Quantitative proteomic analysis of bacterial enzymes released in cheese during ripening.

PubMed

Jardin, Julien; Mollé, Daniel; Piot, Michel; Lortal, Sylvie; Gagnaire, Valérie

2012-04-02

Due to increasingly available bacterial genomes in databases, proteomic tools have recently been used to screen proteins expressed by micro-organisms in food in order to better understand their metabolism in situ. While the main objective is the systematic identification of proteins, the next step will be to bridge the gap between identification and quantification of these proteins. For that purpose, a new mass spectrometry-based approach was applied, using isobaric tagging reagent for quantitative proteomic analysis (iTRAQ), which are amine specific and yield labelled peptides identical in mass. Experimental Swiss-type cheeses were manufactured from microfiltered milk using Streptococcus thermophilus ITG ST20 and Lactobacillus helveticus ITG LH1 as lactic acid starters. At three ripening times (7, 20 and 69 days), cheese aqueous phases were extracted and enriched in bacterial proteins by fractionation. Each sample, standardised in protein amount prior to proteomic analyses, was: i) analysed by 2D-electrophoresis for qualitative analysis and ii) submitted to trypsinolysis, and labelled with specific iTRAQ tag, one per ripening time. The three labelled samples were mixed together and analysed by nano-LC coupled on-line with ESI-QTOF mass spectrometer. Thirty proteins, both from bacterial or bovine origin, were identified and efficiently quantified. The free bacterial proteins detected were enzymes from the central carbon metabolism as well as stress proteins. Depending on the protein considered, the quantity of these proteins in the cheese aqueous extract increased from 2.5 to 20 fold in concentration from day 7 to day 69 of ripening. Copyright © 2012 Elsevier B.V. All rights reserved.

Quantitative proteome analysis using isobaric peptide termini labeling (IPTL).

PubMed

Arntzen, Magnus O; Koehler, Christian J; Treumann, Achim; Thiede, Bernd

2011-01-01

The quantitative comparison of proteome level changes across biological samples has become an essential feature in proteomics that remains challenging. We have recently introduced isobaric peptide termini labeling (IPTL), a novel strategy for isobaric quantification based on the derivatization of peptide termini with complementary isotopically labeled reagents. Unlike non-isobaric quantification methods, sample complexity at the MS level is not increased, providing improved sensitivity and protein coverage. The distinguishing feature of IPTL when comparing it to more established isobaric labeling methods (iTRAQ and TMT) is the presence of quantification signatures in all sequence-determining ions in MS/MS spectra, not only in the low mass reporter ion region. This makes IPTL a quantification method that is accessible to mass spectrometers with limited capabilities in the low mass range. Also, the presence of several quantification points in each MS/MS spectrum increases the robustness of the quantification procedure.

Two independent proteomic approaches provide a comprehensive analysis of the synovial fluid proteome response to Autologous Chondrocyte Implantation.

PubMed

Hulme, Charlotte H; Wilson, Emma L; Fuller, Heidi R; Roberts, Sally; Richardson, James B; Gallacher, Pete; Peffers, Mandy J; Shirran, Sally L; Botting, Catherine H; Wright, Karina T

2018-05-02

Autologous chondrocyte implantation (ACI) has a failure rate of approximately 20%, but it is yet to be fully understood why. Biomarkers are needed that can pre-operatively predict in which patients it is likely to fail, so that alternative or individualised therapies can be offered. We previously used label-free quantitation (LF) with a dynamic range compression proteomic approach to assess the synovial fluid (SF) of ACI responders and non-responders. However, we were able to identify only a few differentially abundant proteins at baseline. In the present study, we built upon these previous findings by assessing higher-abundance proteins within this SF, providing a more global proteomic analysis on the basis of which more of the biology underlying ACI success or failure can be understood. Isobaric tagging for relative and absolute quantitation (iTRAQ) proteomic analysis was used to assess SF from ACI responders (mean Lysholm improvement of 33; n = 14) and non-responders (mean Lysholm decrease of 14; n = 13) at the two stages of surgery (cartilage harvest and chondrocyte implantation). Differentially abundant proteins in iTRAQ and combined iTRAQ and LF datasets were investigated using pathway and network analyses. iTRAQ proteomic analysis confirmed our previous finding that there is a marked proteomic shift in response to cartilage harvest (70 and 54 proteins demonstrating ≥ 2.0-fold change and p < 0.05 between stages I and II in responders and non-responders, respectively). Further, it highlighted 28 proteins that were differentially abundant between responders and non-responders to ACI, which were not found in the LF study, 16 of which were altered at baseline. The differential expression of two proteins (complement C1s subcomponent and matrix metalloproteinase 3) was confirmed biochemically. Combination of the iTRAQ and LF proteomic datasets generated in-depth SF proteome information that was used to generate interactome networks representing ACI success or failure. Functional pathways that are dysregulated in ACI non-responders were identified, including acute-phase response signalling. Several candidate biomarkers for baseline prediction of ACI outcome were identified. A holistic overview of the SF proteome in responders and non-responders to ACI  has been profiled, providing a better understanding of the biological pathways underlying clinical outcome, particularly the differential response to cartilage harvest in non-responders.

Quantitative Analysis of Tissue Samples by Combining iTRAQ Isobaric Labeling with Selected/Multiple Reaction Monitoring (SRM/MRM).

PubMed

Narumi, Ryohei; Tomonaga, Takeshi

2016-01-01

Mass spectrometry-based phosphoproteomics is an indispensible technique used in the discovery and quantification of phosphorylation events on proteins in biological samples. The application of this technique to tissue samples is especially useful for the discovery of biomarkers as well as biological studies. We herein describe the application of a large-scale phosphoproteome analysis and SRM/MRM-based quantitation to develop a strategy for the systematic discovery and validation of biomarkers using tissue samples.

Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics.

PubMed

Prudova, Anna; auf dem Keller, Ulrich; Butler, Georgina S; Overall, Christopher M

2010-05-01

Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute quantitation (iTRAQ) labeling method that simultaneously labels and blocks all primary amines including protein N- termini and lysine side chains. Blocking lysines limits trypsin cleavage to arginine, which effectively elongates the proteolytically truncated peptides for improved MS/MS analysis and peptide identification. Incorporating iTRAQ whole protein labeling with terminal amine isotopic labeling of substrates (iTRAQ-TAILS) to enrich the N-terminome by negative selection of the blocked mature original N-termini and neo-N-termini has many advantages. It enables simultaneous characterization of the natural N-termini of proteins, their N-terminal modifications, and proteolysis product and cleavage site identification. Furthermore, iTRAQ-TAILS also enables multiplex N-terminomics analysis of up to eight samples and allows for quantification in MS2 mode, thus preventing an increase in spectral complexity and extending proteome coverage by signal amplification of low abundance proteins. We compared the substrate degradomes of two closely related matrix metalloproteinases, MMP-2 (gelatinase A) and MMP-9 (gelatinase B), in fibroblast secreted proteins. Among 3,152 unique N-terminal peptides identified corresponding to 1,054 proteins, we detected 201 cleavage products for MMP-2 and unexpectedly only 19 for the homologous MMP-9 under identical conditions. Novel substrates identified and biochemically validated include insulin-like growth factor binding protein-4, complement C1r component A, galectin-1, dickkopf-related protein-3, and thrombospondin-2. Hence, N-terminomics analyses using iTRAQ-TAILS links gelatinases with new mechanisms of action in angiogenesis and reveals unpredicted restrictions in substrate repertoires for these two very similar proteases.

Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics*

PubMed Central

Prudova, Anna; auf dem Keller, Ulrich; Butler, Georgina S.; Overall, Christopher M.

2010-01-01

Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute quantitation (iTRAQ) labeling method that simultaneously labels and blocks all primary amines including protein N- termini and lysine side chains. Blocking lysines limits trypsin cleavage to arginine, which effectively elongates the proteolytically truncated peptides for improved MS/MS analysis and peptide identification. Incorporating iTRAQ whole protein labeling with terminal amine isotopic labeling of substrates (iTRAQ-TAILS) to enrich the N-terminome by negative selection of the blocked mature original N-termini and neo-N-termini has many advantages. It enables simultaneous characterization of the natural N-termini of proteins, their N-terminal modifications, and proteolysis product and cleavage site identification. Furthermore, iTRAQ-TAILS also enables multiplex N-terminomics analysis of up to eight samples and allows for quantification in MS2 mode, thus preventing an increase in spectral complexity and extending proteome coverage by signal amplification of low abundance proteins. We compared the substrate degradomes of two closely related matrix metalloproteinases, MMP-2 (gelatinase A) and MMP-9 (gelatinase B), in fibroblast secreted proteins. Among 3,152 unique N-terminal peptides identified corresponding to 1,054 proteins, we detected 201 cleavage products for MMP-2 and unexpectedly only 19 for the homologous MMP-9 under identical conditions. Novel substrates identified and biochemically validated include insulin-like growth factor binding protein-4, complement C1r component A, galectin-1, dickkopf-related protein-3, and thrombospondin-2. Hence, N-terminomics analyses using iTRAQ-TAILS links gelatinases with new mechanisms of action in angiogenesis and reveals unpredicted restrictions in substrate repertoires for these two very similar proteases. PMID:20305284

iTRAQ-based quantitative proteomic analysis of midgut in silkworm infected with Bombyx mori cytoplasmic polyhedrosis virus.

