ProteomeXchange with identifier PXD001426 (http://proteomecentral.proteomexchange.org/dataset/PXD001426/). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.

Science.gov (United States)

Litichevskiy, Lev; Peckner, Ryan; Abelin, Jennifer G; Asiedu, Jacob K; Creech, Amanda L; Davis, John F; Davison, Desiree; Dunning, Caitlin M; Egertson, Jarrett D; Egri, Shawn; Gould, Joshua; Ko, Tak; Johnson, Sarah A; Lahr, David L; Lam, Daniel; Liu, Zihan; Lyons, Nicholas J; Lu, Xiaodong; MacLean, Brendan X; Mungenast, Alison E; Officer, Adam; Natoli, Ted E; Papanastasiou, Malvina; Patel, Jinal; Sharma, Vagisha; Toder, Courtney; Tubelli, Andrew A; Young, Jennie Z; Carr, Steven A; Golub, Todd R; Subramanian, Aravind; MacCoss, Michael J; Tsai, Li-Huei; Jaffe, Jacob D

2018-04-25

Although the value of proteomics has been demonstrated, cost and scale are typically prohibitive, and gene expression profiling remains dominant for characterizing cellular responses to perturbations. However, high-throughput sentinel assays provide an opportunity for proteomics to contribute at a meaningful scale. We present a systematic library resource (90 drugs × 6 cell lines) of proteomic signatures that measure changes in the reduced-representation phosphoproteome (P100) and changes in epigenetic marks on histones (GCP). A majority of these drugs elicited reproducible signatures, but notable cell line- and assay-specific differences were observed. Using the "connectivity" framework, we compared signatures across cell types and integrated data across assays, including a transcriptional assay (L1000). Consistent connectivity among cell types revealed cellular responses that transcended lineage, and consistent connectivity among assays revealed unexpected associations between drugs. We further leveraged the resource against public data to formulate hypotheses for treatment of multiple myeloma and acute lymphocytic leukemia. This resource is publicly available at https://clue.io/proteomics. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Applied to Quantitative Proteomics of Bacillus subtilis

DEFF Research Database (Denmark)

Soufi, Boumediene; Kumar, C.; Gnad, F.

2010-01-01

We applied stable isotope labeling by amino acids in cell culture (SILAC) to large-scale quantitative proteomics analyses of the model bacterium Bacillus subtilis in two physiological conditions: growth on succinate and growth under phosphate starvation. Using a B. subtilis strain auxotrophic...... of the most comprehensive quantitative proteomics studies in bacteria, covering more than 75% of the B. subtilis genes expressed in the log phase of growth. Furthermore, we detect and quantify dynamics of 35 Ser/Thr/Tyr phosphorylation sites under growth on succinate, and 10 phosphorylation sites under...

Phosphoproteome and transcription factor activity profiling identify actions of the anti-inflammatory agent UTL-5g in LPS stimulated RAW 264.7 cells including disrupting actin remodeling and STAT-3 activation.

Science.gov (United States)

Carruthers, Nicholas J; Stemmer, Paul M; Chen, Ben; Valeriote, Frederick; Gao, Xiaohua; Guatam, Subhash C; Shaw, Jiajiu

2017-09-15

UTL-5g is a novel small-molecule TNF-alpha modulator. It reduces cisplatin-induced side effects by protecting kidney, liver, and platelets, thereby increasing tolerance for cisplatin. UTL-5g also reduces radiation-induced acute liver toxicity. The mechanism of action for UTL-5g is not clear at the present time. A phosphoproteomic analysis to a depth of 4943 phosphopeptides and a luminescence-based transcription factor activity assay were used to provide complementary analyses of signaling events that were disrupted by UTL-5g in RAW 264.7 cells. Transcriptional activity downstream of the interferon gamma, IL-6, type 1 Interferon, TGF-β, PKC/Ca 2+ and the glucocorticoid receptor pathways were disrupted by UTL-5g. Phosphoproteomic analysis indicated that hyperphosphorylation of proteins involved in actin remodeling was suppressed by UTL-5g (gene set analysis, FDR 5g. This global characterization of UTL-5g activity in a macrophage cell line discovered that it disrupts selected aspects of LPS signaling including Stat3 activation and actin remodeling providing new insight on how UTL-5g acts to reduce cisplatin-induced side effects. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics.

Science.gov (United States)

Poss, Zachary C; Ebmeier, Christopher C; Odell, Aaron T; Tangpeerachaikul, Anupong; Lee, Thomas; Pelish, Henry E; Shair, Matthew D; Dowell, Robin D; Old, William M; Taatjes, Dylan J

2016-04-12

Cortistatin A (CA) is a highly selective inhibitor of the Mediator kinases CDK8 and CDK19. Using CA, we now report a large-scale identification of Mediator kinase substrates in human cells (HCT116). We identified over 16,000 quantified phosphosites including 78 high-confidence Mediator kinase targets within 64 proteins, including DNA-binding transcription factors and proteins associated with chromatin, DNA repair, and RNA polymerase II. Although RNA-seq data correlated with Mediator kinase targets, the effects of CA on gene expression were limited and distinct from CDK8 or CDK19 knockdown. Quantitative proteome analyses, tracking around 7,000 proteins across six time points (0-24 hr), revealed that CA selectively affected pathways implicated in inflammation, growth, and metabolic regulation. Contrary to expectations, increased turnover of Mediator kinase targets was not generally observed. Collectively, these data support Mediator kinases as regulators of chromatin and RNA polymerase II activity and suggest their roles extend beyond transcription to metabolism and DNA repair. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Comparative Phosphoproteomics Reveals the Role of AmpC β-lactamase Phosphorylation in the Clinical Imipenem-resistant Strain Acinetobacter baumannii SK17.

Science.gov (United States)

Lai, Juo-Hsin; Yang, Jhih-Tian; Chern, Jeffy; Chen, Te-Li; Wu, Wan-Ling; Liao, Jiahn-Haur; Tsai, Shih-Feng; Liang, Suh-Yuen; Chou, Chi-Chi; Wu, Shih-Hsiung

2016-01-01

Nosocomial infectious outbreaks caused by multidrug-resistant Acinetobacter baumannii have emerged as a serious threat to human health. Phosphoproteomics of pathogenic bacteria has been used to identify the mechanisms of bacterial virulence and antimicrobial resistance. In this study, we used a shotgun strategy combined with high-accuracy mass spectrometry to analyze the phosphoproteomics of the imipenem-susceptible strain SK17-S and -resistant strain SK17-R. We identified 410 phosphosites on 248 unique phosphoproteins in SK17-S and 285 phosphosites on 211 unique phosphoproteins in SK17-R. The distributions of the Ser/Thr/Tyr/Asp/His phosphosites in SK17-S and SK17-R were 47.0%/27.6%/12.4%/8.0%/4.9% versus 41.4%/29.5%/17.5%/6.7%/4.9%, respectively. The Ser-90 phosphosite, located on the catalytic motif S(88)VS(90)K of the AmpC β-lactamase, was first identified in SK17-S. Based on site-directed mutagenesis, the nonphosphorylatable mutant S90A was found to be more resistant to imipenem, whereas the phosphorylation-simulated mutant S90D was sensitive to imipenem. Additionally, the S90A mutant protein exhibited higher β-lactamase activity and conferred greater bacterial protection against imipenem in SK17-S compared with the wild-type. In sum, our results revealed that in A. baumannii, Ser-90 phosphorylation of AmpC negatively regulates both β-lactamase activity and the ability to counteract the antibiotic effects of imipenem. These findings highlight the impact of phosphorylation-mediated regulation in antibiotic-resistant bacteria on future drug design and new therapies. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

DEFF Research Database (Denmark)

Lundby, Alicia; Secher, Anna; Lage, Kasper

2012-01-01

Deregulated cellular signalling is a common hallmark of disease, and delineating tissue phosphoproteomes is key to unravelling the underlying mechanisms. Here we present the broadest tissue catalogue of phosphoproteins to date, covering 31,480 phosphorylation sites on 7,280 proteins quantified ac...

Gel-based phosphoproteomics analysis of sarcoplasmic proteins in postmortem porcine muscle with pH decline rate and time differences

DEFF Research Database (Denmark)

Huang, Honggang; Larsen, Martin Røssel; Karlsson, Anders H

2011-01-01

phosphorylation in sarcoplasmic proteins from three groups of pigs with different pH decline rates from PM 1 to 24¿h. Globally, the fast pH decline group had the highest phosphorylation level at PM 1¿h, but lowest at 24¿h, whereas the slow pH decline group showed the reverse case. The same pattern was also...... observed in most individual bands in 1-DE. The protein phosphorylation levels of 12 bands were significantly affected by the synergy effects of pH and time (p......Meat quality development is highly influenced by the pH decline caused by the postmortem (PM) glycolysis. Protein phosphorylation is an important mechanism in regulating the activity of glycometabolic enzymes. Here, a gel-based phosphoproteomic study was performed to analyze the protein...

Applying quantitative benefit-risk analysis to aid regulatory decision making in diagnostic imaging: methods, challenges, and opportunities.

Science.gov (United States)

Agapova, Maria; Devine, Emily Beth; Bresnahan, Brian W; Higashi, Mitchell K; Garrison, Louis P

2014-09-01

Health agencies making regulatory marketing-authorization decisions use qualitative and quantitative approaches to assess expected benefits and expected risks associated with medical interventions. There is, however, no universal standard approach that regulatory agencies consistently use to conduct benefit-risk assessment (BRA) for pharmaceuticals or medical devices, including for imaging technologies. Economics, health services research, and health outcomes research use quantitative approaches to elicit preferences of stakeholders, identify priorities, and model health conditions and health intervention effects. Challenges to BRA in medical devices are outlined, highlighting additional barriers in radiology. Three quantitative methods--multi-criteria decision analysis, health outcomes modeling and stated-choice survey--are assessed using criteria that are important in balancing benefits and risks of medical devices and imaging technologies. To be useful in regulatory BRA, quantitative methods need to: aggregate multiple benefits and risks, incorporate qualitative considerations, account for uncertainty, and make clear whose preferences/priorities are being used. Each quantitative method performs differently across these criteria and little is known about how BRA estimates and conclusions vary by approach. While no specific quantitative method is likely to be the strongest in all of the important areas, quantitative methods may have a place in BRA of medical devices and radiology. Quantitative BRA approaches have been more widely applied in medicines, with fewer BRAs in devices. Despite substantial differences in characteristics of pharmaceuticals and devices, BRA methods may be as applicable to medical devices and imaging technologies as they are to pharmaceuticals. Further research to guide the development and selection of quantitative BRA methods for medical devices and imaging technologies is needed. Copyright © 2014 AUR. Published by Elsevier Inc. All rights

Comparative Proteome and Phosphoproteome Analyses during Cyprid Development of the Barnacle Balanus ( =Amphibalanus ) amphitrite

KAUST Repository

Zhang, Yu

2010-06-04

The barnacle Balanus amphitrite (=Amphibalanus amphitrite) is a major marine biofouling invertebrate worldwide. It has a complex life cycle during which the larva (called a nauplius) molts six times before transforming into the cyprid stage. The cyprid stage in B. amphitrite is the critical stage for the larval decision to attach and metamorphose. In this study, proteome and phosphoproteome alterations during cyprid development/aging and upon treatment with the antifouling agent butenolide were examined with a two-dimensional electrophoresis (2-DE) multiplexed fluorescent staining approach. Optimized protein separation strategies, including solution-phase isoelectric fractionation and narrow-pH-range 2-DE, were used in a proteomic analysis. Our results show that the differential regulation of the target proteins is highly dynamic on the levels of both protein expression and posttranslational modification. Two groups of proteins, stress-associated and energy metabolism-related proteins, are differentially expressed during cyprid development. Comparison of the control and treatment groups suggests that butenolide exerts its effects by sustaining the expression levels of these proteins. Altogether, our data suggest that proteins involved in stress regulation and energy metabolism play crucial roles in regulating larval attachment and metamorphosis of B. amphitrite. © 2010 American Chemical Society.

Phosphoproteome and Transcriptome of RA-Responsive and RA-Resistant Breast Cancer Cell Lines.

Directory of Open Access Journals (Sweden)

Marilyn Carrier

Full Text Available Retinoic acid (RA, the main active vitamin A metabolite, controls multiple biological processes such as cell proliferation and differentiation through genomic programs and kinase cascades activation. Due to these properties, RA has proven anti-cancer capacity. Several breast cancer cells respond to the antiproliferative effects of RA, while others are RA-resistant. However, the overall signaling and transcriptional pathways that are altered in such cells have not been elucidated. Here, in a large-scale analysis of the phosphoproteins and in a genome-wide analysis of the RA-regulated genes, we compared two human breast cancer cell lines, a RA-responsive one, the MCF7 cell line, and a RA-resistant one, the BT474 cell line, which depicts several alterations of the "kinome". Using high-resolution nano-LC-LTQ-Orbitrap mass spectrometry associated to phosphopeptide enrichment, we found that several proteins involved in signaling and in transcription, are differentially phosphorylated before and after RA addition. The paradigm of these proteins is the RA receptor α (RARα, which was phosphorylated in MCF7 cells but not in BT474 cells after RA addition. The panel of the RA-regulated genes was also different. Overall our results indicate that RA resistance might correlate with the deregulation of the phosphoproteome with consequences on gene expression.

Quantitative Microbial Risk Assessment in Occupational Settings Applied to the Airborne Human Adenovirus Infection

Directory of Open Access Journals (Sweden)

Annalaura Carducci

2016-07-01

Full Text Available Quantitative Microbial Risk Assessment (QMRA methodology, which has already been applied to drinking water and food safety, may also be applied to risk assessment and management at the workplace. The present study developed a preliminary QMRA model to assess microbial risk that is associated with inhaling bioaerosols that are contaminated with human adenovirus (HAdV. This model has been applied to air contamination data from different occupational settings, including wastewater systems, solid waste landfills, and toilets in healthcare settings and offices, with different exposure times. Virological monitoring showed the presence of HAdVs in all the evaluated settings, thus confirming that HAdV is widespread, but with different average concentrations of the virus. The QMRA results, based on these concentrations, showed that toilets had the highest probability of viral infection, followed by wastewater treatment plants and municipal solid waste landfills. Our QMRA approach in occupational settings is novel, and certain caveats should be considered. Nonetheless, we believe it is worthy of further discussions and investigations.

Quantitative Analysis of Signaling Networks across Differentially Embedded Tumors Highlights Interpatient Heterogeneity in Human Glioblastoma

Science.gov (United States)

2015-01-01

Glioblastoma multiforme (GBM) is the most aggressive malignant primary brain tumor, with a dismal mean survival even with the current standard of care. Although in vitro cell systems can provide mechanistic insight into the regulatory networks governing GBM cell proliferation and migration, clinical samples provide a more physiologically relevant view of oncogenic signaling networks. However, clinical samples are not widely available and may be embedded for histopathologic analysis. With the goal of accurately identifying activated signaling networks in GBM tumor samples, we investigated the impact of embedding in optimal cutting temperature (OCT) compound followed by flash freezing in LN2 vs immediate flash freezing (iFF) in LN2 on protein expression and phosphorylation-mediated signaling networks. Quantitative proteomic and phosphoproteomic analysis of 8 pairs of tumor specimens revealed minimal impact of the different sample processing strategies and highlighted the large interpatient heterogeneity present in these tumors. Correlation analyses of the differentially processed tumor sections identified activated signaling networks present in selected tumors and revealed the differential expression of transcription, translation, and degradation associated proteins. This study demonstrates the capability of quantitative mass spectrometry for identification of in vivo oncogenic signaling networks from human tumor specimens that were either OCT-embedded or immediately flash-frozen. PMID:24927040

Effects of the NO/soluble guanylate cyclase/cGMP system on the functions of human platelets.

Science.gov (United States)

Makhoul, Stephanie; Walter, Elena; Pagel, Oliver; Walter, Ulrich; Sickmann, Albert; Gambaryan, Stepan; Smolenski, Albert; Zahedi, René P; Jurk, Kerstin

2018-06-01

Platelets are circulating sentinels of vascular integrity and are activated, inhibited, or modulated by multiple hormones, vasoactive substances or drugs. Endothelium- or drug-derived NO strongly inhibits platelet activation via activation of the soluble guanylate cyclase (sGC) and cGMP elevation, often in synergy with cAMP-elevation by prostacyclin. However, the molecular mechanisms and diversity of cGMP effects in platelets are poorly understood and sometimes controversial. Recently, we established the quantitative human platelet proteome, the iloprost/prostacyclin/cAMP/protein kinase A (PKA)-regulated phosphoproteome, and the interactions of the ADP- and iloprost/prostacyclin-affected phosphoproteome. We also showed that the sGC stimulator riociguat is in vitro a highly specific inhibitor, via cGMP, of various functions of human platelets. Here, we review the regulatory role of the cGMP/protein kinase G (PKG) system in human platelet function, and our current approaches to establish and analyze the phosphoproteome after selective stimulation of the sGC/cGMP pathway by NO donors and riociguat. Present data indicate an extensive and diverse NO/riociguat/cGMP phosphoproteome, which has to be compared with the cAMP phosphoproteome. In particular, sGC/cGMP-regulated phosphorylation of many membrane proteins, G-proteins and their regulators, signaling molecules, protein kinases, and proteins involved in Ca 2+ regulation, suggests that the sGC/cGMP system targets multiple signaling networks rather than a limited number of PKG substrate proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Quantitative phosphoproteomic analysis of early alterations in protein phosphorylation by 2,3,7,8-tetrachlorodibenzo-p-dioxin

DEFF Research Database (Denmark)

Schulz, Melanie; Brandner, Stefanie; Eberhagen, Carola

2013-01-01

A comprehensive quantitative analysis of changes in protein phosphorylation preceding or accompanying transcriptional activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in 5L rat hepatoma cells was performed using the SILAC approach. Following exposure of the cells to DMSO or 1 nM TCDD for 0......-induced gene activation, regulators of small GTPases of the Ras superfamily, UBX domain-containing proteins and the oncogenic protein LYRIC. The results open up new directions for research on the molecular mechanisms of dioxin action and toxicity....

Phosphorylation dynamics during early differentiation of human embryonic stem cells

NARCIS (Netherlands)

van Hoof, D.; Munoz, J.; Braam, S.R.; Pinkse, M.W.H.; Linding, R.; Heck, A.J.R.; Mummery, C.L.; Krijgsveld, J.

2009-01-01

Pluripotent stem cells self-renew indefinitely and possess characteristic protein-protein networks that remodel during differentiation. How this occurs is poorly understood. Using quantitative mass spectrometry, we analyzed the (phospho)proteome of human embryonic stem cells (hESCs) during

Quantitative and comparative visualization applied to cosmological simulations

International Nuclear Information System (INIS)

Ahrens, James; Heitmann, Katrin; Habib, Salman; Ankeny, Lee; McCormick, Patrick; Inman, Jeff; Armstrong, Ryan; Ma, Kwan-Liu

2006-01-01

Cosmological simulations follow the formation of nonlinear structure in dark and luminous matter. The associated simulation volumes and dynamic range are very large, making visualization both a necessary and challenging aspect of the analysis of these datasets. Our goal is to understand sources of inconsistency between different simulation codes that are started from the same initial conditions. Quantitative visualization supports the definition and reasoning about analytically defined features of interest. Comparative visualization supports the ability to visually study, side by side, multiple related visualizations of these simulations. For instance, a scientist can visually distinguish that there are fewer halos (localized lumps of tracer particles) in low-density regions for one simulation code out of a collection. This qualitative result will enable the scientist to develop a hypothesis, such as loss of halos in low-density regions due to limited resolution, to explain the inconsistency between the different simulations. Quantitative support then allows one to confirm or reject the hypothesis. If the hypothesis is rejected, this step may lead to new insights and a new hypothesis, not available from the purely qualitative analysis. We will present methods to significantly improve the Scientific analysis process by incorporating quantitative analysis as the driver for visualization. Aspects of this work are included as part of two visualization tools, ParaView, an open-source large data visualization tool, and Scout, an analysis-language based, hardware-accelerated visualization tool

Quantitative ptychographic reconstruction by applying a probe constraint

Science.gov (United States)

Reinhardt, J.; Schroer, C. G.

2018-04-01

The coherent scanning technique X-ray ptychography has become a routine tool for high-resolution imaging and nanoanalysis in various fields of research such as chemistry, biology or materials science. Often the ptychographic reconstruction results are analysed in order to yield absolute quantitative values for the object transmission and illuminating probe function. In this work, we address a common ambiguity encountered in scaling the object transmission and probe intensity via the application of an additional constraint to the reconstruction algorithm. A ptychographic measurement of a model sample containing nanoparticles is used as a test data set against which to benchmark in the reconstruction results depending on the type of constraint used. Achieving quantitative absolute values for the reconstructed object transmission is essential for advanced investigation of samples that are changing over time, e.g., during in-situ experiments or in general when different data sets are compared.

Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons

NARCIS (Netherlands)

Post, Harm; Penning, Renske; Fitzpatrick, Martin; Garrigues, L.B.; Wu, W.; Mac Gillavry, H.D.; Hoogenraad, C.C.; Heck, A.J.R.; Altelaar, A.F.M.

2017-01-01

Because of the low stoichiometry of protein phosphorylation, targeted enrichment prior to LC–MS/MS analysis is still essential. The trend in phosphoproteome analysis is shifting toward an increasing number of biological replicates per experiment, ideally starting from very low sample amounts,

SILAC-based quantification of changes in protein tyrosine phosphorylation induced by Interleukin-2 (IL-2) and IL-15 in T-lymphocytes

DEFF Research Database (Denmark)

Osinalde, Nerea; Sánchez-Quiles, Virginia; Akimov, Vyacheslav

2015-01-01

This data article presents the first large-scale quantitative phosphoproteomics dataset generated to decipher the signaling networks initiated by IL-2 and IL-15 in T-lymphocytes. Data was collected by combining immunoprecipitation of tyrosine phosphorylated proteins and TiO2-based phosphopeptide...

Comprehensive Quantitative Profiling of Tau and Phosphorylated Tau Peptides in Cerebrospinal Fluid by Mass Spectrometry Provides New Biomarker Candidates.

Science.gov (United States)

Russell, Claire L; Mitra, Vikram; Hansson, Karl; Blennow, Kaj; Gobom, Johan; Zetterberg, Henrik; Hiltunen, Mikko; Ward, Malcolm; Pike, Ian

2017-01-01

Aberrant tau phosphorylation is a hallmark in Alzheimer's disease (AD), believed to promote formation of paired helical filaments, the main constituent of neurofibrillary tangles in the brain. While cerebrospinal fluid (CSF) levels of total tau and tau phosphorylated at threonine residue 181 (pThr181) are established core biomarkers for AD, the value of alternative phosphorylation sites, which may have more direct relevance to pathology, for early diagnosis is not yet known, largely due to their low levels in CSF and lack of standardized detection methods. To overcome sensitivity limitations for analysis of phosphorylated tau in CSF, we have applied an innovative mass spectrometry (MS) workflow, TMTcalibratortrademark, to enrich and enhance the detection of phosphoproteome components of AD brain tissue in CSF, and enable the quantitation of these analytes. We aimed to identify which tau species present in the AD brain are also detectable in CSF and which, if any, are differentially regulated with disease. Over 75% coverage of full-length (2N4R) tau was detected in the CSF with 47 phosphopeptides covering 31 different phosphorylation sites. Of these, 11 phosphopeptides were upregulated by at least 40%, along with an overall increase in tau levels in the CSF of AD patients relative to controls. Use of the TMTcalibratortrademark workflow dramatically improved our ability to detect tau-derived peptides that are directly related to human AD pathology. Further validation of regulated tau peptides as early biomarkers of AD is warranted and is currently being undertaken.

Phosphoproteome profiles of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea during exponential growth in axenic cultures.

Science.gov (United States)

Davanture, Marlène; Dumur, Jérôme; Bataillé-Simoneau, Nelly; Campion, Claire; Valot, Benoît; Zivy, Michel; Simoneau, Philippe; Fillinger, Sabine

2014-07-01

This study describes the gel-free phosphoproteomic analysis of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea grown in vitro under nonlimiting conditions. Using a combination of strong cation exchange and IMAC prior to LC-MS, we identified over 1350 phosphopeptides per fungus representing over 800 phosphoproteins. The preferred phosphorylation sites were found on serine (>80%) and threonine (>15%), whereas phosphorylated tyrosine residues were found at less than 1% in A. brassicicola and at a slightly higher ratio in B. cinerea (1.5%). Biological processes represented principally among the phoshoproteins were those involved in response and transduction of stimuli as well as in regulation of cellular and metabolic processes. Most known elements of signal transduction were found in the datasets of both fungi. This study also revealed unexpected phosphorylation sites in histidine kinases, a category overrepresented in filamentous ascomycetes compared to yeast. The data have been deposited to the ProteomeXchange database with identifier PXD000817 (http://proteomecentral.proteomexchange.org/dataset/PXD000817). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multilayers quantitative X-ray fluorescence analysis applied to easel paintings.

Science.gov (United States)

de Viguerie, Laurence; Sole, V Armando; Walter, Philippe

2009-12-01

X-ray fluorescence spectrometry (XRF) allows a rapid and simple determination of the elemental composition of a material. As a non-destructive tool, it has been extensively used for analysis in art and archaeology since the early 1970s. Whereas it is commonly used for qualitative analysis, recent efforts have been made to develop quantitative treatment even with portable systems. However, the interpretation of the results obtained with this technique can turn out to be problematic in the case of layered structures such as easel paintings. The use of differential X-ray attenuation enables modelling of the various layers: indeed, the absorption of X-rays through different layers will result in modification of intensity ratio between the different characteristic lines. This work focuses on the possibility to use XRF with the fundamental parameters method to reconstruct the composition and thickness of the layers. This method was tested on several multilayers standards and gives a maximum error of 15% for thicknesses and errors of 10% for concentrations. On a painting test sample that was rather inhomogeneous, the XRF analysis provides an average value. This method was applied in situ to estimate the thickness of the layers a painting from Marco d'Oggiono, pupil of Leonardo da Vinci.

The phosphoproteome of Aspergillus nidulans reveals functional association with cellular processes involved in morphology and secretion.

Science.gov (United States)

Ramsubramaniam, Nikhil; Harris, Steven D; Marten, Mark R

2014-11-01

We describe the first phosphoproteome of the model filamentous fungus Aspergillus nidulans. Phosphopeptides were enriched using titanium dioxide, separated using a convenient ultra-long reverse phase gradient, and identified using a "high-high" strategy (high mass accuracy on the parent and fragment ions) with higher-energy collisional dissociation. Using this approach 1801 phosphosites, from 1637 unique phosphopeptides, were identified. Functional classification revealed phosphoproteins were overrepresented under GO categories related to fungal morphogenesis: "sites of polar growth," "vesicle mediated transport," and "cytoskeleton organization." In these same GO categories, kinase-substrate analysis of phosphoproteins revealed the majority were target substrates of CDK and CK2 kinase families, indicating these kinase families play a prominent role in fungal morphogenesis. Kinase-substrate analysis also identified 57 substrates for kinases known to regulate secretion of hydrolytic enzymes (e.g. PkaA, SchA, and An-Snf1). Altogether this data will serve as a benchmark that can be used to elucidate regulatory networks functionally associated with fungal morphogenesis and secretion. All MS data have been deposited in the ProteomeXchange with identifier PXD000715 (http://proteomecentral.proteomexchange.org/dataset/PXD000715). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparative Phosphoproteomic Analysis of the Developing Seeds in Two Indica Rice ( Oryza sativa L.) Cultivars with Different Starch Quality.

Science.gov (United States)

Pang, Yuehan; Zhou, Xin; Chen, Yaling; Bao, Jinsong

2018-03-21

Protein phosphorylation plays important roles in regulation of various molecular events such as plant growth and seed development. However, its involvement in starch biosynthesis is less understood. Here, a comparative phosphoproteomic analysis of two indica rice cultivars during grain development was performed. A total of 2079 and 2434 phosphopeptides from 1273 and 1442 phosphoproteins were identified, covering 2441 and 2808 phosphosites in indica rice 9311 and Guangluai4 (GLA4), respectively. Comparative analysis identified 303 differentially phosphorylated peptides, and 120 and 258 specifically phosphorylated peptides in 9311 and GLA4, respectively. Phosphopeptides in starch biosynthesis related enzymes such as AGPase, SSIIa, SSIIIa, BEI, BEIIb, PUL, and Pho1were identified. GLA4 and 9311 had different amylose content, pasting viscosities, and gelatinization temperature, suggesting subtle difference in starch biosynthesis and regulation between GLA4 and 9311. Our study will give added impetus to further understanding the regulatory mechanism of starch biosynthesis at the phosphorylation level.

Comparative N-glycoproteomic and phosphoproteomic profiling of human placental plasma membrane between normal and preeclampsia pregnancies with high-resolution mass spectrometry.

Directory of Open Access Journals (Sweden)

Fuqiang Wang

Full Text Available Preeclampsia is a serious complication of pregnancy, which affects 2-8% of all pregnancies and is one of the leading causes of maternal and perinatal mortality and morbidity worldwide. To better understand the molecular mechanisms involved in pathological development of placenta in preeclampsia, we used high-resolution LC-MS/MS technologies to construct a comparative N-glycoproteomic and phosphoproteomic profiling of human placental plasma membrane in normal and preeclamptic pregnancies. A total of 1027 N-glyco- and 2094 phospho- sites were detected in human placental plasma membrane, and 5 N-glyco- and 38 phospho- proteins, respectively, with differentially expression were definitively identified between control and preeclamptic placental plasma membrane. Further bioinformatics analysis indicated that these differentially expressed proteins correlate with several specific cellular processes occurring during pathological changes of preeclamptic placental plasma membrane.

Quantitative investment analysis

CERN Document Server

DeFusco, Richard

2007-01-01

In the "Second Edition" of "Quantitative Investment Analysis," financial experts Richard DeFusco, Dennis McLeavey, Jerald Pinto, and David Runkle outline the tools and techniques needed to understand and apply quantitative methods to today's investment process.

Phosphoproteomic dynamics of chickpea (Cicer arietinum L.) reveals shared and distinct components of dehydration response.

Science.gov (United States)

Subba, Pratigya; Barua, Pragya; Kumar, Rajiv; Datta, Asis; Soni, Kamlesh Kumar; Chakraborty, Subhra; Chakraborty, Niranjan

2013-11-01

Reversible protein phosphorylation is a ubiquitous regulatory mechanism that plays critical roles in transducing stress signals to bring about coordinated intracellular responses. To gain better understanding of dehydration response in plants, we have developed a differential phosphoproteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water, and the changes in the phosphorylation status of a large repertoire of proteins were monitored. The proteins were resolved by 2-DE and stained with phosphospecific fluorescent Pro-Q Diamond dye. Mass spectrometric analysis led to the identification of 91 putative phosphoproteins, presumably involved in a variety of functions including cell defense and rescue, photosynthesis and photorespiration, molecular chaperones, and ion transport, among others. Multiple sites of phosphorylation were predicted on several key elements, which include both the regulatory as well as the functional proteins. A critical survey of the phosphorylome revealed a DREPP (developmentally regulated plasma membrane protein) plasma membrane polypeptide family protein, henceforth designated CaDREPP1. The transcripts of CaDREPP1 were found to be differentially regulated under dehydration stress, further corroborating the proteomic results. This work provides new insights into the possible phosphorylation events triggered by the conditions of progressive water-deficit in plants.

Comprehensive quantitative comparison of the membrane proteome, phosphoproteome, and sialiome of human embryonic and neural stem cells

DEFF Research Database (Denmark)

Melo-Braga, Marcella Nunes; Schulz, Melanie; Liu, Qiuyue

2014-01-01

Human embryonic stem cells (hESCs) can differentiate into neural stem cells (NSCs), which can further be differentiated into neurons and glia cells. Therefore, these cells have huge potential as source for treatment of neurological diseases. Membrane-associated proteins are very important......ESCs and NSCs as well as to investigate potential new markers for these two cell stages, we performed large-scale quantitative membrane-proteomic of hESCs and NSCs. This approach employed membrane purification followed by peptide dimethyl labeling and peptide enrichment to study the membrane subproteome as well...... in which 78% of phosphopeptides were identified with ≥99% confidence in site assignment and 1810 unique formerly sialylated N-linked glycopeptides. Several proteins were identified as significantly regulated in hESCs and NSC, including proteins involved in the early embryonic and neural development...

Using Proteomics To Elucidate Critical Signaling Pathways

KAUST Repository

Ahmed, Heba

2012-11-01

Despite important advances in the therapy of acute myeloid leukemia (AML) the majority of patients will die from their disease (Appelbaum, Rowe, Radich, & Dick, 2001). Characterization of the aberrant molecular pathways responsible for this malignancy provides a platform to discover alternative treatments to help alter the fate of patients. AML is characterized by a blockage in the differentiation of myeloid cells resulting in the accumulation of highly proliferating immature hematopoietic cells. Since treatments such as chemotherapy rarely destroy the leukemic cells entirely, differentiation induction therapy has become a very attractive treatment option. Interestingly, previous experiments have shown that ligation of CD44, a cell surface glycoprotein strongly expressed on all AML cells, with anti-CD44 monoclonal antibodies (mAbs) could reverse this block in differentiation of leukemic blasts regardless of the AML subtype. To expand the understanding of the cellular regulation and circuitry involved, we aim to apply quantitative phosphoproteomics to monitor dynamic changes in phosphorylation state in response to anti-CD44 treatment. Protein phosphorylation and dephosphorylation is a highly controlled biochemical process that responds to various intracellular and extracellular stimuli. As phosphorylation is a dynamic process, quantification of these phosphorylation events would be vastly insightful. The main objective of this project is to determine the differentiation-dependent phosphoproteome of AML cells upon treatment of cells with the anti-CD44 mAb.In these experiments, optimization of protein extraction, phosphopeptide enrichment and data processing and analysis has been achieved. The primary results show successful phosphoproteome extraction complemented with efficient phosphopeptide enrichment and informative data processing. Further quantification with stable isotope labeling techniques is anticipated to provide candidates for targeted therapy.

Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis.

Science.gov (United States)

Chen, Yanmei; Hoehenwarter, Wolfgang

2015-12-01

Salinity and oxidative stress are major factors affecting and limiting the productivity of agricultural crops. The molecular and biochemical processes governing the plant response to abiotic stress have often been researched in a reductionist manner. Here, we report a systemic approach combining metabolic labeling and phosphoproteomics to capture early signaling events with quantitative metabolome analysis and enzyme activity assays to determine the effects of salt and oxidative stress on plant physiology. K(+) and Na(+) transporters showed coordinated changes in their phosphorylation pattern, indicating the importance of dynamic ion homeostasis for adaptation to salt stress. Unique phosphorylation sites were found for Arabidopsis (Arabidopsis thaliana) SNF1 kinase homolog10 and 11, indicating their central roles in the stress-regulated responses. Seven Sucrose Non-fermenting1-Related Protein Kinase2 kinases showed varying levels of phosphorylation at multiple serine/threonine residues in their kinase domain upon stress, showing temporally distinct modulation of the various isoforms. Salinity and oxidative stress also lead to changes in protein phosphorylation of proteins central to photosynthesis, in particular the kinase State Transition Protein7 required for state transition and light-harvesting II complex proteins. Furthermore, stress-induced changes of the phosphorylation of enzymes of central metabolism were observed. The phosphorylation patterns of these proteins were concurrent with changes in enzyme activity. This was reflected by altered levels of metabolites, such as the sugars sucrose and fructose, glycolysis intermediates, and amino acids. Together, our study provides evidence for a link between early signaling in the salt and oxidative stress response that regulates the state transition of photosynthesis and the rearrangement of primary metabolism. © 2015 American Society of Plant Biologists. All Rights Reserved.

Quantitative Proteomic and Phosphoproteomic Analysis of Trypanosoma cruzi Amastigogenesis

DEFF Research Database (Denmark)

Queiroz, Rayner M L; Charneau, Sebastien; Mandacaru, Samuel C

2014-01-01

Chagas disease is a tropical neglected disease endemic in Latin America and it is caused by the protozoan Trypanosoma cruzi. The parasite has four major life stages: epimastigote, metacyclic trypomastigote, bloodstream trypomastigote and amastigote. The differentiation from infective trypomastigo......Chagas disease is a tropical neglected disease endemic in Latin America and it is caused by the protozoan Trypanosoma cruzi. The parasite has four major life stages: epimastigote, metacyclic trypomastigote, bloodstream trypomastigote and amastigote. The differentiation from infective...

Identification of BCAP-{sub L} as a negative regulator of the TLR signaling-induced production of IL-6 and IL-10 in macrophages by tyrosine phosphoproteomics

Energy Technology Data Exchange (ETDEWEB)

Matsumura, Takayuki [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan); Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 (Japan); Oyama, Masaaki; Kozuka-Hata, Hiroko [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan); Ishikawa, Kosuke; Inoue, Takafumi [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan); Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 (Japan); Muta, Tatsushi [Laboratory of Cell Recognition and Response, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578 (Japan); Semba, Kentaro, E-mail: ksemba@waseda.jp [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan); Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 (Japan); Inoue, Jun-ichiro, E-mail: jun-i@ims.u-tokyo.ac.jp [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan); Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan)

2010-09-17

Research highlights: {yields} Twenty five tyrosine-phosphorylated proteins in LPS-stimulated macrophages were determined. {yields} BCAP is a novel tyrosine-phosphorylated protein in LPS-stimulated macrophages. {yields} BCAP-{sub L} inhibits IL-6 and IL-10 production in LPS-stimulated macrophages. -- Abstract: Toll-like receptor (TLR) signaling in macrophages is essential for anti-pathogen responses such as cytokine production and antigen presentation. Although numerous reports suggest that protein tyrosine kinases (PTKs) are involved in cytokine induction in response to lipopolysaccharides (LPS; TLR4 ligand) in macrophages, the PTK-mediated signal transduction pathway has yet to be analyzed in detail. Here, we carried out a comprehensive and quantitative dynamic tyrosine phosphoproteomic analysis on the TLR4-mediated host defense system in RAW264.7 macrophages using stable isotope labeling by amino acids in cell culture (SILAC). We determined the temporal profiles of 25 proteins based on SILAC-encoded peptide(s). Of these, we focused on the tyrosine phosphorylation of B-cell adaptor for phosphatidylinositol 3-kinase (BCAP) because the function of BCAP remains unknown in TLR signaling in macrophages. Furthermore, Bcap has two distinct transcripts, a full-length (Bcap-{sub L}) and an alternatively initiated or spliced (Bcap-{sub S}) mRNA, and little is known about the differential functions of the BCAP-{sub L} and BCAP-{sub S} proteins. Our study showed, for the first time, that RNAi-mediated selective depletion of BCAP-{sub L} enhanced IL-6 and IL-10 production but not TNF-{alpha} production in TLR ligand-stimulated macrophages. We propose that BCAP-{sub L} (but not BCAP-{sub S}) is a negative regulator of the TLR-mediated host defense system in macrophages.

Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress.

Science.gov (United States)

Yin, Xiaojian; Sakata, Katsumi; Komatsu, Setsuko

2014-12-05

Flooding has severe negative effects on soybean growth. To explore the flooding-responsive mechanisms in early-stage soybean, a phosphoproteomic approach was used. Two-day-old soybean plants were treated without or with flooding for 3, 6, 12, and 24 h, and root tip proteins were then extracted and analyzed at each time point. After 3 h of flooding exposure, the fresh weight of soybeans increased, whereas the ATP content of soybean root tips decreased. Using a gel-free proteomic technique, a total of 114 phosphoproteins were identified in the root tip samples, and 34 of the phosphoproteins were significantly changed with respect to phosphorylation status after 3 h of flooding stress. Among these phosphoproteins, eukaryotic translation initiation factors were dephosphorylated, whereas several protein synthesis-related proteins were phosphorylated. The mRNA expression levels of sucrose phosphate synthase 1F and eukaryotic translation initiation factor 4 G were down-regulated, whereas UDP-glucose 6-dehydrogenase mRNA expression was up-regulated during growth but down-regulated under flooding stress. Furthermore, bioinformatic protein interaction analysis of flooding-responsive proteins based on temporal phosphorylation patterns indicated that eukaryotic translation initiation factor 4 G was located in the center of the network during flooding. Soybean eukaryotic translation initiation factor 4 G has homology to programmed cell death 4 protein and is implicated in ethylene signaling. The weight of soybeans was increased with treatment by an ethylene-releasing agent under flooding condition, but it was decreased when plants were exposed to an ethylene receptor antagonist. These results suggest that the ethylene signaling pathway plays an important role, via the protein phosphorylation, in mechanisms of plant tolerance to the initial stages of flooding stress in soybean root tips.

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

Science.gov (United States)

Mitsos, Alexander; Melas, Ioannis N; Morris, Melody K; Saez-Rodriguez, Julio; Lauffenburger, Douglas A; Alexopoulos, Leonidas G

2012-01-01

Modeling of signal transduction pathways plays a major role in understanding cells' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i) excessive CPU time requirements and ii) loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP) formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms.

Non Linear Programming (NLP formulation for quantitative modeling of protein signal transduction pathways.

Directory of Open Access Journals (Sweden)

Alexander Mitsos

Full Text Available Modeling of signal transduction pathways plays a major role in understanding cells' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i excessive CPU time requirements and ii loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms.

Applied environmetrics. Simulation applied to the physical environment

Energy Technology Data Exchange (ETDEWEB)

Beer, T

1988-02-01

Environmetrics is the application of quantitative methods to all aspects of the social and natural environment. This includes forecasting, mathematical modelling, data analysis, and statistics. Applied Environmetrics as a discipline involves the analysis of environmental data through the use of packaged, or specially designed computer software. Two case studies of recent implementations of applied environmetrics within the Australian mining industry are dealt with. 3 figs., 5 refs.

Quantitative Portfolio Optimization Techniques Applied to the Brazilian Stock Market

Directory of Open Access Journals (Sweden)

André Alves Portela Santos

2012-09-01

Full Text Available In this paper we assess the out-of-sample performance of two alternative quantitative portfolio optimization techniques - mean-variance and minimum variance optimization – and compare their performance with respect to a naive 1/N (or equally-weighted portfolio and also to the market portfolio given by the Ibovespa. We focus on short selling-constrained portfolios and consider alternative estimators for the covariance matrices: sample covariance matrix, RiskMetrics, and three covariance estimators proposed by Ledoit and Wolf (2003, Ledoit and Wolf (2004a and Ledoit and Wolf (2004b. Taking into account alternative portfolio re-balancing frequencies, we compute out-of-sample performance statistics which indicate that the quantitative approaches delivered improved results in terms of lower portfolio volatility and better risk-adjusted returns. Moreover, the use of more sophisticated estimators for the covariance matrix generated optimal portfolios with lower turnover over time.

Salt-induced changes in cardiac phosphoproteome in a rat model of chronic renal failure.

Directory of Open Access Journals (Sweden)

Zhengxiu Su

Full Text Available Heart damage is widely present in patients with chronic kidney disease. Salt diet is the most important environmental factor affecting development of chronic renal failure and cardiovascular diseases. The proteins involved in chronic kidney disease -induced heart damage, especially their posttranslational modifications, remain largely unknown to date. Sprague-Dawley rats underwent 5/6 nephrectomy (chronic renal failure model or sham operation were treated for 2 weeks with a normal-(0.4% NaCl, or high-salt (4% NaCl diet. We employed TiO2 enrichment, iTRAQ labeling and liquid-chromatography tandem mass spectrometry strategy for phosphoproteomic profiling of left ventricular free walls in these animals. A total of 1724 unique phosphopeptides representing 2551 non-redundant phosphorylation sites corresponding to 763 phosphoproteins were identified. During normal salt feeding, 89 (54% phosphopeptides upregulated and 76 (46% phosphopeptides downregulated in chronic renal failure rats relative to sham rats. In chronic renal failure rats, high salt intake induced upregulation of 84 (49% phosphopeptides and downregulation of 88 (51% phosphopeptides. Database searches revealed that most of the identified phospholproteins were important signaling molecules such as protein kinases, receptors and phosphatases. These phospholproteins were involved in energy metabolism, cell communication, cell differentiation, cell death and other biological processes. The Search Tool for the Retrieval of Interacting Genes analysis revealed functional links among 15 significantly regulated phosphoproteins in chronic renal failure rats compared to sham group, and 23 altered phosphoproteins induced by high salt intake. The altered phosphorylation levels of two proteins involved in heart damage, lamin A and phospholamban were validated. Expression of the downstream genes of these two proteins, desmin and SERCA2a, were also analyzed.

Multivariat least-squares methods applied to the quantitative spectral analysis of multicomponent samples

International Nuclear Information System (INIS)

Haaland, D.M.; Easterling, R.G.; Vopicka, D.A.

1985-01-01

In an extension of earlier work, weighted multivariate least-squares methods of quantitative FT-IR analysis have been developed. A linear least-squares approximation to nonlinearities in the Beer-Lambert law is made by allowing the reference spectra to be a set of known mixtures, The incorporation of nonzero intercepts in the relation between absorbance and concentration further improves the approximation of nonlinearities while simultaneously accounting for nonzero spectra baselines. Pathlength variations are also accommodated in the analysis, and under certain conditions, unknown sample pathlengths can be determined. All spectral data are used to improve the precision and accuracy of the estimated concentrations. During the calibration phase of the analysis, pure component spectra are estimated from the standard mixture spectra. These can be compared with the measured pure component spectra to determine which vibrations experience nonlinear behavior. In the predictive phase of the analysis, the calculated spectra are used in our previous least-squares analysis to estimate sample component concentrations. These methods were applied to the analysis of the IR spectra of binary mixtures of esters. Even with severely overlapping spectral bands and nonlinearities in the Beer-Lambert law, the average relative error in the estimated concentration was <1%

Quantitative autoradiography of neurochemicals

International Nuclear Information System (INIS)

Rainbow, T.C.; Biegon, A.; Bleisch, W.V.