PubMed

Gao, Kun; Deng, Xiang-Yuan; Shang, Meng-Ke; Qin, Guang-Xing; Hou, Cheng-Xiang; Guo, Xi-Jie

2017-01-30

Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) specifically infects the epithelial cells in the midgut of silkworm and causes them to death, which negatively affects the sericulture industry. In order to determine the midgut response at the protein levels to the virus infection, differential proteomes of the silkworm midgut responsive to BmCPV infection were identified with isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). 193, 408, 189 differentially expressed proteins (DEPs) were reliably quantified by iTRAQ analysis in the midgut of BmCPV-infected and control larvae at 24, 48, 72h post infection (hpi) respectively. KEGG enrichment analysis showed that Oxidative phosphorylation, amyotrophic lateral sclerosis, Toll-like receptor signaling pathway, steroid hormone biosynthesis were the significant pathways (Q value≤0.05) both at 24 and 48hpi. qRT-PCR was used to further verify gene transcription of 30 DEPs from iTRAQ, showing that the regulations of 24 genes at the transcript level were consistent with those at the proteomic level. Moreover, the cluster analysis of the three time groups showed that there were seven co-regulated DEPs including BGIBMGA002620-PA, which was a putative p62/sequestosome-1 protein in silkworm. It was upregulated at both the mRNA level and the proteomic level and may play an important role in regulating the autophagy and apoptosis (especially apoptosis) induced by BmCPV infection. This was the first report using an iTRAQ approach to analyze proteomes of the silkworm midgut against BmCPV infection, which contributes to understanding the defense mechanisms of silkworm midgut to virus infection. The domesticated silkworm, Bombyx mori, is renowned for silk production as well as being a traditional lepidopteron model insect served as a subject for morphological, genetic, physiological, and developmental studies. Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) specifically infects the epithelial cells in the midgut of silkworm and causes the silkworm to death, which negatively affects the sericulture industry. Studies on insect antiviral immunity and on interactive mechanisms between host cells and BmCPV are in their infancy and remain insufficient. In order to obtain an overall view of silkworm response to BmCPV infection, we performed a proteomic analysis of the midgut of silkworm responses to BmCPV infection by iTRAQ. This was the first report using an iTRAQ approach to analyze proteomes of the silkworm midgut against BmCPV infection, which contributes to understanding the defense mechanisms of silkworm midgut to virus infection. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparative Analysis of Serum Proteins from Patients with Severe and Mild EV-A71-induced HFMD using iTRAQ-Coupled LC-MS/MS Screening.

PubMed

Fan, Peihu; Chen, Wei; Yu, Pin; Bao, Linlin; Xu, Lili; Qin, Chuan

2017-12-01

This study was designed to provide a rationale for monitoring the development of severe hand, foot, and mouth disease (HFMD) and predicting the onset of this disease via global comparative analysis between patients with severe and mild HFMD. The authors collected serum from five groups: mild (E-M) and severe (E-S) EV-A71-induced HFMD; mild (NE-M) and severe (NE-S) non-EV-A71-induced HFMD; and healthy control subjects (CON). The authors then performed comparative analysis and identified specific differentially expressed proteins (DEPs) of E-S using isobaric mass tag (isobaric tags for relative and absolute quantitation, iTRAQ) labeling coupled with multidimensional liquid chromatography-mass spectrometry (LC-MS/MS). Moreover, The authors validated specific DEPs by multiple reaction monitoring (MRM). The authors identified 10 specific proteins that were significantly altered in E-S patients. Bioinformatics analysis revealed that most of these DEPs are primarily involved in the acute response to infection, which was common to all groups. More importantly, up-regulated proteins associated with neural injury were specifically identified in the E-S group. These findings conclude that severe HFMD symptoms may be caused by EV-A71 infection-mediated injury of the neural system and provide a reference for future research on the course and prognosis of severe HFMD. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Strong, sudden cooling alleviates the inflammatory responses in heat-stressed dairy cows based on iTRAQ proteomic analysis

NASA Astrophysics Data System (ADS)

Cheng, Jianbo; Min, Li; Zheng, Nan; Fan, Caiyun; Zhao, Shengguo; Zhang, Yangdong; Wang, Jiaqi

2018-02-01

This study was designed to investigate the effects of sudden cooling on the physiological responses of 12 heat-stressed Holstein dairy cows using an isobaric tags for relative and absolute quantification (iTRAQ) labeling approach. Plasma samples were collected from these cows during heat stress (HS), and after strong, sudden cooling in the summer (16 days later). We compared plasma proteomic data before and after sudden cooling to identify the differentially abundant proteins. The results showed that sudden cooling in summer effectively alleviated the negative consequences of HS on body temperature and production variables. Expressions of plasma hemoglobin alpha and hemoglobin beta were upregulated, whereas lipopolysaccharide-binding protein (LBP) and haptoglobin were downregulated in this process. The increase of hemoglobin after cooling may improve oxygen transport and alleviate the rise in respiration rates in heat-stressed dairy cows. The decrease of LBP and haptoglobin suggests that the inflammatory responses caused by HS are relieved after cooling. Our findings provide new insight into the physiological changes that occur when heat-stressed dairy cows experience strong, sudden cooling.

Low-molecular-weight color pI markers to monitor on-line the peptide focusing process in OFFGEL fractionation.

PubMed

Michelland, Sylvie; Bourgoin-Voillard, Sandrine; Cunin, Valérie; Tollance, Axel; Bertolino, Pascal; Slais, Karel; Seve, Michel

2017-08-01

High-throughput mass spectrometry-based proteomic analysis requires peptide fractionation to simplify complex biological samples and increase proteome coverage. OFFGEL fractionation technology became a common method to separate peptides or proteins using isoelectric focusing in an immobilized pH gradient. However, the OFFGEL focusing process may be further optimized and controlled in terms of separation time and pI resolution. Here we evaluated OFFGEL technology to separate peptides from different samples in the presence of low-molecular-weight (LMW) color pI markers to visualize the focusing process. LMW color pI markers covering a large pH range were added to the peptide mixture before OFFGEL fractionation using a 24-wells device encompassing the pH range 3-10. We also explored the impact of LMW color pI markers on peptide fractionation labeled previously for iTRAQ. Then, fractionated peptides were separated by RP_HPLC prior to MS analysis using MALDI-TOF/TOF mass spectrometry in MS and MS/MS modes. Here we report the performance of the peptide focusing process in the presence of LMW color pI markers as on-line trackers during the OFFGEL process and the possibility to use them as pI controls for peptide focusing. This method improves the workflow for peptide fractionation in a bottom-up proteomic approach with or without iTRAQ labeling. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stable isotope labelling methods in mass spectrometry-based quantitative proteomics.

PubMed

Chahrour, Osama; Cobice, Diego; Malone, John

2015-09-10

Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons. Copyright © 2015 Elsevier B.V. All rights reserved.

Tissue Proteome Analysis of Different Grades of Human Gliomas Provides Major Cues for Glioma Pathogenesis.

PubMed

Gollapalli, Kishore; Ghantasala, Saicharan; Atak, Apurva; Rapole, Srikanth; Moiyadi, Aliasgar; Epari, Sridhar; Srivastava, Sanjeeva

2017-05-01

Gliomas are heterogeneous and most commonly occurring brain tumors. Blood-brain barrier restricts the entry of brain tumor proteins into blood stream thus limiting the usage of serum or plasma for proteomic analysis. Our study aimed at understanding the molecular basis of aggressiveness of various grades of brain tumors using isobaric tagging for relative and absolute quantification (iTRAQ) based mass spectrometry. Tissue proteomic analysis of various grades of gliomas was performed using four-plex iTRAQ. We labeled five sets (each set consists of control, grade-II, III, and IV tumor samples) of individual glioma patients using iTRAQ reagents. Significantly altered proteins were subjected to bioinformatics analysis using Database for Annotation, Visualization and Integrated Discovery (DAVID). Various metabolic pathways like glycolysis, TCA-cycle, electron transport chain, lactate metabolism, and blood coagulation pathways were majorly observed to be perturbed in gliomas. Most of the identified proteins involved in redox reactions, protein folding, pre-messenger RNA (mRNA) processing, antiapoptosis, and blood coagulation were found to be upregulated in gliomas. Transcriptomics data of glioblastoma multiforme (GBM), low-grade gliomas (LGGs), and controls were downloaded from The Cancer Genome Atlas (TCGA) data portal and further analyzed using BRB-Array tools. Expression levels of a few significantly altered proteins like lactate dehydrogenase, alpha-1 antitrypsin, fibrinogen alpha chain, nucleophosmin, annexin A5, thioredoxin, ferritin light chain, thymosin beta-4-like protein 3, superoxide dismutase-2, and peroxiredoxin-1 and 6 showed a positive correlation with increasing grade of gliomas thereby offering an insight into molecular basis behind their aggressive nature. Several proteins identified in different grades of gliomas are potential grade-specific markers, and perturbed pathways provide comprehensive overview of molecular cues involved in glioma pathogenesis.

Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn.

PubMed

Dong, Yongbin; Wang, Qilei; Zhang, Long; Du, Chunguang; Xiong, Wenwei; Chen, Xinjian; Deng, Fei; Ma, Zhiyan; Qiao, Dahe; Hu, Chunhui; Ren, Yangliu; Li, Yuling

2015-01-01

The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.

Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn

PubMed Central

Du, Chunguang; Xiong, Wenwei; Chen, Xinjian; Deng, Fei; Ma, Zhiyan; Qiao, Dahe; Hu, Chunhui; Ren, Yangliu; Li, Yuling

2015-01-01

The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize. PMID:26587848

Quantitative proteomic analysis of milk fat globule membrane (MFGM) proteins in human and bovine colostrum and mature milk samples through iTRAQ labeling.

PubMed

Yang, Mei; Cong, Min; Peng, Xiuming; Wu, Junrui; Wu, Rina; Liu, Biao; Ye, Wenhui; Yue, Xiqing

2016-05-18

Milk fat globule membrane (MFGM) proteins have many functions. To explore the different proteomics of human and bovine MFGM, MFGM proteins were separated from human and bovine colostrum and mature milk, and analyzed by the iTRAQ proteomic approach. A total of 411 proteins were recognized and quantified. Among these, 232 kinds of differentially expressed proteins were identified. These differentially expressed proteins were analyzed based on multivariate analysis, gene ontology (GO) annotation and KEGG pathway. Biological processes involved were response to stimulus, localization, establishment of localization, and the immune system process. Cellular components engaged were the extracellular space, extracellular region parts, cell fractions, and vesicles. Molecular functions touched upon were protein binding, nucleotide binding, and enzyme inhibitor activity. The KEGG pathway analysis showed several pathways, including regulation of the actin cytoskeleton, focal adhesion, neurotrophin signaling pathway, leukocyte transendothelial migration, tight junction, complement and coagulation cascades, vascular endothelial growth factor signaling pathway, and adherens junction. These results enhance our understanding of different proteomes of human and bovine MFGM across different lactation phases, which could provide important information and potential directions for the infant milk powder and functional food industries.