1982-01-01

Several new methods have been developed that apply quantitative autoradiography to neurochemistry. These methods are derived from the 2-deoxyglucose (2DG) technique of Sokoloff (1), which uses quantitative autoradiography to measure the rate of glucose utilization in brain structures. The new methods allow the measurement of the rate of cerbral protein synthesis and the levels of particular neurotransmitter receptors by quantitative autoradiography. As with the 2DG method, the new techniques can measure molecular levels in micron-sized brain structures; and can be used in conjunction with computerized systems of image processing. It is possible that many neurochemical measurements could be made by computerized analysis of quantitative autoradiograms

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

DEFF Research Database (Denmark)

Miller, Martin Lee; Brunak, Søren; Olsen, JV

2010-01-01

and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global...

PhosphoSiteAnalyzer

DEFF Research Database (Denmark)

Bennetzen, Martin V; Cox, Jürgen; Mann, Matthias

2012-01-01

an algorithm to retrieve kinase predictions from the public NetworKIN webpage in a semiautomated way and applies hereafter advanced statistics to facilitate a user-tailored in-depth analysis of the phosphoproteomic data sets. The interface of the software provides a high degree of analytical flexibility......Phosphoproteomic experiments are routinely conducted in laboratories worldwide, and because of the fast development of mass spectrometric techniques and efficient phosphopeptide enrichment methods, researchers frequently end up having lists with tens of thousands of phosphorylation sites...... and is designed to be intuitive for most users. PhosphoSiteAnalyzer is a freeware program available at http://phosphosite.sourceforge.net ....

Quantitative evaluation of a single-distance phase-retrieval method applied on in-line phase-contrast images of a mouse lung

International Nuclear Information System (INIS)

Mohammadi, Sara; Larsson, Emanuel; Alves, Frauke; Dal Monego, Simeone; Biffi, Stefania; Garrovo, Chiara; Lorenzon, Andrea; Tromba, Giuliana; Dullin, Christian

2014-01-01

Quantitative analysis concerning the application of a single-distance phase-retrieval algorithm on in-line phase-contrast images of a mouse lung at different sample-to-detector distances is presented. Propagation-based X-ray phase-contrast computed tomography (PBI) has already proven its potential in a great variety of soft-tissue-related applications including lung imaging. However, the strong edge enhancement, caused by the phase effects, often hampers image segmentation and therefore the quantitative analysis of data sets. Here, the benefits of applying single-distance phase retrieval prior to the three-dimensional reconstruction (PhR) are discussed and quantified compared with three-dimensional reconstructions of conventional PBI data sets in terms of contrast-to-noise ratio (CNR) and preservation of image features. The PhR data sets show more than a tenfold higher CNR and only minor blurring of the edges when compared with PBI in a predominately absorption-based set-up. Accordingly, phase retrieval increases the sensitivity and provides more functionality in computed tomography imaging

A quantitative performance evaluation of the EM algorithm applied to radiographic images

International Nuclear Information System (INIS)

Brailean, J.C.; Sullivan, B.J.; Giger, M.L.; Chen, C.T.

1991-01-01

In this paper, the authors quantitatively evaluate the performance of the Expectation Maximization (EM) algorithm as a restoration technique for radiographic images. The perceived signal-to-noise ratio (SNR), of simple radiographic patterns processed by the EM algorithm are calculated on the basis of a statistical decision theory model that includes both the observer's visual response function and a noise component internal to the eye-brain system. The relative SNR (ratio of the processed SNR to the original SNR) is calculated and used as a metric to quantitatively compare the effects of the EM algorithm to two popular image enhancement techniques: contrast enhancement (windowing) and unsharp mask filtering

Versatile quantitative phase imaging system applied to high-speed, low noise and multimodal imaging (Conference Presentation)

Science.gov (United States)

Federici, Antoine; Aknoun, Sherazade; Savatier, Julien; Wattellier, Benoit F.

2017-02-01

Quadriwave lateral shearing interferometry (QWLSI) is a well-established quantitative phase imaging (QPI) technique based on the analysis of interference patterns of four diffraction orders by an optical grating set in front of an array detector [1]. As a QPI modality, this is a non-invasive imaging technique which allow to measure the optical path difference (OPD) of semi-transparent samples. We present a system enabling QWLSI with high-performance sCMOS cameras [2] and apply it to perform high-speed imaging, low noise as well as multimodal imaging. This modified QWLSI system contains a versatile optomechanical device which images the optical grating near the detector plane. Such a device is coupled with any kind of camera by varying its magnification. In this paper, we study the use of a sCMOS Zyla5.5 camera from Andor along with our modified QWLSI system. We will present high-speed live cell imaging, up to 200Hz frame rate, in order to follow intracellular fast motions while measuring the quantitative phase information. The structural and density information extracted from the OPD signal is complementary to the specific and localized fluorescence signal [2]. In addition, QPI detects cells even when the fluorophore is not expressed. This is very useful to follow a protein expression with time. The 10 µm spatial pixel resolution of our modified QWLSI associated to the high sensitivity of the Zyla5.5 enabling to perform high quality fluorescence imaging, we have carried out multimodal imaging revealing fine structures cells, like actin filaments, merged with the morphological information of the phase. References [1]. P. Bon, G. Maucort, B. Wattellier, and S. Monneret, "Quadriwave lateral shearing interferometry for quantitative phase microscopy of living cells," Opt. Express, vol. 17, pp. 13080-13094, 2009. [2] P. Bon, S. Lécart, E. Fort and S. Lévêque-Fort, "Fast label-free cytoskeletal network imaging in living mammalian cells," Biophysical journal, 106

Applying real-time quantitative PCR to diagnosis of freemartin in Holstein cattle by quantifying SRY gene: a comparison experiment

Directory of Open Access Journals (Sweden)

Qinghua Qiu

2018-04-01

Full Text Available Background Freemartinism generally occurs in female offspring of dizygotic twins in a mixed-sex pregnancy. Most bovine heterosexual twin females are freemartins. However, about 10% of bovine heterosexual twin females are fertile. Farmers mostly cull bovine fertile heterosexual twin females due to the lack of a practical diagnostic approach. Culling of such animals results in economic and genetic-material losses both for dairy and beef industry. Methods In this study, a comparative test, including qualitative detection of SRY gene by polymerase chain reaction (PCR, quantitative detection of relative content of SRY by real-time quantitative polymerase chain reaction (qPCR, and quantitative detection of H-Y antigen, was performed to establish the most accurate diagnosis for freemartin. Twelve Holstein heterosexual twin females were used in this study, while three normal Holstein bulls and three normal Holstein cows were used as a positive and negative control, respectively. Results Polymerase chain reaction results revealed that SRY gene were absent in three heterosexual twin females and only two of them were verified as fertile in later age. The qPCR results showed that relative content of SRY was more than 14.2% in freemartins and below 0.41% in fertile heterosexual twin females. The H-Y antigen test showed no significant numerical difference between freemartin and fertile heterosexual twin female. Discussion Our results show that relative content of SRY quantified by qPCR is a better detection method for diagnosis of freemartin in Holstein cattle as compare to qualitative detection of SRY gene by PCR or quantitative detection of H-Y antigen. To the authors’ knowledge, this is the first time we applied qPCR to diagnosing freemartin by quantifying SRY gene and got relative SRY content of each freemartin and fertile heterosexual twin female. We concluded that low-level of SRY would not influence fertility of bovine heterosexual twin female.

Quantitative thoracic CT techniques in adults: can they be applied in the pediatric population?

Energy Technology Data Exchange (ETDEWEB)

Yoon, Soon Ho [Seoul National University Medical Research Center, Department of Radiology, Seoul National University College of Medicine, and Institute of Radiation Medicine, Seoul (Korea, Republic of); Goo, Jin Mo [Seoul National University Medical Research Center, Department of Radiology, Seoul National University College of Medicine, and Institute of Radiation Medicine, Seoul (Korea, Republic of); Seoul National University College of Medicine, Cancer Research Institute, Jongno-gu, Seoul (Korea, Republic of); Goo, Hyun Woo [University of Ulsan College of Medicine, Department of Radiology and Research Institute of Radiology, Asan Medical Center, Seoul (Korea, Republic of)

2013-03-15

With the rapid evolution of the multidetector row CT technique, quantitative CT has started to be used in clinical studies for revealing a heterogeneous entity of airflow limitation in chronic obstructive pulmonary disease that is caused by a combination of lung parenchymal destruction and remodeling of the small airways in adults. There is growing evidence of a good correlation between quantitative CT findings and pathological findings, pulmonary function test results and other clinical parameters. This article provides an overview of current quantitative thoracic CT techniques used in adults, and how to translate these CT techniques to the pediatric population. (orig.)

Multivariate calibration applied to the quantitative analysis of infrared spectra

Energy Technology Data Exchange (ETDEWEB)

Haaland, D.M.

1991-01-01

Multivariate calibration methods are very useful for improving the precision, accuracy, and reliability of quantitative spectral analyses. Spectroscopists can more effectively use these sophisticated statistical tools if they have a qualitative understanding of the techniques involved. A qualitative picture of the factor analysis multivariate calibration methods of partial least squares (PLS) and principal component regression (PCR) is presented using infrared calibrations based upon spectra of phosphosilicate glass thin films on silicon wafers. Comparisons of the relative prediction abilities of four different multivariate calibration methods are given based on Monte Carlo simulations of spectral calibration and prediction data. The success of multivariate spectral calibrations is demonstrated for several quantitative infrared studies. The infrared absorption and emission spectra of thin-film dielectrics used in the manufacture of microelectronic devices demonstrate rapid, nondestructive at-line and in-situ analyses using PLS calibrations. Finally, the application of multivariate spectral calibrations to reagentless analysis of blood is presented. We have found that the determination of glucose in whole blood taken from diabetics can be precisely monitored from the PLS calibration of either mind- or near-infrared spectra of the blood. Progress toward the non-invasive determination of glucose levels in diabetics is an ultimate goal of this research. 13 refs., 4 figs.

Quantitative computed tomography applied to interstitial lung diseases.

Science.gov (United States)

Obert, Martin; Kampschulte, Marian; Limburg, Rebekka; Barańczuk, Stefan; Krombach, Gabriele A

2018-03-01

To evaluate a new image marker that retrieves information from computed tomography (CT) density histograms, with respect to classification properties between different lung parenchyma groups. Furthermore, to conduct a comparison of the new image marker with conventional markers. Density histograms from 220 different subjects (normal = 71; emphysema = 73; fibrotic = 76) were used to compare the conventionally applied emphysema index (EI), 15 th percentile value (PV), mean value (MV), variance (V), skewness (S), kurtosis (K), with a new histogram's functional shape (HFS) method. Multinomial logistic regression (MLR) analyses was performed to calculate predictions of different lung parenchyma group membership using the individual methods, as well as combinations thereof, as covariates. Overall correct assigned subjects (OCA), sensitivity (sens), specificity (spec), and Nagelkerke's pseudo R 2 (NR 2 ) effect size were estimated. NR 2 was used to set up a ranking list of the different methods. MLR indicates the highest classification power (OCA of 92%; sens 0.95; spec 0.89; NR 2 0.95) when all histogram analyses methods were applied together in the MLR. Highest classification power among individually applied methods was found using the HFS concept (OCA 86%; sens 0.93; spec 0.79; NR 2 0.80). Conventional methods achieved lower classification potential on their own: EI (OCA 69%; sens 0.95; spec 0.26; NR 2 0.52); PV (OCA 69%; sens 0.90; spec 0.37; NR 2 0.57); MV (OCA 65%; sens 0.71; spec 0.58; NR 2 0.61); V (OCA 66%; sens 0.72; spec 0.53; NR 2 0.66); S (OCA 65%; sens 0.88; spec 0.26; NR 2 0.55); and K (OCA 63%; sens 0.90; spec 0.16; NR 2 0.48). The HFS method, which was so far applied to a CT bone density curve analysis, is also a remarkable information extraction tool for lung density histograms. Presumably, being a principle mathematical approach, the HFS method can extract valuable health related information also from histograms from complete different areas

Changes in the proteome and phosphoproteome expression in the bryozoan Bugula neritina larvae in response to the antifouling agent butenolide

KAUST Repository

Qian, Pei Yuan

2010-09-08

Larval attachment and metamorphosis, commonly referred to as larval settlement, of marine sessile invertebrates can be triggered or blocked by chemical cues and affected by changes in overall protein expression pattern and phosphorylation dynamics. This study focuses on the effects of butenolide, an effective larval settlement inhibitor, on larval settlement at the proteome level in the bryozoan Bugula neritina. Liquid-phase IEF sample prefractionation combined with 2-DE and MALDI-TOF MS was used to identify the differentially expressed proteins. Substantial changes occurred both in protein abundance and in phosphorylation status during larval settlement and when settling larvae were challenged with butenolide. The proteins that responded to treatment were identified as structural proteins, molecular chaperones, mitochondrial peptidases and calcium-binding proteins. Compared with our earlier results, both genistein and butenolide inhibited larval settlement of B. neritina primarily by changes in protein abundance and the phosphorylation status of proteins but have different protein targets in the same species. Clearly, to design potent antifouling compounds and to understand the mode of action of compounds, more studies on the effects of different compounds on proteome and phosphoproteome of different larval species are required. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.

Quantitative Nuclear Medicine. Chapter 17

Energy Technology Data Exchange (ETDEWEB)

Ouyang, J.; El Fakhri, G. [Massachusetts General Hospital and Harvard Medical School, Boston (United States)

2014-12-15

Planar imaging is still used in clinical practice although tomographic imaging (single photon emission computed tomography (SPECT) and positron emission tomography (PET)) is becoming more established. In this chapter, quantitative methods for both imaging techniques are presented. Planar imaging is limited to single photon. For both SPECT and PET, the focus is on the quantitative methods that can be applied to reconstructed images.

Improving data quality and preserving HCD-generated reporter ions with EThcD for isobaric tag-based quantitative proteomics and proteome-wide PTM studies

International Nuclear Information System (INIS)

Yu, Qing; Shi, Xudong; Feng, Yu; Kent, K. Craig; Li, Lingjun

2017-01-01

proteomics. • EThcD preserves HCD-type reporters of DiLeu and TMT tags and improves instrument duty cycle by lowering ETD reaction time. • With EThcD, traditional isobaric tags originally designed for HCD can be readily utilized with ETD. • EThcD is able to provide both b/y and c/z ion series for greatly improved data quality. • EThcD enables quantitative phosphoproteomics with enhanced phosphorylation localization.

Improving data quality and preserving HCD-generated reporter ions with EThcD for isobaric tag-based quantitative proteomics and proteome-wide PTM studies

Energy Technology Data Exchange (ETDEWEB)

Yu, Qing [School of Pharmacy, University of Wisconsin, Madison, WI 53705 (United States); Shi, Xudong [Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705 (United States); Feng, Yu [School of Pharmacy, University of Wisconsin, Madison, WI 53705 (United States); Kent, K. Craig [Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705 (United States); Li, Lingjun, E-mail: lingjun.li@wisc.edu [School of Pharmacy, University of Wisconsin, Madison, WI 53705 (United States); Department of Chemistry, University of Wisconsin, Madison, WI 53706 (United States)

2017-05-22

proteomics. • EThcD preserves HCD-type reporters of DiLeu and TMT tags and improves instrument duty cycle by lowering ETD reaction time. • With EThcD, traditional isobaric tags originally designed for HCD can be readily utilized with ETD. • EThcD is able to provide both b/y and c/z ion series for greatly improved data quality. • EThcD enables quantitative phosphoproteomics with enhanced phosphorylation localization.

Quantitative Finance

Science.gov (United States)

James, Jessica

2017-01-01

Quantitative finance is a field that has risen to prominence over the last few decades. It encompasses the complex models and calculations that value financial contracts, particularly those which reference events in the future, and apply probabilities to these events. While adding greatly to the flexibility of the market available to corporations and investors, it has also been blamed for worsening the impact of financial crises. But what exactly does quantitative finance encompass, and where did these ideas and models originate? We show that the mathematics behind finance and behind games of chance have tracked each other closely over the centuries and that many well-known physicists and mathematicians have contributed to the field.

A HIF-regulated VHL-PTP1B-Src signaling axis identifies a therapeutic target in Renal Cell Carcinoma

OpenAIRE

Suwaki, Natsuko; Vanhecke, Elsa; Atkins, Katelyn M.; Graf, Manuela; Swabey, Katherine; Huang, Paul; Schraml, Peter; Moch, Holger; Cassidy, Amy; Brewer, Daniel; Al-Lazikani, Bissan; Workman, Paul; De-Bono, Johann; Kaye, Stan B.; Larkin, James

2011-01-01

Metastatic renal cell carcinoma (RCC) is a molecularly heterogeneous disease that is intrinsically resistant to chemotherapy and radiotherapy. While VEGF and mTOR targeted therapies have shown clinical activity, their effects are variable and short-lived, underscoring the need for improved treatment strategies for RCC. Here, we used quantitative phosphoproteomics and immunohistochemical profiling of 346 RCC specimens to determine that Src kinase signaling is elevated in RCC cells that retain ...

Dynamic Interaction- and Phospho-Proteomics Reveal Lck as a Major Signaling Hub of CD147 in T Cells.

Science.gov (United States)

Supper, Verena; Hartl, Ingrid; Boulègue, Cyril; Ohradanova-Repic, Anna; Stockinger, Hannes

2017-03-15

Numerous publications have addressed CD147 as a tumor marker and regulator of cytoskeleton, cell growth, stress response, or immune cell function; however, the molecular functionality of CD147 remains incompletely understood. Using affinity purification, mass spectrometry, and phosphopeptide enrichment of isotope-labeled peptides, we examined the dynamic of the CD147 microenvironment and the CD147-dependent phosphoproteome in the Jurkat T cell line upon treatment with T cell stimulating agents. We identified novel dynamic interaction partners of CD147 such as CD45, CD47, GNAI2, Lck, RAP1B, and VAT1 and, furthermore, found 76 CD147-dependent phosphorylation sites on 57 proteins. Using the STRING protein network database, a network between the CD147 microenvironment and the CD147-dependent phosphoproteins was generated and led to the identification of key signaling hubs around the G proteins RAP1B and GNB1, the kinases PKCβ, PAK2, Lck, and CDK1, and the chaperone HSPA5. Gene ontology biological process term analysis revealed that wound healing-, cytoskeleton-, immune system-, stress response-, phosphorylation- and protein modification-, defense response to virus-, and TNF production-associated terms are enriched within the microenvironment and the phosphoproteins of CD147. With the generated signaling network and gene ontology biological process term grouping, we identify potential signaling routes of CD147 affecting T cell growth and function. Copyright © 2017 by The American Association of Immunologists, Inc.

Commenting on Findings in Qualitative and Quantitative Research Articles’ Discussion Sections in Applied Linguistics

Directory of Open Access Journals (Sweden)

Leila Dobakhti

2013-09-01

Full Text Available Research articles have received a wide interest in discourse studies particularly in genre analysis over the last few decades. A vast number of studies have focused on identifying the organizational patterns of research articles in various fields. However, to date, no study has been conducted on generic structure of qualitative and quantitative research articles. This study investigates the importance of commenting on findings in Discussion section of qualitative and quantitative research articles and the strategies that these two types of articles employ in making comments. The analysis shows that while commenting on findings is an important feature in both sets of articles, different strategies of commenting are favored in each type of articles. The differences can be attributed to the different epistemology of qualitative and quantitative research.

Distinct signalling properties of insulin receptor substrate (IRS)-1 and IRS-2 in mediating insulin/IGF-1 action

DEFF Research Database (Denmark)

Rabiee, Atefeh; Krüger, Marcus; Ardenkjær-Larsen, Jacob

2018-01-01

Insulin/IGF-1 action is driven by a complex and highly integrated signalling network. Loss-of-function studies indicate that the major insulin/IGF-1 receptor substrate (IRS) proteins, IRS-1 and IRS-2, mediate different biological functions in vitro and in vivo, suggesting specific signalling...... properties despite their high degree of homology. To identify mechanisms contributing to the differential signalling properties of IRS-1 and IRS-2 in the mediation of insulin/IGF-1 action, we performed comprehensive mass spectrometry (MS)-based phosphoproteomic profiling of brown preadipocytes from wild type......, IRS-1-/-and IRS-2-/-mice in the basal and IGF-1-stimulated states. We applied stable isotope labeling by amino acids in cell culture (SILAC) for the accurate quantitation of changes in protein phosphorylation. We found ~10% of the 6262 unique phosphorylation sites detected to be regulated by IGF-1...

A Cell-Signaling Network Temporally Resolves Specific versus Promiscuous Phosphorylation

Directory of Open Access Journals (Sweden)

Evgeny Kanshin

2015-02-01

Full Text Available If specific and functional kinase- or phosphatase-substrate interactions are optimized for binding compared to promiscuous interactions, then changes in phosphorylation should occur faster on functional versus promiscuous substrates. To test this hypothesis, we designed a high temporal resolution global phosphoproteomics protocol to study the high-osmolarity glycerol (HOG response in the budding yeast Saccharomyces cerevisiae. The method provides accurate, stimulus-specific measurement of phosphoproteome changes, quantitative analysis of phosphodynamics at sub-minute temporal resolution, and detection of more phosphosites. Rates of evolution of dynamic phosphosites were comparable to those of known functional phosphosites and significantly lower than static or longer-time-frame dynamic phosphosites. Kinetic profile analyses indicated that putatively functional kinase- or phosphatase-substrate interactions occur more rapidly, within 60 s, than promiscuous interactions. Finally, we report many changes in phosphorylation of proteins implicated in cytoskeletal and mitotic spindle dynamics that may underlie regulation of cell cycle and morphogenesis.

VIPAR, a quantitative approach to 3D histopathology applied to lymphatic malformations.

Science.gov (United States)

Hägerling, René; Drees, Dominik; Scherzinger, Aaron; Dierkes, Cathrin; Martin-Almedina, Silvia; Butz, Stefan; Gordon, Kristiana; Schäfers, Michael; Hinrichs, Klaus; Ostergaard, Pia; Vestweber, Dietmar; Goerge, Tobias; Mansour, Sahar; Jiang, Xiaoyi; Mortimer, Peter S; Kiefer, Friedemann

2017-08-17

Lack of investigatory and diagnostic tools has been a major contributing factor to the failure to mechanistically understand lymphedema and other lymphatic disorders in order to develop effective drug and surgical therapies. One difficulty has been understanding the true changes in lymph vessel pathology from standard 2D tissue sections. VIPAR (volume information-based histopathological analysis by 3D reconstruction and data extraction), a light-sheet microscopy-based approach for the analysis of tissue biopsies, is based on digital reconstruction and visualization of microscopic image stacks. VIPAR allows semiautomated segmentation of the vasculature and subsequent nonbiased extraction of characteristic vessel shape and connectivity parameters. We applied VIPAR to analyze biopsies from healthy lymphedematous and lymphangiomatous skin. Digital 3D reconstruction provided a directly visually interpretable, comprehensive representation of the lymphatic and blood vessels in the analyzed tissue volumes. The most conspicuous features were disrupted lymphatic vessels in lymphedematous skin and a hyperplasia (4.36-fold lymphatic vessel volume increase) in the lymphangiomatous skin. Both abnormalities were detected by the connectivity analysis based on extracted vessel shape and structure data. The quantitative evaluation of extracted data revealed a significant reduction of lymphatic segment length (51.3% and 54.2%) and straightness (89.2% and 83.7%) for lymphedematous and lymphangiomatous skin, respectively. Blood vessel length was significantly increased in the lymphangiomatous sample (239.3%). VIPAR is a volume-based tissue reconstruction data extraction and analysis approach that successfully distinguished healthy from lymphedematous and lymphangiomatous skin. Its application is not limited to the vascular systems or skin. Max Planck Society, DFG (SFB 656), and Cells-in-Motion Cluster of Excellence EXC 1003.

Applying Mixed Methods Research at the Synthesis Level: An Overview

Science.gov (United States)

Heyvaert, Mieke; Maes, Bea; Onghena, Patrick

2011-01-01

Historically, qualitative and quantitative approaches have been applied relatively separately in synthesizing qualitative and quantitative evidence, respectively, in several research domains. However, mixed methods approaches are becoming increasingly popular nowadays, and practices of combining qualitative and quantitative research components at…

Operation Iraqi Freedom 04 - 06: Opportunities to Apply Quantitative Methods to Intelligence Analysis

National Research Council Canada - National Science Library

Hansen, Eric C

2005-01-01

The purpose of this presentation is to illustrate the need for a quantitative analytical capability within organizations and staffs that provide intelligence analysis to Army, Joint, and Coalition Force headquarters...

Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response.

Science.gov (United States)

Zhang, Xu; Maity, Tapan; Kashyap, Manoj K; Bansal, Mukesh; Venugopalan, Abhilash; Singh, Sahib; Awasthi, Shivangi; Marimuthu, Arivusudar; Charles Jacob, Harrys Kishore; Belkina, Natalya; Pitts, Stephanie; Cultraro, Constance M; Gao, Shaojian; Kirkali, Guldal; Biswas, Romi; Chaerkady, Raghothama; Califano, Andrea; Pandey, Akhilesh; Guha, Udayan

2017-05-01

Mutations in the Epidermal growth factor receptor (EGFR) kinase domain, such as the L858R missense mutation and deletions spanning the conserved sequence 747 LREA 750 , are sensitive to tyrosine kinase inhibitors (TKIs). The gatekeeper site residue mutation, T790M accounts for around 60% of acquired resistance to EGFR TKIs. The first generation EGFR TKIs, erlotinib and gefitinib, and the second generation inhibitor, afatinib are FDA approved for initial treatment of EGFR mutated lung adenocarcinoma. The predominant biomarker of EGFR TKI responsiveness is the presence of EGFR TKI-sensitizing mutations. However, 30-40% of patients with EGFR mutations exhibit primary resistance to these TKIs, underscoring the unmet need of identifying additional biomarkers of treatment response. Here, we sought to characterize the dynamics of tyrosine phosphorylation upon EGFR TKI treatment of mutant EGFR-driven human lung adenocarcinoma cell lines with varying sensitivity to EGFR TKIs, erlotinib and afatinib. We employed stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative mass spectrometry to identify and quantify tyrosine phosphorylated peptides. The proportion of tyrosine phosphorylated sites that had reduced phosphorylation upon erlotinib or afatinib treatment correlated with the degree of TKI-sensitivity. Afatinib, an irreversible EGFR TKI, more effectively inhibited tyrosine phosphorylation of a majority of the substrates. The phosphosites with phosphorylation SILAC ratios that correlated with the TKI-sensitivity of the cell lines include sites on kinases, such as EGFR-Y1197 and MAPK7-Y221, and adaptor proteins, such as SHC1-Y349/350, ERRFI1-Y394, GAB1-Y689, STAT5A-Y694, DLG3-Y705, and DAPP1-Y139, suggesting these are potential biomarkers of TKI sensitivity. DAPP1, is a novel target of mutant EGFR signaling and Y-139 is the major site of DAPP1 tyrosine phosphorylation. We also uncovered several off-target effects of these TKIs, such as MST1R-Y1238

A new standardless quantitative electron probe microanalysis technique applied to III-V compound semiconductors

International Nuclear Information System (INIS)

Zangalis, K.P.; Christou, A.

1982-01-01

The present paper introduces a new standardless quantitative scheme for off-line electron microprobe analysis applications. The analysis is based on standard equations of the type Isub(i)=Csub(i)fsub(ZAF)βsub(i) and is specifically suitable for compound semiconductors. The roots to the resultant nth-degree polynomial are the unknown concentrations. Methods for computing Csub(i) when coefficients βsub(i) are unknown are also outlined. Applications of standardless analysis to GaAs and InP specimens are compared with results obtained by Auger electron spectroscopy and quantitative electron probe analysis with standards. (Auth.)

Quantitative determination of uranium by SIMS

International Nuclear Information System (INIS)

Kuruc, J.; Harvan, D.; Galanda, D.; Matel, L.; Aranyosiova, M.; Velic, D.

2008-01-01

The paper presents results of quantitative measurements of uranium-238 by secondary ion mass spectrometry (SIMS) with using alpha spectrometry as well as complementary technique. Samples with specific activity of uranium-238 were prepared by electrodeposition from aqueous solution of UO 2 (NO 3 ) 2 ·6H 2 O. We tried to apply SIMS to quantitative analysis and search for correlation between intensity obtained from SIMS and activity of uranium-238 in dependence on the surface's weight and possibility of using SIMS in quantitative analysis of environmental samples. The obtained results and correlations as well as results of two real samples measurements are presented in this paper. (authors)

Deterministic quantitative risk assessment development

Energy Technology Data Exchange (ETDEWEB)

Dawson, Jane; Colquhoun, Iain [PII Pipeline Solutions Business of GE Oil and Gas, Cramlington Northumberland (United Kingdom)

2009-07-01

Current risk assessment practice in pipeline integrity management is to use a semi-quantitative index-based or model based methodology. This approach has been found to be very flexible and provide useful results for identifying high risk areas and for prioritizing physical integrity assessments. However, as pipeline operators progressively adopt an operating strategy of continual risk reduction with a view to minimizing total expenditures within safety, environmental, and reliability constraints, the need for quantitative assessments of risk levels is becoming evident. Whereas reliability based quantitative risk assessments can be and are routinely carried out on a site-specific basis, they require significant amounts of quantitative data for the results to be meaningful. This need for detailed and reliable data tends to make these methods unwieldy for system-wide risk k assessment applications. This paper describes methods for estimating risk quantitatively through the calibration of semi-quantitative estimates to failure rates for peer pipeline systems. The methods involve the analysis of the failure rate distribution, and techniques for mapping the rate to the distribution of likelihoods available from currently available semi-quantitative programs. By applying point value probabilities to the failure rates, deterministic quantitative risk assessment (QRA) provides greater rigor and objectivity than can usually be achieved through the implementation of semi-quantitative risk assessment results. The method permits a fully quantitative approach or a mixture of QRA and semi-QRA to suit the operator's data availability and quality, and analysis needs. For example, consequence analysis can be quantitative or can address qualitative ranges for consequence categories. Likewise, failure likelihoods can be output as classical probabilities or as expected failure frequencies as required. (author)

Quantitative autoradiography of semiconductor base material

International Nuclear Information System (INIS)

Treutler, H.C.; Freyer, K.

1983-01-01

Autoradiographic methods for the quantitative determination of elements interesting in semiconductor technology and their distribution in silicon are described. Whereas the local concentration and distribution of phosphorus has been determined with the aid of silver halide films the neutron-induced autoradiography has been applied in the case of boron. Silicon disks containing diffused phosphorus or implanted or diffused boron have been used as standard samples. Different possibilities of the quantitative evaluation of autoradiograms are considered and compared

GPC and quantitative phase imaging

DEFF Research Database (Denmark)

Palima, Darwin; Banas, Andrew Rafael; Villangca, Mark Jayson

2016-01-01

shaper followed by the potential of GPC for biomedical and multispectral applications where we experimentally demonstrate the active light shaping of a supercontinuum laser over most of the visible wavelength range. Finally, we discuss how GPC can be advantageously applied for Quantitative Phase Imaging...

Selective phosphorylation during early macrophage differentiation

KAUST Repository

Zhang, Huoming

2015-08-26

The differentiation of macrophages from monocytes is a tightly controlled and complex biological process. Although numerous studies have been conducted using biochemical approaches or global gene/gene profiling, the mechanisms of the early stages of differentiation remain unclear. Here we used SILAC-based quantitative proteomics approach to perform temporal phosphoproteome profiling of early macrophage differentiation. We identified a large set of phosphoproteins and grouped them as PMA-regulated and non-regulated phosphoproteins in the early stages of differentiation. Further analysis of the PMA-regulated phosphoproteins revealed that transcriptional suppression, cytoskeletal reorganization and cell adhesion were among the most significantly activated pathways. Some key involved regulators of these pathways are mTOR, MYB, STAT1 and CTNNB. Moreover, we were able to classify the roles and activities of several transcriptional factors during different differentiation stages and found that E2F is likely to be an important regulator during the relatively late stages of differentiation. This study provides the first comprehensive picture of the dynamic phosphoproteome during myeloid cells differentiation, and identifies potential molecular targets in leukemic cells.

Characterization of chloroplast phosphoproteins controlling manganese use efficiency using quantitative proteomics

DEFF Research Database (Denmark)

Petersen, Jørgen; Sprenger, Richard Remko; Rogowska-Wrzesinska, Adelina

Manganese is important for molecular functions in plants, i.e. as a co-factor in enzymes and in the oxygen evolving complex of photosystem II, located like most of the photosynthetic machinery, in the thylakoid membranes of chloroplasts. Soils that lack plant available micronutrients such as mang......Manganese is important for molecular functions in plants, i.e. as a co-factor in enzymes and in the oxygen evolving complex of photosystem II, located like most of the photosynthetic machinery, in the thylakoid membranes of chloroplasts. Soils that lack plant available micronutrients...... involved in manganese use efficiency, focusing on the phosphoproteome from thylakoid preparations from two barley genotypes, manganese efficient (Vanessa) and inefficient (Antonia) genotype. Experimental: By monitoring the photosynthetic efficiency (Fv/Fm) a decline in activity is observed as a consequence...

A novel multi-walled carbon nanotube-based antibody conjugate for quantitative and semi-quantitative lateral flow assays.

Science.gov (United States)

Sun, Wenjuan; Hu, Xiaolong; Liu, Jia; Zhang, Yurong; Lu, Jianzhong; Zeng, Libo

2017-10-01

In this study, the multi-walled carbon nanotubes (MWCNTs) were applied in lateral flow strips (LFS) for semi-quantitative and quantitative assays. Firstly, the solubility of MWCNTs was improved using various surfactants to enhance their biocompatibility for practical application. The dispersed MWCNTs were conjugated with the methamphetamine (MET) antibody in a non-covalent manner and then manufactured into the LFS for the quantitative detection of MET. The MWCNTs-based lateral flow assay (MWCNTs-LFA) exhibited an excellent linear relationship between the values of test line and MET when its concentration ranges from 62.5 to 1500 ng/mL. The sensitivity of the LFS was evaluated by conjugating MWCNTs with HCG antibody and the MWCNTs conjugated method is 10 times more sensitive than the one conjugated with classical colloidal gold nanoparticles. Taken together, our data demonstrate that MWCNTs-LFA is a more sensitive and reliable assay for semi-quantitative and quantitative detection which can be used in forensic analysis.

Quantitative analysis of boron by neutron radiography

International Nuclear Information System (INIS)

Bayuelken, A.; Boeck, H.; Schachner, H.; Buchberger, T.

1990-01-01

The quantitative determination of boron in ores is a long process with chemical analysis techniques. As nuclear techniques like X-ray fluorescence and activation analysis are not applicable for boron, only the neutron radiography technique, using the high neutron absorption cross section of this element, can be applied for quantitative determinations. This paper describes preliminary tests and calibration experiments carried out at a 250 kW TRIGA reactor. (orig.) [de

A CT-based method for fully quantitative TI SPECT

International Nuclear Information System (INIS)

Willowson, Kathy; Bailey, Dale; Baldock, Clive

2009-01-01

Full text: Objectives: To develop and validate a method for quantitative 2 0 l TI SPECT data based on corrections derived from X-ray CT data, and to apply the method in the clinic for quantitative determination of recurrence of brain tumours. Method: A previously developed method for achieving quantitative SPECT with 9 9 m Tc based on corrections derived from xray CT data was extended to apply to 2 0 l Tl. Experimental validation was performed on a cylindrical phantom by comparing known injected activity and measured concentration to quantitative calculations. Further evaluation was performed on a RSI Striatal Brain Phantom containing three 'lesions' with activity to background ratios of 1: 1, 1.5: I and 2: I. The method was subsequently applied to a series of scans from patients with suspected recurrence of brain tumours (principally glioma) to determine an SUV-like measure (Standardised Uptake Value). Results: The total activity and concentration in the phantom were calculated to within 3% and I % of the true values, respectively. The calculated values for the concentration of activity in the background and corresponding lesions of the brain phantom (in increasing ratios) were found to be within 2%,10%,1% and 2%, respectively, of the true concentrations. Patient studies showed that an initial SUV greater than 1.5 corresponded to a 56% mortality rate in the first 12 months, as opposed to a 14% mortality rate for those with a SUV less than 1.5. Conclusion: The quantitative technique produces accurate results for the radionuclide 2 0 l Tl. Initial investigation in clinical brain SPECT suggests correlation between quantitative uptake and survival.

Quantitative mass spectrometry: an overview

Science.gov (United States)

Urban, Pawel L.

2016-10-01

Mass spectrometry (MS) is a mainstream chemical analysis technique in the twenty-first century. It has contributed to numerous discoveries in chemistry, physics and biochemistry. Hundreds of research laboratories scattered all over the world use MS every day to investigate fundamental phenomena on the molecular level. MS is also widely used by industry-especially in drug discovery, quality control and food safety protocols. In some cases, mass spectrometers are indispensable and irreplaceable by any other metrological tools. The uniqueness of MS is due to the fact that it enables direct identification of molecules based on the mass-to-charge ratios as well as fragmentation patterns. Thus, for several decades now, MS has been used in qualitative chemical analysis. To address the pressing need for quantitative molecular measurements, a number of laboratories focused on technological and methodological improvements that could render MS a fully quantitative metrological platform. In this theme issue, the experts working for some of those laboratories share their knowledge and enthusiasm about quantitative MS. I hope this theme issue will benefit readers, and foster fundamental and applied research based on quantitative MS measurements. This article is part of the themed issue 'Quantitative mass spectrometry'.

Phosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication.

Directory of Open Access Journals (Sweden)

Denis Avey

2015-07-01

Full Text Available Kaposi's Sarcoma-Associated Herpesvirus (KSHV is an oncogenic virus which has adapted unique mechanisms to modulate the cellular microenvironment of its human host. The pathogenesis of KSHV is intimately linked to its manipulation of cellular signaling pathways, including the extracellular signal-regulated kinase (ERK mitogen-activated protein kinase (MAPK pathway. We have previously shown that KSHV ORF45 contributes to the sustained activation of both ERK and p90 ribosomal S6 kinase (RSK, a major functional mediator of ERK/MAPK signaling during KSHV lytic replication. ORF45-activated RSK is required for optimal KSHV lytic gene expression and progeny virion production, though the underlying mechanisms downstream of this activation are still unclear. We hypothesized that the activation of RSK by ORF45 causes differential phosphorylation of cellular and viral substrates, affecting biological processes essential for efficient KSHV lytic replication. Accordingly, we observed widespread and significant differences in protein phosphorylation upon induction of lytic replication. Mass-spectrometry-based phosphoproteomic screening identified putative substrates of ORF45-activated RSK in KSHV-infected cells. Bioinformatic analyses revealed that nuclear proteins, including several transcriptional regulators, were overrepresented among these candidates. We validated the ORF45/RSK-dependent phosphorylation of several putative substrates by employing KSHV BAC mutagenesis, kinase inhibitor treatments, and/or CRISPR-mediated knockout of RSK in KSHV-infected cells. Furthermore, we assessed the consequences of knocking out these substrates on ORF45/RSK-dependent regulation of gene expression and KSHV progeny virion production. Finally, we show data to support that ORF45 regulates the translational efficiency of a subset of viral/cellular genes with complex secondary structure in their 5' UTR. Altogether, these data shed light on the mechanisms by which KSHV ORF45

Improving the validity of quantitative measures in applied linguistics research

NARCIS (Netherlands)

Purpura, J.E.; Brown, J.D.; Schoonen, R.

2015-01-01

In empirical applied linguistics research it is essential that the key variables are operationalized in a valid and reliable way, and that the scores are treated appropriately, allowing for a proper testing of the hypotheses under investigation. The current article addresses several theoretical and

Stochastic resonance is applied to quantitative analysis for weak chromatographic signal of glyburide in plasma

International Nuclear Information System (INIS)

Zhang Wei; Xiang Bingren; Wu Yanwei; Shang Erxin

2005-01-01

Based on the theory of stochastic resonance, a new method carried on the quantitive analysis to weak chromatographic signal of glyburide in plasma, which was embedded in the noise background and the signal-to-noise ratio (SNR) of HPLC-UV is enhanced remarkably. This method enhances the quantification limit to 1 ng ml -1 , which is the same as HPLC-MS, and makes it possible to detect the weak signal accurately by HPLC-UV, which was not suitable before. The results showed good recovery and linear range from 1 to 50 ng ml -1 of glyburide in plasma and the method can be used for quantitative analysis of glyburide

Phosphoproteomic Analysis Reveals a Novel Mechanism of CaMKIIα Regulation Inversely Induced by Cocaine Memory Extinction versus Reconsolidation

Science.gov (United States)

Rich, Matthew T.; Abbott, Thomas B.; Chung, Lisa; Gulcicek, Erol E.; Stone, Kathryn L.; Colangelo, Christopher M.; Lam, TuKiet T.; Nairn, Angus C.; Taylor, Jane R.

2016-01-01

Successful addiction treatment depends on maintaining long-term abstinence, making relapse prevention an essential therapeutic goal. However, exposure to environmental cues associated with drug use often thwarts abstinence efforts by triggering drug using memories that drive craving and relapse. We sought to develop a dual approach for weakening cocaine memories through phosphoproteomic identification of targets regulated in opposite directions by memory extinction compared with reconsolidation in male Sprague-Dawley rats that had been trained to self-administer cocaine paired with an audiovisual cue. We discovered a novel, inversely regulated, memory-dependent phosphorylation event on calcium-calmodulin-dependent kinase II α (CaMKIIα) at serine (S)331. Correspondingly, extinction-associated S331 phosphorylation inhibited CaMKIIα activity. Intra-basolateral amygdala inhibition of CaMKII promoted memory extinction and disrupted reconsolidation, leading to a reduction in subsequent cue-induced reinstatement. CaMKII inhibition had no effect if the memory was neither retrieved nor extinguished. Therefore, inhibition of CaMKII represents a novel mechanism for memory-based addiction treatment that leverages both extinction enhancement and reconsolidation disruption to reduce relapse-like behavior. SIGNIFICANCE STATEMENT Preventing relapse to drug use is an important goal for the successful treatment of addictive disorders. Relapse-prevention therapies attempt to interfere with drug-associated memories, but are often hindered by unintentional memory strengthening. In this study, we identify phosphorylation events that are bidirectionally regulated by the reconsolidation versus extinction of a cocaine-associated memory, including a novel site on CaMKIIα. Additionally, using a rodent model of addiction, we show that CaMKII inhibition in the amygdala can reduce relapse-like behavior. Together, our data supports the existence of mechanisms that can be used to enhance

Quantitative ion implantation

International Nuclear Information System (INIS)

Gries, W.H.

1976-06-01

This is a report of the study of the implantation of heavy ions at medium keV-energies into electrically conducting mono-elemental solids, at ion doses too small to cause significant loss of the implanted ions by resputtering. The study has been undertaken to investigate the possibility of accurate portioning of matter in submicrogram quantities, with some specific applications in mind. The problem is extensively investigated both on a theoretical level and in practice. A mathematical model is developed for calculating the loss of implanted ions by resputtering as a function of the implanted ion dose and the sputtering yield. Numerical data are produced therefrom which permit a good order-of-magnitude estimate of the loss for any ion/solid combination in which the ions are heavier than the solid atoms, and for any ion energy from 10 to 300 keV. The implanted ion dose is measured by integration of the ion beam current, and equipment and techniques are described which make possible the accurate integration of an ion current in an electromagnetic isotope separator. The methods are applied to two sample cases, one being a stable isotope, the other a radioisotope. In both cases independent methods are used to show that the implantation is indeed quantitative, as predicted. At the same time the sample cases are used to demonstrate two possible applications for quantitative ion implantation, viz. firstly for the manufacture of calibration standards for instrumental micromethods of elemental trace analysis in metals, and secondly for the determination of the half-lives of long-lived radioisotopes by a specific activity method. It is concluded that the present study has advanced quantitative ion implantation to the state where it can be successfully applied to the solution of problems in other fields

Improving the Validity of Quantitative Measures in Applied Linguistics Research

Science.gov (United States)

Purpura, James E.; Brown, James Dean; Schoonen, Rob

2015-01-01

In empirical applied linguistics research it is essential that the key variables are operationalized in a valid and reliable way, and that the scores are treated appropriately, allowing for a proper testing of the hypotheses under investigation. The current article addresses several theoretical and practical issues regarding the use of measurement…

Reflections on Mixing Methods in Applied Linguistics Research

Science.gov (United States)

Hashemi, Mohammad R.