High-coverage quantitative proteomics using amine-specific isotopic labeling.

PubMed

Melanson, Jeremy E; Avery, Steven L; Pinto, Devanand M

2006-08-01

Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.

Urinary amino acid analysis: a comparison of iTRAQ-LC-MS/MS, GC-MS, and amino acid analyzer.

PubMed

Kaspar, Hannelore; Dettmer, Katja; Chan, Queenie; Daniels, Scott; Nimkar, Subodh; Daviglus, Martha L; Stamler, Jeremiah; Elliott, Paul; Oefner, Peter J

2009-07-01

Urinary amino acid analysis is typically done by cation-exchange chromatography followed by post-column derivatization with ninhydrin and UV detection. This method lacks throughput and specificity. Two recently introduced stable isotope ratio mass spectrometric methods promise to overcome those shortcomings. Using two blinded sets of urine replicates and a certified amino acid standard, we compared the precision and accuracy of gas chromatography/mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) of propyl chloroformate and iTRAQ derivatized amino acids, respectively, to conventional amino acid analysis. The GC-MS method builds on the direct derivatization of amino acids in diluted urine with propyl chloroformate, GC separation and mass spectrometric quantification of derivatives using stable isotope labeled standards. The LC-MS/MS method requires prior urinary protein precipitation followed by labeling of urinary and standard amino acids with iTRAQ tags containing different cleavable reporter ions distinguishable by MS/MS fragmentation. Means and standard deviations of percent technical error (%TE) computed for 20 amino acids determined by amino acid analyzer, GC-MS, and iTRAQ-LC-MS/MS analyses of 33 duplicate and triplicate urine specimens were 7.27+/-5.22, 21.18+/-10.94, and 18.34+/-14.67, respectively. Corresponding values for 13 amino acids determined in a second batch of 144 urine specimens measured in duplicate or triplicate were 8.39+/-5.35, 6.23+/-3.84, and 35.37+/-29.42. Both GC-MS and iTRAQ-LC-MS/MS are suited for high-throughput amino acid analysis, with the former offering at present higher reproducibility and completely automated sample pretreatment, while the latter covers more amino acids and related amines.

Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology.

PubMed

Armenta, Jenny M; Hoeschele, Ina; Lazar, Iulia M

2009-07-01

An isotope tags for relative and absolute quantitation (iTRAQ)-based reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) method was developed for differential protein expression profiling in complex cellular extracts. The estrogen positive MCF-7 cell line, cultured in the presence of 17beta-estradiol (E2) and tamoxifen (Tam), was used as a model system. MS analysis was performed with a linear trap quadrupole (LTQ) instrument operated by using pulsed Q dissociation (PQD) detection. Optimization experiments were conducted to maximize the iTRAQ labeling efficiency and the number of quantified proteins. MS data filtering criteria were chosen to result in a false positive identification rate of <4%. The reproducibility of protein identifications was approximately 60%-67% between duplicate, and approximately 50% among triplicate LC-MS/MS runs, respectively. The run-to-run reproducibility, in terms of relative standard deviations (RSD) of global mean iTRAQ ratios, was better than 10%. The quantitation accuracy improved with the number of peptides used for protein identification. From a total of 530 identified proteins (P < 0.001) in the E2/Tam treated MCF-7 cells, a list of 255 proteins (quantified by at least two peptides) was generated for differential expression analysis. A method was developed for the selection, normalization, and statistical evaluation of such datasets. An approximate approximately 2-fold change in protein expression levels was necessary for a protein to be selected as a biomarker candidate. According to this data processing strategy, approximately 16 proteins involved in biological processes such as apoptosis, RNA processing/metabolism, DNA replication/transcription/repair, cell proliferation and metastasis, were found to be up- or down-regulated.

iTRAQ proteomic analysis of the hippocampus in a rat model of nicotine-induced conditioned place preference.

PubMed

Zhu, Beibei; Li, Xiangyu; Chen, Huan; Wang, Hongjuan; Zhu, Xinchao; Hou, Hongwei; Hu, Qingyuan

2017-05-13

Repeated exposures to nicotine are known to result in persistent changes in proteins expression in addiction-related brain regions, such as the striatum, nucleus accumbens and prefrontal cortex, but the changes induced in the protein content of the hippocampus remain poorly studied. This study established a rat model of nicotine-induced conditioned place preference (CPP), and screened for proteins that were differentially expressed in the hippocampus of these rats using isobaric tags for relative and absolute quantitation labeling (iTRAQ) coupled with 2D-LC MS/MS. The nicotine-induced CPP was established by subcutaneously injecting rats with 0.2 mg/kg nicotine. Relative to the control (saline) group, the nicotine group showed 0.67- and 1.5-fold changes in 117 and 10 hippocampal proteins, respectively. These differentially expressed proteins are mainly involved in calcium-mediated signaling, neurotransmitter transport, GABAergic synapse function, long-term synaptic potentiation and nervous system development. Furthermore, RT-PCR was used to confirmed the results of the proteomic analysis. Our findings identify several proteins and cellular signaling pathways potentially involved in the molecular mechanisms in the hippocampus that underlie nicotine addiction. These results provide insights into the mechanisms of nicotine treatment in hippocampus. Copyright © 2017 Elsevier Inc. All rights reserved.

Elevated host lipid metabolism revealed by iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid of tuberculous meningitis patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mu, Jun; Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing; Chongqing Key Laboratory of Neurobiology, Chongqing

Purpose: Tuberculous meningitis (TBM) remains to be one of the most deadly infectious diseases. The pathogen interacts with the host immune system, the process of which is largely unknown. Various cellular processes of Mycobacterium tuberculosis (MTB) centers around lipid metabolism. To determine the lipid metabolism related proteins, a quantitative proteomic study was performed here to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n = 12) and healthy controls (n = 12). Methods: CSF samples were desalted, concentrated, labelled with isobaric tags for relative and absolute quantitation (iTRAQ™), and analyzed by multi-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene ontology andmore » proteomic phenotyping analysis of the differential proteins were conducted using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. ApoE and ApoB were selected for validation by ELISA. Results: Proteomic phenotyping of the 4 differential proteins was invloved in the lipid metabolism. ELISA showed significantly increased ApoB levels in TBM subjects compared to healthy controls. Area under the receiver operating characteristic curve analysis demonstrated ApoB levels could distinguish TBM subjects from healthy controls and viral meningitis subjects with 89.3% sensitivity and 92% specificity. Conclusions: CSF lipid metabolism disregulation, especially elevated expression of ApoB, gives insights into the pathogenesis of TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other center nervous system infectious diseases is required for successful clinical translation. - Highlights: • The first proteomic study on the cerebrospinal fluid of tuberculous meningitis patients using iTRAQ. • Identify 4 differential proteins invloved in the lipid metabolism. • Elevated expression of ApoB gives insights into the pathogenesis of TBM.« less

Complementary proteomic approaches reveal mitochondrial dysfunction, immune and inflammatory dysregulation in a mouse model of Gulf War Illness.

PubMed

Zakirova, Zuchra; Reed, Jon; Crynen, Gogce; Horne, Lauren; Hassan, Samira; Mathura, Venkatarajan; Mullan, Michael; Crawford, Fiona; Ait-Ghezala, Ghania

2017-09-01

Long-term consequences of combined pyridostigmine bromide (PB) and permethrin (PER) exposure in C57BL6/J mice using a well-characterized mouse model of exposure to these Gulf War (GW) agents were explored at the protein level. We used orthogonal proteomic approaches to identify pathways that are chronically impacted in the mouse CNS due to semiacute GW agent exposure early in life. These analyses were performed on soluble and membrane-bound protein fractions from brain samples using two orthogonal isotopic labeling LC-MS/MS proteomic approaches-stable isotope dimethyl labeling and iTRAQ. The use of these approaches allowed for greater coverage of proteins than was possible by either one alone and revealed both distinct and overlapping datasets. This combined analysis identified changes in several mitochondrial, as well as immune and inflammatory pathways after GW agent exposure. The work discussed here provides insight into GW agent exposure dependent mechanisms that adversely affect mitochondrial function and immune and inflammatory regulation. Collectively, our work identified key pathways which were chronically impacted in the mouse CNS following acute GW agent exposure, this may lead to the identification of potential targets for therapeutic intervention in the future. Long-term consequences of combined PB and PER exposure in C57BL6/J mice using a well-characterized mouse model of exposure to these GW agents were explored at the protein level. Expanding on earlier work, we used orthogonal proteomic approaches to identify pathways that are chronically impacted in the mouse CNS due to semiacute GW agent exposure early in life. These analyses were performed on soluble and membrane-bound protein fractions from brain samples using two orthogonal isotopic labeling LC-MS/MS proteomic approaches-stable isotope dimethyl labeling and iTRAQ. The use of these approaches allowed for greater coverage of proteins than was possible by either one alone and revealed both distinct and overlapping datasets. This combined analysis identified changes in several mitochondrial, as well as immune and inflammatory pathways after GW agent exposure. The work discussed here provides insight into GW agent exposure dependent mechanisms that adversely affect mitochondrial function and immune and inflammatory regulation at 5 months postexposure to PB + PER. © 2017 The Authors. PROTEOMICS - Clinical Applications published by WILEY-VCH Verlag GmbH & Co. KGaA.