2012-01-01

This commentary advocates the use of mixed methods research--that is the integration of qualitative and quantitative methods in a single study--in applied linguistics. Based on preliminary findings from a research project in progress, some reflections on the current practice of mixing methods as a new trend in applied linguistics are put forward.…

Quantitative Evidence Synthesis with Power Priors

NARCIS (Netherlands)

Rietbergen, C.|info:eu-repo/dai/nl/322847796

2016-01-01

The aim of this thesis is to provide the applied researcher with a practical approach for quantitative evidence synthesis using the conditional power prior that allows for subjective input and thereby provides an alternative tgbgo deal with the difficulties as- sociated with the joint power prior

Bootstrapping in Applied Linguistics: Assessing Its Potential Using Shared Data

Science.gov (United States)

Plonsky, Luke; Egbert, Jesse; Laflair, Geoffrey T.

2015-01-01

Parametric analyses such as t tests and ANOVAs are the norm--if not the default--statistical tests found in quantitative applied linguistics research (Gass 2009). Applied statisticians and one applied linguist (Larson-Hall 2010, 2012; Larson-Hall and Herrington 2010), however, have argued that this approach may not be appropriate for small samples…

Quantitative X-ray analysis of pigments

International Nuclear Information System (INIS)

Araujo, M. Marrocos de

1987-01-01

The 'matrix-flushing' and the 'adiabatic principle' methods have been applied for the quantitative analysis through X-ray diffraction patterns of pigments and extenders mixtures, frequently used in paint industry. The results obtained have shown the usefulness of these methods, but still ask for improving their accuracy. (Author) [pt

Validity of spherical quantitative refractometry: application to laser-produced plasmas

International Nuclear Information System (INIS)

Benattar, R.; Popovics, C.

1983-01-01

We report an experimental laser technique of quantitative Schlieren imaging of spherical plasmas combined with streak camera recording. We show that quantitative refractometry applies for small values of refraction angles, i.e., when the law giving the refraction angle versus the impact parameter of rays passing through the plasma is a linearly decreasing function

p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage

DEFF Research Database (Denmark)

Borisova, Marina E; Voigt, Andrea; Tollenaere, Maxim A X

2018-01-01

quantitative phosphoproteomics and protein kinase inhibition to provide a systems view on protein phosphorylation patterns induced by UV light and uncover the dependencies of phosphorylation events on the canonical DNA damage signaling by ATM/ATR and the p38 MAP kinase pathway. We identify RNA-binding proteins......Ultraviolet (UV) light radiation induces the formation of bulky photoproducts in the DNA that globally affect transcription and splicing. However, the signaling pathways and mechanisms that link UV-light-induced DNA damage to changes in RNA metabolism remain poorly understood. Here we employ...

Extracting quantitative three-dimensional unsteady flow direction from tuft flow visualizations

Energy Technology Data Exchange (ETDEWEB)

Omata, Noriyasu; Shirayama, Susumu, E-mail: omata@nakl.t.u-tokyo.ac.jp, E-mail: sirayama@sys.t.u-tokyo.ac.jp [Department of Systems Innovation, School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-8656 (Japan)

2017-10-15

We focus on the qualitative but widely used method of tuft flow visualization, and propose a method for quantifying it using information technology. By applying stereo image processing and computer vision, the three-dimensional (3D) flow direction in a real environment can be obtained quantitatively. In addition, we show that the flow can be divided temporally by performing appropriate machine learning on the data. Acquisition of flow information in real environments is important for design development, but it is generally considered difficult to apply simulations or quantitative experiments to such environments. Hence, qualitative methods including the tuft method are still in use today. Although attempts have been made previously to quantify such methods, it has not been possible to acquire 3D information. Furthermore, even if quantitative data could be acquired, analysis was often performed empirically or qualitatively. In contrast, we show that our method can acquire 3D information and analyze the measured data quantitatively. (paper)

Extracting quantitative three-dimensional unsteady flow direction from tuft flow visualizations

International Nuclear Information System (INIS)

Omata, Noriyasu; Shirayama, Susumu

2017-01-01

We focus on the qualitative but widely used method of tuft flow visualization, and propose a method for quantifying it using information technology. By applying stereo image processing and computer vision, the three-dimensional (3D) flow direction in a real environment can be obtained quantitatively. In addition, we show that the flow can be divided temporally by performing appropriate machine learning on the data. Acquisition of flow information in real environments is important for design development, but it is generally considered difficult to apply simulations or quantitative experiments to such environments. Hence, qualitative methods including the tuft method are still in use today. Although attempts have been made previously to quantify such methods, it has not been possible to acquire 3D information. Furthermore, even if quantitative data could be acquired, analysis was often performed empirically or qualitatively. In contrast, we show that our method can acquire 3D information and analyze the measured data quantitatively. (paper)

Development of Three Methods for Simultaneous Quantitative ...

African Journals Online (AJOL)

Development of Three Methods for Simultaneous Quantitative Determination of Chlorpheniramine Maleate and Dexamethasone in the Presence of Parabens in ... Tropical Journal of Pharmaceutical Research ... Results: All the proposed methods were successfully applied to the analysis of raw materials and dosage form.

Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches.

Science.gov (United States)

Tran, Trung T; Bollineni, Ravi C; Strozynski, Margarita; Koehler, Christian J; Thiede, Bernd

2017-07-07

Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant-specific peptide sequences that match to MS data. Furthermore, we combined this database without alternative splice variant-1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies were analyzed using these two databases. Several nonalternative splice variant-1-specific peptides were found in both cell lines, and some of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several nonalternative splice variant-1-specific peptides, and some of them showed clear quantitative differences between the two states.

Review of progress in quantitative nondestructive evaluation

International Nuclear Information System (INIS)

Thompson, D.O.; Chimenti, D.E.

1983-01-01

A comprehensive review of the current state of quantitative nondestructive evaluation (NDE), this volume brings together papers by researchers working in government, private industry, and university laboratories. Their papers cover a wide range of interests and concerns for researchers involved in theoretical and applied aspects of quantitative NDE. Specific topics examined include reliability probability of detection--ultrasonics and eddy currents weldments closure effects in fatigue cracks technology transfer ultrasonic scattering theory acoustic emission ultrasonic scattering, reliability and penetrating radiation metal matrix composites ultrasonic scattering from near-surface flaws ultrasonic multiple scattering

An overview of quantitative approaches in Gestalt perception.

Science.gov (United States)

Jäkel, Frank; Singh, Manish; Wichmann, Felix A; Herzog, Michael H

2016-09-01

Gestalt psychology is often criticized as lacking quantitative measurements and precise mathematical models. While this is true of the early Gestalt school, today there are many quantitative approaches in Gestalt perception and the special issue of Vision Research "Quantitative Approaches in Gestalt Perception" showcases the current state-of-the-art. In this article we give an overview of these current approaches. For example, ideal observer models are one of the standard quantitative tools in vision research and there is a clear trend to try and apply this tool to Gestalt perception and thereby integrate Gestalt perception into mainstream vision research. More generally, Bayesian models, long popular in other areas of vision research, are increasingly being employed to model perceptual grouping as well. Thus, although experimental and theoretical approaches to Gestalt perception remain quite diverse, we are hopeful that these quantitative trends will pave the way for a unified theory. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of Mitosis-Specific Phosphorylation in Mitotic Chromosome-Associated Proteins.

Science.gov (United States)

Ohta, Shinya; Kimura, Michiko; Takagi, Shunsuke; Toramoto, Iyo; Ishihama, Yasushi

2016-09-02

During mitosis, phosphorylation of chromosome-associated proteins is a key regulatory mechanism. Mass spectrometry has been successfully applied to determine the complete protein composition of mitotic chromosomes, but not to identify post-translational modifications. Here, we quantitatively compared the phosphoproteome of isolated mitotic chromosomes with that of chromosomes in nonsynchronized cells. We identified 4274 total phosphorylation sites and 350 mitosis-specific phosphorylation sites in mitotic chromosome-associated proteins. Significant mitosis-specific phosphorylation in centromere/kinetochore proteins was detected, although the chromosomal association of these proteins did not change throughout the cell cycle. This mitosis-specific phosphorylation might play a key role in regulation of mitosis. Further analysis revealed strong dependency of phosphorylation dynamics on kinase consensus patterns, thus linking the identified phosphorylation sites to known key mitotic kinases. Remarkably, chromosomal axial proteins such as non-SMC subunits of condensin, TopoIIα, and Kif4A, together with the chromosomal periphery protein Ki67 involved in the establishment of the mitotic chromosomal structure, demonstrated high phosphorylation during mitosis. These findings suggest a novel mechanism for regulation of chromosome restructuring in mitosis via protein phosphorylation. Our study generated a large quantitative database on protein phosphorylation in mitotic and nonmitotic chromosomes, thus providing insights into the dynamics of chromatin protein phosphorylation at mitosis onset.

Applying analytical ultracentrifugation to nanocrystal suspensions

Energy Technology Data Exchange (ETDEWEB)

Jamison, Jennifer A; Krueger, Karl M; Mayo, J T; Yavuz, Cafer T; Redden, Jacina J; Colvin, Vicki L, E-mail: colvin@rice.ed [Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, TX 77005 (United States)

2009-09-02

While applied frequently in physical biochemistry to the study of protein complexes, the quantitative use of analytical ultracentrifugation (AUC) for nanocrystal analysis is relatively rare. Its application in nanoscience is potentially very powerful as it provides a measure of nanocrystal density, size and structure directly in the solution phase. Towards that end, this paper examines the best practices for applying data collection and analysis methods for AUC, geared towards the study of biomolecules, to the unique problems of nanoparticle analysis. Using uniform nanocrystals of cadmium selenide, we compared several schemes for analyzing raw sedimentation data. Comparable values of the mean sedimentation coefficients (s-value) were found using several popular analytical approaches; however, the distribution in sample s-values is best captured using the van Holde-Weischt algorithm. Measured s-values could be reproducibly collected if sample temperature and concentration were controlled; under these circumstances, the variability for average sedimentation values was typically 5%. The full shape of the distribution in s-values, however, is not easily subjected to quantitative interpretation. Moreover, the selection of the appropriate sedimentation speed is crucial for AUC of nanocrystals as the density of inorganic nanocrystals is much larger than that of solvents. Quantitative analysis of sedimentation properties will allow for better agreement between experimental and theoretical models of nanocrystal solution behavior, as well as providing deeper insight into the hydrodynamic size and solution properties of nanomaterials.

Quantitative phosphoproteomics dissection of 7TM receptor signaling using full and biased agonists

DEFF Research Database (Denmark)

Christensen, Gitte L; Kelstrup, Christian D; Lyngsø, Christina

2010-01-01

only activates the Gaq protein-independent signaling.e quantified more than ten thousand phosphorylation sites of which 1183 were regulated by Angiotensin II or its analogue SII Angiotensin II. 36% of the AT1R regulated phosphorylations were regulated by SII Angiotensin II. Analysis of phosphorylation...... into Angiotensin II signal transduction and is the first study dissecting the differences between a full agonist and a biased agonist from a 7TMR on a systems-wide scale. Importantly, it reveals a previously unappreciated diversity and quantity of Gaq protein-independent signaling and uncovers novel signaling......Seven-transmembrane receptors (7TMRs) signal through the well described heterotrimeric G proteins, but can also activate G protein-independent signaling pathways of which the impact and complexity are less understood. The Angiotensin II type 1 receptor (AT1R) is a prototypical 7TMR and an important...

Quantitative methods in psychology: inevitable and useless

Directory of Open Access Journals (Sweden)

Aaro Toomela

2010-07-01

Full Text Available Science begins with the question, what do I want to know? Science becomes science, however, only when this question is justified and the appropriate methodology is chosen for answering the research question. Research question should precede the other questions; methods should be chosen according to the research question and not vice versa. Modern quantitative psychology has accepted method as primary; research questions are adjusted to the methods. For understanding thinking in modern quantitative psychology, two epistemologies should be distinguished: structural-systemic that is based on Aristotelian thinking, and associative-quantitative that is based on Cartesian-Humean thinking. The first aims at understanding the structure that underlies the studied processes; the second looks for identification of cause-effect relationships between the events with no possible access to the understanding of the structures that underlie the processes. Quantitative methodology in particular as well as mathematical psychology in general, is useless for answering questions about structures and processes that underlie observed behaviors. Nevertheless, quantitative science is almost inevitable in a situation where the systemic-structural basis of behavior is not well understood; all sorts of applied decisions can be made on the basis of quantitative studies. In order to proceed, psychology should study structures; methodologically, constructive experiments should be added to observations and analytic experiments.

Applying quantitative structure–activity relationship approaches to nanotoxicology: Current status and future potential

International Nuclear Information System (INIS)

Winkler, David A.; Mombelli, Enrico; Pietroiusti, Antonio; Tran, Lang; Worth, Andrew; Fadeel, Bengt; McCall, Maxine J.

2013-01-01

The potential (eco)toxicological hazard posed by engineered nanoparticles is a major scientific and societal concern since several industrial sectors (e.g. electronics, biomedicine, and cosmetics) are exploiting the innovative properties of nanostructures resulting in their large-scale production. Many consumer products contain nanomaterials and, given their complex life-cycle, it is essential to anticipate their (eco)toxicological properties in a fast and inexpensive way in order to mitigate adverse effects on human health and the environment. In this context, the application of the structure–toxicity paradigm to nanomaterials represents a promising approach. Indeed, according to this paradigm, it is possible to predict toxicological effects induced by chemicals on the basis of their structural similarity with chemicals for which toxicological endpoints have been previously measured. These structure–toxicity relationships can be quantitative or qualitative in nature and they can predict toxicological effects directly from the physicochemical properties of the entities (e.g. nanoparticles) of interest. Therefore, this approach can aid in prioritizing resources in toxicological investigations while reducing the ethical and monetary costs that are related to animal testing. The purpose of this review is to provide a summary of recent key advances in the field of QSAR modelling of nanomaterial toxicity, to identify the major gaps in research required to accelerate the use of quantitative structure–activity relationship (QSAR) methods, and to provide a roadmap for future research needed to achieve QSAR models useful for regulatory purposes

Distinct signalling properties of insulin receptor substrate (IRS)-1 and IRS-2 in mediating insulin/IGF-1 action.

Science.gov (United States)

Rabiee, Atefeh; Krüger, Marcus; Ardenkjær-Larsen, Jacob; Kahn, C Ronald; Emanuelli, Brice

2018-07-01

Insulin/IGF-1 action is driven by a complex and highly integrated signalling network. Loss-of-function studies indicate that the major insulin/IGF-1 receptor substrate (IRS) proteins, IRS-1 and IRS-2, mediate different biological functions in vitro and in vivo, suggesting specific signalling properties despite their high degree of homology. To identify mechanisms contributing to the differential signalling properties of IRS-1 and IRS-2 in the mediation of insulin/IGF-1 action, we performed comprehensive mass spectrometry (MS)-based phosphoproteomic profiling of brown preadipocytes from wild type, IRS-1 -/- and IRS-2 -/- mice in the basal and IGF-1-stimulated states. We applied stable isotope labeling by amino acids in cell culture (SILAC) for the accurate quantitation of changes in protein phosphorylation. We found ~10% of the 6262 unique phosphorylation sites detected to be regulated by IGF-1. These regulated sites included previously reported substrates of the insulin/IGF-1 signalling pathway, as well as novel substrates including Nuclear Factor I X and Semaphorin-4B. In silico prediction suggests the protein kinase B (PKB), protein kinase C (PKC), and cyclin-dependent kinase (CDK) as the main mediators of these phosphorylation events. Importantly, we found preferential phosphorylation patterns depending on the presence of either IRS-1 or IRS-2, which was associated with specific sets of kinases involved in signal transduction downstream of these substrates such as PDHK1, MAPK3, and PKD1 for IRS-1, and PIN1 and PKC beta for IRS-2. Overall, by generating a comprehensive phosphoproteomic profile from brown preadipocyte cells in response to IGF-1 stimulation, we reveal both common and distinct insulin/IGF-1 signalling events mediated by specific IRS proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Shedding quantitative fluorescence light on novel regulatory mechanisms in skeletal biomedicine and biodentistry.

Science.gov (United States)

Lee, Ji-Won; Iimura, Tadahiro

2017-02-01

Digitalized fluorescence images contain numerical information such as color (wavelength), fluorescence intensity and spatial position. However, quantitative analyses of acquired data and their validation remained to be established. Our research group has applied quantitative fluorescence imaging on tissue sections and uncovered novel findings in skeletal biomedicine and biodentistry. This review paper includes a brief background of quantitative fluorescence imaging and discusses practical applications by introducing our previous research. Finally, the future perspectives of quantitative fluorescence imaging are discussed.

Qualitative and quantitative laser-induced breakdown spectroscopy of bronze objects

International Nuclear Information System (INIS)

Tankova, V; Blagoev, K; Grozeva, M; Malcheva, G; Penkova, P

2016-01-01

Laser-induced breakdown spectroscopy (LIBS) is an analytical technique for qualitative and quantitative elemental analysis of solids, liquids and gases. In this work, the method was applied for investigation of archaeological bronze objects. The analytical information obtained by LIBS was used for qualitative determination of the elements in the material used for manufacturing of the objects under study. Quantitative chemical analysis was also performed after generating calibration curves with standard samples of similar matrix composition. Quantitative estimation of the elemental concentration of the bulk of the samples was performed, together with investigation of the surface layer of the objects. The results of the quantitative analyses gave indications about the manufacturing process of the investigated objects. (paper)

Applying quantitative adiposity feature analysis models to predict benefit of bevacizumab-based chemotherapy in ovarian cancer patients

Science.gov (United States)

Wang, Yunzhi; Qiu, Yuchen; Thai, Theresa; More, Kathleen; Ding, Kai; Liu, Hong; Zheng, Bin

2016-03-01

How to rationally identify epithelial ovarian cancer (EOC) patients who will benefit from bevacizumab or other antiangiogenic therapies is a critical issue in EOC treatments. The motivation of this study is to quantitatively measure adiposity features from CT images and investigate the feasibility of predicting potential benefit of EOC patients with or without receiving bevacizumab-based chemotherapy treatment using multivariate statistical models built based on quantitative adiposity image features. A dataset involving CT images from 59 advanced EOC patients were included. Among them, 32 patients received maintenance bevacizumab after primary chemotherapy and the remaining 27 patients did not. We developed a computer-aided detection (CAD) scheme to automatically segment subcutaneous fat areas (VFA) and visceral fat areas (SFA) and then extracted 7 adiposity-related quantitative features. Three multivariate data analysis models (linear regression, logistic regression and Cox proportional hazards regression) were performed respectively to investigate the potential association between the model-generated prediction results and the patients' progression-free survival (PFS) and overall survival (OS). The results show that using all 3 statistical models, a statistically significant association was detected between the model-generated results and both of the two clinical outcomes in the group of patients receiving maintenance bevacizumab (p<0.01), while there were no significant association for both PFS and OS in the group of patients without receiving maintenance bevacizumab. Therefore, this study demonstrated the feasibility of using quantitative adiposity-related CT image features based statistical prediction models to generate a new clinical marker and predict the clinical outcome of EOC patients receiving maintenance bevacizumab-based chemotherapy.

Neutron radiography applied to qualitative and quantitative non-destructive testing of metals and alloys

International Nuclear Information System (INIS)

Laporte, A.; Bayon, G.; Thierry, D.

1981-01-01

The radiation-material interaction between X-rays, gamma rays and neutrons is compared. The different possibilities of image detection are enumerated. The industrial testing installations associated with the Triton experimental reactor of the Fontenay-aux-Roses Nuclear Research Centre is described. A high performance testing unit is presented -the use of an intense flux of cold neutrons in a special building designed for neutrons radiographic testing- which will enter service in the second half of 1980, in association with the Orphee basic physics reactor of the Saclay Nuclear Research Centre. Concrete examples of manufacturing control on metal parts are given such as: testing of bonds between two metals of comparable density, testing of the homogeneity of high density alloys, testing of the homogeneity of low density alloys, testing of materials with high neutron contrast. Neutron radiographic testing not only achieves qualitative but also quantitative analysis of the films, on two levels, dimensional measurement and homogeneity and/or concentration measurement, by densitometry. Testing methods used for complete quantitative analysis of boronated aluminium plates used in the nuclear industry are examined. Perspectives concerning routine tests, by dealing with fundamental aspects of standardization and the knowledge of the phenomena involved in this testing technique are given [fr

A novel approach to the microdosimetry of neutron capture therapy. Part I. High-resolution quantitative autoradiography applied to microdosimetry in neutron capture therapy

International Nuclear Information System (INIS)

Solares, G.R.; Zamenhof, R.G.

1995-01-01

A novel approach to the microdosimetry of neutron capture therapy has been developed using high-resolution quantitative autoradiography (HRQAR) and two-dimensional Monte Carlo simulation. This approach has been applied using actual cell morophology (nuclear and cytoplasmic cell structures) and the measured microdistribution of boron-10 in a transplanted murine brain tumor (GL261) containing p-boronophenylalanine (BPA) as the boron compound. The 2D Monte Carlo transport code for the α and 7 Li charged particles from the 10 B(n,α) 7 Li reactions has been developed as a surrogate to a full 3D approach to calculate a variety of different microdosimetric parameters. The HRQAR method and the surrogate 2D Monte Carlo approach are described in detail and examples of their use are presented. 27 refs., 11 figs., 1 tab

Quantitative Assays for RAS Pathway Proteins and Phosphorylation States

Science.gov (United States)

The NCI CPTAC program is applying its expertise in quantitative proteomics to develop assays for RAS pathway proteins. Targets include key phosphopeptides that should increase our understanding of how the RAS pathway is regulated.

Quantitative Verification and Synthesis of Attack-Defence Scenarios

DEFF Research Database (Denmark)

Aslanyan, Zaruhi; Nielson, Flemming; Parker, David

2016-01-01

analysis of quantitative properties of complex attack-defence scenarios, using an extension of attack-defence trees which models temporal ordering of actions and allows explicit dependencies in the strategies adopted by attackers and defenders. We adopt a game-theoretic approach, translating attack...... which guarantee or optimise some quantitative property, such as the probability of a successful attack, the expected cost incurred, or some multi-objective trade-off between the two. We implement our approach, building upon the PRISM-games model checker, and apply it to a case study of an RFID goods...

Quantitative DIC microscopy using an off-axis self-interference approach.

Science.gov (United States)

Fu, Dan; Oh, Seungeun; Choi, Wonshik; Yamauchi, Toyohiko; Dorn, August; Yaqoob, Zahid; Dasari, Ramachandra R; Feld, Michael S

2010-07-15

Traditional Normarski differential interference contrast (DIC) microscopy is a very powerful method for imaging nonstained biological samples. However, one of its major limitations is the nonquantitative nature of the imaging. To overcome this problem, we developed a quantitative DIC microscopy method based on off-axis sample self-interference. The digital holography algorithm is applied to obtain quantitative phase gradients in orthogonal directions, which leads to a quantitative phase image through a spiral integration of the phase gradients. This method is practically simple to implement on any standard microscope without stringent requirements on polarization optics. Optical sectioning can be obtained through enlarged illumination NA.

Application of quantitative and qualitative methods for determination ...

African Journals Online (AJOL)

This article covers the issues of integration of qualitative and quantitative methods applied when justifying management decision-making in companies implementing lean manufacturing. The authors defined goals and subgoals and justified the evaluation criteria which lead to the increased company value if achieved.

Misconceived Relationships between Logical Positivism and Quantitative Research: An Analysis in the Framework of Ian Hacking.

Science.gov (United States)

Yu, Chong Ho

Although quantitative research methodology is widely applied by psychological researchers, there is a common misconception that quantitative research is based on logical positivism. This paper examines the relationship between quantitative research and eight major notions of logical positivism: (1) verification; (2) pro-observation; (3)…

Optimization and automation of quantitative NMR data extraction.

Science.gov (United States)

Bernstein, Michael A; Sýkora, Stan; Peng, Chen; Barba, Agustín; Cobas, Carlos

2013-06-18

NMR is routinely used to quantitate chemical species. The necessary experimental procedures to acquire quantitative data are well-known, but relatively little attention has been applied to data processing and analysis. We describe here a robust expert system that can be used to automatically choose the best signals in a sample for overall concentration determination and determine analyte concentration using all accepted methods. The algorithm is based on the complete deconvolution of the spectrum which makes it tolerant of cases where signals are very close to one another and includes robust methods for the automatic classification of NMR resonances and molecule-to-spectrum multiplets assignments. With the functionality in place and optimized, it is then a relatively simple matter to apply the same workflow to data in a fully automatic way. The procedure is desirable for both its inherent performance and applicability to NMR data acquired for very large sample sets.

Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data

Directory of Open Access Journals (Sweden)

Yachie Nozomu

2010-05-01

Full Text Available Abstract Background Phosphorylation is a ubiquitous and fundamental regulatory mechanism that controls signal transduction in living cells. The number of identified phosphoproteins and their phosphosites is rapidly increasing as a result of recent mass spectrometry-based approaches. Results We analyzed time-course phosphoproteome data obtained previously by liquid chromatography mass spectrometry with the stable isotope labeling using amino acids in cell culture (SILAC method. This provides the relative phosphorylation activities of digested peptides at each of five time points after stimulating HeLa cells with epidermal growth factor (EGF. We initially calculated the correlations between the phosphorylation dynamics patterns of every pair of peptides and connected the strongly correlated pairs to construct a network. We found that peptides extracted from the same intracellular fraction (nucleus vs. cytoplasm tended to be close together within this phosphorylation dynamics-based network. The network was then analyzed using graph theory and compared with five known signal-transduction pathways. The dynamics-based network was correlated with known signaling pathways in the NetPath and Phospho.ELM databases, and especially with the EGF receptor (EGFR signaling pathway. Although the phosphorylation patterns of many proteins were drastically changed by the EGF stimulation, our results suggest that only EGFR signaling transduction was both strongly activated and precisely controlled. Conclusions The construction of a phosphorylation dynamics-based network provides a useful overview of condition-specific intracellular signal transduction using quantitative time-course phosphoproteome data under specific experimental conditions. Detailed prediction of signal transduction based on phosphoproteome dynamics remains challenging. However, since the phosphorylation profiles of kinase-substrate pairs on the specific pathway were localized in the dynamics

Quantitative analysis by MRI on condylar motion of the temporomandibular joint in patients applied with occlusal splints

International Nuclear Information System (INIS)

Saito, Hiroki

1999-01-01

The purpose of this study was to assess the feasibility of a newly developed quantitative motion analysis method for the mandibular condyle before and after application of occlusal splints. The subjects were 50 consecutive patients with internal derangement. Stabilization type splints were applied in 23 cases (46%), anterior repositioning type in 18 cases (36%) and pivot type in 9 cases (18%). All patients underwent MR imaging with a 1.5-T MR unit with a 3-inch dual surface coil. Pseudodynamic MR study of the opening cycle was obtained using multiplanar GRASS sequence (MPGR). Incremental and decremental sagittal MR images before and after splint application were transferred to the workstation. Software originally developed by Nakasato and Katsuragawa was used to analyze the condylar motion and path. After splint application, normalized position of displaced discs was seen in 11 cases (22%), and occurred most frequently with anterior repositioning type splints. In patients with anterior repositioning type splints, improvement in the condylar motion was most significant, In patients with normalized disc position after application of occlusal splints, abnormal figure-eight-shaped'' condylar paths were corrected in 9 of 10 cases. In the case with normalized disc position after application of anterior repositioning splint, the maximum rotational angle before application of the splint is larger than that of the case without normalized disc position. Rotational function of the condyle in the inferior joint space may be associated with disc recapturing. (K.H.)

Qualitative versus quantitative methods in psychiatric research.

Science.gov (United States)

Razafsha, Mahdi; Behforuzi, Hura; Azari, Hassan; Zhang, Zhiqun; Wang, Kevin K; Kobeissy, Firas H; Gold, Mark S

2012-01-01

Qualitative studies are gaining their credibility after a period of being misinterpreted as "not being quantitative." Qualitative method is a broad umbrella term for research methodologies that describe and explain individuals' experiences, behaviors, interactions, and social contexts. In-depth interview, focus groups, and participant observation are among the qualitative methods of inquiry commonly used in psychiatry. Researchers measure the frequency of occurring events using quantitative methods; however, qualitative methods provide a broader understanding and a more thorough reasoning behind the event. Hence, it is considered to be of special importance in psychiatry. Besides hypothesis generation in earlier phases of the research, qualitative methods can be employed in questionnaire design, diagnostic criteria establishment, feasibility studies, as well as studies of attitude and beliefs. Animal models are another area that qualitative methods can be employed, especially when naturalistic observation of animal behavior is important. However, since qualitative results can be researcher's own view, they need to be statistically confirmed, quantitative methods. The tendency to combine both qualitative and quantitative methods as complementary methods has emerged over recent years. By applying both methods of research, scientists can take advantage of interpretative characteristics of qualitative methods as well as experimental dimensions of quantitative methods.

The Quantitative and Qualitative Status of Fundamental Movement ...

African Journals Online (AJOL)

South African Journal for Research in Sport, Physical Education and Recreation ... The Bruininks-Oseretsky Test of Motor Proficiency 2 (BOT-2), was used to assess six fundamental movement skills quantitatively, and the Fundamental Movement Pattern Assessment Instrument (FMPAI), was applied to analyse the same ...

NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs.

Science.gov (United States)

Morisset, Dany; Dobnik, David; Hamels, Sandrine; Zel, Jana; Gruden, Kristina

2008-10-01

We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1-25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification.

Quantitative radiography

International Nuclear Information System (INIS)

Brase, J.M.; Martz, H.E.; Waltjen, K.E.; Hurd, R.L.; Wieting, M.G.

1986-01-01

Radiographic techniques have been used in nondestructive evaluation primarily to develop qualitative information (i.e., defect detection). This project applies and extends the techniques developed in medical x-ray imaging, particularly computed tomography (CT), to develop quantitative information (both spatial dimensions and material quantities) on the three-dimensional (3D) structure of solids. Accomplishments in FY 86 include (1) improvements in experimental equipment - an improved microfocus system that will give 20-μm resolution and has potential for increased imaging speed, and (2) development of a simple new technique for displaying 3D images so as to clearly show the structure of the object. Image reconstruction and data analysis for a series of synchrotron CT experiments conducted by LLNL's Chemistry Department has begun

A quantitative phase field model for hydride precipitation in zirconium alloys: Part I. Development of quantitative free energy functional

International Nuclear Information System (INIS)

Shi, San-Qiang; Xiao, Zhihua

2015-01-01

A temperature dependent, quantitative free energy functional was developed for the modeling of hydride precipitation in zirconium alloys within a phase field scheme. The model takes into account crystallographic variants of hydrides, interfacial energy between hydride and matrix, interfacial energy between hydrides, elastoplastic hydride precipitation and interaction with externally applied stress. The model is fully quantitative in real time and real length scale, and simulation results were compared with limited experimental data available in the literature with a reasonable agreement. The work calls for experimental and/or theoretical investigations of some of the key material properties that are not yet available in the literature

Applied multivariate statistical analysis

CERN Document Server

Härdle, Wolfgang Karl

2015-01-01

Focusing on high-dimensional applications, this 4th edition presents the tools and concepts used in multivariate data analysis in a style that is also accessible for non-mathematicians and practitioners.  It surveys the basic principles and emphasizes both exploratory and inferential statistics; a new chapter on Variable Selection (Lasso, SCAD and Elastic Net) has also been added.  All chapters include practical exercises that highlight applications in different multivariate data analysis fields: in quantitative financial studies, where the joint dynamics of assets are observed; in medicine, where recorded observations of subjects in different locations form the basis for reliable diagnoses and medication; and in quantitative marketing, where consumers’ preferences are collected in order to construct models of consumer behavior.  All of these examples involve high to ultra-high dimensions and represent a number of major fields in big data analysis. The fourth edition of this book on Applied Multivariate ...

Challenge in Enhancing the Teaching and Learning of Variable Measurements in Quantitative Research

Science.gov (United States)

Kee, Chang Peng; Osman, Kamisah; Ahmad, Fauziah

2013-01-01

Statistical analysis is one component that cannot be avoided in a quantitative research. Initial observations noted that students in higher education institution faced difficulty analysing quantitative data which were attributed to the confusions of various variable measurements. This paper aims to compare the outcomes of two approaches applied in…

Quantitative EDXS analysis of organic materials using the ζ-factor method

International Nuclear Information System (INIS)

Fladischer, Stefanie; Grogger, Werner

2014-01-01

In this study we successfully applied the ζ-factor method to perform quantitative X-ray analysis of organic thin films consisting of light elements. With its ability to intrinsically correct for X-ray absorption, this method significantly improved the quality of the quantification as well as the accuracy of the results compared to conventional techniques in particular regarding the quantification of light elements. We describe in detail the process of determining sensitivity factors (ζ-factors) using a single standard specimen and the involved parameter optimization for the estimation of ζ-factors for elements not contained in the standard. The ζ-factor method was then applied to perform quantitative analysis of organic semiconducting materials frequently used in organic electronics. Finally, the results were verified and discussed concerning validity and accuracy. - Highlights: • The ζ-factor method is used for quantitative EDXS analysis of light elements. • We describe the process of determining ζ-factors from a single standard in detail. • Organic semiconducting materials are successfully quantified

Noncontact ultrasound imaging applied to cortical bone phantoms

OpenAIRE

Bulman, J. B.; Ganezer, K. S.; Halcrow, P. W.; Neeson, Ian

2012-01-01

Purpose: The purpose of this paper was to take the first steps toward applying noncontact ultrasound (NCU) to the tasks of monitoring osteoporosis and quantitative ultrasound imaging (QUS) of cortical bone. The authors also focused on the advantages of NCU, such as its lack of reliance on a technologist to apply transducers and a layer of acoustical coupling gel, the ability of the transducers to operate autonomously as specified by preprogrammed software, and the likely reduction in statisti...

Quantitative evaluation of degenerative lumbar intervertebral disc applying an equivalent cross-relaxation rate using MRI

International Nuclear Information System (INIS)

Obata, Hideaki; Inaba, Tadashi; Kato, Takaya; Tokuda, Masataka; Matsushima, Shigeru; Yamada, Michiaki; Kinosada, Yasutomi

2004-01-01

The equivalent cross-relaxation rate (ECR) is a measurement method to evaluate a change in organizational structure quantitatively utilizing MRI. The objectives of this study are to understand the characteristics related to water contents in degenerative lumbar intervertebral discs, and to investigate the usefulness of quantitative evaluation using ECR in order to find as early as possible disordered discs. Seven normal volunteers and four asymptomatic volunteers with degeneration in lumbar intervertebral discs, 21 to 26 years of age, were studied using a SIGNA model of GE Medical Systems equipped with a 1.5 T clinical scanner and spine coil. The ECR values were defined as the percentage of signal loss between unsaturated and saturated images. The results showed that the ECR value of annulus fibrosus in an intervertebral disc was higher than nucleus pulposus. Furthermore, it was found that the ECR value of nucleus pulposus (L5-S1) with degeneration was significantly higher than that without degeneration. It was considered that this result reflected an increase of water contents in the degenerative nucleus. This study suggests that the ECR value of a nucleus could be an effective parameter to diagnosis of degenerated discs or grades of disorder. (author)

Electronic imaging systems for quantitative electrophoresis of DNA

International Nuclear Information System (INIS)

Sutherland, J.C.

1989-01-01

Gel electrophoresis is one of the most powerful and widely used methods for the separation of DNA. During the last decade, instruments have been developed that accurately quantitate in digital form the distribution of materials in a gel or on a blot prepared from a gel. In this paper, I review the various physical properties that can be used to quantitate the distribution of DNA on gels or blots and the instrumentation that has been developed to perform these tasks. The emphasis here is on DNA, but much of what is said also applies to RNA, proteins and other molecules. 36 refs

Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase.

Science.gov (United States)

Guo, Xiao; Niemi, Natalie M; Coon, Joshua J; Pagliarini, David J

2017-07-14

The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue ∼50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S. cerevisiae has not been conclusively defined. Here, using comparative mitochondrial phosphoproteomics, analyses of protein-protein interactions by affinity enrichment-mass spectrometry, and in vitro biochemistry, we define Ptc6p as the primary PDC phosphatase in S. cerevisiae Our analyses further suggest additional substrates for related S. cerevisiae phosphatases and describe the overall phosphoproteomic changes that accompany mitochondrial respiratory dysfunction. In summary, our quantitative proteomics and biochemical analyses have identified Ptc6p as the primary-and likely sole- S. cerevisiae PDC phosphatase, closing a key knowledge gap about the regulation of yeast mitochondrial metabolism. Our findings highlight the power of integrative omics and biochemical analyses for annotating the functions of poorly characterized signaling proteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

Directory of Open Access Journals (Sweden)

Fleischmann Robert D

2009-06-01

Full Text Available Abstract The in vitro stationary phase proteome of the human pathogen Shigella dysenteriae serotype 1 (SD1 was quantitatively analyzed in Coomassie Blue G250 (CBB-stained 2D gels. More than four hundred and fifty proteins, of which 271 were associated with distinct gel spots, were identified. In parallel, we employed 2D-LC-MS/MS followed by the label-free computationally modified spectral counting method APEX for absolute protein expression measurements. Of the 4502 genome-predicted SD1 proteins, 1148 proteins were identified with a false positive discovery rate of 5% and quantitated using 2D-LC-MS/MS and APEX. The dynamic range of the APEX method was approximately one order of magnitude higher than that of CBB-stained spot intensity quantitation. A squared Pearson correlation analysis revealed a reasonably good correlation (R2 = 0.67 for protein quantities surveyed by both methods. The correlation was decreased for protein subsets with specific physicochemical properties, such as low Mr values and high hydropathy scores. Stoichiometric ratios of subunits of protein complexes characterized in E. coli were compared with APEX quantitative ratios of orthologous SD1 protein complexes. A high correlation was observed for subunits of soluble cellular protein complexes in several cases, demonstrating versatile applications of the APEX method in quantitative proteomics.

Stable isotope dimethyl labelling for quantitative proteomics and beyond

Science.gov (United States)

Hsu, Jue-Liang; Chen, Shu-Hui

2016-01-01

Stable-isotope reductive dimethylation, a cost-effective, simple, robust, reliable and easy-to- multiplex labelling method, is widely applied to quantitative proteomics using liquid chromatography-mass spectrometry. This review focuses on biological applications of stable-isotope dimethyl labelling for a large-scale comparative analysis of protein expression and post-translational modifications based on its unique properties of the labelling chemistry. Some other applications of the labelling method for sample preparation and mass spectrometry-based protein identification and characterization are also summarized. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644970

Quantitative Preparation in Doctoral Education Programs: A Mixed-Methods Study of Doctoral Student Perspectives on their Quantitative Training

Directory of Open Access Journals (Sweden)

Sarah L Ferguson

2017-07-01

Full Text Available Aim/Purpose: The purpose of the current study is to explore student perceptions of their own doctoral-level education and quantitative proficiency. Background: The challenges of preparing doctoral students in education have been discussed in the literature, but largely from the perspective of university faculty and program administrators. The current study directly explores the student voice on this issue. Methodology: Utilizing a sequential explanatory mixed-methods research design, the present study seeks to better understand doctoral-level education students’ perceptions of their quantitative methods training at a large public university in the southwestern United States. Findings: Results from both phases present the need for more application and consistency in doctoral-level quantitative courses. Additionally, there was a consistent theme of internal motivation in the responses, suggesting students perceive their quantitative training to be valuable beyond their personal interest in the topic. Recommendations for Practitioners: Quantitative methods instructors should emphasize practice in their quantitative courses and consider providing additional support for students through the inclusion of lab sections, tutoring, and/or differentiation. Pre-testing statistical ability at the start of a course is also suggested to better meet student needs. Impact on Society: The ultimate goal of quantitative methods in doctoral education is to produce high-quality educational researchers who are prepared to apply their knowledge to problems and research in education. Results of the present study can inform faculty and administrator decisions in doctoral education to best support this goal. Future Research: Using the student perspectives presented in the present study, future researchers should continue to explore effective instructional strategies and curriculum design within education doctoral programs. The inclusion of student voice can strengthen

Improving quantitative dosimetry in (177)Lu-DOTATATE SPECT by energy window-based scatter corrections

DEFF Research Database (Denmark)

de Nijs, Robin; Lagerburg, Vera; Klausen, Thomas L

2014-01-01

and the activity, which depends on the collimator type, the utilized energy windows and the applied scatter correction techniques. In this study, energy window subtraction-based scatter correction methods are compared experimentally and quantitatively. MATERIALS AND METHODS: (177)Lu SPECT images of a phantom...... technique, the measured ratio was close to the real ratio, and the differences between spheres were small. CONCLUSION: For quantitative (177)Lu imaging MEGP collimators are advised. Both energy peaks can be utilized when the ESSE correction technique is applied. The difference between the calculated...

The Arabidopsis thaliana Cyclic-Nucleotide-Dependent Response – a Quantitative Proteomic and Phosphoproteomic Analysis

KAUST Repository

Alqurashi, May M.

2013-01-01

monophosphate (cAMP), has been shown to be a second messenger in abiotic and biotic stress responses. However, little is known about the precise role of cAMP in plants and in the down-stream activation of kinases, and hence cAMP

Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors.

Science.gov (United States)

Kumar, Sivakumar Prasanth; Jasrai, Yogesh T; Mehta, Vijay P; Pandya, Himanshu A

2015-01-01

Quantitative pharmacophore hypothesis combines the 3D spatial arrangement of pharmacophore features with biological activities of the ligand data-set and predicts the activities of geometrically and/or pharmacophoric similar ligands. Most pharmacophore discovery programs face difficulties in conformational flexibility, molecular alignment, pharmacophore features sampling, and feature selection to score models if the data-set constitutes diverse ligands. Towards this focus, we describe a ligand-based computational procedure to introduce flexibility in aligning the small molecules and generating a pharmacophore hypothesis without geometrical constraints to define pharmacophore space, enriched with chemical features necessary to elucidate common pharmacophore hypotheses (CPHs). Maximal common substructure (MCS)-based alignment method was adopted to guide the alignment of carbon molecules, deciphered the MCS atom connectivity to cluster molecules in bins and subsequently, calculated the pharmacophore similarity matrix with the bin-specific reference molecules. After alignment, the carbon molecules were enriched with original atoms in their respective positions and conventional pharmacophore features were perceived. Distance-based pharmacophoric descriptors were enumerated by computing the interdistance between perceived features and MCS-aligned 'centroid' position. The descriptor set and biological activities were used to develop support vector machine models to predict the activities of the external test set. Finally, fitness score was estimated based on pharmacophore similarity with its bin-specific reference molecules to recognize the best and poor alignments and, also with each reference molecule to predict outliers of the quantitative hypothesis model. We applied this procedure to a diverse data-set of 40 HIV-1 integrase inhibitors and discussed its effectiveness with the reported CPH model.

Digital radiography: a quantitative approach

International Nuclear Information System (INIS)

Retraint, F.

2004-01-01

'Full-text:' In a radiograph the value of each pixel is related to the material thickness crossed by the x-rays. Using this relationship, an object can be characterized by parameters such as depth, surface and volume. Assuming a locally linear detector response and using a radiograph of reference object, the quantitative thickness map of object can be obtained by applying offset and gain corrections. However, for an acquisition system composed of cooled CCD camera optically coupled to a scintillator screen, the radiographic image formation process generates some bias which prevent from obtaining the quantitative information: non uniformity of the x-ray source, beam hardening, Compton scattering, scintillator screen, optical system response. In a first section, we propose a complete model of the radiographic image formation process taking account of these biases. In a second section, we present an inversion scheme of this model for a single material object, which enables to obtain the thickness map of the object crossed by the x-rays. (author)

Quantitative multimodality imaging in cancer research and therapy.

Science.gov (United States)

Yankeelov, Thomas E; Abramson, Richard G; Quarles, C Chad

2014-11-01

Advances in hardware and software have enabled the realization of clinically feasible, quantitative multimodality imaging of tissue pathophysiology. Earlier efforts relating to multimodality imaging of cancer have focused on the integration of anatomical and functional characteristics, such as PET-CT and single-photon emission CT (SPECT-CT), whereas more-recent advances and applications have involved the integration of multiple quantitative, functional measurements (for example, multiple PET tracers, varied MRI contrast mechanisms, and PET-MRI), thereby providing a more-comprehensive characterization of the tumour phenotype. The enormous amount of complementary quantitative data generated by such studies is beginning to offer unique insights into opportunities to optimize care for individual patients. Although important technical optimization and improved biological interpretation of multimodality imaging findings are needed, this approach can already be applied informatively in clinical trials of cancer therapeutics using existing tools. These concepts are discussed herein.

Balance between qualitative and quantitative verification methods

International Nuclear Information System (INIS)

Nidaira, Kazuo

2012-01-01

The amount of inspection effort for verification of declared nuclear material needs to be optimized in the situation where qualitative and quantitative measures are applied. Game theory was referred to investigate the relation of detection probability and deterrence of diversion. Payoffs used in the theory were quantified for cases of conventional safeguards and integrated safeguards by using AHP, Analytical Hierarchy Process. Then, it became possible to estimate detection probability under integrated safeguards which had equivalent deterrence capability for detection probability under conventional safeguards. In addition the distribution of inspection effort for qualitative and quantitative measures was estimated. Although the AHP has some ambiguities in quantifying qualitative factors, its application to optimization in safeguards is useful to reconsider the detection probabilities under integrated safeguards. (author)

Phosphoproteins in extracellular vesicles as candidate markers for breast cancer.

Science.gov (United States)

Chen, I-Hsuan; Xue, Liang; Hsu, Chuan-Chih; Paez, Juan Sebastian Paez; Pan, Li; Andaluz, Hillary; Wendt, Michael K; Iliuk, Anton B; Zhu, Jian-Kang; Tao, W Andy

2017-03-21

The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls. Several biomarkers were validated in individual patients using paralleled reaction monitoring for targeted quantitation. This study demonstrates that the development of phosphoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring.