Complementary proteomic approaches reveal mitochondrial dysfunction, immune and inflammatory dysregulation in a mouse model of Gulf War Illness

PubMed Central

Zakirova, Zuchra; Reed, Jon; Crynen, Gogce; Horne, Lauren; Hassan, Samira; Mathura, Venkatarajan; Mullan, Michael; Crawford, Fiona

2017-01-01

Purpose Long‐term consequences of combined pyridostigmine bromide (PB) and permethrin (PER) exposure in C57BL6/J mice using a well‐characterized mouse model of exposure to these Gulf War (GW) agents were explored at the protein level. Experimental design We used orthogonal proteomic approaches to identify pathways that are chronically impacted in the mouse CNS due to semiacute GW agent exposure early in life. These analyses were performed on soluble and membrane‐bound protein fractions from brain samples using two orthogonal isotopic labeling LC‐MS/MS proteomic approaches—stable isotope dimethyl labeling and iTRAQ. Results The use of these approaches allowed for greater coverage of proteins than was possible by either one alone and revealed both distinct and overlapping datasets. This combined analysis identified changes in several mitochondrial, as well as immune and inflammatory pathways after GW agent exposure. Conclusions and clinical relevance The work discussed here provides insight into GW agent exposure dependent mechanisms that adversely affect mitochondrial function and immune and inflammatory regulation. Collectively, our work identified key pathways which were chronically impacted in the mouse CNS following acute GW agent exposure, this may lead to the identification of potential targets for therapeutic intervention in the future. Long‐term consequences of combined PB and PER exposure in C57BL6/J mice using a well‐characterized mouse model of exposure to these GW agents were explored at the protein level. Expanding on earlier work, we used orthogonal proteomic approaches to identify pathways that are chronically impacted in the mouse CNS due to semiacute GW agent exposure early in life. These analyses were performed on soluble and membrane‐bound protein fractions from brain samples using two orthogonal isotopic labeling LC‐MS/MS proteomic approaches—stable isotope dimethyl labeling and iTRAQ. The use of these approaches allowed for greater coverage of proteins than was possible by either one alone and revealed both distinct and overlapping datasets. This combined analysis identified changes in several mitochondrial, as well as immune and inflammatory pathways after GW agent exposure. The work discussed here provides insight into GW agent exposure dependent mechanisms that adversely affect mitochondrial function and immune and inflammatory regulation at 5 months postexposure to PB + PER. PMID:28371386

Statistical inference from multiple iTRAQ experiments without using common reference standards.

PubMed

Herbrich, Shelley M; Cole, Robert N; West, Keith P; Schulze, Kerry; Yager, James D; Groopman, John D; Christian, Parul; Wu, Lee; O'Meally, Robert N; May, Damon H; McIntosh, Martin W; Ruczinski, Ingo

2013-02-01

Isobaric tags for relative and absolute quantitation (iTRAQ) is a prominent mass spectrometry technology for protein identification and quantification that is capable of analyzing multiple samples in a single experiment. Frequently, iTRAQ experiments are carried out using an aliquot from a pool of all samples, or "masterpool", in one of the channels as a reference sample standard to estimate protein relative abundances in the biological samples and to combine abundance estimates from multiple experiments. In this manuscript, we show that using a masterpool is counterproductive. We obtain more precise estimates of protein relative abundance by using the available biological data instead of the masterpool and do not need to occupy a channel that could otherwise be used for another biological sample. In addition, we introduce a simple statistical method to associate proteomic data from multiple iTRAQ experiments with a numeric response and show that this approach is more powerful than the conventionally employed masterpool-based approach. We illustrate our methods using data from four replicate iTRAQ experiments on aliquots of the same pool of plasma samples and from a 406-sample project designed to identify plasma proteins that covary with nutrient concentrations in chronically undernourished children from South Asia.

iTRAQ Quantitative Proteomic Comparison of Metastatic and Non-Metastatic Uveal Melanoma Tumors

PubMed Central

Crabb, John W.; Hu, Bo; Crabb, John S.; Triozzi, Pierre; Saunthararajah, Yogen; Singh, Arun D.

2015-01-01

Background Uveal melanoma is the most common malignancy of the adult eye. The overall mortality rate is high because this aggressive cancer often metastasizes before ophthalmic diagnosis. Quantitative proteomic analysis of primary metastasizing and non-metastasizing tumors was pursued for insights into mechanisms and biomarkers of uveal melanoma metastasis. Methods Eight metastatic and 7 non-metastatic human primary uveal melanoma tumors were analyzed by LC MS/MS iTRAQ technology with Bruch’s membrane/choroid complex from normal postmortem eyes as control tissue. Tryptic peptides from tumor and control proteins were labeled with iTRAQ tags, fractionated by cation exchange chromatography, and analyzed by LC MS/MS. Protein identification utilized the Mascot search engine and the human Uni-Prot/Swiss-Protein database with false discovery ≤ 1%; protein quantitation utilized the Mascot weighted average method. Proteins designated differentially expressed exhibited quantitative differences (p ≤ 0.05, t-test) in a training set of five metastatic and five non-metastatic tumors. Logistic regression models developed from the training set were used to classify the metastatic status of five independent tumors. Results Of 1644 proteins identified and quantified in 5 metastatic and 5 non-metastatic tumors, 12 proteins were found uniquely in ≥ 3 metastatic tumors, 28 were found significantly elevated and 30 significantly decreased only in metastatic tumors, and 31 were designated differentially expressed between metastatic and non-metastatic tumors. Logistic regression modeling of differentially expressed collagen alpha-3(VI) and heat shock protein beta-1 allowed correct prediction of metastasis status for each of five independent tumor specimens. Conclusions The present data provide new clues to molecular differences in metastatic and non-metastatic uveal melanoma tumors. While sample size is limited and validation required, the results support collagen alpha-3(VI) and heat shock protein beta-1 as candidate biomarkers of uveal melanoma metastasis and establish a quantitative proteomic database for uveal melanoma primary tumors. PMID:26305875

iTRAQ Quantitative Proteomic Analysis of Vitreous from Patients with Retinal Detachment.

PubMed

Santos, Fátima Milhano; Gaspar, Leonor Mesquita; Ciordia, Sergio; Rocha, Ana Sílvia; Castro E Sousa, João Paulo; Paradela, Alberto; Passarinha, Luís António; Tomaz, Cândida Teixeira

2018-04-11

Rhegmatogenous retinal detachment (RRD) is a potentially blinding condition characterized by a physical separation between neurosensory retina and retinal pigment epithelium. Quantitative proteomics can help to understand the changes that occur at the cellular level during RRD, providing additional information about the molecular mechanisms underlying its pathogenesis. In the present study, iTRAQ labeling was combined with two-dimensional LC-ESI-MS/MS to find expression changes in the proteome of vitreous from patients with RRD when compared to control samples. A total of 150 proteins were found differentially expressed in the vitreous of patients with RRD, including 96 overexpressed and 54 underexpressed. Several overexpressed proteins, several such as glycolytic enzymes (fructose-bisphosphate aldolase A, gamma-enolase, and phosphoglycerate kinase 1), glucose transporters (GLUT-1), growth factors (metalloproteinase inhibitor 1), and serine protease inhibitors (plasminogen activator inhibitor 1) are regulated by HIF-1, which suggests that HIF-1 signaling pathway can be triggered in response to RRD. Also, the accumulation of photoreceptor proteins, including phosducin, rhodopsin, and s-arrestin, and vimentin in vitreous may indicate that photoreceptor degeneration occurs in RRD. Also, the accumulation of photoreceptor proteins, including phosducin, rhodopsin, and s-arrestin, and vimentin in vitreous may indicate that photoreceptor degeneration occurs in RRD. Nevertheless, the differentially expressed proteins found in this study suggest that different mechanisms are activated after RRD to promote the survival of retinal cells through complex cellular responses.

iTRAQ Quantitative Proteomic Analysis of Vitreous from Patients with Retinal Detachment

PubMed Central

Gaspar, Leonor Mesquita; Ciordia, Sergio; Rocha, Ana Sílvia; Castro e Sousa, João Paulo; Paradela, Alberto

2018-01-01

Rhegmatogenous retinal detachment (RRD) is a potentially blinding condition characterized by a physical separation between neurosensory retina and retinal pigment epithelium. Quantitative proteomics can help to understand the changes that occur at the cellular level during RRD, providing additional information about the molecular mechanisms underlying its pathogenesis. In the present study, iTRAQ labeling was combined with two-dimensional LC-ESI-MS/MS to find expression changes in the proteome of vitreous from patients with RRD when compared to control samples. A total of 150 proteins were found differentially expressed in the vitreous of patients with RRD, including 96 overexpressed and 54 underexpressed. Several overexpressed proteins, several such as glycolytic enzymes (fructose-bisphosphate aldolase A, gamma-enolase, and phosphoglycerate kinase 1), glucose transporters (GLUT-1), growth factors (metalloproteinase inhibitor 1), and serine protease inhibitors (plasminogen activator inhibitor 1) are regulated by HIF-1, which suggests that HIF-1 signaling pathway can be triggered in response to RRD. Also, the accumulation of photoreceptor proteins, including phosducin, rhodopsin, and s-arrestin, and vimentin in vitreous may indicate that photoreceptor degeneration occurs in RRD. Also, the accumulation of photoreceptor proteins, including phosducin, rhodopsin, and s-arrestin, and vimentin in vitreous may indicate that photoreceptor degeneration occurs in RRD. Nevertheless, the differentially expressed proteins found in this study suggest that different mechanisms are activated after RRD to promote the survival of retinal cells through complex cellular responses. PMID:29641463

Quantitative and temporal proteome analysis of butyrate-treated colorectal cancer cells.