Quantitative Social Dialectology : Explaining Linguistic Variation Geographically and Socially

NARCIS (Netherlands)

Wieling, Martijn; Nerbonne, John; Baayen, R. Harald

2011-01-01

In this study we examine linguistic variation and its dependence on both social and geographic factors. We follow dialectometry in applying a quantitative methodology and focusing on dialect distances, and social dialectology in the choice of factors we examine in building a model to predict word

Quantitative methods for analysing cumulative effects on fish migration success: a review.

Science.gov (United States)

Johnson, J E; Patterson, D A; Martins, E G; Cooke, S J; Hinch, S G

2012-07-01

It is often recognized, but seldom addressed, that a quantitative assessment of the cumulative effects, both additive and non-additive, of multiple stressors on fish survival would provide a more realistic representation of the factors that influence fish migration. This review presents a compilation of analytical methods applied to a well-studied fish migration, a more general review of quantitative multivariable methods, and a synthesis on how to apply new analytical techniques in fish migration studies. A compilation of adult migration papers from Fraser River sockeye salmon Oncorhynchus nerka revealed a limited number of multivariable methods being applied and the sub-optimal reliance on univariable methods for multivariable problems. The literature review of fisheries science, general biology and medicine identified a large number of alternative methods for dealing with cumulative effects, with a limited number of techniques being used in fish migration studies. An evaluation of the different methods revealed that certain classes of multivariable analyses will probably prove useful in future assessments of cumulative effects on fish migration. This overview and evaluation of quantitative methods gathered from the disparate fields should serve as a primer for anyone seeking to quantify cumulative effects on fish migration survival. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Valuing national effects of digital health investments: an applied method.

Science.gov (United States)

Hagens, Simon; Zelmer, Jennifer; Frazer, Cassandra; Gheorghiu, Bobby; Leaver, Chad

2015-01-01

This paper describes an approach which has been applied to value national outcomes of investments by federal, provincial and territorial governments, clinicians and healthcare organizations in digital health. Hypotheses are used to develop a model, which is revised and populated based upon the available evidence. Quantitative national estimates and qualitative findings are produced and validated through structured peer review processes. This methodology has applied in four studies since 2008.

2016 Annual Conference on Experimental and Applied Mechanics

CERN Document Server

Lamberson, Leslie; Kimberley, Jamie; Korach, Chad; Tekalur, Srinivasan; Zavattieri, Pablo; Yoshida, Sanichiro; Lamberti, Luciano; Sciammarella, Cesar; Ralph, W; Singh, Raman; Tandon, Gyaneshwar; Thakre, Piyush; Zavattieri, Pablo; Zhu, Yong; Zehnder, Alan; Zehnder, Alan; Carroll, Jay; Hazeli, Kavan; Berke, Ryan; Pataky, Garrett; Cavalli, Matthew; Beese, Alison; Xia, Shuman; Starman, La; Hay, Jennifer; Karanjgaokar, Nikhil; Quinn, Simon; Balandraud, Xavier; Cloud, Gary; Patterson, Eann; Backman, David

2017-01-01

Dynamic Behavior of Materials, Volume 1 of the Proceedings of the 2016 SEM Annual Conference& Exposition on Experimental and Applied Mechanics, the first volume of ten from the Conference, brings together contributions to this important area of research and engineering. The collection presents early findings and case studies on fundamental and applied aspects of Experimental Mechanics, including papers on: Quantitative Visualization Fracture & Fragmentation Dynamic Behavior of Low Impedance Materials Shock & Blast Dynamic Behavior of Composites Novel Testing Techniques Hybrid Experimental & Computational Methods Dynamic Behavior of Geo-materials General Material Behavior.

Comparison of semi-quantitative and quantitative dynamic contrast-enhanced MRI evaluations of vertebral marrow perfusion in a rat osteoporosis model.

Science.gov (United States)

Zhu, Jingqi; Xiong, Zuogang; Zhang, Jiulong; Qiu, Yuyou; Hua, Ting; Tang, Guangyu

2017-11-14

This study aims to investigate the technical feasibility of semi-quantitative and quantitative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in the assessment of longitudinal changes of marrow perfusion in a rat osteoporosis model, using bone mineral density (BMD) measured by micro-computed tomography (micro-CT) and histopathology as the gold standards. Fifty rats were randomly assigned to the control group (n=25) and ovariectomy (OVX) group whose bilateral ovaries were excised (n=25). Semi-quantitative and quantitative DCE-MRI, micro-CT, and histopathological examinations were performed on lumbar vertebrae at baseline and 3, 6, 9, and 12 weeks after operation. The differences between the two groups in terms of semi-quantitative DCE-MRI parameter (maximum enhancement, E max ), quantitative DCE-MRI parameters (volume transfer constant, K trans ; interstitial volume, V e ; and efflux rate constant, K ep ), micro-CT parameter (BMD), and histopathological parameter (microvessel density, MVD) were compared at each of the time points using an independent-sample t test. The differences in these parameters between baseline and other time points in each group were assessed via Bonferroni's multiple comparison test. A Pearson correlation analysis was applied to assess the relationships between DCE-MRI, micro-CT, and histopathological parameters. In the OVX group, the E max values decreased significantly compared with those of the control group at weeks 6 and 9 (p=0.003 and 0.004, respectively). The K trans values decreased significantly compared with those of the control group from week 3 (pquantitative DCE-MRI, the quantitative DCE-MRI parameter K trans is a more sensitive and accurate index for detecting early reduced perfusion in osteoporotic bone.

Analytical applications of a recycled flow nuclear magnetic resonance system: quantitative analysis of slowly relaxing nuclei

International Nuclear Information System (INIS)

Laude, D.A. Jr.; Lee, R.W.K.; Wilkins, C.L.

1985-01-01

The utility of a recycled flow system for the efficient quantitative analysis of NMR spectra is demonstrated. Requisite conditions are first established for the quantitative flow experiment and then applied to a variety of compounds. An application of the technique to determination of the average polymer chain length for a silicone polymer by quantitative flow 29 Si NMR is also presented. 10 references, 4 figures, 3 tables

Cracking anxiety in the mouse : a quantitative (epi)genetic approach

NARCIS (Netherlands)

Labots, M.

2017-01-01

The aim of this thesis was to improve existing methodologies and apply genetic strategies in order to identify (main-effect, epistatic, multiple and pleiotropic) quantitative trait loci and to decipher functional candidate genes for anxiety-related behavior and baseline blood plasma total

Morphological image processing for quantitative shape analysis of biomedical structures: effective contrast enhancement

International Nuclear Information System (INIS)

Kimori, Yoshitaka

2013-01-01

A contrast enhancement approach utilizing a new type of mathematical morphology called rotational morphological processing is introduced. The method is quantitatively evaluated and then applied to some medical images. Image processing methods significantly contribute to visualization of images captured by biomedical modalities (such as mammography, X-ray computed tomography, magnetic resonance imaging, and light and electron microscopy). Quantitative interpretation of the deluge of complicated biomedical images, however, poses many research challenges, one of which is to enhance structural features that are scarcely perceptible to the human eye. This study introduces a contrast enhancement approach based on a new type of mathematical morphology called rotational morphological processing. The proposed method is applied to medical images for the enhancement of structural features. The effectiveness of the method is evaluated quantitatively by the contrast improvement ratio (CIR). The CIR of the proposed method is 12.1, versus 4.7 and 0.1 for two conventional contrast enhancement methods, clearly indicating the high contrasting capability of the method

The Spectra Count Label-free Quantitation in Cancer Proteomics

OpenAIRE

Zhou, Weidong; Liotta, Lance A.; Petricoin, Emanuel F.

2012-01-01

Mass spectrometry is used routinely for large-scale protein identification from complex biological mixtures. Recently, relative quantitation approach on the basis of spectra count has been applied in several cancer proteomic studies. In this review, we examine the mechanism of this technique and highlight several important parameters associated with its application.

Using Local Data To Advance Quantitative Literacy

Directory of Open Access Journals (Sweden)

Stephen Sweet

2008-07-01

Full Text Available In this article we consider the application of local data as a means of advancing quantitative literacy. We illustrate the use of three different sources of local data: institutional data, Census data, and the National College Health Assessment survey. Our learning modules are applied in courses in sociology and communication, but the strategy of using local data can be integrated beyond these disciplinary boundaries. We demonstrate how these data can be used to stimulate student interests in class discussion, advance analytic skills, as well as develop capacities in written and verbal communication. We conclude by considering concerns that may influence the types of local data used and the challenges of integrating these data in a course in which quantitative analysis is not typically part of the curriculum.

Quantitative in situ magnetization reversal studies in Lorentz microscopy and electron holography

International Nuclear Information System (INIS)

Rodríguez, L.A.; Magén, C.; Snoeck, E.; Gatel, C.; Marín, L.; Serrano-Ramón, L.

2013-01-01

A generalized procedure for the in situ application of magnetic fields by means of the excitation of the objective lens for magnetic imaging experiments in Lorentz microscopy and electron holography is quantitatively described. A protocol for applying magnetic fields with arbitrary in-plane magnitude and orientation is presented, and a freeware script for Digital Micrograph ™ is provided to assist the operation of the microscope. Moreover, a method to accurately reconstruct hysteresis loops is detailed. We show that the out-of-plane component of the magnetic field cannot be always neglected when performing quantitative measurements of the local magnetization. Several examples are shown to demonstrate the accuracy and functionality of the methods. - Highlights: • Generalized procedure for application of magnetic fields with the TEM objective lens. • Arbitrary in-plane magnetic field magnitude and orientation can be applied. • Method to accurately reconstruct hysteresis loops by electron holography. • Out-of-plane field component should be considered in quantitative measurements. • Examples to illustrate the method in Lorentz microscopy and electron holography

Measurement Invariance: A Foundational Principle for Quantitative Theory Building

Science.gov (United States)

Nimon, Kim; Reio, Thomas G., Jr.

2011-01-01

This article describes why measurement invariance is a critical issue to quantitative theory building within the field of human resource development. Readers will learn what measurement invariance is and how to test for its presence using techniques that are accessible to applied researchers. Using data from a LibQUAL+[TM] study of user…

Global regulatory roles of the cAMP/PKA pathway revealed by phenotypic, transcriptomic and phosphoproteomic analyses in a null mutant of the PKA catalytic subunit in Candida albicans.

Science.gov (United States)

Cao, Chengjun; Wu, Mei; Bing, Jian; Tao, Li; Ding, Xuefen; Liu, Xiaoyun; Huang, Guanghua

2017-07-01

The conserved cAMP-dependent protein kinase (PKA) plays critical roles in the regulation of morphological transitions and virulence in the human fungal pathogen Candida albicans. It has long been thought that the PKA catalytic subunit is essential for cell viability in this fungus. Paradoxically, the single adenylyl cyclase-encoding gene, CYR1, which is required for the production of cAMP in C. albicans, is not essential for cell growth. Here, a double mutant of TPK1 and TPK2 (tpk2/tpk2 tpk1/tpk1, t2t1), which encode two isoforms of the PKA catalytic subunit was successfully generated, suggesting that this subunit is not essential for cell viability. Inactivation of the PKA catalytic subunit blocked filamentation and dramatically attenuated white-to-opaque switching, but promoted sexual mating. Comparative transcriptomic analyses demonstrated that the t2t1 and cyr1/cyr1 mutants exhibited similar global gene expression profiles. Compared with the WT strain, the general transcriptional activity and metabolism were significantly decreased in both the t2t1 and cyr1/cyr1 mutants. Using combined phosphoproteomic and bioinformatic analyses, we identified 181 potential PKA phosphorylation targets, which represent 148 unique proteins involved in a wide spectrum of biological processes. The study sheds new insights into the global regulatory features of the cAMP/PKA pathway in C. albicans. © 2017 John Wiley & Sons Ltd.

Toward methodological emancipation in applied health research.

Science.gov (United States)

Thorne, Sally

2011-04-01

In this article, I trace the historical groundings of what have become methodological conventions in the use of qualitative approaches to answer questions arising from the applied health disciplines and advocate an alternative logic more strategically grounded in the epistemological orientations of the professional health disciplines. I argue for an increasing emphasis on the modification of conventional qualitative approaches to the particular knowledge demands of the applied practice domain, challenging the merits of what may have become unwarranted attachment to theorizing. Reorienting our methodological toolkits toward the questions arising within an evidence-dominated policy agenda, I encourage my applied health disciplinary colleagues to make themselves useful to that larger project by illuminating that which quantitative research renders invisible, problematizing the assumptions on which it generates conclusions, and filling in the gaps in knowledge needed to make decisions on behalf of people and populations.

Identification and quantitation of anhydrosugars in biomass pyrolytic oils using carbon-13 NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Castola, V.; Bighelli, A. [Universite de Corse, Equipe Chimie et Biomasse, Ajaccio (France); Conti, L.; Scano, G.; Mascia, S. [Universita di Sassari, Dipartimento di Chimica, Sassari (Italy); Casanova, J. [Universite de Corse, Equipe Chimie et Biomasse, Ajaccio (France)

2000-07-01

We described a method which allowed identification and quantitation of anhydrosugars in biomass pyrolysis liquids using carbon-13 NMR spectroscopy. The quantitative procedure was checked and validated (accuracy, precision and response linearity) with pure compounds and artificial mixtures. This method was then applied to the analysis of the glucidic fraction obtained after a simple and rapid fractionation of the bio oil. (author)

Quantitative XPS analysis of high Tc superconductor surfaces

International Nuclear Information System (INIS)

Jablonski, A.; Sanada, N.; Suzuki, Y.; Fukuda, Y.; Nagoshi, M.

1993-01-01

The procedure of quantitative XPS analysis involving the relative sensitivity factors is most convenient to apply to high T c superconductor surfaces because this procedure does not require standards. However, a considerable limitation of such an approach is its relatively low accuracy. In the present work, a proposition is made to use for this purpose a modification of the relative sensitivity factor approach accounting for the matrix and the instrumental effects. The accuracy of this modification when applied to the binary metal alloys is 2% or better. A quantitative XPS analysis was made for surfaces of the compounds Bi 2 Sr 2 CuO 6 , Bi 2 Sr 2 CaCu 2 O 8 , and YBa 2 Cu 3 O Y . The surface composition determined for the polycrystalline samples corresponds reasonably well to the bulk stoichiometry. Slight deficiency of oxygen was found for the Bi-based compounds. The surface exposed on cleavage of the Bi 2 Sr 2 CaCu 2 O 8 single crystal was found to be enriched with bismuth, which indicates that the cleavage occurs along the BiO planes. This result is in agreement with the STM studies published in the literature

Quantitative phase analysis by neutron diffraction

Energy Technology Data Exchange (ETDEWEB)

Lee, Chang Hee; Song, Su Ho; Lee, Jin Ho; Shim, Hae Seop [Korea Atomic Energy Research Institute, Taejon (Korea)

1999-06-01

This study is to apply quantitative phase analysis (QPA) by neutron diffraction to the round robin samples provided by the International Union of Crystallography(IUCr). We measured neutron diffraction patterns for mixed samples which have several different weight percentages and their unique characteristic features. Neutron diffraction method has been known to be superior to its complementary methods such as X-ray or Synchrotron, but it is still accepted as highly reliable under limited conditions or samples. Neutron diffraction has strong capability especially on oxides due to its scattering cross-section of the oxygen and it can become a more strong tool for analysis on the industrial materials with this quantitative phase analysis techniques. By doing this study, we hope not only to do one of instrument performance tests on our HRPD but also to improve our ability on the analysis of neutron diffraction data by comparing our QPA results with others from any advanced reactor facilities. 14 refs., 4 figs., 6 tabs. (Author)

Assessing the impact of natural policy experiments on socioeconomic inequalities in health: how to apply commonly used quantitative analytical methods?

Directory of Open Access Journals (Sweden)

Yannan Hu

2017-04-01

Full Text Available Abstract Background The scientific evidence-base for policies to tackle health inequalities is limited. Natural policy experiments (NPE have drawn increasing attention as a means to evaluating the effects of policies on health. Several analytical methods can be used to evaluate the outcomes of NPEs in terms of average population health, but it is unclear whether they can also be used to assess the outcomes of NPEs in terms of health inequalities. The aim of this study therefore was to assess whether, and to demonstrate how, a number of commonly used analytical methods for the evaluation of NPEs can be applied to quantify the effect of policies on health inequalities. Methods We identified seven quantitative analytical methods for the evaluation of NPEs: regression adjustment, propensity score matching, difference-in-differences analysis, fixed effects analysis, instrumental variable analysis, regression discontinuity and interrupted time-series. We assessed whether these methods can be used to quantify the effect of policies on the magnitude of health inequalities either by conducting a stratified analysis or by including an interaction term, and illustrated both approaches in a fictitious numerical example. Results All seven methods can be used to quantify the equity impact of policies on absolute and relative inequalities in health by conducting an analysis stratified by socioeconomic position, and all but one (propensity score matching can be used to quantify equity impacts by inclusion of an interaction term between socioeconomic position and policy exposure. Conclusion Methods commonly used in economics and econometrics for the evaluation of NPEs can also be applied to assess the equity impact of policies, and our illustrations provide guidance on how to do this appropriately. The low external validity of results from instrumental variable analysis and regression discontinuity makes these methods less desirable for assessing policy effects

Assessing the impact of natural policy experiments on socioeconomic inequalities in health: how to apply commonly used quantitative analytical methods?

Science.gov (United States)

Hu, Yannan; van Lenthe, Frank J; Hoffmann, Rasmus; van Hedel, Karen; Mackenbach, Johan P

2017-04-20

The scientific evidence-base for policies to tackle health inequalities is limited. Natural policy experiments (NPE) have drawn increasing attention as a means to evaluating the effects of policies on health. Several analytical methods can be used to evaluate the outcomes of NPEs in terms of average population health, but it is unclear whether they can also be used to assess the outcomes of NPEs in terms of health inequalities. The aim of this study therefore was to assess whether, and to demonstrate how, a number of commonly used analytical methods for the evaluation of NPEs can be applied to quantify the effect of policies on health inequalities. We identified seven quantitative analytical methods for the evaluation of NPEs: regression adjustment, propensity score matching, difference-in-differences analysis, fixed effects analysis, instrumental variable analysis, regression discontinuity and interrupted time-series. We assessed whether these methods can be used to quantify the effect of policies on the magnitude of health inequalities either by conducting a stratified analysis or by including an interaction term, and illustrated both approaches in a fictitious numerical example. All seven methods can be used to quantify the equity impact of policies on absolute and relative inequalities in health by conducting an analysis stratified by socioeconomic position, and all but one (propensity score matching) can be used to quantify equity impacts by inclusion of an interaction term between socioeconomic position and policy exposure. Methods commonly used in economics and econometrics for the evaluation of NPEs can also be applied to assess the equity impact of policies, and our illustrations provide guidance on how to do this appropriately. The low external validity of results from instrumental variable analysis and regression discontinuity makes these methods less desirable for assessing policy effects on population-level health inequalities. Increased use of the

Quantitative kinetics of proteolytic enzymes determined by a surface concentration-based assay using peptide arrays.

Science.gov (United States)

Jung, Se-Hui; Kong, Deok-Hoon; Park, Seoung-Woo; Kim, Young-Myeong; Ha, Kwon-Soo

2012-08-21

Peptide arrays have emerged as a key technology for drug discovery, diagnosis, and cell biology. Despite the promise of these arrays, applications of peptide arrays to quantitative analysis of enzyme kinetics have been limited due to the difficulty in obtaining quantitative information of enzymatic reaction products. In this study, we developed a new approach for the quantitative kinetics analysis of proteases using fluorescence-conjugated peptide arrays, a surface concentration-based assay with solid-phase peptide standards using dry-off measurements, and compared it with an applied concentration-based assay. For fabrication of the peptide arrays, substrate peptides of cMMP-3, caspase-3, caspase-9, and calpain-1 were functionalized with TAMRA and cysteine, and were immobilized onto amine-functionalized arrays using a heterobifunctional linker, N-[γ-maleimidobutyloxy]succinimide ester. The proteolytic activities of the four enzymes were quantitatively analyzed by calculating changes induced by enzymatic reactions in the concentrations of peptides bound to array surfaces. In addition, this assay was successfully applied for calculating the Michaelis constant (K(m,surf)) for the four enzymes. Thus, this new assay has a strong potential for use in the quantitative evaluation of proteases, and for drug discovery through kinetics studies including the determination of K(m) and V(max).

Quantitative mixture fraction measurements in combustion system via laser induced breakdown spectroscopy

KAUST Repository

Mansour, Mohy S.; Imam, Hisham; Elsayed, Khaled A.; Elbaz, Ayman M.; Abbass, Wafaa

2015-01-01

Laser induced breakdown spectroscopy (LIBS) technique has been applied to quantitative mixture fraction measurements in flames. The measured spectra of different mixtures of natural gas and air are used to obtain the calibration parameters for local

The role of SANRAD facility in quantitative and morphological investigation

International Nuclear Information System (INIS)

Nshimirimana, Robert; Beer, Frikkie de; Radebe, Mabuti

2011-01-01

The SANRAD (South African Neutron Radiography) facility hosts a neutron/X-ray tomography system, which is extensively being utilized in non-destructive examination experiments where it is necessary to determine the properties (e.g. size, porosity, permeability and morphology) of samples. Those properties have a great importance in a variety of fields such as nuclear shielding, paleontology, geosciences, anatomy and reverse engineering studies. Quantitative and morphological investigations require a tomography system capable of producing tomograms with a high spatial resolution and free of artefacts where specialized imaging software is applied in the investigations. The SANRAD facility is used by the scientific and engineering communities in their qualitative, quantitative and morphological investigations. The capability of the SANRAD facility to investigate qualitatively and quantitatively the internal structure of several objects non-destructively is demonstrated with special emphasis on the precision and accuracy of the system.

Parts of the Whole: Quantitative Literacy on a Desert Island

Directory of Open Access Journals (Sweden)

Dorothy Wallace

2015-07-01

Full Text Available Some of the specific institutional problems faced by quantitative reasoning courses, programs and requirements arise from the fragile intellectual position of “quantitative reasoning” as an idea, or meme. The process of isolation and reintroduction explains both the proliferation of living species and the way in which some difficult ideas take their place in a culture. Using evolutionary explanations as metaphor and the Copernican revolution as an example of a difficult idea, we draw lessons that can be applied to the “quantitative reasoning” meme, including the function of the National Numeracy Network as an island of protected discourse favoring the growth of the QR meme. We conclude that the mission of the National Numeracy Network should focus on attributes of that island, and in particular extend the mission beyond being a network, to being an actual community.

Multimodal quantitative phase and fluorescence imaging of cell apoptosis

Science.gov (United States)

Fu, Xinye; Zuo, Chao; Yan, Hao

2017-06-01

Fluorescence microscopy, utilizing fluorescence labeling, has the capability to observe intercellular changes which transmitted and reflected light microscopy techniques cannot resolve. However, the parts without fluorescence labeling are not imaged. Hence, the processes simultaneously happen in these parts cannot be revealed. Meanwhile, fluorescence imaging is 2D imaging where information in the depth is missing. Therefore the information in labeling parts is also not complete. On the other hand, quantitative phase imaging is capable to image cells in 3D in real time through phase calculation. However, its resolution is limited by the optical diffraction and cannot observe intercellular changes below 200 nanometers. In this work, fluorescence imaging and quantitative phase imaging are combined to build a multimodal imaging system. Such system has the capability to simultaneously observe the detailed intercellular phenomenon and 3D cell morphology. In this study the proposed multimodal imaging system is used to observe the cell behavior in the cell apoptosis. The aim is to highlight the limitations of fluorescence microscopy and to point out the advantages of multimodal quantitative phase and fluorescence imaging. The proposed multimodal quantitative phase imaging could be further applied in cell related biomedical research, such as tumor.

Quantitative influence of risk factors on blood glucose level.

Science.gov (United States)

Chen, Songjing; Luo, Senlin; Pan, Limin; Zhang, Tiemei; Han, Longfei; Zhao, Haixiu

2014-01-01

The aim of this study is to quantitatively analyze the influence of risk factors on the blood glucose level, and to provide theory basis for understanding the characteristics of blood glucose change and confirming the intervention index for type 2 diabetes. The quantitative method is proposed to analyze the influence of risk factors on blood glucose using back propagation (BP) neural network. Ten risk factors are screened first. Then the cohort is divided into nine groups by gender and age. According to the minimum error principle, nine BP models are trained respectively. The quantitative values of the influence of different risk factors on the blood glucose change can be obtained by sensitivity calculation. The experiment results indicate that weight is the leading cause of blood glucose change (0.2449). The second factors are cholesterol, age and triglyceride. The total ratio of these four factors reaches to 77% of the nine screened risk factors. And the sensitivity sequences can provide judgment method for individual intervention. This method can be applied to risk factors quantitative analysis of other diseases and potentially used for clinical practitioners to identify high risk populations for type 2 diabetes as well as other disease.

Pungency Quantitation of Hot Pepper Sauces Using HPLC

Science.gov (United States)

Betts, Thomas A.

1999-02-01

A class of compounds known as capsaicinoids are responsible for the "heat" of hot peppers. To determine the pungency of a particular pepper or pepper product, one may quantify the capsaicinoids and relate those concentrations to the perceived heat. The format of the laboratory described here allows students to collectively develop an HPLC method for the quantitation of the two predominant capsaicinoids (capsaicin and dihydrocapsaicin) in hot-pepper products. Each small group of students investigated one of the following aspects of the method: detector wavelength, mobile-phase composition, extraction of capsaicinoids, calibration, and quantitation. The format of the lab forced students to communicate and cooperate to develop this method. The resulting HPLC method involves extraction with acetonitrile followed by solid-phase extraction clean-up, an isocratic 80:20 methanol-water mobile phase, a 4.6 mm by 25 cm C-18 column, and UV absorbance detection at 284 nm. The method developed by the students was then applied to the quantitation of capsaicinoids in a variety of hot pepper sauces. Editor's Note on Hazards in our April 2000 issue addresses the above.

Quantitative reliability assessment for safety critical system software

International Nuclear Information System (INIS)

Chung, Dae Won; Kwon, Soon Man

2005-01-01

An essential issue in the replacement of the old analogue I and C to computer-based digital systems in nuclear power plants is the quantitative software reliability assessment. Software reliability models have been successfully applied to many industrial applications, but have the unfortunate drawback of requiring data from which one can formulate a model. Software which is developed for safety critical applications is frequently unable to produce such data for at least two reasons. First, the software is frequently one-of-a-kind, and second, it rarely fails. Safety critical software is normally expected to pass every unit test producing precious little failure data. The basic premise of the rare events approach is that well-tested software does not fail under normal routine and input signals, which means that failures must be triggered by unusual input data and computer states. The failure data found under the reasonable testing cases and testing time for these conditions should be considered for the quantitative reliability assessment. We will present the quantitative reliability assessment methodology of safety critical software for rare failure cases in this paper

Constrained energy minimization applied to apparent reflectance and single-scattering albedo spectra: a comparison

Science.gov (United States)

Resmini, Ronald G.; Graver, William R.; Kappus, Mary E.; Anderson, Mark E.

1996-11-01

Constrained energy minimization (CEM) has been applied to the mapping of the quantitative areal distribution of the mineral alunite in an approximately 1.8 km2 area of the Cuprite mining district, Nevada. CEM is a powerful technique for rapid quantitative mineral mapping which requires only the spectrum of the mineral to be mapped. A priori knowledge of background spectral signatures is not required. Our investigation applies CEM to calibrated radiance data converted to apparent reflectance (AR) and to single scattering albedo (SSA) spectra. The radiance data were acquired by the 210 channel, 0.4 micrometers to 2.5 micrometers airborne Hyperspectral Digital Imagery Collection Experiment sensor. CEM applied to AR spectra assumes linear mixing of the spectra of the materials exposed at the surface. This assumption is likely invalid as surface materials, which are often mixtures of particulates of different substances, are more properly modeled as intimate mixtures and thus spectral mixing analyses must take account of nonlinear effects. One technique for approximating nonlinear mixing requires the conversion of AR spectra to SSA spectra. The results of CEM applied to SSA spectra are compared to those of CEM applied to AR spectra. The occurrence of alunite is similar though not identical to mineral maps produced with both the SSA and AR spectra. Alunite is slightly more widespread based on processing with the SSA spectra. Further, fractional abundances derived from the SSA spectra are, in general, higher than those derived from AR spectra. Implications for the interpretation of quantitative mineral mapping with hyperspectral remote sensing data are discussed.

A study on quantitative V and V of safety-critical software

International Nuclear Information System (INIS)

Eom, H. S.; Kang, H. G.; Chang, S. C.; Ha, J. J.; Son, H. S.

2004-03-01

Recently practical needs have required quantitative features for the software reliability for Probabilistic Safety Assessment which is one of the important methods being used in assessing the overall safety of nuclear power plant. But the conventional assessment methods of software reliability could not provide enough information for PSA of NPP, therefore current assessments of a digital system which includes safety-critical software usually exclude the software part or use arbitrary values. This paper describes a Bayesian Belief Networks based method that models the rule-based qualitative software assessment method for a practical use and can produce quantitative results for PSA. The framework was constructed by utilizing BBN that can combine the qualitative and quantitative evidence relevant to the reliability of safety-critical software and can infer a conclusion in a formal and a quantitative way. The case study was performed by applying the method for assessing the quality of software requirement specification of safety-critical software that will be embedded in reactor protection system

Corrosion of non-irradiated UAl{sub x}-Al fuel in the presence of clay pore solution. A quantitative XRD secondary phase analysis applying the DDM method

Energy Technology Data Exchange (ETDEWEB)

Neumann, Andreas [Halle-Wittenberg Univ. (Germany). Dept. of Mineralogy and Geochemistry; RWTH Aachen Univ. (Germany). Inst. of Crystallography; Klinkenberg, Martina; Curtius, Hildegard [Forschungszentrum Juelich GmbH (Germany). Inst. of Energy and Climate Research, IEK-6 Nuclear Waste Management

2017-04-01

Corrosion experiments with non-irradiated metallic UAl{sub x}-Al research reactor fuel elements were carried out in autoclaves to identify and quantify the corrosion products. Such compounds, considering the long-term safety assessment of final repositories, can interact with the released inventory and this constitutes a sink for radionuclide migration in formation waters. Therefore, the metallic fuel sample was subjected to clay pore solution to investigate its process of disintegration by analyzing the resulting products and the remnants, i.e. the secondary phases. Due to the fast corrosion rate a full sample disintegration was observed within the experimental period of 1 year at 90 C. The obtained solids were subdivided into different grain size fractions and prepared for analysis. The elemental analysis of the suspension showed that, uranium and aluminum are concentrated in the solids, whereas iron was mainly dissolved. Non-ambient X-ray diffraction (XRD) combined with the derivative difference minimization (DDM) method was applied for the qualitative and quantitative phase analysis (QPA) of the secondary phases. Gypsum and hemihydrate (bassanite), residues of non-corroded nuclear fuel, hematite, and goethite were identified. The quantitative phase analysis showed that goethite is the major crystalline phase. The amorphous content exceeded 80 wt% and hosted the uranium. All other compounds were present to a minor content. The obtained results by XRD were well supported by complementary scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS) analysis.

Quantitative Analysis of Mixtures of Monoprotic Acids Applying Modified Model-Based Rank Annihilation Factor Analysis on Variation Matrices of Spectrophotometric Acid-Base Titrations

Directory of Open Access Journals (Sweden)

Ebrahim Ghorbani-Kalhor

2015-04-01

Full Text Available In the current work, a new version of rank annihilation factor analysis was developedto circumvent the rank deficiency problem in multivariate data measurements.Simultaneous determination of dissociation constant and concentration of monoprotic acids was performed by applying model-based rank annihilation factor analysis on variation matrices of spectrophotometric acid-base titrations data. Variation matrices can be obtained by subtracting first row of data matrix from all rows of the main data matrix. This method uses variation matrices instead of multivariate spectrophotometric acid-base titrations matrices to circumvent the rank deficiency problem in the rank quantitation step. The applicability of this approach was evaluated by simulated data at first stage, then the binary mixtures of ascorbic and sorbic acids as model compounds were investigated by the proposed method. At the end, the proposed method was successfully applied for resolving the ascorbic and sorbic acid in an orange juice real sample. Therefore, unique results were achieved by applying rank annihilation factor analysis on variation matrix and using hard soft model combination advantage without any problem and difficulty in rank determination. Normal 0 false false false EN-US X-NONE AR-SA /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi; mso-bidi-language:AR-SA;}    

Applying Organizational Commitment and Human Capital Theories to Emigration Research

Science.gov (United States)

Verkhohlyad, Olga; McLean, Gary N.

2012-01-01

Purpose: This study aims to bring some additional insight into the issue of emigration by establishing a relationship between emigration and psychic return of citizens to their human capital investment in the country. Design/methodology/approach: The article adopts a quantitative research strategy. It applies organizational commitment and human…

Network analysis of cancer PSB 2014 Poster

OpenAIRE

McDermott, Jason

2014-01-01

Cancer is, in general, a complex disease; it operates on pathways and systems, not solely on the individual components of those systems (genes or proteins). We have gathered global proteomic and phosphoproteomic data from a set of tumors with existing genomic data (sequencing, methylation, miRNA and mRNA expression) associated with a range of survival phenotypes. We report on our recent progress in analyzing proteomic, phosphoproteomic, and accompanying genomic data in terms of pathways that ...

Classification of quantitative light-induced fluorescence images using convolutional neural network

NARCIS (Netherlands)

Imangaliyev, S.; van der Veen, M.H.; Volgenant, C.M.C.; Loos, B.G.; Keijser, B.J.F.; Crielaard, W.; Levin, E.; Lintas, A.; Rovetta, S.; Verschure, P.F.M.J.; Villa, A.E.P.

2017-01-01

Images are an important data source for diagnosis of oral diseases. The manual classification of images may lead to suboptimal treatment procedures due to subjective errors. In this paper an image classification algorithm based on Deep Learning framework is applied to Quantitative Light-induced

Risk assessment and food allergy: the probabilistic model applied to allergens

NARCIS (Netherlands)

Spanjersberg, M.Q.I.; Kruizinga, A.G.; Rennen, M.A.J.; Houben, G.F.

2007-01-01

In order to assess the risk of unintended exposure to food allergens, traditional deterministic risk assessment is usually applied, leading to inconsequential conclusions as 'an allergic reaction cannot be excluded'. TNO therefore developed a quantitative risk assessment model for allergens based on

High performance liquid chromatographic assay for the quantitation of total glutathione in plasma

Science.gov (United States)

Abukhalaf, Imad K.; Silvestrov, Natalia A.; Menter, Julian M.; von Deutsch, Daniel A.; Bayorh, Mohamed A.; Socci, Robin R.; Ganafa, Agaba A.

2002-01-01

A simple and widely used homocysteine HPLC procedure was applied for the HPLC identification and quantitation of glutathione in plasma. The method, which utilizes SBDF as a derivatizing agent utilizes only 50 microl of sample volume. Linear quantitative response curve was generated for glutathione over a concentration range of 0.3125-62.50 micromol/l. Linear regression analysis of the standard curve exhibited correlation coefficient of 0.999. Limit of detection (LOD) and limit of quantitation (LOQ) values were 5.0 and 15 pmol, respectively. Glutathione recovery using this method was nearly complete (above 96%). Intra-assay and inter-assay precision studies reflected a high level of reliability and reproducibility of the method. The applicability of the method for the quantitation of glutathione was demonstrated successfully using human and rat plasma samples.

Artificial intelligence methods applied for quantitative analysis of natural radioactive sources

International Nuclear Information System (INIS)

Medhat, M.E.

2012-01-01

Highlights: ► Basic description of artificial neural networks. ► Natural gamma ray sources and problem of detections. ► Application of neural network for peak detection and activity determination. - Abstract: Artificial neural network (ANN) represents one of artificial intelligence methods in the field of modeling and uncertainty in different applications. The objective of the proposed work was focused to apply ANN to identify isotopes and to predict uncertainties of their activities of some natural radioactive sources. The method was tested for analyzing gamma-ray spectra emitted from natural radionuclides in soil samples detected by a high-resolution gamma-ray spectrometry based on HPGe (high purity germanium). The principle of the suggested method is described, including, relevant input parameters definition, input data scaling and networks training. It is clear that there is satisfactory agreement between obtained and predicted results using neural network.

Quantitative site-specific phosphoproteomics of Trichoderma reesei signaling pathways upon induction of hydrolytic enzyme production

NARCIS (Netherlands)

Nguyen, E.V.; Imanishi, S.Y.; Haapaniemi, P.; Yadav, A.; Saloheimo, M.; Corthals, G.L.; Pakula, T.M.

2016-01-01

The filamentous fungus Trichoderma reesei is used for industrial production of secreted enzymes including carbohydrate active enzymes, such as cellulases and hemicellulases. The production of many of these enzymes by T. reesei is influenced by the carbon source it grows on, where the regulation

SET mediates TCE-induced liver cell apoptosis through dephosphorylation and upregulation of nucleolin.

Science.gov (United States)

Ren, Xiaohu; Huang, Xinfeng; Yang, Xifei; Liu, Yungang; Liu, Wei; Huang, Haiyan; Wu, Desheng; Zou, Fei; Liu, Jianjun

2017-06-20

Trichloroethylene (TCE) is an occupational and environmental chemical that can cause severe hepatotoxicity. While our previous studies showed that the phosphatase inhibitor SET is a key mediator of TCE-induced liver cell apoptosis, the molecular mechanisms remain elusive. Using quantitative phosphoproteomic analysis, we report here that nucleolin is a SET-regulated phosphoprotein in human liver HL-7702 cells. Functional analysis suggested that SET promoted dephosphorylation of nucleolin, decreased its binding to its transcriptional activator, c-myc, and upregulated nucleolin expression in TCE-treated cells. Importantly, TCE-induced hepatocyte apoptosis was significantly attenuated when nucleolin was downregulated with specific siRNAs. These findings indicate that TCE may induce hepatocyte apoptosis via SET-mediated dephosphorylation and overexpression of nucleolin.

Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking

DEFF Research Database (Denmark)

Francavilla, Chiara; Papetti, Moreno; Rigbolt, Kristoffer T G

2016-01-01

, we devised an integrated multilayered proteomics approach (IMPA). We analyzed dynamic changes in the receptor interactome, ubiquitinome, phosphoproteome, and late proteome in response to both ligands in human cells by quantitative MS and identified 67 proteins regulated at multiple levels. We...... identified RAB7 phosphorylation and RCP recruitment to EGFR as switches for EGF and TGF-α outputs, controlling receptor trafficking, signaling duration, proliferation, and migration. By manipulating RCP levels or phosphorylation of RAB7 in EGFR-positive cancer cells, we were able to switch a TGF......-α-mediated response to an EGF-like response or vice versa as EGFR trafficking was rerouted. We propose IMPA as an approach to uncover fine-tuned regulatory mechanisms in cell signaling....

Quantitative research versus quality assurance, quality improvement, total quality management, and continuous quality improvement.

Science.gov (United States)

Vogelsang, J

1999-04-01

The purpose of this report is to provide a review of the scientific method used in the quantitative research studies for consumers, evaluators, and applied nurse researchers. The fundamental characteristics of the problem-solving/ performance-improvement processes of quality assurance, quality improvement, total quality management, and continuous quality improvement are described. Research is compared with these processes, and is followed by a discussion about the publication of quantitative research findings.

Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples.

Science.gov (United States)

Zellner, Maria; Babeluk, Rita; Diestinger, Michael; Pirchegger, Petra; Skeledzic, Senada; Oehler, Rudolf

2008-09-01

Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.

Expressing Certainty in Discussion Sections of Qualitative and Quantitative Research Articles

Science.gov (United States)

Dobakhti, Leila

2013-01-01

This paper investigates how boosters are used by qualitative and quantitative research article writers to express certainty. Boosters are words such as "definitely," "sure," "demonstrate" which signal writers' assurance in what they say. Drawing on a corpus of 200 research articles in Applied Linguistics, this study…

Quantitative Peptidomics with Five-plex Reductive Methylation labels

Science.gov (United States)

Tashima, Alexandre K.; Fricker, Lloyd D.

2018-05-01

Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of 13C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach. [Figure not available: see fulltext.

Quantitative information in medical imaging

International Nuclear Information System (INIS)

Deconinck, F.

1985-01-01

When developing new imaging or image processing techniques, one constantly has in mind that the new technique should provide a better, or more optimal answer to medical tasks than existing techniques do 'Better' or 'more optimal' imply some kind of standard by which one can measure imaging or image processing performance. The choice of a particular imaging modality to answer a diagnostic task, such as the detection of coronary artery stenosis is also based on an implicit optimalisation of performance criteria. Performance is measured by the ability to provide information about an object (patient) to the person (referring doctor) who ordered a particular task. In medical imaging the task is generally to find quantitative information on bodily function (biochemistry, physiology) and structure (histology, anatomy). In medical imaging, a wide range of techniques is available. Each technique has it's own characteristics. The techniques discussed in this paper are: nuclear magnetic resonance, X-ray fluorescence, scintigraphy, positron emission tomography, applied potential tomography, computerized tomography, and compton tomography. This paper provides a framework for the comparison of imaging performance, based on the way the quantitative information flow is altered by the characteristics of the modality

Quantitative standard-less XRF analysis

International Nuclear Information System (INIS)

Ulitzka, S.

2002-01-01

Full text: For most analytical tasks in the mining and associated industries matrix-matched calibrations are used for the monitoring of ore grades and process control. In general, such calibrations are product specific (iron ore, bauxite, alumina, mineral sands, cement etc.) and apply to a relatively narrow concentration range but give the best precision and accuracy for those materials. A wide range of CRMs is available and for less common materials synthetic standards can be made up from 'pure' chemicals. At times, analysis of materials with varying matrices (powders, scales, fly ash, alloys, polymers, liquors, etc.) and diverse physical shapes (non-flat, metal drillings, thin layers on substrates etc.) is required that could also contain elements which are not part of a specific calibration. A qualitative analysis can provide information about the presence of certain elements and the relative intensities of element peaks in a scan can give a rough idea about their concentrations. More often however, quantitative values are required. The paper will look into the basics of quantitative standardless analysis and show results for some well-defined CRMs. Copyright (2002) Australian X-ray Analytical Association Inc

Quantitative estimation of time-variable earthquake hazard by using fuzzy set theory

Science.gov (United States)

Deyi, Feng; Ichikawa, M.

1989-11-01

In this paper, the various methods of fuzzy set theory, called fuzzy mathematics, have been applied to the quantitative estimation of the time-variable earthquake hazard. The results obtained consist of the following. (1) Quantitative estimation of the earthquake hazard on the basis of seismicity data. By using some methods of fuzzy mathematics, seismicity patterns before large earthquakes can be studied more clearly and more quantitatively, highly active periods in a given region and quiet periods of seismic activity before large earthquakes can be recognized, similarities in temporal variation of seismic activity and seismic gaps can be examined and, on the other hand, the time-variable earthquake hazard can be assessed directly on the basis of a series of statistical indices of seismicity. Two methods of fuzzy clustering analysis, the method of fuzzy similarity, and the direct method of fuzzy pattern recognition, have been studied is particular. One method of fuzzy clustering analysis is based on fuzzy netting, and another is based on the fuzzy equivalent relation. (2) Quantitative estimation of the earthquake hazard on the basis of observational data for different precursors. The direct method of fuzzy pattern recognition has been applied to research on earthquake precursors of different kinds. On the basis of the temporal and spatial characteristics of recognized precursors, earthquake hazards in different terms can be estimated. This paper mainly deals with medium-short-term precursors observed in Japan and China.

Quantitative analysis of soluble elements in environmental waters by PIXE

International Nuclear Information System (INIS)

Niizeki, T.; Kawasaki, K.; Adachi, M.; Tsuji, M.; Hattori, T.

1999-01-01

We have started PIXE research for environmental science at Van de Graaff accelerator facility in Tokyo Institute of Technology. Quantitative measurements of soluble fractions in river waters have been carried out using the preconcentrate method developed in Tohoku University. We reveal that this PIXE target preparation can be also applied to waste water samples. (author)

Joint analysis of binary and quantitative traits with data sharing and outcome-dependent sampling.

Science.gov (United States)

Zheng, Gang; Wu, Colin O; Kwak, Minjung; Jiang, Wenhua; Joo, Jungnam; Lima, Joao A C

2012-04-01

We study the analysis of a joint association between a genetic marker with both binary (case-control) and quantitative (continuous) traits, where the quantitative trait values are only available for the cases due to data sharing and outcome-dependent sampling. Data sharing becomes common in genetic association studies, and the outcome-dependent sampling is the consequence of data sharing, under which a phenotype of interest is not measured for some subgroup. The trend test (or Pearson's test) and F-test are often, respectively, used to analyze the binary and quantitative traits. Because of the outcome-dependent sampling, the usual F-test can be applied using the subgroup with the observed quantitative traits. We propose a modified F-test by also incorporating the genotype frequencies of the subgroup whose traits are not observed. Further, a combination of this modified F-test and Pearson's test is proposed by Fisher's combination of their P-values as a joint analysis. Because of the correlation of the two analyses, we propose to use a Gamma (scaled chi-squared) distribution to fit the asymptotic null distribution for the joint analysis. The proposed modified F-test and the joint analysis can also be applied to test single trait association (either binary or quantitative trait). Through simulations, we identify the situations under which the proposed tests are more powerful than the existing ones. Application to a real dataset of rheumatoid arthritis is presented. © 2012 Wiley Periodicals, Inc.