PubMed

Tan, Hwee Tong; Tan, Sandra; Lin, Qingsong; Lim, Teck Kwang; Hew, Choy Leong; Chung, Maxey C M

2008-06-01

Colorectal cancer is one of the most common cancers in developed countries, and its incidence is negatively associated with high dietary fiber intake. Butyrate, a short-chain fatty acid fermentation by-product of fiber induces cell maturation with the promotion of growth arrest, differentiation, and/or apoptosis of cancer cells. The stimulation of cell maturation by butyrate in colonic cancer cells follows a temporal progression from the early phase of growth arrest to the activation of apoptotic cascades. Previously we performed two-dimensional DIGE to identify differentially expressed proteins induced by 24-h butyrate treatment of HCT-116 colorectal cancer cells. Herein we used quantitative proteomics approaches using iTRAQ (isobaric tags for relative and absolute quantitation), a stable isotope labeling methodology that enables multiplexing of four samples, for a temporal study of HCT-116 cells treated with butyrate. In addition, cleavable ICAT, which selectively tags cysteine-containing proteins, was also used, and the results complemented those obtained from the iTRAQ strategy. Selected protein targets were validated by real time PCR and Western blotting. A model is proposed to illustrate our findings from this temporal analysis of the butyrate-responsive proteome that uncovered several integrated cellular processes and pathways involved in growth arrest, apoptosis, and metastasis. These signature clusters of butyrate-regulated pathways are potential targets for novel chemopreventive and therapeutic drugs for treatment of colorectal cancer.

Find Pairs: The Module for Protein Quantification of the PeakQuant Software Suite

PubMed Central

Eisenacher, Martin; Kohl, Michael; Wiese, Sebastian; Hebeler, Romano; Meyer, Helmut E.

2012-01-01

Abstract Accurate quantification of proteins is one of the major tasks in current proteomics research. To address this issue, a wide range of stable isotope labeling techniques have been developed, allowing one to quantitatively study thousands of proteins by means of mass spectrometry. In this article, the FindPairs module of the PeakQuant software suite is detailed. It facilitates the automatic determination of protein abundance ratios based on the automated analysis of stable isotope-coded mass spectrometric data. Furthermore, it implements statistical methods to determine outliers due to biological as well as technical variance of proteome data obtained in replicate experiments. This provides an important means to evaluate the significance in obtained protein expression data. For demonstrating the high applicability of FindPairs, we focused on the quantitative analysis of proteome data acquired in 14N/15N labeling experiments. We further provide a comprehensive overview of the features of the FindPairs software, and compare these with existing quantification packages. The software presented here supports a wide range of proteomics applications, allowing one to quantitatively assess data derived from different stable isotope labeling approaches, such as 14N/15N labeling, SILAC, and iTRAQ. The software is publicly available at http://www.medizinisches-proteom-center.de/software and free for academic use. PMID:22909347

Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry.

PubMed

Pfammatter, Sibylle; Bonneil, Eric; Thibault, Pierre

2016-12-02

Quantitative proteomics using isobaric reagent tandem mass tags (TMT) or isobaric tags for relative and absolute quantitation (iTRAQ) provides a convenient approach to compare changes in protein abundance across multiple samples. However, the analysis of complex protein digests by isobaric labeling can be undermined by the relative large proportion of co-selected peptide ions that lead to distorted reporter ion ratios and affect the accuracy and precision of quantitative measurements. Here, we investigated the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS) in proteomic experiments to reduce sample complexity and improve protein quantification using TMT isobaric labeling. LC-FAIMS-MS/MS analyses of human and yeast protein digests led to significant reductions in interfering ions, which increased the number of quantifiable peptides by up to 68% while significantly improving the accuracy of abundance measurements compared to that with conventional LC-MS/MS. The improvement in quantitative measurements using FAIMS is further demonstrated for the temporal profiling of protein abundance of HEK293 cells following heat shock treatment.

Analysis of Reproducibility of Proteome Coverage and Quantitation Using Isobaric Mass Tags (iTRAQ and TMT).

PubMed

Casey, Tammy M; Khan, Javed M; Bringans, Scott D; Koudelka, Tomas; Takle, Pari S; Downs, Rachael A; Livk, Andreja; Syme, Robert A; Tan, Kar-Chun; Lipscombe, Richard J

2017-02-03

This study aimed to compare the depth and reproducibility of total proteome and differentially expressed protein coverage in technical duplicates and triplicates using iTRAQ 4-plex, iTRAQ 8-plex, and TMT 6-plex reagents. The analysis was undertaken because comprehensive comparisons of isobaric mass tag reproducibility have not been widely reported in the literature. The highest number of proteins was identified with 4-plex, followed by 8-plex and then 6-plex reagents. Quantitative analyses revealed that more differentially expressed proteins were identified with 4-plex reagents than 8-plex reagents and 6-plex reagents. Replicate reproducibility was determined to be ≥69% for technical duplicates and ≥57% for technical triplicates. The results indicate that running an 8-plex or 6-plex experiment instead of a 4-plex experiment resulted in 26 or 39% fewer protein identifications, respectively. When 4-plex spectra were searched with three software tools-ProteinPilot, Mascot, and Proteome Discoverer-the highest number of protein identifications were obtained with Mascot. The analysis of negative controls demonstrated the importance of running experiments as replicates. Overall, this study demonstrates the advantages of using iTRAQ 4-plex reagents over iTRAQ 8-plex and TMT 6-plex reagents, provides estimates of technical duplicate and triplicate reproducibility, and emphasizes the value of running replicate samples.

Toxicoproteomics in Aquatic Toxicology: iTRAQ Reveals Insight into Proteins Affected by 17alpha-ethinylestradiol, Dieldrin, and 17â-trenbolone

EPA Science Inventory

Toxicoproteomics is an emerging discipline in toxicology for characterizing chemical modes of action at the molecular level. We have successfully utilized a quantitative proteomics method termed isobaric tagging for relative and absolute quantitation (iTRAQ) to measure protein re...

An accurate proteomic quantification method: fluorescence labeling absolute quantification (FLAQ) using multidimensional liquid chromatography and tandem mass spectrometry.

PubMed

Liu, Junyan; Liu, Yang; Gao, Mingxia; Zhang, Xiangmin

2012-08-01

A facile proteomic quantification method, fluorescent labeling absolute quantification (FLAQ), was developed. Instead of using MS for quantification, the FLAQ method is a chromatography-based quantification in combination with MS for identification. Multidimensional liquid chromatography (MDLC) with laser-induced fluorescence (LIF) detection with high accuracy and tandem MS system were employed for FLAQ. Several requirements should be met for fluorescent labeling in MS identification: Labeling completeness, minimum side-reactions, simple MS spectra, and no extra tandem MS fragmentations for structure elucidations. A fluorescence dye, 5-iodoacetamidofluorescein, was finally chosen to label proteins on all cysteine residues. The fluorescent dye was compatible with the process of the trypsin digestion and MALDI MS identification. Quantitative labeling was achieved with optimization of reacting conditions. A synthesized peptide and model proteins, BSA (35 cysteines), OVA (five cysteines), were used for verifying the completeness of labeling. Proteins were separated through MDLC and quantified based on fluorescent intensities, followed by MS identification. High accuracy (RSD% < 1.58) and wide linearity of quantification (1-10(5) ) were achieved by LIF detection. The limit of quantitation for the model protein was as low as 0.34 amol. Parts of proteins in human liver proteome were quantified and demonstrated using FLAQ. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics

PubMed Central

Frost, Dustin C.; Greer, Tyler; Xiang, Feng; Liang, Zhidan; Li, Lingjun

2015-01-01

Rationale Relative quantification of proteins via their enzymatically digested peptide products determines disease biomarker candidate lists in discovery studies. Isobaric label-based strategies using TMT and iTRAQ allow for up to 10 samples to be multiplexed in one experiment, but their expense limits their use. The demand for cost-effective tagging reagents capable of multiplexing many samples led us to develop an 8-plex version of our isobaric labeling reagent, DiLeu. Methods The original 4-plex DiLeu reagent was extended to an 8-plex set by coupling isotopic variants of dimethylated leucine to an alanine balance group designed to offset the increasing mass of the label’s reporter group. Tryptic peptides from a single protein digest, a protein mixture digest, and Saccharomyces cerevisiae lysate digest were labeled with 8-plex DiLeu and analyzed via nanoLC-MS2 on a Q-Exactive Orbitrap mass spectrometer. Characteristics of 8-plex DiLeu-labeled peptides, including quantitative accuracy and fragmentation, were examined. Results An 8-plex set of DiLeu reagents with 1 Da-spaced reporters was synthesized at a yield of 36%. The average cost to label eight 100 μg peptide samples was calculated to be approximately $15. Normalized collision energy tests on the Q-Exactive revealed that a higher-energy collisional dissociation value of 27 generated the optimum number of high-quality spectral matches. Relative quantification of DiLeu-labeled peptides yielded normalized median ratios accurate to within 12% of their expected values. Conclusions Cost-effective 8-plex DiLeu reagents can be synthesized and applied to relative peptide and protein quantification. These labels increase the multiplexing capacity of our previous 4-plex implementation without requiring high-resolution instrumentation to resolve reporter ion signals. PMID:25981542

Quantitative analysis of UV-A shock and short term stress using iTRAQ, pseudo selective reaction monitoring (pSRM) and GC-MS based metabolite analysis of the cyanobacterium Nostoc punctiforme ATCC 29133.

PubMed

Wase, Nishikant; Pham, Trong Khoa; Ow, Saw Yen; Wright, Phillip C

2014-09-23

A quantitative proteomics and metabolomics analysis was performed using iTRAQ, HPLC and GC-MS in the filamentous cyanobacterium Nostoc punctiforme ATCC 29133 to understand the effect of short and long term UV-A exposure. Changes in the proteome were measured for short-term stress (4-24h) using iTRAQ. Changes in the photosynthetic pigments and intracellular metabolites were observed at exposures of up to 7days (pigments) and up to 11days (intracellular metabolites). To assess iTRAQ measurement quality, pseudo selected reaction monitoring (pSRM) was used, with this confirming underestimation of protein abundance levels by iTRAQ. Our results suggest that short term UV-A radiation lowers the abundance of PS-I and PS-II proteins. We also observed an increase in abundance of intracellular redox homeostasis proteins and plastocyanin. Additionally, we observed statistically significant changes in scytonemin, Chlorophyll A, astaxanthin, zeaxanthin, and β-carotene. Assessment of intracellular metabolites showed significant changes in several, suggesting their potential role in the Nostoc's stress mitigation strategy. Cyanobacteria under UV-A radiation have reduced growth due to intensive damage to essential functions, but the organism shows a defense response by remodeling bioenergetics pathway, induction of the UV protection compound scytonemin and increased levels of proline and tyrosine as a mitigation response. The effect of UV-A radiation on the proteome and intracellular metabolites of N. punctiforme ATCC 29133 including photosynthetic pigments has been described. We also verify the expression of 13 iTRAQ quantified protein using LC-pSRM. Overall we observed that UV-A radiation has a drastic effect on the photosynthetic machinery, photosynthetic pigments and intracellular amino acids. As a mitigation strategy against UV-A radiation, proline, glycine, and tyrosine were accumulated. Copyright © 2014. Published by Elsevier B.V.