Fluorescent foci quantitation for high-throughput analysis

Directory of Open Access Journals (Sweden)

Elena Ledesma-Fernández

2015-06-01

Full Text Available A number of cellular proteins localize to discrete foci within cells, for example DNA repair proteins, microtubule organizing centers, P bodies or kinetochores. It is often possible to measure the fluorescence emission from tagged proteins within these foci as a surrogate for the concentration of that specific protein. We wished to develop tools that would allow quantitation of fluorescence foci intensities in high-throughput studies. As proof of principle we have examined the kinetochore, a large multi-subunit complex that is critical for the accurate segregation of chromosomes during cell division. Kinetochore perturbations lead to aneuploidy, which is a hallmark of cancer cells. Hence, understanding kinetochore homeostasis and regulation are important for a global understanding of cell division and genome integrity. The 16 budding yeast kinetochores colocalize within the nucleus to form a single focus. Here we have created a set of freely-available tools to allow high-throughput quantitation of kinetochore foci fluorescence. We use this ‘FociQuant’ tool to compare methods of kinetochore quantitation and we show proof of principle that FociQuant can be used to identify changes in kinetochore protein levels in a mutant that affects kinetochore function. This analysis can be applied to any protein that forms discrete foci in cells.

Limitations of quantitative CT in corticosteroid induced osteopenia

International Nuclear Information System (INIS)

Karantanas, A.H.; Kalef-Ezra, J.; Glaros, D.; Ioannina Univ.

1991-01-01

Single energy spectrum quantitative CT (SES-QCT) was applied for the assessment of the trabecular bone mineral status in patients under long-term corticosteroid treatment. Seventeen renal graft recipients (RGR) and 12 patients receiving corticosteroid treatment for collagen disease were studied. A reduction of about 40% in the spinal trabecular bone density relative to matched controls was found, associated with the corticosteroid administration. Repeated measurements showed significant reduction in density 4 months after transplantation, and an increase in density after graft rejection. Radiologic or clinical evidence of osteopenia in the spine was not found. Other noninvasive techniques, applied in the upper extremities of the RGR, showed only minor bone reduction compared to controls. The findings of the present study suggest that adipose tissue deposition in the spinal trabeculae can introduce errors in the measurements. Therefore, SES-QCT should not be applied during corticosteroid therapy. (orig.)

Preliminary research on eddy current bobbin quantitative test for heat exchange tube in nuclear power plant

Science.gov (United States)

Qi, Pan; Shao, Wenbin; Liao, Shusheng

2016-02-01

For quantitative defects detection research on heat transfer tube in nuclear power plants (NPP), two parts of work are carried out based on the crack as the main research objects. (1) Production optimization of calibration tube. Firstly, ASME, RSEM and homemade crack calibration tubes are applied to quantitatively analyze the defects depth on other designed crack test tubes, and then the judgment with quantitative results under crack calibration tube with more accuracy is given. Base on that, weight analysis of influence factors for crack depth quantitative test such as crack orientation, length, volume and so on can be undertaken, which will optimize manufacture technology of calibration tubes. (2) Quantitative optimization of crack depth. Neural network model with multi-calibration curve adopted to optimize natural crack test depth generated in in-service tubes shows preliminary ability to improve quantitative accuracy.

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

Science.gov (United States)

Trinkle-Mulcahy, Laura; Boulon, Séverine; Lam, Yun Wah; Urcia, Roby; Boisvert, François-Michel; Vandermoere, Franck; Morrice, Nick A.; Swift, Sam; Rothbauer, Ulrich; Leonhardt, Heinrich; Lamond, Angus

2008-01-01

The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments. PMID:18936248

Effects of applying three-dimensional seismic isolation system on the seismic design of FBR

International Nuclear Information System (INIS)

Hirata, Kazuta; Yabana, Shuichi; Kanazawa, Kenji; Matsuda, Akihiro

1997-01-01

In this study conceptional three-dimensional seismic isolation system for fast breeder reactor (FBR) is proposed. Effects of applying three-dimensional seismic isolation system on the seismic design for the FBR equipment are evaluated quantitatively. From the evaluation, it is concluded following effects are expected by applying the three-dimensional seismic isolation system to the FBR and the effects are evaluated quantitatively. (1) Reduction of membrane thickness of the reactor vessel (2) Suppression of uplift of fuels by reducing vertical seismic response of the core (3) Reduction of the supports for the piping system (4) Three-dimensional base isolation system for the whole reactor building is advantageous to the combined isolation system of horizontal base isolation for the reactor building and vertical isolation for the equipment. (author)

Qualitative and quantitative assessment of interior moisture buffering by enclosures

DEFF Research Database (Denmark)

Janssen, Hans; Roels, Staf

2009-01-01

The significance of interior humidity in attaining sustainable, durable, healthy and comfortable buildings is increasingly recognised. Given their significant interaction, interior humidity appraisals need a qualitative and/or quantitative assessment of interior moisture buffering. While the effe......The significance of interior humidity in attaining sustainable, durable, healthy and comfortable buildings is increasingly recognised. Given their significant interaction, interior humidity appraisals need a qualitative and/or quantitative assessment of interior moisture buffering. While...... the effective moisture penetration depth and effective capacitance models allow quantified assessment, their reliance on the ‘moisture penetration depth’ necessitates comprehensive material properties and hampers their application to multi-dimensional interior objects. On the other hand, while various recently...... an alternative basis for quantitative evaluation of interior moisture buffering by the effective moisture penetration depth and effective capacitance models. The presented methodology uses simple and fast measurements only and can also be applied to multimaterial and/or multidimensional interior elements....

An Applied Physicist Does Econometrics

Science.gov (United States)

Taff, L. G.

2010-02-01

The biggest problem those attempting to understand econometric data, via modeling, have is that economics has no F = ma. Without a theoretical underpinning, econometricians have no way to build a good model to fit observations to. Physicists do, and when F = ma failed, we knew it. Still desiring to comprehend econometric data, applied economists turn to mis-applying probability theory---especially with regard to the assumptions concerning random errors---and choosing extremely simplistic analytical formulations of inter-relationships. This introduces model bias to an unknown degree. An applied physicist, used to having to match observations to a numerical or analytical model with a firm theoretical basis, modify the model, re-perform the analysis, and then know why, and when, to delete ``outliers'', is at a considerable advantage when quantitatively analyzing econometric data. I treat two cases. One is to determine the household density distribution of total assets, annual income, age, level of education, race, and marital status. Each of these ``independent'' variables is highly correlated with every other but only current annual income and level of education follow a linear relationship. The other is to discover the functional dependence of total assets on the distribution of assets: total assets has an amazingly tight power law dependence on a quadratic function of portfolio composition. Who knew? )

Towards quantitative laser-induced breakdown spectroscopy analysis of soil samples

International Nuclear Information System (INIS)

Bousquet, B.; Sirven, J.-B.; Canioni, L.

2007-01-01

A quantitative analysis of chromium in soil samples is presented. Different emission lines related to chromium are studied in order to select the best one for quantitative features. Important matrix effects are demonstrated from one soil to the other, preventing any prediction of concentration in different soils on the basis of a univariate calibration curve. Finally, a classification of the LIBS data based on a series of Principal Component Analyses (PCA) is applied to a reduced dataset of selected spectral lines related to the major chemical elements in the soils. LIBS data of heterogeneous soils appear to be widely dispersed, which leads to a reconsideration of the sampling step in the analysis process

Quantitation: clinical applications

International Nuclear Information System (INIS)

Britton, K.E.

1982-01-01

Single photon emission tomography may be used quantitatively if its limitations are recognized and quantitation is made in relation to some reference area on the image. Relative quantitation is discussed in outline in relation to the liver, brain and pituitary, thyroid, adrenals, and heart. (U.K.)

EVALUATION OF STACHYBOTRYS CHARTARUM IN THE HOUSE OF AN INFANT WITH PULMONARY HEMORRHAGE: QUANTITATIVE ASSESSMENT BEFORE, DURING, AND AFTER REMEDIATION

Science.gov (United States)

Stachybotrys chartarum is an indoor mold that has been associated with pulmonary hemorrhage (PH) cases in the Cleveland, Ohio area. This study applied two new quantitative measurements to air samples from a home where an infant developed PH. Quantitative polymerase chain reacti...

The quantitative Morse theorem

OpenAIRE

Loi, Ta Le; Phien, Phan

2013-01-01

In this paper, we give a proof of the quantitative Morse theorem stated by {Y. Yomdin} in \\cite{Y1}. The proof is based on the quantitative Sard theorem, the quantitative inverse function theorem and the quantitative Morse lemma.

Quantitative phenotyping via deep barcode sequencing.

Science.gov (United States)

Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

2009-10-01

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

Science.gov (United States)

Bergholt, Mads Sylvest; Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

2013-12-03

We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in

Quantitative high-resolution genomic analysis of single cancer cells.

Science.gov (United States)

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

Applying a radiomics approach to predict prognosis of lung cancer patients

Science.gov (United States)

Emaminejad, Nastaran; Yan, Shiju; Wang, Yunzhi; Qian, Wei; Guan, Yubao; Zheng, Bin

2016-03-01

Radiomics is an emerging technology to decode tumor phenotype based on quantitative analysis of image features computed from radiographic images. In this study, we applied Radiomics concept to investigate the association among the CT image features of lung tumors, which are either quantitatively computed or subjectively rated by radiologists, and two genomic biomarkers namely, protein expression of the excision repair cross-complementing 1 (ERCC1) genes and a regulatory subunit of ribonucleotide reductase (RRM1), in predicting disease-free survival (DFS) of lung cancer patients after surgery. An image dataset involving 94 patients was used. Among them, 20 had cancer recurrence within 3 years, while 74 patients remained DFS. After tumor segmentation, 35 image features were computed from CT images. Using the Weka data mining software package, we selected 10 non-redundant image features. Applying a SMOTE algorithm to generate synthetic data to balance case numbers in two DFS ("yes" and "no") groups and a leave-one-case-out training/testing method, we optimized and compared a number of machine learning classifiers using (1) quantitative image (QI) features, (2) subjective rated (SR) features, and (3) genomic biomarkers (GB). Data analyses showed relatively lower correlation among the QI, SR and GB prediction results (with Pearson correlation coefficients 0.5). Among them, using QI yielded the highest performance.

A method of quantitative prediction for sandstone type uranium deposit in Russia and its application

International Nuclear Information System (INIS)

Chang Shushuai; Jiang Minzhong; Li Xiaolu

2008-01-01

The paper presents the foundational principle of quantitative predication for sandstone type uranium deposits in Russia. Some key methods such as physical-mathematical model construction and deposits prediction are described. The method has been applied to deposits prediction in Dahongshan region of Chaoshui basin. It is concluded that the technique can fortify the method of quantitative predication for sandstone type uranium deposits, and it could be used as a new technique in China. (authors)

Balancing the Quantitative and Qualitative Aspects of Social Network Analysis to Study Complex Social Systems

OpenAIRE

Schipper, Danny; Spekkink, Wouter

2015-01-01

Social Network Analysis (SNA) can be used to investigate complex social systems. SNA is typically applied as a quantitative method, which has important limitations. First, quantitative methods are capable of capturing the form of relationships (e.g. strength and frequency), but they are less suitable for capturing the content of relationships (e.g. interests and motivations). Second, while complex social systems are highly dynamic, the representations that SNA creates of such systems are ofte...

Quantitative atom probe analysis of nanostructure containing clusters and precipitates with multiple length scales

International Nuclear Information System (INIS)

Marceau, R.K.W.; Stephenson, L.T.; Hutchinson, C.R.; Ringer, S.P.

2011-01-01

A model Al-3Cu-(0.05 Sn) (wt%) alloy containing a bimodal distribution of relatively shear-resistant θ' precipitates and shearable GP zones is considered in this study. It has recently been shown that the addition of the GP zones to such microstructures can lead to significant increases in strength without a decrease in the uniform elongation. In this study, atom probe tomography (APT) has been used to quantitatively characterise the evolution of the GP zones and the solute distribution in the bimodal microstructure as a function of applied plastic strain. Recent nuclear magnetic resonance (NMR) analysis has clearly shown strain-induced dissolution of the GP zones, which is supported by the current APT data with additional spatial information. There is significant repartitioning of Cu from the GP zones into the solid solution during deformation. A new approach for cluster finding in APT data has been used to quantitatively characterise the evolution of the sizes and shapes of the Cu containing features in the solid solution solute as a function of applied strain. -- Research highlights: → A new approach for cluster finding in atom probe tomography (APT) data has been used to quantitatively characterise the evolution of the sizes and shapes of the Cu containing features with multiple length scales. → In this study, a model Al-3Cu-(0.05 Sn) (wt%) alloy containing a bimodal distribution of relatively shear-resistant θ' precipitates and shearable GP zones is considered. → APT has been used to quantitatively characterise the evolution of the GP zones and the solute distribution in the bimodal microstructure as a function of applied plastic strain. → It is clearly shown that there is strain-induced dissolution of the GP zones with significant repartitioning of Cu from the GP zones into the solid solution during deformation.

Statistical shape analysis using 3D Poisson equation--A quantitatively validated approach.

Science.gov (United States)

Gao, Yi; Bouix, Sylvain

2016-05-01

Statistical shape analysis has been an important area of research with applications in biology, anatomy, neuroscience, agriculture, paleontology, etc. Unfortunately, the proposed methods are rarely quantitatively evaluated, and as shown in recent studies, when they are evaluated, significant discrepancies exist in their outputs. In this work, we concentrate on the problem of finding the consistent location of deformation between two population of shapes. We propose a new shape analysis algorithm along with a framework to perform a quantitative evaluation of its performance. Specifically, the algorithm constructs a Signed Poisson Map (SPoM) by solving two Poisson equations on the volumetric shapes of arbitrary topology, and statistical analysis is then carried out on the SPoMs. The method is quantitatively evaluated on synthetic shapes and applied on real shape data sets in brain structures. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative Algebraic Reasoning

DEFF Research Database (Denmark)

Mardare, Radu Iulian; Panangaden, Prakash; Plotkin, Gordon

2016-01-01

We develop a quantitative analogue of equational reasoning which we call quantitative algebra. We define an equality relation indexed by rationals: a =ε b which we think of as saying that “a is approximately equal to b up to an error of ε”. We have 4 interesting examples where we have a quantitative...... equational theory whose free algebras correspond to well known structures. In each case we have finitary and continuous versions. The four cases are: Hausdorff metrics from quantitive semilattices; pWasserstein metrics (hence also the Kantorovich metric) from barycentric algebras and also from pointed...

Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions

Directory of Open Access Journals (Sweden)

Frédéric Barraquand

2014-03-01

Full Text Available Proficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists who studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75% were not satisfied with their understanding of mathematical models; 75% felt that the level of mathematics was “too low” in their ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more statistics classes. Respondents thought that 30% of classes in ecology-related degrees should be focused on quantitative disciplines, which is likely higher than for most existing programs. The main suggestion to improve quantitative training was to relate theoretical and statistical modeling to applied ecological problems. Improving quantitative training will require dedicated, quantitative classes for ecology-related degrees that contain good mathematical and statistical practice.

Quantitative fluorescence microscopy and image deconvolution.

Science.gov (United States)

Swedlow, Jason R

2013-01-01

Quantitative imaging and image deconvolution have become standard techniques for the modern cell biologist because they can form the basis of an increasing number of assays for molecular function in a cellular context. There are two major types of deconvolution approaches--deblurring and restoration algorithms. Deblurring algorithms remove blur but treat a series of optical sections as individual two-dimensional entities and therefore sometimes mishandle blurred light. Restoration algorithms determine an object that, when convolved with the point-spread function of the microscope, could produce the image data. The advantages and disadvantages of these methods are discussed in this chapter. Image deconvolution in fluorescence microscopy has usually been applied to high-resolution imaging to improve contrast and thus detect small, dim objects that might otherwise be obscured. Their proper use demands some consideration of the imaging hardware, the acquisition process, fundamental aspects of photon detection, and image processing. This can prove daunting for some cell biologists, but the power of these techniques has been proven many times in the works cited in the chapter and elsewhere. Their usage is now well defined, so they can be incorporated into the capabilities of most laboratories. A major application of fluorescence microscopy is the quantitative measurement of the localization, dynamics, and interactions of cellular factors. The introduction of green fluorescent protein and its spectral variants has led to a significant increase in the use of fluorescence microscopy as a quantitative assay system. For quantitative imaging assays, it is critical to consider the nature of the image-acquisition system and to validate its response to known standards. Any image-processing algorithms used before quantitative analysis should preserve the relative signal levels in different parts of the image. A very common image-processing algorithm, image deconvolution, is used

Quantitative risk in radiation protection standards

International Nuclear Information System (INIS)

Bond, V.P.

1978-01-01

The bases for developing quantitative assessment of exposure risks in the human being, and the several problems that accompany the assessment and introduction of the risk of exposure to high and low LET radiation into radiation protection, will be evaluated. The extension of the pioneering radiation protection philosophies to the control of other hazardous agents that cannot be eliminated from the environment will be discussed, as will the serious misunderstandings and misuse of concepts and facts that have inevitably surrounded the application to one agent alone, of the protection philosophy that must in time be applied to a broad spectrum of potentially hazardous agents. (orig.) [de

Phosphorylation site dynamics of early T-cell receptor signaling

DEFF Research Database (Denmark)

Chylek, Lily A; Akimov, Vyacheslav; Dengjel, Jörn

2014-01-01

In adaptive immune responses, T-cell receptor (TCR) signaling impacts multiple cellular processes and results in T-cell differentiation, proliferation, and cytokine production. Although individual protein-protein interactions and phosphorylation events have been studied extensively, we lack...... that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites...... a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found...

Genomic value prediction for quantitative traits under the epistatic model

Directory of Open Access Journals (Sweden)

Xu Shizhong

2011-01-01

Full Text Available Abstract Background Most quantitative traits are controlled by multiple quantitative trait loci (QTL. The contribution of each locus may be negligible but the collective contribution of all loci is usually significant. Genome selection that uses markers of the entire genome to predict the genomic values of individual plants or animals can be more efficient than selection on phenotypic values and pedigree information alone for genetic improvement. When a quantitative trait is contributed by epistatic effects, using all markers (main effects and marker pairs (epistatic effects to predict the genomic values of plants can achieve the maximum efficiency for genetic improvement. Results In this study, we created 126 recombinant inbred lines of soybean and genotyped 80 makers across the genome. We applied the genome selection technique to predict the genomic value of somatic embryo number (a quantitative trait for each line. Cross validation analysis showed that the squared correlation coefficient between the observed and predicted embryo numbers was 0.33 when only main (additive effects were used for prediction. When the interaction (epistatic effects were also included in the model, the squared correlation coefficient reached 0.78. Conclusions This study provided an excellent example for the application of genome selection to plant breeding.

Connecting qualitative observation and quantitative measurement for enhancing quantitative literacy in plant anatomy course

Science.gov (United States)

Nuraeni, E.; Rahmat, A.

2018-05-01

Forming of cognitive schemes of plant anatomy concepts is performed by processing of qualitative and quantitative data obtained from microscopic observations. To enhancing student’s quantitative literacy, strategy of plant anatomy course was modified by adding the task to analyze quantitative data produced by quantitative measurement of plant anatomy guided by material course. Participant in this study was 24 biology students and 35 biology education students. Quantitative Literacy test, complex thinking in plant anatomy test and questioner used to evaluate the course. Quantitative literacy capability data was collected by quantitative literacy test with the rubric from the Association of American Colleges and Universities, Complex thinking in plant anatomy by test according to Marzano and questioner. Quantitative literacy data are categorized according to modified Rhodes and Finley categories. The results showed that quantitative literacy of biology education students is better than biology students.

Ultrasonic and densimetric titration applied for acid-base reactions.

Science.gov (United States)

Burakowski, Andrzej; Gliński, Jacek

2014-01-01

Classical acoustic acid-base titration was monitored using sound speed and density measurements. Plots of these parameters, as well as of the adiabatic compressibility coefficient calculated from them, exhibit changes with the volume of added titrant. Compressibility changes can be explained and quantitatively predicted theoretically in terms of Pasynski theory of non-compressible hydrates combined with that of the additivity of the hydration numbers with the amount and type of ions and molecules present in solution. It also seems that this development could be applied in chemical engineering for monitoring the course of chemical processes, since the applied experimental methods can be carried out almost independently on the medium under test (harmful, aggressive, etc.).

Multicomponent quantitative spectroscopic analysis without reference substances based on ICA modelling.

Science.gov (United States)

Monakhova, Yulia B; Mushtakova, Svetlana P

2017-05-01

A fast and reliable spectroscopic method for multicomponent quantitative analysis of targeted compounds with overlapping signals in complex mixtures has been established. The innovative analytical approach is based on the preliminary chemometric extraction of qualitative and quantitative information from UV-vis and IR spectral profiles of a calibration system using independent component analysis (ICA). Using this quantitative model and ICA resolution results of spectral profiling of "unknown" model mixtures, the absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated without reference solutions. Good recoveries generally between 95% and 105% were obtained. The method can be applied to any spectroscopic data that obey the Beer-Lambert-Bouguer law. The proposed method was tested on analysis of vitamins and caffeine in energy drinks and aromatic hydrocarbons in motor fuel with 10% error. The results demonstrated that the proposed method is a promising tool for rapid simultaneous multicomponent analysis in the case of spectral overlap and the absence/inaccessibility of reference materials.

Quantitative sexing (Q-Sexing) and relative quantitative sexing (RQ ...

African Journals Online (AJOL)

samer

Key words: Polymerase chain reaction (PCR), quantitative real time polymerase chain reaction (qPCR), quantitative sexing, Siberian tiger. INTRODUCTION. Animal molecular sexing .... 43:3-12. Ellegren H (1996). First gene on the avian W chromosome (CHD) provides a tag for universal sexing of non-ratite birds. Proc.

Quantitative high-resolution genomic analysis of single cancer cells.

Directory of Open Access Journals (Sweden)

Juliane Hannemann

Full Text Available During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

Quantitative measurement of cerebral blood flow on patients with early syphilis

International Nuclear Information System (INIS)

Zhong Jijun; Wu Jinchang; Yang Yi; Tang Jun; Liu Zengli; Shi Xin

2005-01-01

To study quantitative change of cerebral blood flow (CBF) on patients with early syphilis, the authors have established a method on absolute measurement of rCBF by using SPECT with Ethyl Cysteinate Dimmer (ECD) as imaging agent, and the method was applied to measure rCBF on patients with early syphilis. The rCBF values measured by this method are highly consistent with the values measured by other classical methods such as SPECT ( 123 I-IMP) and PET( 15 O-H 2 O). The rCBF values for early syphilis patients and the normal control show some statistical differences. A routine quantitative absolute measurement of rCBF featured with simple procedures is therefore on the way of maturation. (authors)

Assessment of policy makers' individual and organizational capacity to acquire, assess, adapt and apply research evidence for maternal and child health policy making in Nigeria: a cross-sectional quantitative survey.

Science.gov (United States)

Uneke, Chigozie Jesse; Sombie, Issiaka; Keita, Namoudou; Lokossou, Virgil; Johnson, Ermel; Ongolo-Zogo, Pierre; Uro-Chukwu, Henry Chukwuemeka

2017-09-01

Throughout the world, there is increasing awareness and acknowledgement of the value of research evidence in the development of effective health policy and in quality health care practice and administration. Among the major challenges associated with the lack of uptake of research evidence into policy and practice in Nigeria is the capacity constraints of policymakers to use research evidence in policy making. To assess the capacity of maternal and child health policy makers to acquire, access, adapt and apply available research evidence. This cross-sectional quantitative survey was conducted at a national maternal, newborn and child health (MNCH) stakeholders' engagement event. An evidence to policy self-assessment questionnaire was used to assess the capacity of forty MNCH policy makers to acquire, assess, adapt and apply research evidence for policy making. Low mean ratings were observed ranging from 2.68-3.53 on a scale of 5 for knowledge about initiating/conducting research and capacity to assess authenticity, validity, reliability, relevance and applicability of research evidence and for organizational capacity for promoting and using of research for policy making. There is need to institute policy makers' capacity development programmes to improve evidence-informed policymaking.

Phase analysis in duplex stainless steel: comparison of EBSD and quantitative metallography methods

International Nuclear Information System (INIS)

Michalska, J; Chmiela, B

2014-01-01

The purpose of the research was to work out the qualitative and quantitative analysis of phases in DSS in as-received state and after thermal aging. For quantitative purposes, SEM observations, EDS analyses and electron backscattered diffraction (EBSD) methods were employed. Qualitative analysis of phases was performed by two methods: EBSD and classical quantitative metallography. A juxtaposition of different etchants for the revealing of microstructure and brief review of sample preparation methods for EBSD studies were presented. Different ways of sample preparation were tested and based on these results a detailed methodology of DSS phase analysis was developed including: surface finishing, selective etching methods and image acquisition. The advantages and disadvantages of applied methods were pointed out and compared the accuracy of the analysis phase performed by both methods

Applying quantitative metabolomics based on chemical isotope labeling LC-MS for detecting potential milk adulterant in human milk.

Science.gov (United States)

Mung, Dorothea; Li, Liang

2018-02-25

There is an increasing demand for donor human milk to feed infants for various reasons including that a mother may be unable to provide sufficient amounts of milk for their child or the milk is considered unsafe for the baby. Selling and buying human milk via the Internet has gained popularity. However, there is a risk of human milk sold containing other adulterants such as animal or plant milk. Analytical tools for rapid detection of adulterants in human milk are needed. We report a quantitative metabolomics method for detecting potential milk adulterants (soy, almond, cow, goat and infant formula milk) in human milk. It is based on the use of a high-performance chemical isotope labeling (CIL) LC-MS platform to profile the metabolome of an unknown milk sample, followed by multivariate or univariate comparison of the resultant metabolomic profile with that of human milk to determine the differences. Using dansylation LC-MS to profile the amine/phenol submetabolome, we could detect an average of 4129 ± 297 (n = 9) soy metabolites, 3080 ± 470 (n = 9) almond metabolites, 4256 ± 136 (n = 18) cow metabolites, 4318 ± 198 (n = 9) goat metabolites, 4444 ± 563 (n = 9) infant formula metabolites, and 4020 ± 375 (n = 30) human metabolites. This high level of coverage allowed us to readily differentiate the six different types of samples. From the analysis of binary mixtures of human milk containing 5, 10, 25, 50 and 75% other type of milk, we demonstrated that this method could be used to detect the presence of as low as 5% adulterant in human milk. We envisage that this method could be applied to detect contaminant or adulterant in other types of food or drinks. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative diagnosis of skeletons with demineralizing osteopathy

International Nuclear Information System (INIS)

Banzer, D.

1979-01-01

The quantitative diagnosis of bone diseases must be assessed according to the accuracy of the applied method, the expense in apparatus, personnel and financial resources and the comparability of results. Nuclide absorptiometry and in the future perhaps computed tomography represent the most accurate methods for determining the mineral content of bones. Their application is the clinics' prerogative because of the costs. Morphometry provides quantiative information, in particular in course control, and enables an objective judgement of visual pictures. It requires little expenditure and should be combined with microradioscopy. Direct comparability of the findings of different working groups is most easy in morphometry; it depends on the equipment in computerized tomography and is still hardly possible in nuclide absorptiometry. For fundamental physical reason, it will hardly be possible to produce a low-cost, fast and easy-to-handle instrument for the determination of the mineral salt concentration in bones. Instead, there is rather a trend towards more expensive equipment, e.g. CT instruments; the universal use of these instruments, however, will help to promote quantitative diagnoses. (orig.) [de

Quantitative analysis method for ship construction quality

Directory of Open Access Journals (Sweden)

FU Senzong

2017-03-01

Full Text Available The excellent performance of a ship is assured by the accurate evaluation of its construction quality. For a long time, research into the construction quality of ships has mainly focused on qualitative analysis due to a shortage of process data, which results from limited samples, varied process types and non-standardized processes. Aiming at predicting and controlling the influence of the construction process on the construction quality of ships, this article proposes a reliability quantitative analysis flow path for the ship construction process and fuzzy calculation method. Based on the process-quality factor model proposed by the Function-Oriented Quality Control (FOQC method, we combine fuzzy mathematics with the expert grading method to deduce formulations calculating the fuzzy process reliability of the ordinal connection model, series connection model and mixed connection model. The quantitative analysis method is applied in analyzing the process reliability of a ship's shaft gear box installation, which proves the applicability and effectiveness of the method. The analysis results can be a useful reference for setting key quality inspection points and optimizing key processes.

Quantitative Image Restoration in Bright Field Optical Microscopy.

Science.gov (United States)

Gutiérrez-Medina, Braulio; Sánchez Miranda, Manuel de Jesús

2017-11-07

Bright field (BF) optical microscopy is regarded as a poor method to observe unstained biological samples due to intrinsic low image contrast. We introduce quantitative image restoration in bright field (QRBF), a digital image processing method that restores out-of-focus BF images of unstained cells. Our procedure is based on deconvolution, using a point spread function modeled from theory. By comparing with reference images of bacteria observed in fluorescence, we show that QRBF faithfully recovers shape and enables quantify size of individual cells, even from a single input image. We applied QRBF in a high-throughput image cytometer to assess shape changes in Escherichia coli during hyperosmotic shock, finding size heterogeneity. We demonstrate that QRBF is also applicable to eukaryotic cells (yeast). Altogether, digital restoration emerges as a straightforward alternative to methods designed to generate contrast in BF imaging for quantitative analysis. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Quantitative analysis of water heavy by NMR spectroscopy

International Nuclear Information System (INIS)

Gomez Gil, V.

1975-01-01

Nuclear Magnetic Resonance has been applied to a wide variety of quantitative problems. A typical example has been the determination of isotopic composition. In this paper two different analytical methods for the determination of water in deuterium oxide are described. The first one, employs acetonitril as an internal standard compound and in the second one calibration curve of signal integral curve versus amount of D 2 O is constructed. Both methods give results comparable to those of mass spectrometry of IR spectroscopy. (Author) 5 refs

Quantitative analysis chemistry

International Nuclear Information System (INIS)

Ko, Wansuk; Lee, Choongyoung; Jun, Kwangsik; Hwang, Taeksung

1995-02-01

This book is about quantitative analysis chemistry. It is divided into ten chapters, which deal with the basic conception of material with the meaning of analysis chemistry and SI units, chemical equilibrium, basic preparation for quantitative analysis, introduction of volumetric analysis, acid-base titration of outline and experiment examples, chelate titration, oxidation-reduction titration with introduction, titration curve, and diazotization titration, precipitation titration, electrometric titration and quantitative analysis.

Identification of novel PAMP-triggered phosphorylation and dephosphorylation events in arabidopsis thaliana by quantitative phosphoproteomic analysis

KAUST Repository

Rayapuram, Naganand; Bonhomme, Ludovic; Bigeard, Jean; Haddadou, Kahina; Przybylski, Cé dric; Hirt, Heribert; Pflieger, Delphine

2014-01-01

Signaling cascades rely strongly on protein kinase-mediated substrate phosphorylation. Currently a major challenge in signal transduction research is to obtain high confidence substrate phosphorylation sites and assign them to specific kinases. In response to bacterial flagellin, a pathogen-associated molecular pattern (PAMP), we searched for rapidly phosphorylated proteins in Arabidopsis thaliana by combining multistage activation (MSA) and electron transfer dissociation (ETD) fragmentation modes, which generate complementary spectra and identify phosphopeptide sites with increased reliability. Of a total of 825 phosphopeptides, we identified 58 to be differentially phosphorylated. These peptides harbor kinase motifs of mitogen-activated protein kinases (MAPKs) and calcium-dependent protein kinases (CDPKs), as well as yet unknown protein kinases. Importantly, 12 of the phosphopeptides show reduced phosphorylation upon flagellin treatment. Since protein abundance levels did not change, these results indicate that flagellin induces not only various protein kinases but also protein phosphatases, even though a scenario of inhibited kinase activity may also be possible. © 2014 American Chemical Society.

Identification of novel PAMP-triggered phosphorylation and dephosphorylation events in arabidopsis thaliana by quantitative phosphoproteomic analysis

KAUST Repository

Rayapuram, Naganand

2014-04-04

Signaling cascades rely strongly on protein kinase-mediated substrate phosphorylation. Currently a major challenge in signal transduction research is to obtain high confidence substrate phosphorylation sites and assign them to specific kinases. In response to bacterial flagellin, a pathogen-associated molecular pattern (PAMP), we searched for rapidly phosphorylated proteins in Arabidopsis thaliana by combining multistage activation (MSA) and electron transfer dissociation (ETD) fragmentation modes, which generate complementary spectra and identify phosphopeptide sites with increased reliability. Of a total of 825 phosphopeptides, we identified 58 to be differentially phosphorylated. These peptides harbor kinase motifs of mitogen-activated protein kinases (MAPKs) and calcium-dependent protein kinases (CDPKs), as well as yet unknown protein kinases. Importantly, 12 of the phosphopeptides show reduced phosphorylation upon flagellin treatment. Since protein abundance levels did not change, these results indicate that flagellin induces not only various protein kinases but also protein phosphatases, even though a scenario of inhibited kinase activity may also be possible. © 2014 American Chemical Society.

Quantitative research.

Science.gov (United States)

Watson, Roger

2015-04-01

This article describes the basic tenets of quantitative research. The concepts of dependent and independent variables are addressed and the concept of measurement and its associated issues, such as error, reliability and validity, are explored. Experiments and surveys – the principal research designs in quantitative research – are described and key features explained. The importance of the double-blind randomised controlled trial is emphasised, alongside the importance of longitudinal surveys, as opposed to cross-sectional surveys. Essential features of data storage are covered, with an emphasis on safe, anonymous storage. Finally, the article explores the analysis of quantitative data, considering what may be analysed and the main uses of statistics in analysis.

Quantitative film radiography

International Nuclear Information System (INIS)

Devine, G.; Dobie, D.; Fugina, J.; Hernandez, J.; Logan, C.; Mohr, P.; Moss, R.; Schumacher, B.; Updike, E.; Weirup, D.

1991-01-01

We have developed a system of quantitative radiography in order to produce quantitative images displaying homogeneity of parts. The materials that we characterize are synthetic composites and may contain important subtle density variations not discernible by examining a raw film x-radiograph. In order to quantitatively interpret film radiographs, it is necessary to digitize, interpret, and display the images. Our integrated system of quantitative radiography displays accurate, high-resolution pseudo-color images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. This report discusses: the method; film processor monitoring and control; verifying film and processor performance; and correction of scatter effects

Modified HS-SPME for determination of quantitative relations between low-molecular oxygen compounds in various matrices.

Science.gov (United States)

Dawidowicz, Andrzej L; Szewczyk, Joanna; Dybowski, Michal P

2016-09-07

Similar quantitative relations between individual constituents of the liquid sample established by its direct injection can be obtained applying Polydimethylsiloxane (PDMS) fiber in the headspace solid phase microextraction (HS-SPME) system containing the examined sample suspended in methyl silica oil. This paper proves that the analogous system composed of sample suspension/emulsion in polyethylene glycol (PEG) and Carbowax fiber allows to get similar quantitative relations between components of the mixture as those established by its direct analysis, but only for polar constituents. It is demonstrated for essential oil (EO) components of savory, sage, mint and thyme, and of artificial liquid mixture of polar constituents. The observed differences in quantitative relations between polar constituents estimated by both applied procedures are insignificant (Fexp < Fcrit). The presented results indicates that wider applicability of the system composed of a sample suspended in the oil of the same physicochemical character as that of used SPME fiber coating strongly depends on the character of interactions between analytes-suspending liquid and analytes-fiber coating. Copyright © 2016 Elsevier B.V. All rights reserved.

The controlled incorporation of foreign elements in metal surfaces by means of quantitative ion implantation

International Nuclear Information System (INIS)

Gries, W.H.

1977-01-01

Quantitative ion implantation is a powerful new method for the doping of metal surfaces with accurately known quantities of an element or one of its isotopes. It can be applied for the preparation of standards for various uses in instrumental methods of surface and bulk analysis. This paper provides selected information on some theoretical and practical aspects of quantitative ion implantation with the object of promoting the application of the method and stimulating further purposeful research on the subject. (Auth.)

Quantitative assessment of key parameters in qualitative vulnerability methods applied in karst systems based on an integrated numerical modelling approach

Science.gov (United States)

Doummar, Joanna; Kassem, Assaad

2017-04-01

In the framework of a three-year PEER (USAID/NSF) funded project, flow in a Karst system in Lebanon (Assal) dominated by snow and semi arid conditions was simulated and successfully calibrated using an integrated numerical model (MIKE-She 2016) based on high resolution input data and detailed catchment characterization. Point source infiltration and fast flow pathways were simulated by a bypass function and a high conductive lens respectively. The approach consisted of identifying all the factors used in qualitative vulnerability methods (COP, EPIK, PI, DRASTIC, GOD) applied in karst systems and to assess their influence on recharge signals in the different hydrological karst compartments (Atmosphere, Unsaturated zone and Saturated zone) based on the integrated numerical model. These parameters are usually attributed different weights according to their estimated impact on Groundwater vulnerability. The aim of this work is to quantify the importance of each of these parameters and outline parameters that are not accounted for in standard methods, but that might play a role in the vulnerability of a system. The spatial distribution of the detailed evapotranspiration, infiltration, and recharge signals from atmosphere to unsaturated zone to saturated zone was compared and contrasted among different surface settings and under varying flow conditions (e.g., in varying slopes, land cover, precipitation intensity, and soil properties as well point source infiltration). Furthermore a sensitivity analysis of individual or coupled major parameters allows quantifying their impact on recharge and indirectly on vulnerability. The preliminary analysis yields a new methodology that accounts for most of the factors influencing vulnerability while refining the weights attributed to each one of them, based on a quantitative approach.

Water volume quantitation using nuclear magnetic resonance imaging: application to cerebrospinal fluid

International Nuclear Information System (INIS)

Lecouffe, P.; Huglo, D.; Dubois, P.; Rousseau, J.; Marchandise, X.

1990-01-01

Quantitation in proton NMR imaging is applied to cerebrospinal fluid (CSF). Total intracranial CSF volume was measured from Condon's method: CSF signal was compared with distilled water standard signal in a single sagittal thick slice. Brain signal was reduced to minimum using a 5000/360/400 sequence. Software constraints did not permit easy implementing on imager and uniformity correction was performed on a microcomputer. Accuracy was better than 4%. Total intracranial CSF was found between 91 and 164 ml in 5 healthy volunteers. Extraventricular CSF quantitation appears very improved by this method, but planimetric methods seem better in order to quantify ventricular CSF. This technique is compared to total lung water measurement from proton density according to Mac Lennan's method. Water volume quantitation confirms ability of NMR imaging to quantify biologic parameters but image defects have to be known by strict quality control [fr

A quantitative method for evaluating alternatives. [aid to decision making

Science.gov (United States)

Forthofer, M. J.

1981-01-01

When faced with choosing between alternatives, people tend to use a number of criteria (often subjective, rather than objective) to decide which is the best alternative for them given their unique situation. The subjectivity inherent in the decision-making process can be reduced by the definition and use of a quantitative method for evaluating alternatives. This type of method can help decision makers achieve degree of uniformity and completeness in the evaluation process, as well as an increased sensitivity to the factors involved. Additional side-effects are better documentation and visibility of the rationale behind the resulting decisions. General guidelines for defining a quantitative method are presented and a particular method (called 'hierarchical weighted average') is defined and applied to the evaluation of design alternatives for a hypothetical computer system capability.

A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

Energy Technology Data Exchange (ETDEWEB)

Beasley, D.G., E-mail: dgbeasley@ctn.ist.utl.pt [IST/C2TN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Alves, L.C. [IST/C2TN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Le Trequesser, Q. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB, UPR9048) CNRS, Université de Bordeaux, 87 avenue du Dr. A. Schweitzer, Pessac F-33608 (France); Marques, A.C. [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Seznec, H. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Silva, R.C. da [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal)

2014-07-15

The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans – a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

Real time quantitative phase microscopy based on single-shot transport of intensity equation (ssTIE) method

Science.gov (United States)

Yu, Wei; Tian, Xiaolin; He, Xiaoliang; Song, Xiaojun; Xue, Liang; Liu, Cheng; Wang, Shouyu

2016-08-01

Microscopy based on transport of intensity equation provides quantitative phase distributions which opens another perspective for cellular observations. However, it requires multi-focal image capturing while mechanical and electrical scanning limits its real time capacity in sample detections. Here, in order to break through this restriction, real time quantitative phase microscopy based on single-shot transport of the intensity equation method is proposed. A programmed phase mask is designed to realize simultaneous multi-focal image recording without any scanning; thus, phase distributions can be quantitatively retrieved in real time. It is believed the proposed method can be potentially applied in various biological and medical applications, especially for live cell imaging.

Leaving Quietly? A Quantitative Study of Retirement Rituals and How They Affect Life Satisfaction

NARCIS (Netherlands)

van den Bogaard, L.

2017-01-01

This study quantitatively explores the understudied topic of retirement rituals, what factors influence them, and how the experience of such rites of passage may affect postretirement satisfaction with life (SWL). Various regression techniques are applied to 2 waves of Dutch panel data gathered

Decay of Correlations, Quantitative Recurrence and Logarithm Law for Contracting Lorenz Attractors

Science.gov (United States)

Galatolo, Stefano; Nisoli, Isaia; Pacifico, Maria Jose

2018-03-01

In this paper we prove that a class of skew products maps with non uniformly hyperbolic base has exponential decay of correlations. We apply this to obtain a logarithm law for the hitting time associated to a contracting Lorenz attractor at all the points having a well defined local dimension, and a quantitative recurrence estimation.

Qualitative and quantitative combined nonlinear dynamics model and its application in analysis of price, supply–demand ratio and selling rate

International Nuclear Information System (INIS)

Zhu, Dingju

2016-01-01

The qualitative and quantitative combined nonlinear dynamics model proposed in this paper fill the gap in nonlinear dynamics model in terms of qualitative and quantitative combined methods, allowing the qualitative model and quantitative model to perfectly combine and overcome their weaknesses by learning from each other. These two types of models use their strengths to make up for the other’s deficiencies. The qualitative and quantitative combined models can surmount the weakness that the qualitative model cannot be applied and verified in a quantitative manner, and the high costs and long time of multiple construction as well as verification of the quantitative model. The combined model is more practical and efficient, which is of great significance for nonlinear dynamics. The qualitative and quantitative combined modeling and model analytical method raised in this paper is not only applied to nonlinear dynamics, but can be adopted and drawn on in the modeling and model analysis of other fields. Additionally, the analytical method of qualitative and quantitative combined nonlinear dynamics model proposed in this paper can satisfactorily resolve the problems with the price system’s existing nonlinear dynamics model analytical method. The three-dimensional dynamics model of price, supply–demand ratio and selling rate established in this paper make estimates about the best commodity prices using the model results, thereby providing a theoretical basis for the government’s macro-control of price. Meanwhile, this model also offer theoretical guidance to how to enhance people’s purchasing power and consumption levels through price regulation and hence to improve people’s living standards.

Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis.

Science.gov (United States)

Liu, Shichang; Yu, Fengchao; Yang, Zhu; Wang, Tingliang; Xiong, Hairong; Chang, Caren; Yu, Weichuan; Li, Ning

2018-05-01

Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we applied both C sCl d ensity g radient (CDG) centrifugation-based protein fractionation and a dimethyl-labeling-based 4C quantitative PTM proteomics workflow in the study of dynamic acetylproteomic changes in Arabidopsis. This workflow integrates the dimethyl c hemical labeling with c hromatography-based acetylpeptide separation and enrichment followed by mass spectrometry (MS) analysis, the extracted ion chromatogram (XIC) quantitation-based c omputational analysis of mass spectrometry data to measure dynamic changes of acetylpeptide level using an in-house software program, named S table isotope-based Qua ntitation- D imethyl labeling (SQUA-D), and finally the c onfirmation of ethylene hormone-regulated acetylation using immunoblot analysis. Eventually, using this proteomic approach, 7456 unambiguous acetylation sites were found from 2638 different acetylproteins, and 5250 acetylation sites, including 5233 sites on lysine side chain and 17 sites on protein N termini, were identified repetitively. Out of these repetitively discovered acetylation sites, 4228 sites on lysine side chain ( i.e. 80.5%) are novel. These acetylproteins are exemplified by the histone superfamily, ribosomal and heat shock proteins, and proteins related to stress/stimulus responses and energy metabolism. The novel acetylproteins enriched by the CDG centrifugation fractionation contain many cellular trafficking proteins, membrane-bound receptors, and receptor-like kinases, which are mostly involved in brassinosteroid, light, gravity, and development signaling. In addition, we identified 12 highly conserved acetylation site motifs within histones, P-glycoproteins, actin depolymerizing factors, ATPases, transcription factors, and receptor-like kinases. Using SQUA-D software, we have quantified 33 ethylene hormone-enhanced and

New possibilities for quantitative measurements of regional cerebral blood flow with gold-195m

International Nuclear Information System (INIS)

Lindner, P.; Nickel, O.

1985-01-01

A previously reported theory for quantitative cerebral blood flow measurement for nondiffusible radiotracers has been applied to patients after stroke and to volunteers undergoing a mental stimulation exercise. The energy spectrum of gold-195m shows two strong photon peaks, one at an energy level of 68 keV and a second at an energy-level of 262 keV. The low energy peak is suitable for perfusion studies in lateral views of the hemispheres; no look-through effect is seen. The high energy level is good for studies in posterior-anterior positions. Parametric images for quantitative regional cerebral blood flow can be generated. The area of occluded vessels in the case of stroke can be detected. Quantitative activation patterns of cerebral blood flow during mental stimulation can be generated. The results prove that, not only with freely diffusible indicators like xenon but also with nondiffusible indicators, it is possible to measure quantitatively cerebral blood flow patterns

Quantitatively characterizing the microstructural features of breast ductal carcinoma tissues in different progression stages by Mueller matrix microscope.

Science.gov (United States)

Dong, Yang; Qi, Ji; He, Honghui; He, Chao; Liu, Shaoxiong; Wu, Jian; Elson, Daniel S; Ma, Hui

2017-08-01

Polarization imaging has been recognized as a potentially powerful technique for probing the microstructural information and optical properties of complex biological specimens. Recently, we have reported a Mueller matrix microscope by adding the polarization state generator and analyzer (PSG and PSA) to a commercial transmission-light microscope, and applied it to differentiate human liver and cervical cancerous tissues with fibrosis. In this paper, we apply the Mueller matrix microscope for quantitative detection of human breast ductal carcinoma samples at different stages. The Mueller matrix polar decomposition and transformation parameters of the breast ductal tissues in different regions and at different stages are calculated and analyzed. For more quantitative comparisons, several widely-used image texture feature parameters are also calculated to characterize the difference in the polarimetric images. The experimental results indicate that the Mueller matrix microscope and the polarization parameters can facilitate the quantitative detection of breast ductal carcinoma tissues at different stages.

Single particle transfer for quantitative analysis with total-reflection X-ray fluorescence spectrometry

International Nuclear Information System (INIS)

Esaka, Fumitaka; Esaka, Konomi T.; Magara, Masaaki; Sakurai, Satoshi; Usuda, Shigekazu; Watanabe, Kazuo

2006-01-01

The technique of single particle transfer was applied to quantitative analysis with total-reflection X-ray fluorescence (TXRF) spectrometry. The technique was evaluated by performing quantitative analysis of individual Cu particles with diameters between 3.9 and 13.2 μm. The direct quantitative analysis of the Cu particle transferred onto a Si carrier gave a discrepancy between measured and calculated Cu amounts due to the absorption effects of incident and fluorescent X-rays within the particle. By the correction for the absorption effects, the Cu amounts in individual particles could be determined with the deviation within 10.5%. When the Cu particles were dissolved with HNO 3 solution prior to the TXRF analysis, the deviation was improved to be within 3.8%. In this case, no correction for the absorption effects was needed for quantification

A study on framework for assessing limiting condition for operation(LCOs) quantitatively in a CANDU reactor

International Nuclear Information System (INIS)

Kang, Kyung Min

2003-02-01

Limiting conditions for operations define the allowed outage times and the actions to be taken if the repair cannot be completed within the AOT. Typically the actions required are plant shutdown. In situations where the risk associated with the action, i.e., the risk of plant shutdown given a failure in the safety system, may be substantial, a strategy is needed to control the risk implications. In this study the strategy is evaluated quantitatively using a tool of system dynamics. The strategic actions associated with LCO needs to be assessed dynamically. System dynamics technique is easy enough to be applied for quantitative assessment of LCO, where the system dynamics is an important factor in evaluating operational modes of nuclear power plants. The review on the improvements of overly conservative technical specification has been performed in this study. The VENSIM tool has been applied to evaluate quantitatively the LCO of the auxiliary feed water systems in the Wol-Sung nuclear power plant. A value of core damage frequency in PSA is used as risk measure. The analysis of both full power operation and shutdown operation has been compared for the value of the CDF. This study shows a plot of LCO full power operating and shutdown risks in term of core damage probability for failure of AFWS (auxiliary feedwater system). Obtaining a lower risk level in a stable mode, compared to the LCO operation alternative, is the principal motivation of going to full power operational mode or shutdown operational mode. A time dependent framework developed in this study has been applied to assess the LCO of the example problem and it is shown that it is very flexible in that it can be applied to assess LCO quantitatively under any operational context of the technical specifications. This study contributes risk informed regulation to enhance and optimize the LCO of previous technical specifications for CANDU through developing framework in application proposed in this methodology

Susceptibility-Weighted Imaging and Quantitative Susceptibility Mapping in the Brain

Science.gov (United States)

Liu, Chunlei; Li, Wei; Tong, Karen A.; Yeom, Kristen W.; Kuzminski, Samuel

2015-01-01

Susceptibility-weighted imaging (SWI) is a magnetic resonance imaging (MRI) technique that enhances image contrast by using the susceptibility differences between tissues. It is created by combining both magnitude and phase in the gradient echo data. SWI is sensitive to both paramagnetic and diamagnetic substances which generate different phase shift in MRI data. SWI images can be displayed as a minimum intensity projection that provides high resolution delineation of the cerebral venous architecture, a feature that is not available in other MRI techniques. As such, SWI has been widely applied to diagnose various venous abnormalities. SWI is especially sensitive to deoxygenated blood and intracranial mineral deposition and, for that reason, has been applied to image various pathologies including intracranial hemorrhage, traumatic brain injury, stroke, neoplasm, and multiple sclerosis. SWI, however, does not provide quantitative measures of magnetic susceptibility. This limitation is currently being addressed with the development of quantitative susceptibility mapping (QSM) and susceptibility tensor imaging (STI). While QSM treats susceptibility as isotropic, STI treats susceptibility as generally anisotropic characterized by a tensor quantity. This article reviews the basic principles of SWI, its clinical and research applications, the mechanisms governing brain susceptibility properties, and its practical implementation, with a focus on brain imaging. PMID:25270052

Susceptibility-weighted imaging and quantitative susceptibility mapping in the brain.

Science.gov (United States)

Liu, Chunlei; Li, Wei; Tong, Karen A; Yeom, Kristen W; Kuzminski, Samuel

2015-07-01

Susceptibility-weighted imaging (SWI) is a magnetic resonance imaging (MRI) technique that enhances image contrast by using the susceptibility differences between tissues. It is created by combining both magnitude and phase in the gradient echo data. SWI is sensitive to both paramagnetic and diamagnetic substances which generate different phase shift in MRI data. SWI images can be displayed as a minimum intensity projection that provides high resolution delineation of the cerebral venous architecture, a feature that is not available in other MRI techniques. As such, SWI has been widely applied to diagnose various venous abnormalities. SWI is especially sensitive to deoxygenated blood and intracranial mineral deposition and, for that reason, has been applied to image various pathologies including intracranial hemorrhage, traumatic brain injury, stroke, neoplasm, and multiple sclerosis. SWI, however, does not provide quantitative measures of magnetic susceptibility. This limitation is currently being addressed with the development of quantitative susceptibility mapping (QSM) and susceptibility tensor imaging (STI). While QSM treats susceptibility as isotropic, STI treats susceptibility as generally anisotropic characterized by a tensor quantity. This article reviews the basic principles of SWI, its clinical and research applications, the mechanisms governing brain susceptibility properties, and its practical implementation, with a focus on brain imaging. © 2014 Wiley Periodicals, Inc.

A quantitative assessment method for the NPP operators' diagnosis of accidents

International Nuclear Information System (INIS)

Kim, M. C.; Seong, P. H.

2003-01-01

In this research, we developed a quantitative model for the operators' diagnosis of the accident situation when an accident occurs in a nuclear power plant. After identifying the occurrence probabilities of accidents, the unavailabilities of various information sources, and the causal relationship between accidents and information sources, Bayesian network is used for the analysis of the change in the occurrence probabilities of accidents as the operators receive the information related to the status of the plant. The developed method is applied to a simple example case and it turned out that the developed method is a systematic quantitative analysis method which can cope with complex relationship between the accidents and information sources and various variables such accident occurrence probabilities and unavailabilities of various information sources

Automated Quantitative Rare Earth Elements Mineralogy by Scanning Electron Microscopy

Science.gov (United States)

Sindern, Sven; Meyer, F. Michael

2016-09-01

Increasing industrial demand of rare earth elements (REEs) stems from the central role they play for advanced technologies and the accelerating move away from carbon-based fuels. However, REE production is often hampered by the chemical, mineralogical as well as textural complexity of the ores with a need for better understanding of their salient properties. This is not only essential for in-depth genetic interpretations but also for a robust assessment of ore quality and economic viability. The design of energy and cost-efficient processing of REE ores depends heavily on information about REE element deportment that can be made available employing automated quantitative process mineralogy. Quantitative mineralogy assigns numeric values to compositional and textural properties of mineral matter. Scanning electron microscopy (SEM) combined with a suitable software package for acquisition of backscatter electron and X-ray signals, phase assignment and image analysis is one of the most efficient tools for quantitative mineralogy. The four different SEM-based automated quantitative mineralogy systems, i.e. FEI QEMSCAN and MLA, Tescan TIMA and Zeiss Mineralogic Mining, which are commercially available, are briefly characterized. Using examples of quantitative REE mineralogy, this chapter illustrates capabilities and limitations of automated SEM-based systems. Chemical variability of REE minerals and analytical uncertainty can reduce performance of phase assignment. This is shown for the REE phases parisite and synchysite. In another example from a monazite REE deposit, the quantitative mineralogical parameters surface roughness and mineral association derived from image analysis are applied for automated discrimination of apatite formed in a breakdown reaction of monazite and apatite formed by metamorphism prior to monazite breakdown. SEM-based automated mineralogy fulfils all requirements for characterization of complex unconventional REE ores that will become

Matrix effect and correction by standard addition in quantitative liquid chromatographic-mass spectrometric analysis of diarrhetic shellfish poisoning toxins.

Science.gov (United States)

Ito, Shinya; Tsukada, Katsuo

2002-01-11

An evaluation of the feasibility of liquid chromatography-mass spectrometry (LC-MS) with atmospheric pressure ionization was made for quantitation of four diarrhetic shellfish poisoning toxins, okadaic acid, dinophysistoxin-1, pectenotoxin-6 and yessotoxin in scallops. When LC-MS was applied to the analysis of scallop extracts, large signal suppressions were observed due to coeluting substances from the column. To compensate for these matrix signal suppressions, the standard addition method was applied. First, the sample was analyzed and then the sample involving the addition of calibration standards is analyzed. Although this method requires two LC-MS runs per analysis, effective correction of quantitative errors was found.

Quantitative studies with the gamma-camera: correction for spatial and energy distortion

International Nuclear Information System (INIS)

Soussaline, F.; Todd-Pokropek, A.E.; Raynaud, C.

1977-01-01

The gamma camera sensitivity distribution is an important source of error in quantitative studies. In addition, spatial distortion produces apparent variations in count density which degrades quantitative studies. The flood field image takes into account both effects and is influenced by the pile-up of the tail distribution. It is essential to measure separately each of these parameters. These were investigated using a point source displaced by a special scanning table with two X, Y stepping motors of 10 micron precision. The spatial distribution of the sensitivity, spatial distortion and photopeak in the field of view were measured and compared for different setting-up of the camera and PM gains. For well-tuned cameras, the sensitivity is fairly constant, while the variations appearing in the flood field image are primarily due to spatial distortion, the former more dependent than the latter on the energy window setting. This indicates why conventional flood field uniformity correction must not be applied. A correction technique to improve the results in quantitative studies has been tested using a continuously matched energy window at every point within the field. A method for correcting spatial distortion is also proposed, where, after an adequately sampled measurement of this error, a transformation can be applied to calculate the true position of events. The knowledge of the magnitude of these parameters is essential in the routine use and design of detector systems

Rigour in quantitative research.

Science.gov (United States)

Claydon, Leica Sarah

2015-07-22

This article which forms part of the research series addresses scientific rigour in quantitative research. It explores the basis and use of quantitative research and the nature of scientific rigour. It examines how the reader may determine whether quantitative research results are accurate, the questions that should be asked to determine accuracy and the checklists that may be used in this process. Quantitative research has advantages in nursing, since it can provide numerical data to help answer questions encountered in everyday practice.

A Monte Carlo error simulation applied to calibration-free X-ray diffraction phase analysis

International Nuclear Information System (INIS)

Braun, G.E.

1986-01-01

Quantitative phase analysis of a system of n phases can be effected without the need for calibration standards provided at least n different mixtures of these phases are available. A series of linear equations relating diffracted X-ray intensities, weight fractions and quantitation factors coupled with mass balance relationships can be solved for the unknown weight fractions and factors. Uncertainties associated with the measured X-ray intensities, owing to counting of random X-ray quanta, are used to estimate the errors in the calculated parameters utilizing a Monte Carlo simulation. The Monte Carlo approach can be generalized and applied to any quantitative X-ray diffraction phase analysis method. Two examples utilizing mixtures of CaCO 3 , Fe 2 O 3 and CaF 2 with an α-SiO 2 (quartz) internal standard illustrate the quantitative method and corresponding error analysis. One example is well conditioned; the other is poorly conditioned and, therefore, very sensitive to errors in the measured intensities. (orig.)

Self-Normalized Photoacoustic Technique for the Quantitative Analysis of Paper Pigments

Science.gov (United States)

Balderas-López, J. A.; Gómez y Gómez, Y. M.; Bautista-Ramírez, M. E.; Pescador-Rojas, J. A.; Martínez-Pérez, L.; Lomelí-Mejía, P. A.

2018-03-01

A self-normalized photoacoustic technique was applied for quantitative analysis of pigments embedded in solids. Paper samples (filter paper, Whatman No. 1), attached with the pigment: Direct Fast Turquoise Blue GL, were used for this study. This pigment is a blue dye commonly used in industry to dye paper and other fabrics. The optical absorption coefficient, at a wavelength of 660 nm, was measured for this pigment at various concentrations in the paper substrate. It was shown that Beer-Lambert model for light absorption applies well for pigments in solid substrates and optical absorption coefficients as large as 220 cm^{-1} can be measured with this photoacoustic technique.

Applied photometry, radiometry, and measurements of optical losses

CERN Document Server

Bukshtab, Michael

2012-01-01

Applied Photometry, Radiometry, and Measurements of Optical Losses reviews and analyzes physical concepts of radiation transfer, providing quantitative foundation for the means of measurements of optical losses, which affect propagation and distribution of light waves in various media and in diverse optical systems and components. The comprehensive analysis of advanced methodologies for low-loss detection is outlined in comparison with the classic photometric and radiometric observations, having a broad range of techniques examined and summarized: from interferometric and calorimetric, resonator and polarization, phase-shift and ring-down decay, wavelength and frequency modulation to pulse separation and resonant, acousto-optic and emissive - subsequently compared to direct and balancing methods for studying free-space and polarization optics, fibers and waveguides. The material is focused on applying optical methods and procedures for evaluation of transparent, reflecting, scattering, absorbing, and aggregat...

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.

Science.gov (United States)

Chaudhuri, Rima; Sadrieh, Arash; Hoffman, Nolan J; Parker, Benjamin L; Humphrey, Sean J; Stöckli, Jacqueline; Hill, Adam P; James, David E; Yang, Jean Yee Hwa

2015-08-19

Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community. Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites

A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.

Science.gov (United States)

Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li

2013-01-21

A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments.

A Study of Cognitive Load for Enhancing Student’s Quantitative Literacy in Inquiry Lab Learning

Science.gov (United States)

Nuraeni, E.; Rahman, T.; Alifiani, D. P.; Khoerunnisa, R. S.

2017-09-01

Students often find it difficult to appreciate the relevance of the role of quantitative analysis and concept attainment in the science class. This study measured student cognitive load during the inquiry lab of the respiratory system to improve quantitative literacy. Participants in this study were 40 11th graders from senior high school in Indonesia. After students learned, their feelings about the degree of mental effort that it took to complete the learning tasks were measured by 28 self-report on a 4-point Likert scale. The Task Complexity Worksheet were used to asses processing quantitative information and paper based test were applied to assess participants’ concept achievements. The results showed that inquiry instructional induced a relatively low mental effort, high processing information and high concept achievments.

A quantitative approach to evolution of music and philosophy

International Nuclear Information System (INIS)

Vieira, Vilson; Fabbri, Renato; Travieso, Gonzalo; Oliveira Jr, Osvaldo N; Costa, Luciano da Fontoura

2012-01-01

The development of new statistical and computational methods is increasingly making it possible to bridge the gap between hard sciences and humanities. In this study, we propose an approach based on a quantitative evaluation of attributes of objects in fields of humanities, from which concepts such as dialectics and opposition are formally defined mathematically. As case studies, we analyzed the temporal evolution of classical music and philosophy by obtaining data for 8 features characterizing the corresponding fields for 7 well-known composers and philosophers, which were treated with multivariate statistics and pattern recognition methods. A bootstrap method was applied to avoid statistical bias caused by the small sample data set, with which hundreds of artificial composers and philosophers were generated, influenced by the 7 names originally chosen. Upon defining indices for opposition, skewness and counter-dialectics, we confirmed the intuitive analysis of historians in that classical music evolved according to a master–apprentice tradition, while in philosophy changes were driven by opposition. Though these case studies were meant only to show the possibility of treating phenomena in humanities quantitatively, including a quantitative measure of concepts such as dialectics and opposition, the results are encouraging for further application of the approach presented here to many other areas, since it is entirely generic. (paper)

Critical Quantitative Inquiry in Context

Science.gov (United States)

Stage, Frances K.; Wells, Ryan S.

2014-01-01

This chapter briefly traces the development of the concept of critical quantitative inquiry, provides an expanded conceptualization of the tasks of critical quantitative research, offers theoretical explanation and justification for critical research using quantitative methods, and previews the work of quantitative criticalists presented in this…

Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

Directory of Open Access Journals (Sweden)

Jaeyong Yee

2015-01-01

Full Text Available A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait.

Marker-assisted selection for improving quantitative traits of forage crops

International Nuclear Information System (INIS)

Dolstra, O.; Denneboom, C.; Vos, Ab L.F. de; Loo, E.N. van

2007-01-01

This chapter provides an example of using marker-assisted selection (MAS) for breeding perennial ryegrass (Lolium perenne), a pasture species. A mapping study had shown the presence of quantitative trait loci (QTL) for seven component traits of nitrogen use efficiency (NUE). The NUE-related QTL clustered in five chromosomal regions. These QTL were validated through divergent marker selection in an F 2 population. The criterion used for plant selection was a summation index based on the number of positive QTL alleles. The evaluation studies showed a strong indirect response of marker selection on NUE. Marker selection using a summation index such as applied here proved to be very effective for difficult and complex quantitative traits such as NUE. The strategy is easily applicable in outbreeding crops to raise the frequency of several desirable alleles simultaneously. (author)

A Quantitative Features Analysis of Recommended No- and Low-Cost Preschool E-Books

Science.gov (United States)

Parette, Howard P.; Blum, Craig; Luthin, Katie

2015-01-01

In recent years, recommended e-books have drawn increasing attention from early childhood education professionals. This study applied a quantitative descriptive features analysis of cost (n = 70) and no-cost (n = 60) e-books recommended by the Texas Computer Education Association. While t tests revealed no statistically significant differences…

Quantitative Risk reduction estimation Tool For Control Systems, Suggested Approach and Research Needs

Energy Technology Data Exchange (ETDEWEB)

Miles McQueen; Wayne Boyer; Mark Flynn; Sam Alessi

2006-03-01

For the past year we have applied a variety of risk assessment technologies to evaluate the risk to critical infrastructure from cyber attacks on control systems. More recently, we identified the need for a stand alone control system risk reduction estimation tool to provide owners and operators of control systems with a more useable, reliable, and credible method for managing the risks from cyber attack. Risk is defined as the probability of a successful attack times the value of the resulting loss, typically measured in lives and dollars. Qualitative and ad hoc techniques for measuring risk do not provide sufficient support for cost benefit analyses associated with cyber security mitigation actions. To address the need for better quantitative risk reduction models we surveyed previous quantitative risk assessment research; evaluated currently available tools; developed new quantitative techniques [17] [18]; implemented a prototype analysis tool to demonstrate how such a tool might be used; used the prototype to test a variety of underlying risk calculational engines (e.g. attack tree, attack graph); and identified technical and research needs. We concluded that significant gaps still exist and difficult research problems remain for quantitatively assessing the risk to control system components and networks, but that a useable quantitative risk reduction estimation tool is not beyond reach.

Quantitative interface models for simulating microstructure evolution

International Nuclear Information System (INIS)

Zhu, J.Z.; Wang, T.; Zhou, S.H.; Liu, Z.K.; Chen, L.Q.

2004-01-01

To quantitatively simulate microstructural evolution in real systems, we investigated three different interface models: a sharp-interface model implemented by the software DICTRA and two diffuse-interface models which use either physical order parameters or artificial order parameters. A particular example is considered, the diffusion-controlled growth of a γ ' precipitate in a supersaturated γ matrix in Ni-Al binary alloys. All three models use the thermodynamic and kinetic parameters from the same databases. The temporal evolution profiles of composition from different models are shown to agree with each other. The focus is on examining the advantages and disadvantages of each model as applied to microstructure evolution in alloys

Non-linear changes in rhythmic variability of European art music: Quantitative support for historical musicology

DEFF Research Database (Denmark)

Hansen, Niels Chr.; Sadakata, Makiko; Pearce, Marcus

It is a long-held belief in historical musicology that the prosody of composers’ native languages is reflected in the rhythmic and melodic properties of their music. Applying the normalised Pairwise Variability Index (nPVI) to speech alongside musical scores, research has established quantitative...... music up until the mid-19th century, after which French music diverged into an Austro-German school and a French nationalist school. In sum, using musical nPVI analysis, we provide quantitative support for music-historical descriptions of an Italian-dominated Baroque (composer birth years: 1600...

Global protein phosphorylation dynamics during deoxynivalenol-induced ribotoxic stress response in the macrophage

Energy Technology Data Exchange (ETDEWEB)

Pan, Xiao [Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 (United States); Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States); Whitten, Douglas A. [Research Technology Support Facility, Proteomics Core, Michigan State University, East Lansing, MI 48824 (United States); Wu, Ming [Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824 (United States); Chan, Christina [Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 (United States); Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824 (United States); Wilkerson, Curtis G. [Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 (United States); Research Technology Support Facility, Proteomics Core, Michigan State University, East Lansing, MI 48824 (United States); Pestka, James J., E-mail: pestka@msu.edu [Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States); Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 (United States); Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824 (United States)

2013-04-15

Deoxynivalenol (DON), a trichothecene mycotoxin produced by Fusarium that commonly contaminates food, is capable of activating mononuclear phagocytes of the innate immune system via a process termed the ribotoxic stress response (RSR). To encapture global signaling events mediating RSR, we quantified the early temporal (≤ 30 min) phosphoproteome changes that occurred in RAW 264.7 murine macrophage during exposure to a toxicologically relevant concentration of DON (250 ng/mL). Large-scale phosphoproteomic analysis employing stable isotope labeling of amino acids in cell culture (SILAC) in conjunction with titanium dioxide chromatography revealed that DON significantly upregulated or downregulated phosphorylation of 188 proteins at both known and yet-to-be functionally characterized phosphosites. DON-induced RSR is extremely complex and goes far beyond its prior known capacity to inhibit translation and activate MAPKs. Transcriptional regulation was the main target during early DON-induced RSR, covering over 20% of the altered phosphoproteins as indicated by Gene Ontology annotation and including transcription factors/cofactors and epigenetic modulators. Other biological processes impacted included cell cycle, RNA processing, translation, ribosome biogenesis, monocyte differentiation and cytoskeleton organization. Some of these processes could be mediated by signaling networks involving MAPK-, NFκB-, AKT- and AMPK-linked pathways. Fuzzy c-means clustering revealed that DON-regulated phosphosites could be discretely classified with regard to the kinetics of phosphorylation/dephosphorylation. The cellular response networks identified provide a template for further exploration of the mechanisms of trichothecenemycotoxins and other ribotoxins, and ultimately, could contribute to improved mechanism-based human health risk assessment. - Highlights: ► Mycotoxin deoxynivalenol (DON) induces immunotoxicity via ribotoxic stress response. ► SILAC phosphoproteomics using

Global protein phosphorylation dynamics during deoxynivalenol-induced ribotoxic stress response in the macrophage

International Nuclear Information System (INIS)

Pan, Xiao; Whitten, Douglas A.; Wu, Ming; Chan, Christina; Wilkerson, Curtis G.; Pestka, James J.

2013-01-01

Deoxynivalenol (DON), a trichothecene mycotoxin produced by Fusarium that commonly contaminates food, is capable of activating mononuclear phagocytes of the innate immune system via a process termed the ribotoxic stress response (RSR). To encapture global signaling events mediating RSR, we quantified the early temporal (≤ 30 min) phosphoproteome changes that occurred in RAW 264.7 murine macrophage during exposure to a toxicologically relevant concentration of DON (250 ng/mL). Large-scale phosphoproteomic analysis employing stable isotope labeling of amino acids in cell culture (SILAC) in conjunction with titanium dioxide chromatography revealed that DON significantly upregulated or downregulated phosphorylation of 188 proteins at both known and yet-to-be functionally characterized phosphosites. DON-induced RSR is extremely complex and goes far beyond its prior known capacity to inhibit translation and activate MAPKs. Transcriptional regulation was the main target during early DON-induced RSR, covering over 20% of the altered phosphoproteins as indicated by Gene Ontology annotation and including transcription factors/cofactors and epigenetic modulators. Other biological processes impacted included cell cycle, RNA processing, translation, ribosome biogenesis, monocyte differentiation and cytoskeleton organization. Some of these processes could be mediated by signaling networks involving MAPK-, NFκB-, AKT- and AMPK-linked pathways. Fuzzy c-means clustering revealed that DON-regulated phosphosites could be discretely classified with regard to the kinetics of phosphorylation/dephosphorylation. The cellular response networks identified provide a template for further exploration of the mechanisms of trichothecenemycotoxins and other ribotoxins, and ultimately, could contribute to improved mechanism-based human health risk assessment. - Highlights: ► Mycotoxin deoxynivalenol (DON) induces immunotoxicity via ribotoxic stress response. ► SILAC phosphoproteomics using

Systematic inference of functional phosphorylation events in yeast metabolism.

Science.gov (United States)

Chen, Yu; Wang, Yonghong; Nielsen, Jens

2017-07-01

Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics has received increased attention. We developed a mathematical framework that describes the relationship between phosphorylation level of a metabolic enzyme and the corresponding flux through the enzyme. Using this framework, it is possible to quantitatively estimate contribution of phosphorylation events to flux changes. We showed that phosphorylation regulation analysis, combined with a systematic workflow and correlation analysis, can be used for inference of functional phosphorylation events in steady and dynamic conditions, respectively. Using this analysis, we assigned functionality to phosphorylation events of 17 metabolic enzymes in the yeast Saccharomyces cerevisiae , among which 10 are novel. Phosphorylation regulation analysis cannot only be extended for inference of other functional post-translational modifications but also be a promising scaffold for multi-omics data integration in systems biology. Matlab codes for flux balance analysis in this study are available in Supplementary material. yhwang@ecust.edu.cn or nielsenj@chalmers.se. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Proteomic Dissection of Nanotopography-Sensitive Mechanotransductive Signaling Hubs that Foster Neuronal Differentiation in PC12 Cells

Directory of Open Access Journals (Sweden)

Elisa Maffioli

2018-01-01

Full Text Available Neuronal cells are competent in precisely sensing nanotopographical features of their microenvironment. The perceived microenvironmental information will be “interpreted” by mechanotransductive processes and impacts on neuronal functioning and differentiation. Attempts to influence neuronal differentiation by engineering substrates that mimic appropriate extracellular matrix (ECM topographies are hampered by the fact that profound details of mechanosensing/-transduction complexity remain elusive. Introducing omics methods into these biomaterial approaches has the potential to provide a deeper insight into the molecular processes and signaling cascades underlying mechanosensing/-transduction but their exigence in cellular material is often opposed by technical limitations of major substrate top-down fabrication methods. Supersonic cluster beam deposition (SCBD allows instead the bottom-up fabrication of nanostructured substrates over large areas characterized by a quantitatively controllable ECM-like nanoroughness that has been recently shown to foster neuron differentiation and maturation. Exploiting this capacity of SCBD, we challenged mechanosensing/-transduction and differentiative behavior of neuron-like PC12 cells with diverse nanotopographies and/or changes of their biomechanical status, and analyzed their phosphoproteomic profiles in these settings. Versatile proteins that can be associated to significant processes along the mechanotransductive signal sequence, i.e., cell/cell interaction, glycocalyx and ECM, membrane/f-actin linkage and integrin activation, cell/substrate interaction, integrin adhesion complex, actomyosin organization/cellular mechanics, nuclear organization, and transcriptional regulation, were affected. The phosphoproteomic data suggested furthermore an involvement of ILK, mTOR, Wnt, and calcium signaling in these nanotopography- and/or cell mechanics-related processes. Altogether, potential nanotopography

Quantitative determination of minor and trace elements in rocks and soils by spark source mass spectrometry

International Nuclear Information System (INIS)

Ure, A.M.; Bacon, J.R.

1978-01-01

Experimental details are given of the quantitative determination of minor and trace elements in rocks and soils by spark source mass spectrometry. The effects of interfering species, and corrections that can be applied, are discussed. (U.K.)

Applying a new ensemble approach to estimating stock status of marine fisheries around the world

DEFF Research Database (Denmark)

Rosenberg, Andrew A.; Kleisner, Kristin M.; Afflerbach, Jamie

2018-01-01

The exploitation status of marine fisheries stocks worldwide is of critical importance for food security, ecosystem conservation, and fishery sustainability. Applying a suite of data-limited methods to global catch data, combined through an ensemble modeling approach, we provide quantitative esti...

Application of Fault Management Theory to the Quantitive Selection of a Launch Vehicle Abort Trigger Suite

Science.gov (United States)

Lo, Yunnhon; Johnson, Stephen B.; Breckenridge, Jonathan T.

2014-01-01

SHM/FM theory has been successfully applied to the selection of the baseline set Abort Triggers for the NASA SLS center dot Quantitative assessment played a useful role in the decision process ? M&FM, which is new within NASA MSFC, required the most "new" work, as this quantitative analysis had never been done before center dot Required development of the methodology and tool to mechanize the process center dot Established new relationships to the other groups ? The process is now an accepted part of the SLS design process, and will likely be applied to similar programs in the future at NASA MSFC ? Future improvements center dot Improve technical accuracy ?Differentiate crew survivability due to an abort, vs. survivability even no immediate abort occurs (small explosion with little debris) ?Account for contingent dependence of secondary triggers on primary triggers ?Allocate "? LOC Benefit" of each trigger when added to the previously selected triggers. center dot Reduce future costs through the development of a specialized tool ? Methodology can be applied to any manned/unmanned vehicle, in space or terrestrial

Power System Oscillation Modes Identifications: Guidelines for Applying TLS-ESPRIT Method

Science.gov (United States)

Gajjar, Gopal R.; Soman, Shreevardhan

2013-05-01

Fast measurements of power system quantities available through wide-area measurement systems enables direct observations for power system electromechanical oscillations. But the raw observations data need to be processed to obtain the quantitative measures required to make any inference regarding the power system state. A detailed discussion is presented for the theory behind the general problem of oscillatory mode indentification. This paper presents some results on oscillation mode identification applied to a wide-area frequency measurements system. Guidelines for selection of parametes for obtaining most reliable results from the applied method are provided. Finally, some results on real measurements are presented with our inference on them.

Quantitative evaluation of risks for individuals in diagnostic radiology

Energy Technology Data Exchange (ETDEWEB)

Iinuma, T A; Tateno, Y; Hashizume, T [National Inst. of Radiological Sciences, Chiba (Japan)

1980-05-01

A method to estimate quantitatively risks of individual patients due to exposure to diagnostic radiation (carcinogenetic and genetic effects of radiation) was proposed on the basis of ICRP-26. Carcinogenetic effect of radiation was calculated by multiplying mean dose equivalent for each organ per each radiological examination by shortening of average life-expectancy which was calculated from incidence of fetal carcinoma of each organ, latent period of carcinoma, and incidence period of carcinoma. Genetic effect of radiation was calculated by multiplying mean dose equivalent for gonad per each radiological examination by incidence of genetically severe radiation damages due to parent's exposure and child expectancy rate. Three examples were shown on calculations of risks in the photofluorographic examinations of the stomach and chest, and mammography. The same method of calculation could be applied to the in-vivo nuclear medicine examinations. Further investigation was required to calculate the risks quantitatively for various types of diagnostic procedures using radiation.

Quantitative evaluation of risks for individuals in diagnostic radiology

International Nuclear Information System (INIS)

Iinuma, T.A.; Tateno, Yukio; Hashizume, Tadashi

1980-01-01

A method to estimate quantitatively risks of individual patients due to exposure to diagnostic radiation (carcinogenetic and genetic effects of radiation) was proposed on the basis of ICRP-26. Carcinogenetic effect of radiation was calculated by multiplying mean dose equivalent for each organ per each radiological examination by shortening of average life-expectancy which was calculated from incidence of fetal carcinoma of each organ, latent period of carcinoma, and incidence period of carcinoma. Genetic effect of radiation was calculated by multiplying mean dose equivalent for gonad per each radiological examination by incidence of genetically severe radiation damages due to parent's exposure and child expectancy rate. Three examples were shown on calculations of risks in the photofluorographic examinations of the stomach and chest, and mammography. The same method of calculation could be applied to the in-vivo nuclear medicine examinations. Further investigation was required to calculate the risks quantitatively for various types of diagnostic procedures using radiation. (Tsunoda, M.)

Model for Quantitative Evaluation of Enzyme Replacement Treatment

Directory of Open Access Journals (Sweden)

Radeva B.

2009-12-01

Full Text Available Gaucher disease is the most frequent lysosomal disorder. Its enzyme replacement treatment was the new progress of modern biotechnology, successfully used in the last years. The evaluation of optimal dose of each patient is important due to health and economical reasons. The enzyme replacement is the most expensive treatment. It must be held continuously and without interruption. Since 2001, the enzyme replacement therapy with Cerezyme*Genzyme was formally introduced in Bulgaria, but after some time it was interrupted for 1-2 months. The dose of the patients was not optimal. The aim of our work is to find a mathematical model for quantitative evaluation of ERT of Gaucher disease. The model applies a kind of software called "Statistika 6" via the input of the individual data of 5-year-old children having the Gaucher disease treated with Cerezyme. The output results of the model gave possibilities for quantitative evaluation of the individual trends in the development of the disease of each child and its correlation. On the basis of this results, we might recommend suitable changes in ERT.

A quantitative in vitro assay for the evaluation of phototoxic potential of topically applied materials.

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Tenenbaum, S; DiNardo, J; Morris, W E; Wolf, B A; Schnetzinger, R W

1984-10-01

A quantitative in vitro method for phototoxic evaluation of chemicals has been developed and validated. The assay uses Saccharomyces cerevisiae, seeded in an agar overlay on top of a plate count agar base. 8-Methoxy psoralen is used as a reference standard against which materials are measured. Activity is quantified by cytotoxicity measured as zones of inhibition. Several known phototoxins (heliotropine, lyral, phantolid, and bergamot oil) and photoallergens (6-methyl coumarin and musk ambrette) are used to validate the assay. An excellent correlation is observed between in vivo studies employing Hartley albino guinea pigs and the in vitro assay for several fragrance raw materials and other chemicals. The in vitro assay exhibits a greater sensitivity from 2-500 fold. For three fragrance oils, the in vitro assay detects low levels of photobiological activity while the in vivo assay is negative. Although the in vitro assay does not discriminate between phototoxins and photoallergens, it can be used for screening of raw materials so that reduction in animal usage can be achieved while maintaining the protection of the consumer.

Problems of Understanding English Ironic Expressions by M.A. Students of Applied Linguistics at Mu'tah University in Jordan

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Al Khawaldeh, Suhaib

2015-01-01

The present study attempts to investigate the problems of understanding English ironic expressions M.A. of Applied Linguistics students at Mu'tah University in Jordan. This quantitative and qualitative study includes 15 of M.A. students of Applied Linguistics at Mu'tah University. The participants were selected randomly. Two research instruments…

Automated quantitative assessment of proteins' biological function in protein knowledge bases.

Science.gov (United States)

Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter

2008-01-01

Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

Directory of Open Access Journals (Sweden)

Gabriele Mayr

2008-01-01

Full Text Available Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Quantitative aspects of myocardial perfusion imaging

International Nuclear Information System (INIS)

Vogel, R.A.

1980-01-01

Myocardial perfusion measurements have traditionally been performed in a quantitative fashion using application of the Sapirstein, Fick, Kety-Schmidt, or compartmental analysis principles. Although global myocardial blood flow measurements have not proven clinically useful, regional determinations have substantially advanced our understanding of and ability to detect myocardial ischemia. With the introduction of thallium-201, such studies have become widely available, although these have generally undergone qualitative evaluation. Using computer-digitized data, several methods for the quantification of myocardial perfusion images have been introduced. These include orthogonal and polar coordinate systems and anatomically oriented region of interest segmentation. Statistical ranges of normal and time-activity analyses have been applied to these data, resulting in objective and reproducible means of data evaluation

Quantitative cerebral blood flow patterns with the short lived isotope 195m Au

International Nuclear Information System (INIS)

Lindner, P.; Nickel, O.

1984-01-01

A previously reported theory for quantitative cerebral blood flow measurements using intravenously injected nondiffusible radiotracers has been applied on patients after stroke and on volunteers undergoing a mental stimulation exercise. Quantitative measurements of cerebral blood flow patterns (in ml/min/100g) not only in p.a. but also in lateral views of the brain are possible by using of the short-lived (30 sec) isotope Au 195m. The energy spectrum of the eluate of the generator shows two strong photon peaks, one at 68 keV and a second at 262 keV. The 68 keV peak is suitable for perfusion studies in lateral views of the hemispheres, no 'look through' effect is seen. The 262 keV peak is good for studies in p.a. positions. The studies last less than 1 minute and can be repeated after 3 minutes. Parametric images for quantitative regional cerebral blood flow can be generated. The area of occluded vessels in the case of stroke can be made visible. Quantitative activation patterns of cerebral blood flow during mental stimulation can be generated. After optical stimulation a clear increase of blood flow was seen in the visual cortex. The results prove that not only with freely diffusible (like Xenon) but also with nondiffusible indicators like 195m Au it is possible to measure quantitatively cerebral blood flow patterns. Au 195m is very advantageous for quantitative clinical investigations of cerebrovascular disease. (Author)

Quantitative Ultrasound for Measuring Obstructive Severity in Children with Hydronephrosis.

Science.gov (United States)

Cerrolaza, Juan J; Peters, Craig A; Martin, Aaron D; Myers, Emmarie; Safdar, Nabile; Linguraru, Marius George

2016-04-01

We define sonographic biomarkers for hydronephrotic renal units that can predict the necessity of diuretic nuclear renography. We selected a cohort of 50 consecutive patients with hydronephrosis of varying severity in whom 2-dimensional sonography and diuretic mercaptoacetyltriglycine renography had been performed. A total of 131 morphological parameters were computed using quantitative image analysis algorithms. Machine learning techniques were then applied to identify ultrasound based safety thresholds that agreed with the t½ for washout. A best fit model was then derived for each threshold level of t½ that would be clinically relevant at 20, 30 and 40 minutes. Receiver operating characteristic curve analysis was performed. Sensitivity, specificity and area under the receiver operating characteristic curve were determined. Improvement obtained by the quantitative imaging method compared to the Society for Fetal Urology grading system and the hydronephrosis index was statistically verified. For the 3 thresholds considered and at 100% sensitivity the specificities of the quantitative imaging method were 94%, 70% and 74%, respectively. Corresponding area under the receiver operating characteristic curve values were 0.98, 0.94 and 0.94, respectively. Improvement obtained by the quantitative imaging method over the Society for Fetal Urology grade and hydronephrosis index was statistically significant (p hydronephrosis can identify thresholds of clinically significant washout times with 100% sensitivity to decrease the number of diuretic renograms in up to 62% of children. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Integrating quantitative thinking into an introductory biology course improves students' mathematical reasoning in biological contexts.

Science.gov (United States)

Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

2014-01-01

Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students' apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students' understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students' inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students' biology learning.

Integrating Quantitative Thinking into an Introductory Biology Course Improves Students’ Mathematical Reasoning in Biological Contexts

Science.gov (United States)

Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

2014-01-01

Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students’ apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students’ understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students’ inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students’ biology learning. PMID:24591504

Problem-based learning on quantitative analytical chemistry course

Science.gov (United States)

Fitri, Noor

2017-12-01

This research applies problem-based learning method on chemical quantitative analytical chemistry, so called as "Analytical Chemistry II" course, especially related to essential oil analysis. The learning outcomes of this course include aspects of understanding of lectures, the skills of applying course materials, and the ability to identify, formulate and solve chemical analysis problems. The role of study groups is quite important in improving students' learning ability and in completing independent tasks and group tasks. Thus, students are not only aware of the basic concepts of Analytical Chemistry II, but also able to understand and apply analytical concepts that have been studied to solve given analytical chemistry problems, and have the attitude and ability to work together to solve the problems. Based on the learning outcome, it can be concluded that the problem-based learning method in Analytical Chemistry II course has been proven to improve students' knowledge, skill, ability and attitude. Students are not only skilled at solving problems in analytical chemistry especially in essential oil analysis in accordance with local genius of Chemistry Department, Universitas Islam Indonesia, but also have skilled work with computer program and able to understand material and problem in English.

Quantitative Analysis of Piroxicam Using Temperature-Controlled Ionic Liquid Dispersive Liquid Phase Microextraction Followed By Stopped-Flow Injection Spectrofluorimetry

Directory of Open Access Journals (Sweden)

Mohammad Reza Ganjali

2013-07-01

Full Text Available Background:Piroxicam (PXM belongs to the wide class of non-steroidal anti-inflammatory drugs (NSAIDs. PXM has been widely applied in the treatment of rheumatoid arthritis, gonarthrosis, osteoarthritis, backaches, neuralgia, mialgia. In the presented work, a green and benign sample pretreatment method called temperature-controlled ionic liquid dispersive liquid phase microextraction (TCIL-DLPME was followed with stopped-flow injection spectrofluorimetry (SFIS for quantitation of PXM in pharmaceutical formulations and biological samples.Methods:Temperature-controlled ionic liquid dispersive liquid phase microextraction (TCIL-DLPME was applied as an environmentally friendly sample enrichment method to extract and isolate PXM prior to quantitation. Dispersion of 1-hexyl-3-methylimidazolium hexafluorophosphate ([Hmim][PF6] ionic liquid (IL through the sample aqueous solution was performed by applying a relatively high temperature. PXM was extracted into the extractor, and after phase separation, PXM in the final solution was determined by stopped-flow injection spectrofluorimetry (SFIS.Results and Major Conclusion:Different factors affecting the designed method such as IL amount, diluting agent, pH and temperature were investigated in details and optimized. The method provided a linear dynamic range of 0.2-150 μg l-1, a limit of detection (LOD of 0.046 μg l-1 and a relative standard deviation (RSD of 3.1%. Furthermore, in order to demonstrate the analytical applicability of the recommended method, it was applied for quantitation of PXM in real samples.

Quantitative MRI in refractory temporal lobe epilepsy: relationship with surgical outcomes

Science.gov (United States)

Bonilha, Leonardo

2015-01-01

Medically intractable temporal lobe epilepsy (TLE) remains a serious health problem. Across treatment centers, up to 40% of patients with TLE will continue to experience persistent postoperative seizures at 2-year follow-up. It is unknown why such a large number of patients continue to experience seizures despite being suitable candidates for resective surgery. Preoperative quantitative MRI techniques may provide useful information on why some patients continue to experience disabling seizures, and may have the potential to develop prognostic markers of surgical outcome. In this article, we provide an overview of how quantitative MRI morphometric and diffusion tensor imaging (DTI) data have improved the understanding of brain structural alterations in patients with refractory TLE. We subsequently review the studies that have applied quantitative structural imaging techniques to identify the neuroanatomical factors that are most strongly related to a poor postoperative prognosis. In summary, quantitative imaging studies strongly suggest that TLE is a disorder affecting a network of neurobiological systems, characterized by multiple and inter-related limbic and extra-limbic network abnormalities. The relationship between brain alterations and postoperative outcome are less consistent, but there is emerging evidence suggesting that seizures are less likely to remit with surgery when presurgical abnormalities are observed in the connectivity supporting brain regions serving as network nodes located outside the resected temporal lobe. Future work, possibly harnessing the potential from multimodal imaging approaches, may further elucidate the etiology of persistent postoperative seizures in patients with refractory TLE. Furthermore, quantitative imaging techniques may be explored to provide individualized measures of postoperative seizure freedom outcome. PMID:25853080

Quantitative in situ magnetization reversal studies in Lorentz microscopy and electron holography.

Science.gov (United States)

Rodríguez, L A; Magén, C; Snoeck, E; Gatel, C; Marín, L; Serrano-Ramón, L; Prieto, J L; Muñoz, M; Algarabel, P A; Morellon, L; De Teresa, J M; Ibarra, M R

2013-11-01

A generalized procedure for the in situ application of magnetic fields by means of the excitation of the objective lens for magnetic imaging experiments in Lorentz microscopy and electron holography is quantitatively described. A protocol for applying magnetic fields with arbitrary in-plane magnitude and orientation is presented, and a freeware script for Digital Micrograph(™) is provided to assist the operation of the microscope. Moreover, a method to accurately reconstruct hysteresis loops is detailed. We show that the out-of-plane component of the magnetic field cannot be always neglected when performing quantitative measurements of the local magnetization. Several examples are shown to demonstrate the accuracy and functionality of the methods. © 2013 Elsevier B.V. All rights reserved.