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates.

PubMed

Kleifeld, Oded; Doucet, Alain; Prudova, Anna; auf dem Keller, Ulrich; Gioia, Magda; Kizhakkedathu, Jayachandran N; Overall, Christopher M

2011-09-22

Analysis of the sequence and nature of protein N termini has many applications. Defining the termini of proteins for proteome annotation in the Human Proteome Project is of increasing importance. Terminomics analysis of protease cleavage sites in degradomics for substrate discovery is a key new application. Here we describe the step-by-step procedures for performing terminal amine isotopic labeling of substrates (TAILS), a 2- to 3-d (depending on method of labeling) high-throughput method to identify and distinguish protease-generated neo-N termini from mature protein N termini with all natural modifications with high confidence. TAILS uses negative selection to enrich for all N-terminal peptides and uses primary amine labeling-based quantification as the discriminating factor. Labeling is versatile and suited to many applications, including biochemical and cell culture analyses in vitro; in vivo analyses using tissue samples from animal and human sources can also be readily performed. At the protein level, N-terminal and lysine amines are blocked by dimethylation (formaldehyde/sodium cyanoborohydride) and isotopically labeled by incorporating heavy and light dimethylation reagents or stable isotope labeling with amino acids in cell culture labels. Alternatively, easy multiplex sample analysis can be achieved using amine blocking and labeling with isobaric tags for relative and absolute quantification, also known as iTRAQ. After tryptic digestion, N-terminal peptide separation is achieved using a high-molecular-weight dendritic polyglycerol aldehyde polymer that binds internal tryptic and C-terminal peptides that now have N-terminal alpha amines. The unbound naturally blocked (acetylation, cyclization, methylation and so on) or labeled mature N-terminal and neo-N-terminal peptides are recovered by ultrafiltration and analyzed by tandem mass spectrometry (MS/MS). Hierarchical substrate winnowing discriminates substrates from the background proteolysis products and non-cleaved proteins by peptide isotope quantification and bioinformatics search criteria.

Plant proteome analysis: a 2006 update.

PubMed

Jorrín, Jesús V; Maldonado, Ana M; Castillejo, Ma Angeles

2007-08-01

This 2006 'Plant Proteomics Update' is a continuation of the two previously published in 'Proteomics' by 2004 (Canovas et al., Proteomics 2004, 4, 285-298) and 2006 (Rossignol et al., Proteomics 2006, 6, 5529-5548) and it aims to bring up-to-date the contribution of proteomics to plant biology on the basis of the original research papers published throughout 2006, with references to those appearing last year. According to the published papers and topics addressed, we can conclude that, as observed for the three previous years, there has been a quantitative, but not qualitative leap in plant proteomics. The full potential of proteomics is far from being exploited in plant biology research, especially if compared to other organisms, mainly yeast and humans, and a number of challenges, mainly technological, remain to be tackled. The original papers published last year numbered nearly 100 and deal with the proteome of at least 26 plant species, with a high percentage for Arabidopsis thaliana (28) and rice (11). Scientific objectives ranged from proteomic analysis of organs/tissues/cell suspensions (57) or subcellular fractions (29), to the study of plant development (12), the effect of hormones and signalling molecules (8) and response to symbionts (4) and stresses (27). A small number of contributions have covered PTMs (8) and protein interactions (4). 2-DE (specifically IEF-SDS-PAGE) coupled to MS still constitutes the almost unique platform utilized in plant proteome analysis. The application of gel-free protein separation methods and 'second generation' proteomic techniques such as multidimensional protein identification technology (MudPIT), and those for quantitative proteomics including DIGE, isotope-coded affinity tags (ICAT), iTRAQ and stable isotope labelling by amino acids in cell culture (SILAC) still remains anecdotal. This review is divided into seven sections: Introduction, Methodology, Subcellular proteomes, Development, Responses to biotic and abiotic stresses, PTMs and Protein interactions. Section 8 summarizes the major pitfalls and challenges of plant proteomics.

Elucidation of the Mechanisms and Environmental Relevance of cis-Dichloroethene and Vinyl Chloride Biodegradation

DTIC Science & Technology

2012-11-01

in iTRAQ study Table 3-12: Ratio of aldehyde and alcohol dehydrogenases from iTRAQ study Table 3-13: Proteins involved in proposed glyoxal...pathway for cDCE degradation proceeds through chloro-, or dichloroacetaldehyde. Multiple aldehyde dehydrogenases are annotated in the genome of...dichloroacetaldehyde is a fortuitous reaction. However, if the initial reaction is monooxygenation to an aldehyde then the true intermediate would be

Xarray: multi-dimensional data analysis in Python

NASA Astrophysics Data System (ADS)

Hoyer, Stephan; Hamman, Joe; Maussion, Fabien

2017-04-01

xarray (http://xarray.pydata.org) is an open source project and Python package that provides a toolkit and data structures for N-dimensional labeled arrays, which are the bread and butter of modern geoscientific data analysis. Key features of the package include label-based indexing and arithmetic, interoperability with the core scientific Python packages (e.g., pandas, NumPy, Matplotlib, Cartopy), out-of-core computation on datasets that don't fit into memory, a wide range of input/output options, and advanced multi-dimensional data manipulation tools such as group-by and resampling. In this contribution we will present the key features of the library and demonstrate its great potential for a wide range of applications, from (big-)data processing on super computers to data exploration in front of a classroom.

Mining the human urine proteome for monitoring renal transplant injury

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sigdel, Tara K.; Gao, Yuqian; He, Jintang

The human urinary proteome reflects systemic and inherent renal injury perturbations and can be analyzed to harness specific biomarkers for different kidney transplant injury states. 396 unique urine samples were collected contemporaneously with an allograft biopsy from 396 unique kidney transplant recipients. Centralized, blinded histology on the graft was used to classify matched urine samples into categories of acute rejection (AR), chronic allograft nephropathy (CAN), BK virus nephritis (BKVN), and stable graft (STA). Liquid chromatography–mass spectrometry (LC-MS) based proteomics using iTRAQ based discovery (n=108) and global label-free LC-MS analyses of individual samples (n=137) for quantitative proteome assessment were used inmore » the discovery step. Selected reaction monitoring (SRM) was applied to identify and validate minimal urine protein/peptide biomarkers to accurately segregate organ injury causation and pathology on unique urine samples (n=151). A total of 958 proteins were initially quantified by iTRAQ, 87% of which were also identified among 1574 urine proteins detected in LC-MS validation. 103 urine proteins were significantly (p<0.05) perturbed in injury and enriched for humoral immunity, complement activation, and lymphocyte trafficking. A set of 131 peptides corresponding to 78 proteins were assessed by SRM for their significance in an independent sample cohort. A minimal set of 35 peptides mapping to 33 proteins, were modeled to segregate different injury groups (AUC =93% for AR, 99% for CAN, 83% for BKVN). Urinary proteome discovery and targeted validation identified urine protein fingerprints for non-invasive differentiation of kidney transplant injuries, thus opening the door for personalized immune risk assessment and therapy.« less

Proteomic Analysis of Lipid Raft-Like Detergent-Resistant Membranes of Lens Fiber Cells.

PubMed

Wang, Zhen; Schey, Kevin L

2015-12-01

Plasma membranes of lens fiber cells have high levels of long-chain saturated fatty acids, cholesterol, and sphingolipids-key components of lipid rafts. Thus, lipid rafts are expected to constitute a significant portion of fiber cell membranes and play important roles in lens biology. The purpose of this study was to characterize the lens lipid raft proteome. Quantitative proteomics, both label-free and iTRAQ methods, were used to characterize lens fiber cell lipid raft proteins. Detergent-resistant, lipid raft membrane (DRM) fractions were isolated by sucrose gradient centrifugation. To confirm protein localization to lipid rafts, protein sensitivity to cholesterol removal by methyl-β-cyclodextrin was quantified by iTRAQ analysis. A total of 506 proteins were identified in raft-like detergent-resistant membranes. Proteins identified support important functions of raft domains in fiber cells, including trafficking, signal transduction, and cytoskeletal organization. In cholesterol-sensitivity studies, 200 proteins were quantified and 71 proteins were strongly affected by cholesterol removal. Lipid raft markers flotillin-1 and flotillin-2 and a significant fraction of AQP0, MP20, and AQP5 were found in the DRM fraction and were highly sensitive to cholesterol removal. Connexins 46 and 50 were more abundant in nonraft fractions, but a small fraction of each was found in the DRM fraction and was strongly affected by cholesterol removal. Quantification of modified AQP0 confirmed that fatty acylation targeted this protein to membrane raft domains. These data represent the first comprehensive profile of the lipid raft proteome of lens fiber cells and provide information on membrane protein organization in these cells.

Elucidation of the Mechanisms and Environmental Relevance of cis-Dichloroethene and Vinyl Chloride Biodegradation

DTIC Science & Technology

2012-11-01

iTRAQ study Table 3-12: Ratio of aldehyde and alcohol dehydrogenases from iTRAQ study Table 3-13: Proteins involved in proposed glyoxal transformation...pathway for cDCE degradation proceeds through chloro-, or dichloroacetaldehyde. Multiple aldehyde dehydrogenases are annotated in the genome of JS666...is a fortuitous reaction. However, if the initial reaction is monooxygenation to an aldehyde then the true intermediate would be

Strigolactone-regulated proteins revealed by iTRAQ-based quantitative proteomics in Arabidopsis.