Quantitative analysis of patient-specific dosimetric IMRT verification

International Nuclear Information System (INIS)

Budgell, G J; Perrin, B A; Mott, J H L; Fairfoul, J; Mackay, R I

2005-01-01

Patient-specific dosimetric verification methods for IMRT treatments are variable, time-consuming and frequently qualitative, preventing evidence-based reduction in the amount of verification performed. This paper addresses some of these issues by applying a quantitative analysis parameter to the dosimetric verification procedure. Film measurements in different planes were acquired for a series of ten IMRT prostate patients, analysed using the quantitative parameter, and compared to determine the most suitable verification plane. Film and ion chamber verification results for 61 patients were analysed to determine long-term accuracy, reproducibility and stability of the planning and delivery system. The reproducibility of the measurement and analysis system was also studied. The results show that verification results are strongly dependent on the plane chosen, with the coronal plane particularly insensitive to delivery error. Unexpectedly, no correlation could be found between the levels of error in different verification planes. Longer term verification results showed consistent patterns which suggest that the amount of patient-specific verification can be safely reduced, provided proper caution is exercised: an evidence-based model for such reduction is proposed. It is concluded that dose/distance to agreement (e.g., 3%/3 mm) should be used as a criterion of acceptability. Quantitative parameters calculated for a given criterion of acceptability should be adopted in conjunction with displays that show where discrepancies occur. Planning and delivery systems which cannot meet the required standards of accuracy, reproducibility and stability to reduce verification will not be accepted by the radiotherapy community

Synthesis of Thermally Switchable Chromatographic Materials with Immobilized Ti4+ for Enrichment of Phosphopeptides by Reversible Addition Fragmentation Chain Transfer Polymerization

Science.gov (United States)

Wang, Di; Cao, Zhihan; Pang, Xinzhu; Deng, Yulin; Li, Bo; Dai, Rongji

2018-01-01

Reversible phosphorylation of proteins is one of the most crucial types of post-translational modifications (PTMs). And it shows significant work in diversified biological processes. However, the separation technology of phosphorylated peptides is still an analytical challenge in phosphoproteomics, because phosphopeptides are alway in low stoichiometry. Thus, enrichment of phosphopeptides before detection is indispensable. In this study, a novel temperature regulated separation protocol was developed. Silica@p (NIPAAm-co-IPPA)-Ti4+, a new Ti(IV)-IMAC (Immobilized Metal Affinity chromatography) materials was synthesized by reversible addition fragmentation chain transfer polymerization (RAFT). By the unique thermally responsive properties of poly(N-isopropylacrylamide) (PNIPAAm), the captured phosphorylated peptides could be released by changing temperature only without applying any other eluant which could damage the phosphopeptides. We employed isopropanol phosphonic acid (IPPA) as an IMAC ligand for the immobilization of Ti(IV) which could increase the specific adsorption of phosphopeptides. The enrichment and release properties were examined by treatment with pyridoxal 5’-phosphate (PLP) and casein phosphopeptides (CPP). Two phosphorylated compounds above have temperature-stimulated binding to Ti4+. Finally, silica@p (NIPAAm-co-IPPA)-Ti4+ was successfully employed in pretreatment of phosphopeptides in a tryptic digest of a-casein and human serum albumin (HSA). The results indicated a great potential of this new temperature-responsive material in phosphoproteomics study.

Weighing evidence: quantitative measures of the importance of bitemark evidence.

Science.gov (United States)

Kittelson, J M; Kieser, J A; Buckingham, D M; Herbison, G P

2002-12-01

Quantitative measures of the importance of evidence such as the "likelihood ratio" have become increasingly popular in the courtroom. These measures have been used by expert witnesses formally to describe their certainty about a piece of evidence. These measures are commonly interpreted as the amount by which the evidence should revise the opinion of guilt, and thereby summarize the importance of a particular piece of evidence. Unlike DNA evidence, quantitative measures have not been widely used by forensic dentists to describe their certainty when testifying about bitemark evidence. There is, however, no inherent reason why they should not be used to evaluate bitemarks. The purpose of this paper is to describe the likelihood ratio as it might be applied to bitemark evidence. We use a simple bitemark example to define the likelihood ratio, its application, and interpretation. In particular we describe how the jury interprets the likelihood ratio from a Bayesian perspective when evaluating the impact of the evidence on the odds that the accused is guilty. We describe how the dentist would calculate the likelihood ratio based on frequentist interpretations. We also illustrate some of the limitations of the likelihood ratio, and show how those limitations apply to bitemark evidence. We conclude that the quality of bitemark evidence cannot be adequately summarized by the likelihood ratio, and argue that its application in this setting may be more misleading than helpful.

Quantitative Surface Analysis by Xps (X-Ray Photoelectron Spectroscopy: Application to Hydrotreating Catalysts

Directory of Open Access Journals (Sweden)

Beccat P.

1999-07-01

Full Text Available XPS is an ideal technique to provide the chemical composition of the extreme surface of solid materials, vastly applied to the study of catalysts. In this article, we will show that a quantitative approach, based upon fundamental expression of the XPS signal, has enabled us to obtain a consistent set of response factors for the elements of the periodic table. In-depth spadework has been necessary to know precisely the transmission function of the spectrometer used at IFP. The set of response factors obtained enables to perform, on a routine basis, a quantitative analysis with approximately 20% relative accuracy, which is quite acceptable for an analysis of such a nature. While using this quantitative approach, we have developed an analytical method specific to hydrotreating catalysts that allows obtaining the sulphiding degree of molybdenum quite reliably and reproducibly. The usage of this method is illustrated by two examples for which XPS spectroscopy has provided with information sufficiently accurate and quantitative to help understand the reactivity differences between certain MoS2/Al2O3 or NiMoS/Al2O3-type hydrotreating catalysts.

A quantitative genetic approach to assess the evolutionary potential of a coastal marine fish to ocean acidification

KAUST Repository

Malvezzi, Alex J.; Murray, Christopher S.; Feldheim, Kevin A.; DiBattista, Joseph; Garant, Dany; Gobler, Christopher J.; Chapman, Demian D.; Baumann, Hannes

2015-01-01

Assessing the potential of marine organisms to adapt genetically to increasing oceanic CO2 levels requires proxies such as heritability of fitness-related traits under ocean acidification (OA). We applied a quantitative genetic method to derive

MR Imaging-based Semi-quantitative Methods for Knee Osteoarthritis

Science.gov (United States)

JARRAYA, Mohamed; HAYASHI, Daichi; ROEMER, Frank Wolfgang; GUERMAZI, Ali

2016-01-01

Magnetic resonance imaging (MRI)-based semi-quantitative (SQ) methods applied to knee osteoarthritis (OA) have been introduced during the last decade and have fundamentally changed our understanding of knee OA pathology since then. Several epidemiological studies and clinical trials have used MRI-based SQ methods to evaluate different outcome measures. Interest in MRI-based SQ scoring system has led to continuous update and refinement. This article reviews the different SQ approaches for MRI-based whole organ assessment of knee OA and also discuss practical aspects of whole joint assessment. PMID:26632537

Real-time quantitative PCR of Staphylococcus aureus and application in restaurant meals.

Science.gov (United States)

Berrada, H; Soriano, J M; Mañes, J; Picó, Y

2006-01-01

Staphylococcus aureus is considered the second most common pathogen to cause outbreaks of food poisoning, exceeded only by Campylobacter. Consumption of foods containing this microorganism is often identified as the cause of illness. In this study, a rapid, reliable, and sensitive real-time quantitative PCR was developed and compared with conventional culture methods. Real-time quantitative PCR was carried out by purifying DNA extracts of S. aureus with a Staphylococcus sample preparation kit and quantifying it in the LightCycler system with hybridization probes. The assay was linear from a range of 10 to 10(6) S. aureus cells (r2 > 0.997). The PCR reaction presented an efficiency of >85%. Accuracy of the PCR-based assay, expressed as percent bias, was around 13%, and the precision, expressed as a percentage of the coefficient of variation, was 7 to 10%. Intraday and interday variability were studied at 10(2) CFU/g and was 12 and 14%, respectively. The proposed method was applied to the analysis of 77 samples of restaurant meals in Valencia (Spain). In 11.6% of samples S. aureus was detected by real-time quantitative PCR, as well as by the conventional microbiological method. An excellent correspondence between real-time quantitative PCR and microbiological numbers (CFU/g) was observed with deviations of < 28%.

Quantitative analysis of titanium concentration using calibration-free laser-induced breakdown spectroscopy (LIBS)

Science.gov (United States)

Zaitun; Prasetyo, S.; Suliyanti, M. M.; Isnaeni; Herbani, Y.

2018-03-01

Laser-induced breakdown spectroscopy (LIBS) can be used for quantitative and qualitative analysis. Calibration-free LIBS (CF-LIBS) is a method to quantitatively analyze concentration of elements in a sample in local thermodynamic equilibrium conditions without using available matrix-matched calibration. In this study, we apply CF-LIBS for quantitative analysis of Ti in TiO2 sample. TiO2 powder sample was mixed with polyvinyl alcohol and formed into pellets. An Nd:YAG pulsed laser at a wavelength of 1064 nm was focused onto the sample to generate plasma. The spectrum of plasma was recorded using spectrophotometer then compared to NIST spectral line to determine energy levels and other parameters. The value of plasma temperature obtained using Boltzmann plot is 8127.29 K and electron density from calculation is 2.49×1016 cm-3. Finally, the concentration of Ti in TiO2 sample from this study is 97% that is in proximity with the sample certificate.

Urea-modified metal-organic framework of type MIL-101(Cr) for the preconcentration of phosphorylated peptides

International Nuclear Information System (INIS)

Yang, Xiaoqing; Xia, Yan

2016-01-01

Mass spectrometry (MS) is the most powerful tool in phosphoproteomics research. However, phosphopeptides usually are present in low concentrations and their preconcentration therefore is highly desired. We describe a two-step method for the synthesis of a metal organic framework of the type MIL-101(Cr) that is modified with urea (then designated as MIL-101(Cr)-UR 2 ). It possesses large surface area, good solvent stability and high affinity for some phosphates. Due to the presence of modified urea functions, this material allows for selective and effective enrichment of phosphorylated peptides. It was successfully applied to the enrichment of phosphopeptides from non-fat-milk. The method was applied to the detection of phosphopeptides in a tryptic digest of β-casein where is showed a detection sensitivity as low as 10 −10 M. (author)

Solid-phase peptide quantitation assay using labeled monoclonal antibody and glutaraldehyde fixation

International Nuclear Information System (INIS)

Kasprzyk, P.G.; Cuttitta, F.; Avis, I.; Nakanishi, Y.; Treston, A.; Wong, H.; Walsh, J.H.; Mulshine, J.L.

1988-01-01

A solid-phase radioimmunoassay utilizing iodinated peptide-specific monoclonal antibody as a detection system instead of labeled peptide has been developed. Regional specific monoclonal antibodies to either gastrin-releasing peptide or gastrin were used as models to validate the general application of our modified assay. Conditions for radioactive labeling of the monoclonal antibody were determined to minimize oxidant damage, which compromises the sensitivity of other reported peptide quantitation assays. Pretreatment of 96-well polyvinyl chloride test plates with a 5% glutaraldehyde solution resulted in consistent retention of sufficient target peptide on the solid-phase matrix to allow precise quantitation. This quantitative method is completed within 1 h of peptide solid phasing. Pretreatment of assay plates with glutaraldehyde increased binding of target peptide and maximized antibody binding by optimizing antigen presentation. The hypothesis that glutaraldehyde affects both peptide binding to the plate and orientation of the peptide was confirmed by analysis of several peptide analogs. These studies indicate that peptide binding was mediated through a free amino group leaving the carboxy-terminal portion of the target peptide accessible for antibody binding. It was observed that the length of the peptide also affects the amount of monoclonal antibody that will bind. Under the optimal conditions, results from quantitation of gastrin-releasing peptide in relevant samples agree well with those from previously reported techniques. Thus, we report here a modified microplate assay which may be generally applied for the rapid and sensitive quantitation of peptide hormones

Optimized IMAC-IMAC protocol for phosphopeptide recovery from complex biological samples

DEFF Research Database (Denmark)

Ye, Juanying; Zhang, Xumin; Young, Clifford

2010-01-01

using Fe(III)-NTA IMAC resin and it proved to be highly selective in the phosphopeptide enrichment of a highly diluted standard sample (1:1000) prior to MALDI MS analysis. We also observed that a higher iron purity led to an increased IMAC enrichment efficiency. The optimized method was then adapted...... to phosphoproteome analyses of cell lysates of high protein complexity. From either 20 microg of mouse sample or 50 microg of Drosophila melanogaster sample, more than 1000 phosphorylation sites were identified in each study using IMAC-IMAC and LC-MS/MS. We demonstrate efficient separation of multiply phosphorylated...... characterization of phosphoproteins in functional phosphoproteomics research projects....

Quantitative assessment of growth plate activity

International Nuclear Information System (INIS)

Harcke, H.T.; Macy, N.J.; Mandell, G.A.; MacEwen, G.D.

1984-01-01

In the immature skeleton the physis or growth plate is the area of bone least able to withstand external forces and is therefore prone to trauma. Such trauma often leads to premature closure of the plate and results in limb shortening and/or angular deformity (varus or valgus). Active localization of bone seeking tracers in the physis makes bone scintigraphy an excellent method for assessing growth plate physiology. To be most effective, however, physeal activity should be quantified so that serial evaluations are accurate and comparable. The authors have developed a quantitative method for assessing physeal activity and have applied it ot the hip and knee. Using computer acquired pinhole images of the abnormal and contralateral normal joints, ten regions of interest are placed at key locations around each joint and comparative ratios are generated to form a growth plate profile. The ratios compare segmental physeal activity to total growth plate activity on both ipsilateral and contralateral sides and to adjacent bone. In 25 patients, ages 2 to 15 years, with angular deformities of the legs secondary to trauma, Blount's disease, and Perthes disease, this technique is able to differentiate abnormal segmental physeal activity. This is important since plate closure does not usually occur uniformly across the physis. The technique may permit the use of scintigraphy in the prediction of early closure through the quantitative analysis of serial studies

Dominant Epistasis Between Two Quantitative Trait Loci Governing Sporulation Efficiency in Yeast Saccharomyces cerevisiae

Science.gov (United States)

Bergman, Juraj; Mitrikeski, Petar T.

2015-01-01

Summary Sporulation efficiency in the yeast Saccharomyces cerevisiae is a well-established model for studying quantitative traits. A variety of genes and nucleotides causing different sporulation efficiencies in laboratory, as well as in wild strains, has already been extensively characterised (mainly by reciprocal hemizygosity analysis and nucleotide exchange methods). We applied a different strategy in order to analyze the variation in sporulation efficiency of laboratory yeast strains. Coupling classical quantitative genetic analysis with simulations of phenotypic distributions (a method we call phenotype modelling) enabled us to obtain a detailed picture of the quantitative trait loci (QTLs) relationships underlying the phenotypic variation of this trait. Using this approach, we were able to uncover a dominant epistatic inheritance of loci governing the phenotype. Moreover, a molecular analysis of known causative quantitative trait genes and nucleotides allowed for the detection of novel alleles, potentially responsible for the observed phenotypic variation. Based on the molecular data, we hypothesise that the observed dominant epistatic relationship could be caused by the interaction of multiple quantitative trait nucleotides distributed across a 60--kb QTL region located on chromosome XIV and the RME1 locus on chromosome VII. Furthermore, we propose a model of molecular pathways which possibly underlie the phenotypic variation of this trait. PMID:27904371

New possibilities for quantitative measurements of regional cerebral blood flow with Au-195 m

International Nuclear Information System (INIS)

Lindner, P.; Nickel, O.

1984-01-01

A previously reported theory for quantitative cerebral blood flow measurement for nondiffusible radiotracers has been applied on patients after stroke and an volunteers undergoing a mental stimulation exercise. Quantitative measurements of cerebral blood flow patterns not only in p-a. but also in lateral views of the brain are possible by the use of the recently developed generator for the short lived (30 sec) isotope Au-195 m. The energy spectrum of the eluate of the generator shows two strong photon peaks, one at an energy level of 68 KeV and a second at an energy-level of 262 KeV. The low energy peak is suitable for perfusion studies in lateral views of the hemispheres, no ''look through'' effect is seen. The high energy level is good for studies in p-a-positions. The studies last less than 1 minute and can be repeated after 3 minutes. Parametric images for quantitative regional cerebral blood flow can be generated. The area of occluded vessels in the case of stroke can be detected. Quantitative activation patterns of cerebral blood flow during mental stimulation can be generated. The results prove that not only with freely diffusible indicators like Xenon but also with nondiffusible indicators it is possible to measure quantitatively cerebral blood flow patterns. (orig.)

Quantitative MR imaging in fracture dating--Initial results.

Science.gov (United States)

Baron, Katharina; Neumayer, Bernhard; Widek, Thomas; Schick, Fritz; Scheicher, Sylvia; Hassler, Eva; Scheurer, Eva

2016-04-01

For exact age determinations of bone fractures in a forensic context (e.g. in cases of child abuse) improved knowledge of the time course of the healing process and use of non-invasive modern imaging technology is of high importance. To date, fracture dating is based on radiographic methods by determining the callus status and thereby relying on an expert's experience. As a novel approach, this study aims to investigate the applicability of magnetic resonance imaging (MRI) for bone fracture dating by systematically investigating time-resolved changes in quantitative MR characteristics after a fracture event. Prior to investigating fracture healing in children, adults were examined for this study in order to test the methodology for this application. Altogether, 31 MR examinations in 17 subjects (♀: 11 ♂: 6; median age 34 ± 15 y, scanned 1-5 times over a period of up to 200 days after the fracture event) were performed on a clinical 3T MR scanner (TimTrio, Siemens AG, Germany). All subjects were treated conservatively for a fracture in either a long bone or in the collar bone. Both, qualitative and quantitative MR measurements were performed in all subjects. MR sequences for a quantitative measurement of relaxation times T1 and T2 in the fracture gap and musculature were applied. Maps of quantitative MR parameters T1, T2, and magnetisation transfer ratio (MTR) were calculated and evaluated by investigating changes over time in the fractured area by defined ROIs. Additionally, muscle areas were examined as reference regions to validate this approach. Quantitative evaluation of 23 MR data sets (12 test subjects, ♀: 7 ♂: 5) showed an initial peak in T1 values in the fractured area (T1=1895 ± 607 ms), which decreased over time to a value of 1094 ± 182 ms (200 days after the fracture event). T2 values also peaked for early-stage fractures (T2=115 ± 80 ms) and decreased to 73 ± 33 ms within 21 days after the fracture event. After that time point, no

The Performance of Indian Equity Funds in the Era of Quantitative Easing

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Ömer Faruk Tan

2015-10-01

Full Text Available This study aims to evaluate the performance of Indian equity funds between January 2009 and October 2014. This study period coincides with the period of quantitative easing during which the developing economies in financial markets have been influenced. After the global financial crisis of 2008 came a period of quantitative easing (QE, creating an increase in the money supply and leading to a capital flow from developed countries to developing countries. During this 5-year 10-month period, in which the relevant quantitative easing continued, Indian CNX500 price index yielded approximately 21% compounded on average, per annum. In this study, Indian equity funds are examined in order to compare these funds’ performance within this period. Within this scope, 12 Indian equity funds are chosen. In order to measure these funds’ performances, the Sharpe ratio (1966, Treynor ratio (1965, Jensen’s alpha (1968 methods are used. Jensen’s alpha is also used in identifying selectivity skills of fund managers. Additionally, the Treynor & Mazuy (1966 regression analysis method is applied to show the market timing ability of fund managers.

Can Transformational Leadership Influence on Teachers' Commitment towards Organization, Teaching Profession, and Students Learning? A Quantitative Analysis

Science.gov (United States)

Ibrahim, Mohammed Sani; Ghavifekr, Simin; Ling, Sii; Siraj, Saedah; Azeez, Mohd Ibrahim K.

2014-01-01

This study investigates the impact of transformational leadership as idealized influence, inspirational motivation, intellectual stimulation, and individualized consideration on teachers' commitment towards organization, teaching profession, and students' learning. A quantitative survey method was applied, and four broadly hypothesized…

Quantitative flow visualization of fluidized-bed heat exchanger by neutron radiography

International Nuclear Information System (INIS)

Ozawa, M.; Umekawa, H.; Furui, S.; Hayashi, K.; Takenaka, N.

2004-01-01

Quantitative flow visualization of a gas-solid fluidized-bed installed vertical tube-bank has been successfully conducted using neutron radiography and image processing technique. The quantitative data of void fraction distribution as well as the fluctuation data are presented. The time-averaged void fraction is well correlated by the drift-flux model. The bubbles formed in the bed, rise along the vertical tubes and the observed bubble size is smaller than that in a free bubbling bed without tube-banks. The bubble diameter is well correlated by the modified Mori and Wen's correlation taking into account the pitch of tube arrangement. The bubble rise velocity is also well correlated by applying the drift-flux model. These results are consistent for both bed materials of Geldart's B- and A-particles, while the bubble size is significantly different between two kinds of particles

Preparation of Biological Samples Containing Metoprolol and Bisoprolol for Applying Methods for Quantitative Analysis

Directory of Open Access Journals (Sweden)

Corina Mahu Ştefania

2015-12-01

Full Text Available Arterial hypertension is a complex disease with many serious complications, representing a leading cause of mortality. Selective beta-blockers such as metoprolol and bisoprolol are frequently used in the management of hypertension. Numerous analytical methods have been developed for the determination of these substances in biological fluids, such as liquid chromatography coupled with mass spectrometry, gas chromatography coupled with mass spectrometry, high performance liquid chromatography. Due to the complex composition of biological fluids a biological sample pre-treatment before the use of the method for quantitative determination is required in order to remove proteins and potential interferences. The most commonly used methods for processing biological samples containing metoprolol and bisoprolol were identified through a thorough literature search using PubMed, ScienceDirect, and Willey Journals databases. Articles published between years 2005-2015 were reviewed. Protein precipitation, liquid-liquid extraction and solid phase extraction are the main techniques for the extraction of these drugs from plasma, serum, whole blood and urine samples. In addition, numerous other techniques have been developed for the preparation of biological samples, such as dispersive liquid-liquid microextraction, carrier-mediated liquid phase microextraction, hollow fiber-protected liquid phase microextraction, on-line molecularly imprinted solid phase extraction. The analysis of metoprolol and bisoprolol in human plasma, urine and other biological fluids provides important information in clinical and toxicological trials, thus requiring the application of appropriate extraction techniques for the detection of these antihypertensive substances at nanogram and picogram levels.

Quantitative structure-property relationship (correlation analysis) of phosphonic acid-based chelates in design of MRI contrast agent.

Science.gov (United States)

Tiwari, Anjani K; Ojha, Himanshu; Kaul, Ankur; Dutta, Anupama; Srivastava, Pooja; Shukla, Gauri; Srivastava, Rakesh; Mishra, Anil K

2009-07-01

Nuclear magnetic resonance imaging is a very useful tool in modern medical diagnostics, especially when gadolinium (III)-based contrast agents are administered to the patient with the aim of increasing the image contrast between normal and diseased tissues. With the use of soft modelling techniques such as quantitative structure-activity relationship/quantitative structure-property relationship after a suitable description of their molecular structure, we have studied a series of phosphonic acid for designing new MRI contrast agent. Quantitative structure-property relationship studies with multiple linear regression analysis were applied to find correlation between different calculated molecular descriptors of the phosphonic acid-based chelating agent and their stability constants. The final quantitative structure-property relationship mathematical models were found as--quantitative structure-property relationship Model for phosphonic acid series (Model 1)--log K(ML) = {5.00243(+/-0.7102)}- MR {0.0263(+/-0.540)}n = 12 l r l = 0.942 s = 0.183 F = 99.165 quantitative structure-property relationship Model for phosphonic acid series (Model 2)--log K(ML) = {5.06280(+/-0.3418)}- MR {0.0252(+/- .198)}n = 12 l r l = 0.956 s = 0.186 F = 99.256.

Quantitative tomographic measurements of opaque multiphase flows

Energy Technology Data Exchange (ETDEWEB)

GEORGE,DARIN L.; TORCZYNSKI,JOHN R.; SHOLLENBERGER,KIM ANN; O' HERN,TIMOTHY J.; CECCIO,STEVEN L.

2000-03-01

An electrical-impedance tomography (EIT) system has been developed for quantitative measurements of radial phase distribution profiles in two-phase and three-phase vertical column flows. The EIT system is described along with the computer algorithm used for reconstructing phase volume fraction profiles. EIT measurements were validated by comparison with a gamma-densitometry tomography (GDT) system. The EIT system was used to accurately measure average solid volume fractions up to 0.05 in solid-liquid flows, and radial gas volume fraction profiles in gas-liquid flows with gas volume fractions up to 0.15. In both flows, average phase volume fractions and radial volume fraction profiles from GDT and EIT were in good agreement. A minor modification to the formula used to relate conductivity data to phase volume fractions was found to improve agreement between the methods. GDT and EIT were then applied together to simultaneously measure the solid, liquid, and gas radial distributions within several vertical three-phase flows. For average solid volume fractions up to 0.30, the gas distribution for each gas flow rate was approximately independent of the amount of solids in the column. Measurements made with this EIT system demonstrate that EIT may be used successfully for noninvasive, quantitative measurements of dispersed multiphase flows.

Affinity for Quantitative Tools: Undergraduate Marketing Students Moving beyond Quantitative Anxiety

Science.gov (United States)

Tarasi, Crina O.; Wilson, J. Holton; Puri, Cheenu; Divine, Richard L.

2013-01-01

Marketing students are known as less likely to have an affinity for the quantitative aspects of the marketing discipline. In this article, we study the reasons why this might be true and develop a parsimonious 20-item scale for measuring quantitative affinity in undergraduate marketing students. The scale was administered to a sample of business…

Brain microstructure mapping using quantitative and diffusion MRI

International Nuclear Information System (INIS)

Lebois, Alice

2014-01-01

), in order to better understand their relations and to explain the observed variability along the fascicles and the interhemispheric asymmetries. The second part was focused on the brain tissue modeling at the cell scale to extract the quantitative parameters characterizing the geometry of the cellular membranes, such as the axonal diameter and the axonal density. A diffusion MRI sequence was developed on the 3 Teslas and 7 Teslas Siemens clinical systems of NeuroSpin which is able to apply any kind of gradient waveforms to fall within an approach where the gradient waveform results from an optimization under the hypothesis of a geometrical tissue model, hardware and time constraints induced by clinical applications. This sequence was applied in the study of fourteen healthy subjects in order to build the first quantitative atlas of the axonal diameter and the local axonal density at 7 T. We also proposed a new geometrical model to model the axon, dividing the axonal compartment, usually modelled using a simple cylinder, into two compartments: one being near the membranes with low diffusivity and one farther from the membranes, less restricted and with higher diffusivity. We conducted a theoretical study showing that under clinical conditions, this new model allows, in part, to overcome the bias induced by the simple cylindrical model leading to a systematic overestimation of the smallest diameters. Finally, in the aim of going further in the physiopathology of the autism, we added to the current 3 T imaging protocol the dMRI sequence developed in the framework of this thesis in order to map the axonal diameter and density. This study is ongoing and should validate shortly the contribution of these new quantitative measures of the microstructure in the comprehension of the atrophies of the corpus callosum, initially observed using less specific diffusion parameters such as the generalized fractional anisotropy. There will be other clinical applications in the future

[Statistical analysis of articles in "Chinese journal of applied physiology" from 1999 to 2008].

Science.gov (United States)

Du, Fei; Fang, Tao; Ge, Xue-ming; Jin, Peng; Zhang, Xiao-hong; Sun, Jin-li

2010-05-01

To evaluate the academic level and influence of "Chinese Journal of Applied Physiology" through statistical analysis for the fund sponsored articles published in the recent ten years. The articles of "Chinese Journal of Applied Physiology" from 1999 to 2008 were investigated. The number and the percentage of the fund sponsored articles, the fund organization and the author region were quantitatively analyzed by using the literature metrology method. The number of the fund sponsored articles increased unceasingly. The ratio of the fund from local government significantly enhanced in the latter five years. Most of the articles were from institutes located at Beijing, Zhejiang and Tianjin. "Chinese Journal of Applied Physiology" has a fine academic level and social influence.

Isotropic differential phase contrast microscopy for quantitative phase bio-imaging.

Science.gov (United States)

Chen, Hsi-Hsun; Lin, Yu-Zi; Luo, Yuan

2018-05-16

Quantitative phase imaging (QPI) has been investigated to retrieve optical phase information of an object and applied to biological microscopy and related medical studies. In recent examples, differential phase contrast (DPC) microscopy can recover phase image of thin sample under multi-axis intensity measurements in wide-field scheme. Unlike conventional DPC, based on theoretical approach under partially coherent condition, we propose a new method to achieve isotropic differential phase contrast (iDPC) with high accuracy and stability for phase recovery in simple and high-speed fashion. The iDPC is simply implemented with a partially coherent microscopy and a programmable thin-film transistor (TFT) shield to digitally modulate structured illumination patterns for QPI. In this article, simulation results show consistency of our theoretical approach for iDPC under partial coherence. In addition, we further demonstrate experiments of quantitative phase images of a standard micro-lens array, as well as label-free live human cell samples. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative mixture fraction measurements in combustion system via laser induced breakdown spectroscopy

KAUST Repository

Mansour, Mohy S.

2015-01-01

Laser induced breakdown spectroscopy (LIBS) technique has been applied to quantitative mixture fraction measurements in flames. The measured spectra of different mixtures of natural gas and air are used to obtain the calibration parameters for local elemental mass fraction measurements and hence calculate the mixture fraction. The results are compared with the mixture fraction calculations based on the ratios of the spectral lines of H/N elements, H/O elements and C/(N+O) and they show good agreement within the reaction zone of the flames. Some deviations are observed outside the reaction zone. The ability of LIBS technique as a tool for quantitative mixture fraction as well as elemental fraction measurements in reacting and non-reacting of turbulent flames is feasible. © 2014 Elsevier Ltd. All rights reserved.

Quantitative Analysis of Microbes in Water Tank of G.A. Siwabessy Reactor

International Nuclear Information System (INIS)

Itjeu Karliana; Diah Dwiana Lestiani

2003-01-01

The quality of water in reactor system has an important role because it could effect the function as a coolant and the operation of reactor indirectly. The study of microbe analyzes has been carried out to detect the existence of microbes in water tank and quantitative analyzes of microbes also has been applied as a continuation of the previous study. The samples is taken out from the end side of reactor GA Siwabessy's tank, inoculated in TSA (Tripcase Soy Agar) medium, put in incubator at 30 - 35 o C for 4 days. The results of experiment show the reconfirmation for the existence of bacteria and the un-existence of yield. The quantitative analysis with TPC method show the growth rate of bacteria is twice in 24 hours. (author)

Ion-solid interaction at low energies: principles and application of quantitative ISS

International Nuclear Information System (INIS)

Niehus, H.; Spitzl, R.

1991-01-01

Quantitative surface analysis with low-energy (500-5000 eV) ion scattering spectroscopy is known to be difficult, most often because of strong charge transfer and multiple scattering effects occurring during ion-surface interaction. In order to avoid neutralization problems, either alkali primary ions or noble gas ions in combination with the detection of all scattered particles was applied. Multiple scattering occurs predominantly at forward scattering and might confound the analysis. Backward scattering (i.e. 180 o impact collision ion scattering) bypasses strongly the multiple scattering complication and has been used successfully for the analysis of a number of surface structures for metals, semiconductors and binary alloys. A simple triangulation concept gives access to mass-selective qualitative surface crystallography. Quantitative surface structures were determined by comparison with computer simulations. (author)

A Mixed-Methods Analysis in Assessing Students' Professional Development by Applying an Assessment for Learning Approach.

Science.gov (United States)

Peeters, Michael J; Vaidya, Varun A

2016-06-25

Objective. To describe an approach for assessing the Accreditation Council for Pharmacy Education's (ACPE) doctor of pharmacy (PharmD) Standard 4.4, which focuses on students' professional development. Methods. This investigation used mixed methods with triangulation of qualitative and quantitative data to assess professional development. Qualitative data came from an electronic developmental portfolio of professionalism and ethics, completed by PharmD students during their didactic studies. Quantitative confirmation came from the Defining Issues Test (DIT)-an assessment of pharmacists' professional development. Results. Qualitatively, students' development reflections described growth through this course series. Quantitatively, the 2015 PharmD class's DIT N2-scores illustrated positive development overall; the lower 50% had a large initial improvement compared to the upper 50%. Subsequently, the 2016 PharmD class confirmed these average initial improvements of students and also showed further substantial development among students thereafter. Conclusion. Applying an assessment for learning approach, triangulation of qualitative and quantitative assessments confirmed that PharmD students developed professionally during this course series.

Public and Public Utility Enterprises Restructuring: Statistical and Quantitative Aid for Ensuring Human Resource Sustainability

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Mladen Čudanov

2014-04-01

Full Text Available This article presents a quantitative approach to restructuring public and public utility enterprises, particularly during downsizing requests. The large number of employees in the public sector can be one of the causes for economic instability at country level. That is particularly visible in the context of the euro zone crisis and economic/political instability in countries like Greece, Portugal, Ireland, Spain and Italy. Our approach is based on the statistical analysis of productivity oscillation and setting of performance standards in public and public utility enterprises based on the aforementioned productivity. Data background is given through job descriptions, organizational charts, salary reports and monthly performance reports, in most cases part of organizational information systems. It is recommended for quantitative data to be analyzed on a monthly basis, during a period of 30 or more months. Our method increases procedural fairness and accuracy, because quantitative, statistical, impartial and objective approach is applied for estimating parameters which could be related to downsizing. However, the application of this method is not limited to downsizing, as during its application in more than 20 public and public utility enterprises it was sometimes applied to increase output or reduce costs not necessarily connected to labour. Although it finally refers to downsizing, this method can provide fairer and more impartial approach than the subjective estimate of employee surplus, and its arbitral distribution within the enterprise.

SPECT myocardial blood flow quantitation toward clinical use: a comparative study with {sup 13}N-Ammonia PET myocardial blood flow quantitation

Energy Technology Data Exchange (ETDEWEB)

Hsu, Bailing [University of Missouri-Columbia, Nuclear Science and Engineering Institute, Columbia, Missouri (United States); Hu, Lien-Hsin; Yang, Bang-Hung; Ting, Chien-Hsin; Huang, Wen-Sheng [Taipei Veterans General Hospital, Department of Nuclear Medicine, Taipei (China); Chen, Lung-Ching [Shin Kong Wu-Ho Su Memorial Hospital, Division of Cardiology, Taipei (China); Chen, Yen-Kung [Shin Kong Wu-Ho Su Memorial Hospital, Department of Nuclear Medicine, Taipei (China); Hung, Guang-Uei [Chang Bing Show Chwan Memorial Hospital, Department of Nuclear Medicine, Changhua (China); Wu, Tao-Cheng [National Yang-Ming University, Cardiovascular Research Center, Taipei (China)

2017-01-15

The aim of this study was to evaluate the accuracy of myocardial blood flow (MBF) quantitation of {sup 99m}Tc-Sestamibi (MIBI) single photon emission computed tomography (SPECT) compared with {sup 13}N-Ammonia (NH3) position emission tomography (PET) on the same cohorts. Recent advances of SPECT technologies have been applied to develop MBF quantitation as a promising tool to diagnose coronary artery disease (CAD) for areas where PET MBF quantitation is not available. However, whether the SPECT approach can achieve the same level of accuracy as the PET approach for clinical use still needs further investigations. Twelve healthy volunteers (HVT) and 16 clinical patients with CAD received both MIBI SPECT and NH3 PET flow scans. Dynamic SPECT images acquired with high temporary resolution were fully corrected for physical factors and processed to quantify K1 using the standard compartmental modeling. Human MIBI tracer extraction fraction (EF) was determined by comparing MIBI K1 and NH3 flow on the HVT group and then used to convert flow values from K1 for all subjects. MIBI and NH3 flow values were systematically compared to validate the SPECT approach. The human MIBI EF was determined as [1.0-0.816*exp(-0.267/MBF)]. Global and regional MBF and myocardial flow reserve (MFR) of MIBI SPECT and NH3 PET were highly correlated for all subjects (global R{sup 2}: MBF = 0.92, MFR = 0.78; regional R{sup 2}: MBF ≥ 0.88, MFR ≥ 0.71). No significant differences for rest flow, stress flow, and MFR between these two approaches were observed (All p ≥ 0.088). Bland-Altman plots overall revealed small bias between MIBI SPECT and NH3 PET (global: ΔMBF = -0.03Lml/min/g, ΔMFR = 0.07; regional: ΔMBF = -0.07 - 0.06, ΔMFR = -0.02 - 0.22). Quantitation with SPECT technologies can be accurate to measure myocardial blood flow as PET quantitation while comprehensive imaging factors of SPECT to derive the variability between these two approaches were fully addressed and corrected

SPECT myocardial blood flow quantitation toward clinical use: a comparative study with "1"3N-Ammonia PET myocardial blood flow quantitation

International Nuclear Information System (INIS)

Hsu, Bailing; Hu, Lien-Hsin; Yang, Bang-Hung; Ting, Chien-Hsin; Huang, Wen-Sheng; Chen, Lung-Ching; Chen, Yen-Kung; Hung, Guang-Uei; Wu, Tao-Cheng

2017-01-01

The aim of this study was to evaluate the accuracy of myocardial blood flow (MBF) quantitation of "9"9"mTc-Sestamibi (MIBI) single photon emission computed tomography (SPECT) compared with "1"3N-Ammonia (NH3) position emission tomography (PET) on the same cohorts. Recent advances of SPECT technologies have been applied to develop MBF quantitation as a promising tool to diagnose coronary artery disease (CAD) for areas where PET MBF quantitation is not available. However, whether the SPECT approach can achieve the same level of accuracy as the PET approach for clinical use still needs further investigations. Twelve healthy volunteers (HVT) and 16 clinical patients with CAD received both MIBI SPECT and NH3 PET flow scans. Dynamic SPECT images acquired with high temporary resolution were fully corrected for physical factors and processed to quantify K1 using the standard compartmental modeling. Human MIBI tracer extraction fraction (EF) was determined by comparing MIBI K1 and NH3 flow on the HVT group and then used to convert flow values from K1 for all subjects. MIBI and NH3 flow values were systematically compared to validate the SPECT approach. The human MIBI EF was determined as [1.0-0.816*exp(-0.267/MBF)]. Global and regional MBF and myocardial flow reserve (MFR) of MIBI SPECT and NH3 PET were highly correlated for all subjects (global R"2: MBF = 0.92, MFR = 0.78; regional R"2: MBF ≥ 0.88, MFR ≥ 0.71). No significant differences for rest flow, stress flow, and MFR between these two approaches were observed (All p ≥ 0.088). Bland-Altman plots overall revealed small bias between MIBI SPECT and NH3 PET (global: ΔMBF = -0.03Lml/min/g, ΔMFR = 0.07; regional: ΔMBF = -0.07 - 0.06, ΔMFR = -0.02 - 0.22). Quantitation with SPECT technologies can be accurate to measure myocardial blood flow as PET quantitation while comprehensive imaging factors of SPECT to derive the variability between these two approaches were fully addressed and corrected. (orig.)

Comparative gel-based phosphoproteomics in response to signaling molecules

KAUST Repository

Marondedze, Claudius; Lilley, Kathryn S.; Thomas, Ludivine

2013-01-01

The gel-based proteomics approach is a valuable technique for studying the characteristics of proteins. This technique has diverse applications ranging from analysis of a single protein to the study of the total cellular proteins. Further, protein quality and to some extent distribution can be first assessed by means of one-dimensional gel electrophoresis and then more informatively, for comparative analysis, using the two-dimensional gel electrophoresis technique. Here, we describe how to take advantage of the availability of fluorescent dyes to stain for a selective class of proteins on the same gel for the detection of both phospho- and total proteomes. This enables the co-detection of phosphoproteins as well as total proteins from the same gel and is accomplished by utilizing two different fluorescent stains, the ProQ-Diamond, which stains only phosphorylated proteins, and Sypro Ruby, which stains the entire subset of proteins. This workflow can be applied to gain insights into the regulatory mechanisms induced by signaling molecules such as cyclic nucleotides through the quantification and subsequent identification of responsive phospho- and total proteins. © Springer Science+Business Media New York 2013.

Comparative gel-based phosphoproteomics in response to signaling molecules

KAUST Repository

Marondedze, Claudius

2013-09-03

The gel-based proteomics approach is a valuable technique for studying the characteristics of proteins. This technique has diverse applications ranging from analysis of a single protein to the study of the total cellular proteins. Further, protein quality and to some extent distribution can be first assessed by means of one-dimensional gel electrophoresis and then more informatively, for comparative analysis, using the two-dimensional gel electrophoresis technique. Here, we describe how to take advantage of the availability of fluorescent dyes to stain for a selective class of proteins on the same gel for the detection of both phospho- and total proteomes. This enables the co-detection of phosphoproteins as well as total proteins from the same gel and is accomplished by utilizing two different fluorescent stains, the ProQ-Diamond, which stains only phosphorylated proteins, and Sypro Ruby, which stains the entire subset of proteins. This workflow can be applied to gain insights into the regulatory mechanisms induced by signaling molecules such as cyclic nucleotides through the quantification and subsequent identification of responsive phospho- and total proteins. © Springer Science+Business Media New York 2013.

Quantitive DNA Fiber Mapping

Energy Technology Data Exchange (ETDEWEB)

Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

2008-01-28

Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

Analytical robustness of quantitative NIR chemical imaging for Islamic paper characterization

Science.gov (United States)

Mahgoub, Hend; Gilchrist, John R.; Fearn, Thomas; Strlič, Matija

2017-07-01

Recently, spectral imaging techniques such as Multispectral (MSI) and Hyperspectral Imaging (HSI) have gained importance in the field of heritage conservation. This paper explores the analytical robustness of quantitative chemical imaging for Islamic paper characterization by focusing on the effect of different measurement and processing parameters, i.e. acquisition conditions and calibration on the accuracy of the collected spectral data. This will provide a better understanding of the technique that can provide a measure of change in collections through imaging. For the quantitative model, special calibration target was devised using 105 samples from a well-characterized reference Islamic paper collection. Two material properties were of interest: starch sizing and cellulose degree of polymerization (DP). Multivariate data analysis methods were used to develop discrimination and regression models which were used as an evaluation methodology for the metrology of quantitative NIR chemical imaging. Spectral data were collected using a pushbroom HSI scanner (Gilden Photonics Ltd) in the 1000-2500 nm range with a spectral resolution of 6.3 nm using a mirror scanning setup and halogen illumination. Data were acquired at different measurement conditions and acquisition parameters. Preliminary results showed the potential of the evaluation methodology to show that measurement parameters such as the use of different lenses and different scanning backgrounds may not have a great influence on the quantitative results. Moreover, the evaluation methodology allowed for the selection of the best pre-treatment method to be applied to the data.

Mixed methods in gerontological research: Do the qualitative and quantitative data “touch”?

Science.gov (United States)

Happ, Mary Beth

2010-01-01

This paper distinguishes between parallel and integrated mixed methods research approaches. Barriers to integrated mixed methods approaches in gerontological research are discussed and critiqued. The author presents examples of mixed methods gerontological research to illustrate approaches to data integration at the levels of data analysis, interpretation, and research reporting. As a summary of the methodological literature, four basic levels of mixed methods data combination are proposed. Opportunities for mixing qualitative and quantitative data are explored using contemporary examples from published studies. Data transformation and visual display, judiciously applied, are proposed as pathways to fuller mixed methods data integration and analysis. Finally, practical strategies for mixing qualitative and quantitative data types are explicated as gerontological research moves beyond parallel mixed methods approaches to achieve data integration. PMID:20077973

Identification and Quantitation of Malonic Acid Biomarkers of In-Born Error Metabolism by Targeted Metabolomics

Science.gov (United States)

Ambati, Chandra Shekar R.; Yuan, Furong; Abu-Elheiga, Lutfi A.; Zhang, Yiqing; Shetty, Vivekananda

2017-05-01

Malonic acid (MA), methylmalonic acid (MMA), and ethylmalonic acid (EMA) metabolites are implicated in various non-cancer disorders that are associated with inborn-error metabolism. In this study, we have slightly modified the published 3-nitrophenylhydrazine (3NPH) derivatization method and applied it to derivatize MA, MMA, and EMA to their hydrazone derivatives, which were amenable for liquid chromatography- mass spectrometry (LC-MS) quantitation. 3NPH was used to derivatize MA, MMA, and EMA, and multiple reaction monitoring (MRM) transitions of the corresponding derivatives were determined by product-ion experiments. Data normalization and absolute quantitation were achieved by using 3NPH derivatized isotopic labeled compounds 13C2-MA, MMA-D3, and EMA-D3. The detection limits were found to be at nanomolar concentrations and a good linearity was achieved from nanomolar to millimolar concentrations. As a proof of concept study, we have investigated the levels of malonic acids in mouse plasma with malonyl-CoA decarboxylase deficiency (MCD-D), and we have successfully applied 3NPH method to identify and quantitate all three malonic acids in wild type (WT) and MCD-D plasma with high accuracy. The results of this method were compared with that of underivatized malonic acid standards experiments that were performed using hydrophilic interaction liquid chromatography (HILIC)-MRM. Compared with HILIC method, 3NPH derivatization strategy was found to be very efficient to identify these molecules as it greatly improved the sensitivity, quantitation accuracy, as well as peak shape and resolution. Furthermore, there was no matrix effect in LC-MS analysis and the derivatized metabolites were found to be very stable for longer time.

Time-Gated Raman Spectroscopy for Quantitative Determination of Solid-State Forms of Fluorescent Pharmaceuticals.

Science.gov (United States)

Lipiäinen, Tiina; Pessi, Jenni; Movahedi, Parisa; Koivistoinen, Juha; Kurki, Lauri; Tenhunen, Mari; Yliruusi, Jouko; Juppo, Anne M; Heikkonen, Jukka; Pahikkala, Tapio; Strachan, Clare J

2018-04-03

Raman spectroscopy is widely used for quantitative pharmaceutical analysis, but a common obstacle to its use is sample fluorescence masking the Raman signal. Time-gating provides an instrument-based method for rejecting fluorescence through temporal resolution of the spectral signal and allows Raman spectra of fluorescent materials to be obtained. An additional practical advantage is that analysis is possible in ambient lighting. This study assesses the efficacy of time-gated Raman spectroscopy for the quantitative measurement of fluorescent pharmaceuticals. Time-gated Raman spectroscopy with a 128 × (2) × 4 CMOS SPAD detector was applied for quantitative analysis of ternary mixtures of solid-state forms of the model drug, piroxicam (PRX). Partial least-squares (PLS) regression allowed quantification, with Raman-active time domain selection (based on visual inspection) improving performance. Model performance was further improved by using kernel-based regularized least-squares (RLS) regression with greedy feature selection in which the data use in both the Raman shift and time dimensions was statistically optimized. Overall, time-gated Raman spectroscopy, especially with optimized data analysis in both the spectral and time dimensions, shows potential for sensitive and relatively routine quantitative analysis of photoluminescent pharmaceuticals during drug development and manufacturing.

Quantitative Model for Economic Analyses of Information Security Investment in an Enterprise Information System

Directory of Open Access Journals (Sweden)

Bojanc Rok

2012-11-01

Full Text Available The paper presents a mathematical model for the optimal security-technology investment evaluation and decision-making processes based on the quantitative analysis of security risks and digital asset assessments in an enterprise. The model makes use of the quantitative analysis of different security measures that counteract individual risks by identifying the information system processes in an enterprise and the potential threats. The model comprises the target security levels for all identified business processes and the probability of a security accident together with the possible loss the enterprise may suffer. The selection of security technology is based on the efficiency of selected security measures. Economic metrics are applied for the efficiency assessment and comparative analysis of different protection technologies. Unlike the existing models for evaluation of the security investment, the proposed model allows direct comparison and quantitative assessment of different security measures. The model allows deep analyses and computations providing quantitative assessments of different options for investments, which translate into recommendations facilitating the selection of the best solution and the decision-making thereof. The model was tested using empirical examples with data from real business environment.

A simplified method for quantitative assessment of the relative health and safety risk of environmental management activities

International Nuclear Information System (INIS)

Eide, S.A.; Smith, T.H.; Peatross, R.G.; Stepan, I.E.

1996-09-01

This report presents a simplified method to assess the health and safety risk of Environmental Management activities of the US Department of Energy (DOE). The method applies to all types of Environmental Management activities including waste management, environmental restoration, and decontamination and decommissioning. The method is particularly useful for planning or tradeoff studies involving multiple conceptual options because it combines rapid evaluation with a quantitative approach. The method is also potentially applicable to risk assessments of activities other than DOE Environmental Management activities if rapid quantitative results are desired

Quantitative multi-waves migration in elastic anisotropic media; Migration quantitative multi-ondes en milieu elastique anisotrope

Energy Technology Data Exchange (ETDEWEB)

Borgne, H.

2004-12-01

Seismic imaging is an important tool for ail exploration. From the filtered seismic traces and a subsurface velocity model, migration allows to localize the reflectors and to estimate physical properties of these interfaces. The subsurface is split up into a reference medium, corresponding to the low spatial frequencies (a smooth medium), and a perturbation medium, corresponding to the high spatial frequencies. The propagation of elastic waves in the medium of reference is modelled by the ray theory. The association of this theory with a principle of diffraction or reflection allows to take into account the high spatial frequencies: the Kirchhoff approach represents so the medium of perturbations with continuous surfaces, characterized by reflection coefficients. The target of the quantitative migration is to reconstruct this reflection coefficient, notably its behaviour according to the incidence angle. These information will open the way to seismic characterization of the reservoir domain, with. a stratigraphic inversion for instance. In order to improve the qualitative and quantitative migration results, one of the current challenges is to take into account the anisotropy of the subsurface. Taking into account rocks anisotropy in the imaging process of seismic data requires two improvements from the isotropic case. The first one roughly concerns the modelling aspect: an anisotropic propagator should be used to avoid a mis-positioning or bad focusing of the imaged reflectors. The second correction concerns the migration aspect: as anisotropy affects the reflectivity of subsurface, a specific anisotropic imaging formula should be applied in the migration kernel, in order to recover the correct A V A behavior of the subsurface reflectors, If the first correction is DOW made in most so-called anisotropic imaging algorithms, the second one is currently ignored. The first part of my work concerns theoretical aspects. 1 study first the preservation of amplitudes in the

A Bayesian belief nets based quantitative software reliability assessment for PSA: COTS case study

International Nuclear Information System (INIS)

Eom, H. S.; Sung, T. Y.; Jeong, H. S.; Park, J. H.; Kang, H. G.; Lee, K. Y.; Park, J. K

2002-03-01

Current reliability assessments of safety critical software embedded in the digital systems in nuclear power plants are based on the rule-based qualitative assessment methods. Then recently practical needs require the quantitative features of software reliability for Probabilistic Safety Assessment (PSA) that is one of important methods being used in assessing the whole safety of nuclear power plant. But conventional quantitative software reliability assessment methods are not enough to get the necessary results in assessing the safety critical software used in nuclear power plants. Thus, current reliability assessment methods for these digital systems exclude the software part or use arbitrary values for the software reliability in the assessment. This reports discusses a Bayesian Belief Nets (BBN) based quantification method that models current qualitative software assessment in formal way and produces quantitative results required for PSA. Commercial Off-The-Shelf (COTS) software dedication process that KAERI developed was applied to the discussed BBN based method for evaluating the plausibility of the proposed method in PSA

Quantitative model analysis with diverse biological data: applications in developmental pattern formation.

Science.gov (United States)

Pargett, Michael; Umulis, David M

2013-07-15

Mathematical modeling of transcription factor and signaling networks is widely used to understand if and how a mechanism works, and to infer regulatory interactions that produce a model consistent with the observed data. Both of these approaches to modeling are informed by experimental data, however, much of the data available or even acquirable are not quantitative. Data that is not strictly quantitative cannot be used by classical, quantitative, model-based analyses that measure a difference between the measured observation and the model prediction for that observation. To bridge the model-to-data gap, a variety of techniques have been developed to measure model "fitness" and provide numerical values that can subsequently be used in model optimization or model inference studies. Here, we discuss a selection of traditional and novel techniques to transform data of varied quality and enable quantitative comparison with mathematical models. This review is intended to both inform the use of these model analysis methods, focused on parameter estimation, and to help guide the choice of method to use for a given study based on the type of data available. Applying techniques such as normalization or optimal scaling may significantly improve the utility of current biological data in model-based study and allow greater integration between disparate types of data. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantitative magneto-optical investigation of superconductor/ferromagnet hybrid structures.

Science.gov (United States)

Shaw, G; Brisbois, J; Pinheiro, L B G L; Müller, J; Blanco Alvarez, S; Devillers, T; Dempsey, N M; Scheerder, J E; Van de Vondel, J; Melinte, S; Vanderbemden, P; Motta, M; Ortiz, W A; Hasselbach, K; Kramer, R B G; Silhanek, A V

2018-02-01

We present a detailed quantitative magneto-optical imaging study of several superconductor/ferromagnet hybrid structures, including Nb deposited on top of thermomagnetically patterned NdFeB and permalloy/niobium with erasable and tailored magnetic landscapes imprinted in the permalloy layer. The magneto-optical imaging data are complemented with and compared to scanning Hall probe microscopy measurements. Comprehensive protocols have been developed for calibrating, testing, and converting Faraday rotation data to magnetic field maps. Applied to the acquired data, they reveal the comparatively weaker magnetic response of the superconductor from the background of larger fields and field gradients generated by the magnetic layer.

Quantitative magneto-optical investigation of superconductor/ferromagnet hybrid structures

Science.gov (United States)

Shaw, G.; Brisbois, J.; Pinheiro, L. B. G. L.; Müller, J.; Blanco Alvarez, S.; Devillers, T.; Dempsey, N. M.; Scheerder, J. E.; Van de Vondel, J.; Melinte, S.; Vanderbemden, P.; Motta, M.; Ortiz, W. A.; Hasselbach, K.; Kramer, R. B. G.; Silhanek, A. V.

2018-02-01

We present a detailed quantitative magneto-optical imaging study of several superconductor/ferromagnet hybrid structures, including Nb deposited on top of thermomagnetically patterned NdFeB and permalloy/niobium with erasable and tailored magnetic landscapes imprinted in the permalloy layer. The magneto-optical imaging data are complemented with and compared to scanning Hall probe microscopy measurements. Comprehensive protocols have been developed for calibrating, testing, and converting Faraday rotation data to magnetic field maps. Applied to the acquired data, they reveal the comparatively weaker magnetic response of the superconductor from the background of larger fields and field gradients generated by the magnetic layer.

Applying quranic contemplation in counseling

Directory of Open Access Journals (Sweden)

Daris Tamin

2016-12-01

Full Text Available The intent of this research project was to explore the use of Quranic contemplation practices in counseling. In Islamic terminology that mean Quranic contemplation known as Tadabbur Al-Quran. Referring to this objective, this research is on the continuum between basic research and applied research. The research method that has been applied mix method beetwen quantitative and qualitative approaches. Integrating the two methods were considered appropriate for pragmatism paradigm adopted in this research. Based on the results of the research found that: Quranic Contemplation in Counseling that applicable on four general phases, namely: Exploration, Reading Scripture, Developing, and Supplication. In particular, at each session consists of seven steps, namely: (1 build engagement counselee to open his/her heart to accept the Quran as a heart medicine, the instructions for the peace of mind and happiness in life; (2 exposing the problems of the counselee; (3 identify the norms adopted counselee; (4 guiding the counselee for contemplations with Quran in the order: recited, guiding understand the meaning of the verse, raised the focus on words related to the problem, the main message conveyed paragraph, reflecting the message of verses in everyday life; and expand the discussion; (5 made a commitment to change the behavior of current and future; (6 invited to join in the spiritual community; and (7 guided prayer.

Quantitative evaluation of orbital hybridization in carbon nanotubes under radial deformation using π-orbital axis vector

Directory of Open Access Journals (Sweden)

Masato Ohnishi

2015-04-01

Full Text Available When a radial strain is applied to a carbon nanotube (CNT, the increase in local curvature induces orbital hybridization. The effect of the curvature-induced orbital hybridization on the electronic properties of CNTs, however, has not been evaluated quantitatively. In this study, the strength of orbital hybridization in CNTs under homogeneous radial strain was evaluated quantitatively. Our analyses revealed the detailed procedure of the change in electronic structure of CNTs. In addition, the dihedral angle, the angle between π-orbital axis vectors of adjacent atoms, was found to effectively predict the strength of local orbital hybridization in deformed CNTs.

Quantitative assessment for pneumoconiosis severity diagnosis using 3D CT images

Science.gov (United States)

Hino, Koki; Matsuhiro, Mikio; Suzuki, Hidenobu; Kawata, Yoshiki; Niki, Noboru; Kato, Katsuya; Kishimoto, Takumi; Ashizawa, Kazuto

2018-02-01

Pneumoconiosis is an occupational respiratory illness that occur by inhaling dust to the lungs. 240,000 participants are screened for diagnosis of pneumoconiosis every year in Japan. Radiograph is used for staging of severity rate in pneumoconiosis worldwide. CT imaging is useful for the differentiation of requirements for industrial accident approval because it can detect small lesions in comparison with radiograph. In this paper, we extracted lung nodules from 3D pneumoconiosis CT images by two manual processes and automatic process, and created a database of pneumoconiosis CT images. We used the database to analyze, compare, and evaluate visual diagnostic results of radiographs and quantitative assessment (number, size and volume) of lung nodules. This method was applied to twenty pneumoconiosis patients. Initial results showed that the proposed method can assess severity rate in pneumoconiosis quantitatively. This study demonstrates effectiveness on diagnosis and prognosis of pneumoconiosis in CT screening.

Analysis of vaginal microbicide film hydration kinetics by quantitative imaging refractometry.

Science.gov (United States)

Rinehart, Matthew; Grab, Sheila; Rohan, Lisa; Katz, David; Wax, Adam

2014-01-01

We have developed a quantitative imaging refractometry technique, based on holographic phase microscopy, as a tool for investigating microscopic structural changes in water-soluble polymeric materials. Here we apply the approach to analyze the structural degradation of vaginal topical microbicide films due to water uptake. We implemented transmission imaging of 1-mm diameter film samples loaded into a flow chamber with a 1.5×2 mm field of view. After water was flooded into the chamber, interference images were captured and analyzed to obtain high resolution maps of the local refractive index and subsequently the volume fraction and mass density of film material at each spatial location. Here, we compare the hydration dynamics of a panel of films with varying thicknesses and polymer compositions, demonstrating that quantitative imaging refractometry can be an effective tool for evaluating and characterizing the performance of candidate microbicide film designs for anti-HIV drug delivery.

A qualitative and quantitative assessment for a bone marrow harvest simulator.

Science.gov (United States)

Machado, Liliane S; Moraes, Ronei M

2009-01-01

Several approaches to perform assessment in training simulators based on virtual reality have been proposed. There are two kinds of assessment methods: offline and online. The main requirements related to online training assessment methodologies applied to virtual reality systems are the low computational complexity and the high accuracy. In the literature it can be found several approaches for general cases which can satisfy such requirements. An inconvenient about those approaches is related to an unsatisfactory solution for specific cases, as in some medical procedures, where there are quantitative and qualitative information available to perform the assessment. In this paper, we present an approach to online training assessment based on a Modified Naive Bayes which can manipulate qualitative and quantitative variables simultaneously. A special medical case was simulated in a bone marrow harvest simulator. The results obtained were satisfactory and evidenced the applicability of the method.

Quantitative Estimation for the Effectiveness of Automation

International Nuclear Information System (INIS)

Lee, Seung Min; Seong, Poong Hyun

2012-01-01

In advanced MCR, various automation systems are applied to enhance the human performance and reduce the human errors in industrial fields. It is expected that automation provides greater efficiency, lower workload, and fewer human errors. However, these promises are not always fulfilled. As the new types of events related to application of the imperfect and complex automation are occurred, it is required to analyze the effects of automation system for the performance of human operators. Therefore, we suggest the quantitative estimation method to analyze the effectiveness of the automation systems according to Level of Automation (LOA) classification, which has been developed over 30 years. The estimation of the effectiveness of automation will be achieved by calculating the failure probability of human performance related to the cognitive activities

Cartilage Repair Surgery: Outcome Evaluation by Using Noninvasive Cartilage Biomarkers Based on Quantitative MRI Techniques?

Science.gov (United States)

Jungmann, Pia M.; Baum, Thomas; Bauer, Jan S.; Karampinos, Dimitrios C.; Link, Thomas M.; Li, Xiaojuan; Trattnig, Siegfried; Rummeny, Ernst J.; Woertler, Klaus; Welsch, Goetz H.

2014-01-01

Background. New quantitative magnetic resonance imaging (MRI) techniques are increasingly applied as outcome measures after cartilage repair. Objective. To review the current literature on the use of quantitative MRI biomarkers for evaluation of cartilage repair at the knee and ankle. Methods. Using PubMed literature research, studies on biochemical, quantitative MR imaging of cartilage repair were identified and reviewed. Results. Quantitative MR biomarkers detect early degeneration of articular cartilage, mainly represented by an increasing water content, collagen disruption, and proteoglycan loss. Recently, feasibility of biochemical MR imaging of cartilage repair tissue and surrounding cartilage was demonstrated. Ultrastructural properties of the tissue after different repair procedures resulted in differences in imaging characteristics. T2 mapping, T1rho mapping, delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), and diffusion weighted imaging (DWI) are applicable on most clinical 1.5 T and 3 T MR scanners. Currently, a standard of reference is difficult to define and knowledge is limited concerning correlation of clinical and MR findings. The lack of histological correlations complicates the identification of the exact tissue composition. Conclusions. A multimodal approach combining several quantitative MRI techniques in addition to morphological and clinical evaluation might be promising. Further investigations are required to demonstrate the potential for outcome evaluation after cartilage repair. PMID:24877139

Cartilage Repair Surgery: Outcome Evaluation by Using Noninvasive Cartilage Biomarkers Based on Quantitative MRI Techniques?

Directory of Open Access Journals (Sweden)

Pia M. Jungmann

2014-01-01

Full Text Available Background. New quantitative magnetic resonance imaging (MRI techniques are increasingly applied as outcome measures after cartilage repair. Objective. To review the current literature on the use of quantitative MRI biomarkers for evaluation of cartilage repair at the knee and ankle. Methods. Using PubMed literature research, studies on biochemical, quantitative MR imaging of cartilage repair were identified and reviewed. Results. Quantitative MR biomarkers detect early degeneration of articular cartilage, mainly represented by an increasing water content, collagen disruption, and proteoglycan loss. Recently, feasibility of biochemical MR imaging of cartilage repair tissue and surrounding cartilage was demonstrated. Ultrastructural properties of the tissue after different repair procedures resulted in differences in imaging characteristics. T2 mapping, T1rho mapping, delayed gadolinium-enhanced MRI of cartilage (dGEMRIC, and diffusion weighted imaging (DWI are applicable on most clinical 1.5 T and 3 T MR scanners. Currently, a standard of reference is difficult to define and knowledge is limited concerning correlation of clinical and MR findings. The lack of histological correlations complicates the identification of the exact tissue composition. Conclusions. A multimodal approach combining several quantitative MRI techniques in addition to morphological and clinical evaluation might be promising. Further investigations are required to demonstrate the potential for outcome evaluation after cartilage repair.

Quantitative imaging of magnetic nanoparticles by magneto-relaxometric tomography for biomedical applications; Quantitative Bildgebung magnetischer Nanopartikel mittels magnetrelaxometrischer Tomographie fuer biomedizinische Anwendungen

Energy Technology Data Exchange (ETDEWEB)

Liebl, Maik

2016-11-18

Current biomedical research focuses on the development of novel biomedical applications based on magnetic nanoparticles (MNPs), e.g. for local cancer treatment. These therapy approaches employ MNPs as remotely controlled drug carriers or local heat generators. Since location and quantity of MNPs determine drug enrichment and heat production, quantitative knowledge of the MNP distribution inside a body is essential for the development and success of these therapies. Magnetorelaxometry (MRX) is capable to provide such quantitative information based on the specific response of the MNPs after switching-off an applied magnetic field. Applying a uniform (homogeneous) magnetic field to a MNP distribution and measuring the MNP response by multiple sensors at different locations allows for spatially resolved MNP quantification. However, to reconstruct the MNP distribution from this spatially resolved MRX data, an ill posed inverse problem has to be solved. So far, the solution of this problem was stabilized incorporating a-priori knowledge in the forward model, e.g. by setting priors on the vertical position of the distribution using a 2D reconstruction grid or setting priors on the number and geometry of the MNP sources inside the body. MRX tomography represents a novel approach for quantitative 3D imaging of MNPs, where the inverse solution is stabilized by a series of MRX measurements. In MRX tomography, only parts of the MNP distribution are sequentially magnetized by the use of inhomogeneous magnetic fields. Each magnetizing is followed by detection of the response of the corresponding part of the distribution by multiple sensors. The 3D reconstruction of the MNP distribution is then accomplished by a common evaluation of the distinct MRX measurement series. In this thesis the first experimental setup for MRX tomography was developed for quantitative 3D imaging of biomedical MNP distributions. It is based on a multi-channel magnetizing unit which has been engineered to

Verification of practicability of quantitative reliability evaluation method (De-BDA) in nuclear power plants

International Nuclear Information System (INIS)

Takahashi, Kinshiro; Yukimachi, Takeo.

1988-01-01

A variety of methods have been applied to study of reliability analysis in which human factors are included in order to enhance the safety and availability of nuclear power plants. De-BDA (Detailed Block Diagram Analysis) is one of such mehtods developed with the objective of creating a more comprehensive and understandable tool for quantitative analysis of reliability associated with plant operations. The practicability of this method has been verified by applying it to reliability analysis of various phases of plant operation as well as evaluation of enhanced man-machine interface in the central control room. (author)

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis.

Science.gov (United States)

Tucker, George; Loh, Po-Ru; Berger, Bonnie

2013-10-04

Comprehensive protein-protein interaction (PPI) maps are a powerful resource for uncovering the molecular basis of genetic interactions and providing mechanistic insights. Over the past decade, high-throughput experimental techniques have been developed to generate PPI maps at proteome scale, first using yeast two-hybrid approaches and more recently via affinity purification combined with mass spectrometry (AP-MS). Unfortunately, data from both protocols are prone to both high false positive and false negative rates. To address these issues, many methods have been developed to post-process raw PPI data. However, with few exceptions, these methods only analyze binary experimental data (in which each potential interaction tested is deemed either observed or unobserved), neglecting quantitative information available from AP-MS such as spectral counts. We propose a novel method for incorporating quantitative information from AP-MS data into existing PPI inference methods that analyze binary interaction data. Our approach introduces a probabilistic framework that models the statistical noise inherent in observations of co-purifications. Using a sampling-based approach, we model the uncertainty of interactions with low spectral counts by generating an ensemble of possible alternative experimental outcomes. We then apply the existing method of choice to each alternative outcome and aggregate results over the ensemble. We validate our approach on three recent AP-MS data sets and demonstrate performance comparable to or better than state-of-the-art methods. Additionally, we provide an in-depth discussion comparing the theoretical bases of existing approaches and identify common aspects that may be key to their performance. Our sampling framework extends the existing body of work on PPI analysis using binary interaction data to apply to the richer quantitative data now commonly available through AP-MS assays. This framework is quite general, and many enhancements are likely

Practical quantitative measures of ALARA

International Nuclear Information System (INIS)

Kathren, R.L.; Larson, H.V.

1982-06-01

Twenty specific quantitative measures to assist in evaluating the effectiveness of as low as reasonably achievable (ALARA) programs are described along with their applicability, practicality, advantages, disadvantages, and potential for misinterpretation or dortion. Although no single index or combination of indices is suitable for all facilities, generally, these five: (1) mean individual dose equivalent (MIDE) to the total body from penetrating radiations; (2) statistical distribution of MIDE to the whole body from penetrating radiations; (3) cumulative penetrating whole body dose equivalent; (4) MIDE evaluated by job classification; and (5) MIDE evaluated by work location-apply to most programs. Evaluation of other programs may require other specific dose equivalent based indices, including extremity exposure data, cumulative dose equivalent to organs or to the general population, and nonpenetrating radiation dose equivalents. Certain nondose equivalent indices, such as the size of the radiation or contamination area, may also be used; an airborne activity index based on air concentration, room volume, and radiotoxicity is developed for application in some ALARA programs

Quantitative determination of α and f parameters for κo NAA

International Nuclear Information System (INIS)

Moon, J. H.; Kim, S. H.; Jeong, Y. S.

2002-01-01

Instrumental Neutron Activation Analysis as a representative method of nuclear analytical techniques, has advantages of non-destructive, simultaneous multi-element analysis with the characteristics of absolute measurement. Recently, use of κ o quantitative method which is accurate, convenient and user-friendly has been generalized world-widely. In this study, α and f parameters which is indispensable to implement κ o NAA were experimentally measured at NAA No.1-irradiation hole of HANARO research reactor. In addition, it was intended to apply routine analysis by the establishment of reliable and effective procedure of the measurement

Development of quantitative evaluation procedure of in-service materials degradation

International Nuclear Information System (INIS)

Takahashi, Hideaki

1992-01-01

The quantitative nondestructive evaluation procedure for detecting in-service materials degradation of low alloy structural steels by both small punch test and the electrochemical method has been developed. The static and dynamic small punch test method have been developed in order to apply this technique to R and D study for fusion reactor material development, such as 14 MeV irradiation damage evaluation. The characteristic changes in polarization curves attributed to IGC have an excellent correlation with shifts in FATT caused by temper embrittlement for Cr-Mo and Cr-Mo-V steels. (author)

TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells

DEFF Research Database (Denmark)

Hekmat, Omid; Munk, Stephanie; Fogh, Louise

2013-01-01

may explain the resistance phenotype to topoisomerase inhibitors that was observed in cells with high TIMP-1 levels. Pathway analysis showed an enrichment of proteins from functional categories such as apoptosis, cell cycle, DNA repair, transcription factors, drug targets and proteins associated......Tissue inhibitor of metalloproteinase 1 (TIMP-1) is a protein with a potential biological role in drug resistance. To elucidate the unknown molecular mechanisms underlying the association between high TIMP-1 levels and increased chemotherapy resistance, we employed SILAC-based quantitative mass...... spectrometry to analyze global proteome and phosphoproteome differences of MCF-7 breast cancer cells expressing high or low levels of TIMP-1. In TIMP-1 high expressing cells, 312 proteins and 452 phosphorylation sites were up-regulated. Among these were the cancer drug targets topoisomerase 1, 2A and 2B, which...

Comprehensive analysis of signal transduction in three-dimensional ECM-based tumor cell cultures

Directory of Open Access Journals (Sweden)

Iris Eke

2015-11-01

Full Text Available Analysis of signal transduction and protein phosphorylation is fundamental to understand physiological and pathological cell behavior as well as identification of novel therapeutic targets. Despite the fact that more physiological three-dimensional cell culture assays are increasingly used, particularly proteomics and phosphoproteomics remain challenging due to easy, robust and reproducible sample preparation. Here, we present an easy-to-perform, reliable and time-efficient method for the production of 3D cell lysates without compromising cell adhesion before cell lysis. The samples can be used for Western blotting as well as phosphoproteome array technology. This technique would be of interest for researchers working in all fields of biology and drug development.

Phospho.ELM: a database of phosphorylation sites--update 2011

DEFF Research Database (Denmark)

Dinkel, Holger; Chica, Claudia; Via, Allegra

2011-01-01

The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises ...... sequence alignment used for the score calculation. Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases.......The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42...

Quantitative imaging of turbulent and reacting flows

Energy Technology Data Exchange (ETDEWEB)

Paul, P.H. [Sandia National Laboratories, Livermore, CA (United States)

1993-12-01

Quantitative digital imaging, using planar laser light scattering techniques is being developed for the analysis of turbulent and reacting flows. Quantitative image data, implying both a direct relation to flowfield variables as well as sufficient signal and spatial dynamic range, can be readily processed to yield two-dimensional distributions of flowfield scalars and in turn two-dimensional images of gradients and turbulence scales. Much of the development of imaging techniques to date has concentrated on understanding the requisite molecular spectroscopy and collision dynamics to be able to determine how flowfield variable information is encoded into the measured signal. From this standpoint the image is seen as a collection of single point measurements. The present effort aims at realizing necessary improvements in signal and spatial dynamic range, signal-to-noise ratio and spatial resolution in the imaging system as well as developing excitation/detection strategies which provide for a quantitative measure of particular flowfield scalars. The standard camera used for the study is an intensified CCD array operated in a conventional video format. The design of the system was based on detailed modeling of signal and image transfer properties of fast UV imaging lenses, image intensifiers and CCD detector arrays. While this system is suitable for direct scalar imaging, derived quantities (e.g. temperature or velocity images) require an exceptionally wide dynamic range imaging detector. To apply these diagnostics to reacting flows also requires a very fast shuttered camera. The authors have developed and successfully tested a new type of gated low-light level detector. This system relies on fast switching of proximity focused image-diode which is direct fiber-optic coupled to a cooled CCD array. Tests on this new detector show significant improvements in detection limit, dynamic range and spatial resolution as compared to microchannel plate intensified arrays.

A method for three-dimensional quantitative observation of the microstructure of biological samples

Science.gov (United States)

Wang, Pengfei; Chen, Dieyan; Ma, Wanyun; Wu, Hongxin; Ji, Liang; Sun, Jialin; Lv, Danyu; Zhang, Lu; Li, Ying; Tian, Ning; Zheng, Jinggao; Zhao, Fengying

2009-07-01

Contemporary biology has developed into the era of cell biology and molecular biology, and people try to study the mechanism of all kinds of biological phenomena at the microcosmic level now. Accurate description of the microstructure of biological samples is exigent need from many biomedical experiments. This paper introduces a method for 3-dimensional quantitative observation on the microstructure of vital biological samples based on two photon laser scanning microscopy (TPLSM). TPLSM is a novel kind of fluorescence microscopy, which has excellence in its low optical damage, high resolution, deep penetration depth and suitability for 3-dimensional (3D) imaging. Fluorescent stained samples were observed by TPLSM, and afterward the original shapes of them were obtained through 3D image reconstruction. The spatial distribution of all objects in samples as well as their volumes could be derived by image segmentation and mathematic calculation. Thus the 3-dimensionally and quantitatively depicted microstructure of the samples was finally derived. We applied this method to quantitative analysis of the spatial distribution of chromosomes in meiotic mouse oocytes at metaphase, and wonderful results came out last.

Reconciling Anti-essentialism and Quantitative Methodology

DEFF Research Database (Denmark)

Jensen, Mathias Fjællegaard

2017-01-01

Quantitative methodology has a contested role in feminist scholarship which remains almost exclusively qualitative. Considering Irigaray’s notion of mimicry, Spivak’s strategic essentialism, and Butler’s contingent foundations, the essentialising implications of quantitative methodology may prove...... the potential to reconcile anti-essentialism and quantitative methodology, and thus, to make peace in the quantitative/qualitative Paradigm Wars....

Expert judgement models in quantitative risk assessment

Energy Technology Data Exchange (ETDEWEB)

Rosqvist, T. [VTT Automation, Helsinki (Finland); Tuominen, R. [VTT Automation, Tampere (Finland)

1999-12-01

Expert judgement is a valuable source of information in risk management. Especially, risk-based decision making relies significantly on quantitative risk assessment, which requires numerical data describing the initiator event frequencies and conditional probabilities in the risk model. This data is seldom found in databases and has to be elicited from qualified experts. In this report, we discuss some modelling approaches to expert judgement in risk modelling. A classical and a Bayesian expert model is presented and applied to real case expert judgement data. The cornerstone in the models is the log-normal distribution, which is argued to be a satisfactory choice for modelling degree-of-belief type probability distributions with respect to the unknown parameters in a risk model. Expert judgements are qualified according to bias, dispersion, and dependency, which are treated differently in the classical and Bayesian approaches. The differences are pointed out and related to the application task. Differences in the results obtained from the different approaches, as applied to real case expert judgement data, are discussed. Also, the role of a degree-of-belief type probability in risk decision making is discussed.

Expert judgement models in quantitative risk assessment

International Nuclear Information System (INIS)

Rosqvist, T.; Tuominen, R.

1999-01-01

Expert judgement is a valuable source of information in risk management. Especially, risk-based decision making relies significantly on quantitative risk assessment, which requires numerical data describing the initiator event frequencies and conditional probabilities in the risk model. This data is seldom found in databases and has to be elicited from qualified experts. In this report, we discuss some modelling approaches to expert judgement in risk modelling. A classical and a Bayesian expert model is presented and applied to real case expert judgement data. The cornerstone in the models is the log-normal distribution, which is argued to be a satisfactory choice for modelling degree-of-belief type probability distributions with respect to the unknown parameters in a risk model. Expert judgements are qualified according to bias, dispersion, and dependency, which are treated differently in the classical and Bayesian approaches. The differences are pointed out and related to the application task. Differences in the results obtained from the different approaches, as applied to real case expert judgement data, are discussed. Also, the role of a degree-of-belief type probability in risk decision making is discussed

Quantitative habitability.

Science.gov (United States)

Shock, Everett L; Holland, Melanie E

2007-12-01

A framework is proposed for a quantitative approach to studying habitability. Considerations of environmental supply and organismal demand of energy lead to the conclusions that power units are most appropriate and that the units for habitability become watts per organism. Extreme and plush environments are revealed to be on a habitability continuum, and extreme environments can be quantified as those where power supply only barely exceeds demand. Strategies for laboratory and field experiments are outlined that would quantify power supplies, power demands, and habitability. An example involving a comparison of various metabolisms pursued by halophiles is shown to be well on the way to a quantitative habitability analysis.

Quantitative bioanalytical and analytical method development of dibenzazepine derivative, carbamazepine: A review

Directory of Open Access Journals (Sweden)

Prasanna A. Datar

2015-08-01

Full Text Available Bioanalytical methods are widely used for quantitative estimation of drugs and their metabolites in physiological matrices. These methods could be applied to studies in areas of human clinical pharmacology and toxicology. The major bioanalytical services are method development, method validation and sample analysis (method application. Various methods such as GC, LC–MS/MS, HPLC, HPTLC, micellar electrokinetic chromatography, and UFLC have been used in laboratories for the qualitative and quantitative analysis of carbamazepine in biological samples throughout all phases of clinical research and quality control. The article incorporates various reported methods developed to help analysts in choosing crucial parameters for new method development of carbamazepine and its derivatives and also enumerates metabolites, and impurities reported so far. Keywords: Carbamazepine, HPLC, LC–MS/MS, HPTLC, RP-UFLC, Micellar electrokinetic chromatography

Evaluation of the potential for bioaerosols from land applied biosolids

Energy Technology Data Exchange (ETDEWEB)

Tanner, Benjamin; Brooks, John; Josephseon, Karen; Gerba, Charles; Pepper, Ian

2003-07-01

The overall objective of this study was to quantitatively and qualitatively document the potential hazards of biological aerosols derived from land applied biosolids, and ultimately develop risk assessment models and land-management strategies for safe, effective use of biosolids. The specific objectives were: i) Quantify bacterial and viral microorganisms emitted as bioaerosols from point sources of biosolids, and area (land-applied) sources of biosolids; ii) Develop risk assessment models based on a) hazard identification, b) dose response, c) exposure assessment; d) risk characterization. Research has consisted of laboratory studies at the University of Arizona and field studies at several regional U.S. locations. Bioaerosol samples have been collected via ''Impingement'' using SKC biosamplers. The biologicals monitored for included: i) viruses: enteroviruses, calciviruses; ii) phage e.g, MS2; iii) E. coil; iv) Salmonella; v) total coliforms; vi) Clostridium perfringens; vii) Aspergillus spp.; viii) Endotoxin. Air samples were collected at discrete distances torn both biosolid piles (point sources), or land applied biosolids (area sources). (author)

Quantitative analysis of styrene butadiene copolymers using S-SIMS and LA-FTICRMS

International Nuclear Information System (INIS)

Ruch, D.; Boes, C.; Zimmer, R.; Muller, J.F.; Migeon, H.-N.

2003-01-01

Styrene butadiene copolymers (SBR) have been analyzed by static secondary ion mass spectrometry (S-SIMS) and laser ablation Fourier transform ion cyclotron resonance mass spectrometry (LA-FTICRMS) to obtain quantitative information based on specific peaks knowing that the complication of this system is that there are no characteristic SIMS peaks unique to each styrene and butadiene monomer. So, to overcome this problem, a silver deposition has been applied into polystyrene (PS), butadiene rubber (BR) and SBR. By this way, new secondary ions are detected in particular silver cationized butadiene and styrene monomers at m/z 161/163 and 211/213, respectively. The LA-FTICRMS experiments do not require pre-treatment. At high laser power density, UV photons (193, 266 and 355 nm) allow to detect directly the styrene and butadiene ions at m/z 104 and 54, respectively. Using these SIMS and LA-FTICRMS peaks, it is possible to obtain quantitative results. However, the silver coating in the SIMS experiment seems to have a great influence on the obtention of quantitative information. For LA-FTICRMS experiments, the best results seem to be obtained at the 355 nm wavelength

A quantitative study of nanoparticle skin penetration with interactive segmentation.

Science.gov (United States)

Lee, Onseok; Lee, See Hyun; Jeong, Sang Hoon; Kim, Jaeyoung; Ryu, Hwa Jung; Oh, Chilhwan; Son, Sang Wook

2016-10-01

In the last decade, the application of nanotechnology techniques has expanded within diverse areas such as pharmacology, medicine, and optical science. Despite such wide-ranging possibilities for implementation into practice, the mechanisms behind nanoparticle skin absorption remain unknown. Moreover, the main mode of investigation has been qualitative analysis. Using interactive segmentation, this study suggests a method of objectively and quantitatively analyzing the mechanisms underlying the skin absorption of nanoparticles. Silica nanoparticles (SNPs) were assessed using transmission electron microscopy and applied to the human skin equivalent model. Captured fluorescence images of this model were used to evaluate degrees of skin penetration. These images underwent interactive segmentation and image processing in addition to statistical quantitative analyses of calculated image parameters including the mean, integrated density, skewness, kurtosis, and area fraction. In images from both groups, the distribution area and intensity of fluorescent silica gradually increased in proportion to time. Since statistical significance was achieved after 2 days in the negative charge group and after 4 days in the positive charge group, there is a periodic difference. Furthermore, the quantity of silica per unit area showed a dramatic change after 6 days in the negative charge group. Although this quantitative result is identical to results obtained by qualitative assessment, it is meaningful in that it was proven by statistical analysis with quantitation by using image processing. The present study suggests that the surface charge of SNPs could play an important role in the percutaneous absorption of NPs. These findings can help achieve a better understanding of the percutaneous transport of NPs. In addition, these results provide important guidance for the design of NPs for biomedical applications.

[Reconsidering evaluation criteria regarding health care research: toward an integrative framework of quantitative and qualitative criteria].

Science.gov (United States)

Miyata, Hiroaki; Kai, Ichiro

2006-05-01

Debate about the relationship between quantitative and qualitative paradigms is often muddled and confused and the clutter of terms and arguments has resulted in the concepts becoming obscure and unrecognizable. It is therefore very important to reconsider evaluation criteria regarding rigor in social science. As Lincoln & Guba have already compared quantitative paradigms (validity, reliability, neutrality, generalizability) with qualitative paradigms (credibility, dependability, confirmability, transferability), we have discuss use of evaluation criteria based on pragmatic perspective. Validity/Credibility is the paradigm concerned to observational framework, while Reliability/Dependability refer to the range of stability in observations, Neutrality/Confirmability reflect influences between observers and subjects, Generalizability/Transferability have epistemological difference in the way findings are applied. Qualitative studies, however, does not always chose the qualitative paradigms. If we assume the stability to some extent, it is better to use the quantitative paradigm (reliability). Moreover as a quantitative study can not always guarantee a perfect observational framework, with stability in all phases of observations, it is useful to use qualitative paradigms to enhance the rigor in the study.

R - evolution in Time Series Analysis Software Applied on R - omanian Capital Market

Directory of Open Access Journals (Sweden)

Ciprian ALEXANDRU

2014-06-01

Full Text Available Worldwide and during the last decade, R has developed in a balanced way and nowadays it represents the most powerful tool for computational statistics, data science and visualization. Millions of data scientists use R to face their most challenging problems in topics ranging from economics to engineering and genetics. In this study, R was used to compute data on stock market prices in order to build trading models and to estimate the evolution of the quantitative financial market. These models were already applied on the international capital markets. In Romania, the quantitative modeling of capital market is available only for clients of trading brokers because the time series data are collected for the commercial purpose; in that circumstance, the statistical computing tools meet the inertia to change. This paper aims to expose a small part of the capability of R to use mix-and-match models and cutting-edge methods in statistics and quantitative modeling in order to build an alternative way to analyze capital market in Romania over the commercial threshold.

Analysis of Nanobody-Epitope Interactions in Living Cells via Quantitative Protein Transport Assays.

Science.gov (United States)

Früholz, Simone; Pimpl, Peter

2017-01-01

Over the past few decades, quantitative protein transport analyses have been used to elucidate the sorting and transport of proteins in the endomembrane system of plants. Here, we have applied our knowledge about transport routes and the corresponding sorting signals to establish an in vivo system for testing specific interactions between soluble proteins.Here, we describe the use of quantitative protein transport assays in tobacco mesophyll protoplasts to test for interactions occurring between a GFP-binding nanobody and its GFP epitope. For this, we use a secreted GFP-tagged α-amylase as a reporter together with a vacuolar-targeted RFP-tagged nanobody. The interaction between these proteins is then revealed by a transport alteration of the secretory reporter due to the interaction-triggered attachment of the vacuolar sorting signal.

Quantitative bioanalytical and analytical method development of dibenzazepine derivative, carbamazepine: A review ☆

OpenAIRE

Datar, Prasanna A.

2015-01-01

Bioanalytical methods are widely used for quantitative estimation of drugs and their metabolites in physiological matrices. These methods could be applied to studies in areas of human clinical pharmacology and toxicology. The major bioanalytical services are method development, method validation and sample analysis (method application). Various methods such as GC, LC–MS/MS, HPLC, HPTLC, micellar electrokinetic chromatography, and UFLC have been used in laboratories for the qualitative and qua...

Micro photometer's automation for quantitative spectrograph analysis

International Nuclear Information System (INIS)

Gutierrez E, C.Y.A.

1996-01-01

A Microphotometer is used to increase the sharpness of dark spectral lines. Analyzing these lines one sample content and its concentration could be determined and the analysis is known as Quantitative Spectrographic Analysis. The Quantitative Spectrographic Analysis is carried out in 3 steps, as follows. 1. Emulsion calibration. This consists of gauging a photographic emulsion, to determine the intensity variations in terms of the incident radiation. For the procedure of emulsion calibration an adjustment with square minimum to the data obtained is applied to obtain a graph. It is possible to determine the density of dark spectral line against the incident light intensity shown by the microphotometer. 2. Working curves. The values of known concentration of an element against incident light intensity are plotted. Since the sample contains several elements, it is necessary to find a work curve for each one of them. 3. Analytical results. The calibration curve and working curves are compared and the concentration of the studied element is determined. The automatic data acquisition, calculation and obtaining of resulting, is done by means of a computer (PC) and a computer program. The conditioning signal circuits have the function of delivering TTL levels (Transistor Transistor Logic) to make the communication between the microphotometer and the computer possible. Data calculation is done using a computer programm

Quantitative analysis of protein-ligand interactions by NMR.

Science.gov (United States)

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

Embedding the perceptions of people with dementia into quantitative research design.

Science.gov (United States)

O'Rourke, Hannah M; Duggleby, Wendy; Fraser, Kimberly D

2015-05-01

Patient perspectives about quality of life are often found in the results of qualitative research and could be applied to steer the direction of future research. The purpose of this paper was to describe how findings from a body of qualitative research on patient perspectives about quality of life were linked to a clinical administrative dataset and then used to design a subsequent quantitative study. Themes from two systematic reviews of qualitative evidence (i.e., metasyntheses) identified what affects quality of life according to people with dementia. Selected themes and their sub-concepts were then mapped to an administrative dataset (the Resident Assessment Instrument 2.0) to determine the study focus, formulate nine hypotheses, and select a patient-reported outcome. A literature review followed to confirm existence of a knowledge gap, identify adjustment variables, and support design decisions. A quantitative study to test the association between conflict and sadness for people with dementia in long-term care was derived from metasynthesis themes. Challenges included (1) mapping broad themes to the administrative dataset; (2) decisions associated with inclusion of variables not identified by people with dementia from the qualitative research; and (3) selecting a patient-reported outcome, when the dataset lacked a valid subjective quality-of-life measure. Themes derived from a body of qualitative research capturing a target populations' perspective can be linked to administrative data and used to design a quantitative study. Using this approach, the quantitative findings will be meaningful with respect to the quality of life of the target population.

Applied spectrophotometry: analysis of a biochemical mixture.

Science.gov (United States)

Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

2013-01-01

Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software. Copyright © 2013 Wiley Periodicals, Inc.

Proficiency testing as a basis for estimating uncertainty of measurement: application to forensic alcohol and toxicology quantitations.

Science.gov (United States)

Wallace, Jack

2010-05-01

While forensic laboratories will soon be required to estimate uncertainties of measurement for those quantitations reported to the end users of the information, the procedures for estimating this have been little discussed in the forensic literature. This article illustrates how proficiency test results provide the basis for estimating uncertainties in three instances: (i) For breath alcohol analyzers the interlaboratory precision is taken as a direct measure of uncertainty. This approach applies when the number of proficiency tests is small. (ii) For blood alcohol, the uncertainty is calculated from the differences between the laboratory's proficiency testing results and the mean quantitations determined by the participants; this approach applies when the laboratory has participated in a large number of tests. (iii) For toxicology, either of these approaches is useful for estimating comparability between laboratories, but not for estimating absolute accuracy. It is seen that data from proficiency tests enable estimates of uncertainty that are empirical, simple, thorough, and applicable to a wide range of concentrations.