PubMed

Li, Zhou; Czarnecki, Olaf; Chourey, Karuna; Yang, Jun; Tuskan, Gerald A; Hurst, Gregory B; Pan, Chongle; Chen, Jin-Gui

2014-03-07

Strigolactones (SLs) are a new class of plant hormones. In addition to acting as a key inhibitor of shoot branching, SLs stimulate seed germination of root parasitic plants and promote hyphal branching and root colonization of symbiotic arbuscular mycorrhizal fungi. They also regulate many other aspects of plant growth and development. At the transcription level, SL-regulated genes have been reported. However, nothing is known about the proteome regulated by this new class of plant hormones. A quantitative proteomics approach using an isobaric chemical labeling reagent, iTRAQ, to identify the proteome regulated by SLs in Arabidopsis seedlings is presented. It was found that SLs regulate the expression of about three dozen proteins that have not been previously assigned to SL pathways. These findings provide a new tool to investigate the molecular mechanism of action of SLs.

Profiling the Aspergillus fumigatus Proteome in Response to Caspofungin ▿ †

PubMed Central

Cagas, Steven E.; Jain, Mohit Raja; Li, Hong; Perlin, David S.

2011-01-01

The proteomic response of Aspergillus fumigatus to caspofungin was evaluated by gel-free isobaric tagging for relative and absolute quantitation (iTRAQ) as a means to determine potential biomarkers of drug action. A cell fractionation approach yielding 4 subcellular compartment fractions was used to enhance the resolution of proteins for proteomic analysis. Using iTRAQ, a total of 471 unique proteins were identified in soluble and cell wall/plasma membrane fractions at 24 and 48 h of growth in rich media in a wild-type drug-susceptible strain. A total of 122 proteins showed at least a 2-fold change in relative abundance following exposure to caspofungin (CSF) at just below the minimum effective concentration (0.12 μg/ml). The largest changes were seen in the mitochondrial hypoxia response domain protein (AFUA_1G12250), the level of which decreased >16-fold in the secreted fraction, and ChiA1, the level of which decreased 12.1-fold in the cell wall/plasma membrane fraction. The level of the major allergen and cytotoxin AspF1 was also shown to decrease by 12.1-fold upon the addition of drug. A subsequent iTRAQ analysis of an echinocandin-resistant strain (fks1-S678P) was used to validate proteins specific to drug action. A total of 103 proteins in the 2 fractions tested by iTRAQ were differentially expressed in the wild-type susceptible strain but not significantly changed in the resistant strain. Of these potential biomarkers, 11 had levels that changed at least 12-fold. Microarray analysis of the susceptible strain was performed to evaluate the correlation between proteomics and genomics, with a total of 117 genes found to be changing at least 2-fold. Of these, a total of 22 proteins with significant changes identified by iTRAQ also showed significant gene expression level changes by microarray. Overall, these data have the potential to identify biomarkers that assess the relative efficacy of echinocandin drug therapy. PMID:20974863

SPECHT - single-stage phosphopeptide enrichment and stable-isotope chemical tagging: quantitative phosphoproteomics of insulin action in muscle.

PubMed

Kettenbach, Arminja N; Sano, Hiroyuki; Keller, Susanna R; Lienhard, Gustav E; Gerber, Scott A

2015-01-30

The study of cellular signaling remains a significant challenge for translational and clinical research. In particular, robust and accurate methods for quantitative phosphoproteomics in tissues and tumors represent significant hurdles for such efforts. In the present work, we design, implement and validate a method for single-stage phosphopeptide enrichment and stable isotope chemical tagging, or SPECHT, that enables the use of iTRAQ, TMT and/or reductive dimethyl-labeling strategies to be applied to phosphoproteomics experiments performed on primary tissue. We develop and validate our approach using reductive dimethyl-labeling and HeLa cells in culture, and find these results indistinguishable from data generated from more traditional SILAC-labeled HeLa cells mixed at the cell level. We apply the SPECHT approach to the quantitative analysis of insulin signaling in a murine myotube cell line and muscle tissue, identify known as well as new phosphorylation events, and validate these phosphorylation sites using phospho-specific antibodies. Taken together, our work validates chemical tagging post-single-stage phosphoenrichment as a general strategy for studying cellular signaling in primary tissues. Through the use of a quantitatively reproducible, proteome-wide phosphopeptide enrichment strategy, we demonstrated the feasibility of post-phosphopeptide purification chemical labeling and tagging as an enabling approach for quantitative phosphoproteomics of primary tissues. Using reductive dimethyl labeling as a generalized chemical tagging strategy, we compared the performance of post-phosphopeptide purification chemical tagging to the well established community standard, SILAC, in insulin-stimulated tissue culture cells. We then extended our method to the analysis of low-dose insulin signaling in murine muscle tissue, and report on the analytical and biological significance of our results. Copyright © 2014 Elsevier B.V. All rights reserved.

A comparative proteomics method for multiple samples based on a 18O-reference strategy and a quantitation and identification-decoupled strategy.

PubMed

Wang, Hongbin; Zhang, Yongqian; Gui, Shuqi; Zhang, Yong; Lu, Fuping; Deng, Yulin

2017-08-15

Comparisons across large numbers of samples are frequently necessary in quantitative proteomics. Many quantitative methods used in proteomics are based on stable isotope labeling, but most of these are only useful for comparing two samples. For up to eight samples, the iTRAQ labeling technique can be used. For greater numbers of samples, the label-free method has been used, but this method was criticized for low reproducibility and accuracy. An ingenious strategy has been introduced, comparing each sample against a 18 O-labeled reference sample that was created by pooling equal amounts of all samples. However, it is necessary to use proportion-known protein mixtures to investigate and evaluate this new strategy. Another problem for comparative proteomics of multiple samples is the poor coincidence and reproducibility in protein identification results across samples. In present study, a method combining 18 O-reference strategy and a quantitation and identification-decoupled strategy was investigated with proportion-known protein mixtures. The results obviously demonstrated that the 18 O-reference strategy had greater accuracy and reliability than other previously used comparison methods based on transferring comparison or label-free strategies. By the decoupling strategy, the quantification data acquired by LC-MS and the identification data acquired by LC-MS/MS are matched and correlated to identify differential expressed proteins, according to retention time and accurate mass. This strategy made protein identification possible for all samples using a single pooled sample, and therefore gave a good reproducibility in protein identification across multiple samples, and allowed for optimizing peptide identification separately so as to identify more proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

MilQuant: a free, generic software tool for isobaric tagging-based quantitation.

PubMed

Zou, Xiao; Zhao, Minzhi; Shen, Hongyan; Zhao, Xuyang; Tong, Yuanpeng; Wang, Qingsong; Wei, Shicheng; Ji, Jianguo

2012-09-18

Isobaric tagging techniques such as iTRAQ and TMT are widely used in quantitative proteomics and especially useful for samples that demand in vitro labeling. Due to diversity in choices of MS acquisition approaches, identification algorithms, and relative abundance deduction strategies, researchers are faced with a plethora of possibilities when it comes to data analysis. However, the lack of generic and flexible software tool often makes it cumbersome for researchers to perform the analysis entirely as desired. In this paper, we present MilQuant, mzXML-based isobaric labeling quantitator, a pipeline of freely available programs that supports native acquisition files produced by all mass spectrometer types and collection approaches currently used in isobaric tagging based MS data collection. Moreover, aside from effective normalization and abundance ratio deduction algorithms, MilQuant exports various intermediate results along each step of the pipeline, making it easy for researchers to customize the analysis. The functionality of MilQuant was demonstrated by four distinct datasets from different laboratories. The compatibility and extendibility of MilQuant makes it a generic and flexible tool that can serve as a full solution to data analysis of isobaric tagging-based quantitation. Copyright © 2012 Elsevier B.V. All rights reserved.

Modelling atherosclerosis by proteomics: Molecular changes in the ascending aortas of cholesterol-fed rabbits.

PubMed

Xu, Jingshu; Jüllig, Mia; Middleditch, Martin J; Cooper, Garth J S

2015-09-01

The cholesterol-fed rabbit is commonly used as a model to study the vascular effects of hypercholesterolemia and resulting atherosclerotic lesions. Here we undertook a proteomic case-control investigation of ascending aortas from male New Zealand White rabbits after 10 weeks on a high-cholesterol (2% w/w) diet (HCD, n = 5) or control diet (n = 5), in order to determine the changes in response to the HCD. Histology confirmed intimal thickening in the HCD group consistent with atherosclerosis, and LC-MS/MS analysis of individually-obtained ascending aortic extracts labelled with isobaric (iTRAQ) tags enabled the identification and quantitation of 453 unique proteins above the 1% false discovery rate threshold. Of 67 proteins showing significant differences in relative abundance (p < 0.05), 62 were elevated and five decreased in ascending aortas from HCD-fed rabbits compared to controls. Six proteins were selected for validation using Multiple Reaction Monitoring, which confirmed the iTRAQ results. Many of the observed protein changes are consistent with known molecular perturbations in the ascending aorta that occur in response to hypercholesterolemia, e.g. elevation of tissue levels of apolipoproteins, extracellular matrix adhesion proteins, glycolytic enzymes, heat shock proteins and proteins involved in immune defense. We also made a number of novel observations, including a 15-fold elevation of glycoprotein (trans-membrane) nmb-like (Gpnmb) in response to HCD. Gpnmb has previously been linked to angiogenesis but not to atherosclerosis. This and additional novel observations merit further investigation as these perturbations may play important and as yet undiscovered roles in the pathogenesis of atherosclerosis in rabbits as well as humans. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Quantitative chemical proteomics profiling of de novo protein synthesis during starvation-mediated autophagy.

PubMed

Wang, Jigang; Zhang, Jianbin; Lee, Yew-Mun; Koh, Pin-Lang; Ng, Shukie; Bao, Feichao; Lin, Qingsong; Shen, Han-Ming

2016-10-02

Autophagy is an intracellular degradation mechanism in response to nutrient starvation. Via autophagy, some nonessential cellular constituents are degraded in a lysosome-dependent manner to generate biomolecules that can be utilized for maintaining the metabolic homeostasis. Although it is known that under starvation the global protein synthesis is significantly reduced mainly due to suppression of MTOR (mechanistic target of rapamycin serine/threonine kinase), emerging evidence demonstrates that de novo protein synthesis is involved in the autophagic process. However, characterizing these de novo proteins has been an issue with current techniques. Here, we developed a novel method to identify newly synthesized proteins during starvation-mediated autophagy by combining bio-orthogonal noncanonical amino acid tagging (BONCAT) and isobaric tags for relative and absolute quantitation (iTRAQ TM ). Using bio-orthogonal metabolic tagging, L-azidohomoalanine (AHA) was incorporated into newly synthesized proteins which were then enriched with avidin beads after a click reaction between alkyne-bearing biotin and AHA's bio-orthogonal azide moiety. The enriched proteins were subjected to iTRAQ labeling for protein identification and quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Via the above approach, we identified and quantified a total of 1176 proteins and among them 711 proteins were found to meet our defined criteria as de novo synthesized proteins during starvation-mediated autophagy. The characterized functional profiles of the 711 newly synthesized proteins by bioinformatics analysis suggest their roles in ensuring the prosurvival outcome of autophagy. Finally, we performed validation assays for some selected proteins and found that knockdown of some genes has a significant impact on starvation-induced autophagy. Thus, we think that the BONCAT-iTRAQ approach is effective in the identification of newly synthesized proteins and provides useful insights to the molecular mechanisms and biological functions of autophagy.

Proteomic Analysis of Lipid Raft-Like Detergent-Resistant Membranes of Lens Fiber Cells

PubMed Central

Wang, Zhen; Schey, Kevin L.

2015-01-01

Purpose Plasma membranes of lens fiber cells have high levels of long-chain saturated fatty acids, cholesterol, and sphingolipids—key components of lipid rafts. Thus, lipid rafts are expected to constitute a significant portion of fiber cell membranes and play important roles in lens biology. The purpose of this study was to characterize the lens lipid raft proteome. Methods Quantitative proteomics, both label-free and iTRAQ methods, were used to characterize lens fiber cell lipid raft proteins. Detergent-resistant, lipid raft membrane (DRM) fractions were isolated by sucrose gradient centrifugation. To confirm protein localization to lipid rafts, protein sensitivity to cholesterol removal by methyl-β-cyclodextrin was quantified by iTRAQ analysis. Results A total of 506 proteins were identified in raft-like detergent-resistant membranes. Proteins identified support important functions of raft domains in fiber cells, including trafficking, signal transduction, and cytoskeletal organization. In cholesterol-sensitivity studies, 200 proteins were quantified and 71 proteins were strongly affected by cholesterol removal. Lipid raft markers flotillin-1 and flotillin-2 and a significant fraction of AQP0, MP20, and AQP5 were found in the DRM fraction and were highly sensitive to cholesterol removal. Connexins 46 and 50 were more abundant in nonraft fractions, but a small fraction of each was found in the DRM fraction and was strongly affected by cholesterol removal. Quantification of modified AQP0 confirmed that fatty acylation targeted this protein to membrane raft domains. Conclusions These data represent the first comprehensive profile of the lipid raft proteome of lens fiber cells and provide information on membrane protein organization in these cells. PMID:26747763

Recent 5-year Findings and Technological Advances in the Proteomic Study of HIV-associated Disorders.

PubMed

Zhang, Lijun; Jia, Xiaofang; Jin, Jun-O; Lu, Hongzhou; Tan, Zhimi

2017-04-01

Human immunodeficiency virus-1 (HIV-1) mainly relies on host factors to complete its life cycle. Hence, it is very important to identify HIV-regulated host proteins. Proteomics is an excellent technique for this purpose because of its high throughput and sensitivity. In this review, we summarized current technological advances in proteomics, including general isobaric tags for relative and absolute quantitation (iTRAQ) and stable isotope labeling by amino acids in cell culture (SILAC), as well as subcellular proteomics and investigation of posttranslational modifications. Furthermore, we reviewed the applications of proteomics in the discovery of HIV-related diseases and HIV infection mechanisms. Proteins identified by proteomic studies might offer new avenues for the diagnosis and treatment of HIV infection and the related diseases. Copyright © 2017 The Authors. Production and hosting by Elsevier B.V. All rights reserved.

Proteomic biomarkers in lung cancer.

PubMed

Pastor, M D; Nogal, A; Molina-Pinelo, S; Carnero, A; Paz-Ares, L

2013-09-01

The correct understanding of tumour development relies on the comprehensive study of proteins. They are the main orchestrators of vital processes, such as signalling pathways, which drive the carcinogenic process. Proteomic technologies can be applied to cancer research to detect differential protein expression and to assess different responses to treatment. Lung cancer is the number one cause of cancer-related death in the world. Mostly diagnosed at late stages of the disease, lung cancer has one of the lowest 5-year survival rates at 15 %. The use of different proteomic techniques such as two-dimensional gel electrophoresis (2D-PAGE), isotope labelling (ICAT, SILAC, iTRAQ) and mass spectrometry may yield new knowledge on the underlying biology of lung cancer and also allow the development of new early detection tests and the identification of changes in the cancer protein network that are associated with prognosis and drug resistance.

Quantitative proteomics analysis by iTRAQ in human nuclear cataracts of different ages and normal lens nuclei.

PubMed

Zhou, Hai Yan; Yan, Hong; Wang, Li Li; Yan, Wei Jia; Shui, Ying Bo; Beebe, David C

2015-08-01

The goal of this study was to quantitatively identify the differentially expressed proteins in nuclear cataracts of different ages and normal lens nuclei in humans. Forty-eight human lens nucleus samples with hardness grades III, IV were obtained during cataract surgery by extracapsular cataract extraction. Seven normal transparent human lens nuclei were obtained from fresh normal cadaver eyes during corneal transplantation surgery. Lens nuclei were divided into seven groups according to age and optic axis: Group A (average age 80.8 ± 1.2 years), Group B (average age 57.0 ± 4.0 years), Group C average age 80.3 ± 4.5 years), Group D (average age 56.9 ± 4.2 years), Group E (average age 78.1 ± 2.5 years), Group F (average age 57.6 ± 3.3 years) and Group G (seven normal transparent human lenses from normal cadaver eyes, average age 34.7 ± 4.2 years). Water-soluble, water-insoluble, and water-insoluble-urea-soluble protein fractions were extracted from samples. The three-part protein fractions from the individual lenses were combined to form the total proteins of each sample. The proteomic profiles of each group were further analyzed using 8-plex iTRAQ labeling combined with 2D-LC-MS/MS. The data were analyzed with the ProteinPilot software for peptide matching, protein identification, and quantification. Differentially expressed proteins were validated by Western blotting. We employed biological and technical replicates and selected the intersection of the two results, which included 80 proteins. Nine proteins were differentially expressed among the 80 proteins identified using proteomic techniques. In age-related nuclear cataracts (ARNC), the expression levels of fatty acid-binding protein and pterin-4-alpha-carbinolamine dehydratase were upregulated, whereas the levels of alpha-crystallin B chain (CRYAB), GSH synthetase, phakinin, gamma-crystallin C, phosphoglycerate kinase 1, betaine-homocysteine S-methyltransferase 1 (BHMT1), and spectrin beta chain were downregulated. These proteins may be associated with abnormal protein aggregation and oxidative stress. GSH synthetase and CRYAB expression levels in the nuclear cataract decreased with age. The mass spectrometric analysis results were consistent with the Western blot validation. The results indicate that CRYAB and GSH synthetase may be involved in ARNC pathogenesis. iTRAQ combined with 2D-LC-MS/MS provides new methods for future studies of pathological mechanisms and protective drug development for ARNC. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-throughput quantitation of amino acids in rat and mouse biological matrices using stable isotope labeling and UPLC-MS/MS analysis.

PubMed

Takach, Edward; O'Shea, Thomas; Liu, Hanlan

2014-08-01

Quantifying amino acids in biological matrices is typically performed using liquid chromatography (LC) coupled with fluorescent detection (FLD), requiring both derivatization and complete baseline separation of all amino acids. Due to its high specificity and sensitivity, the use of UPLC-MS/MS eliminates the derivatization step and allows for overlapping amino acid retention times thereby shortening the analysis time. Furthermore, combining UPLC-MS/MS with stable isotope labeling (e.g., isobaric tag for relative and absolute quantitation, i.e., iTRAQ) of amino acids enables quantitation while maintaining sensitivity, selectivity and speed of analysis. In this study, we report combining UPLC-MS/MS analysis with iTRAQ labeling of amino acids resulting in the elution and quantitation of 44 amino acids within 5 min demonstrating the speed and convenience of this assay over established approaches. This chromatographic analysis time represented a 5-fold improvement over the conventional HPLC-MS/MS method developed in our laboratory. In addition, the UPLC-MS/MS method demonstrated improvements in both specificity and sensitivity without loss of precision. In comparing UPLC-MS/MS and HPLC-MS/MS results of 32 detected amino acids, only 2 amino acids exhibited imprecision (RSD) >15% using UPLC-MS/MS, while 9 amino acids exhibited RSD >15% using HPLC-MS/MS. Evaluating intra- and inter-assay precision over 3 days, the quantitation range for 32 detected amino acids in rat plasma was 0.90-497 μM, with overall mean intra-day precision of less than 15% and mean inter-day precision of 12%. This UPLC-MS/MS assay was successfully implemented for the quantitative analysis of amino acids in rat and mouse plasma, along with mouse urine and tissue samples, resulting in the following concentration ranges: 0.98-431 μM in mouse plasma for 32 detected amino acids; 0.62-443 μM in rat plasma for 32 detected amino acids; 0.44-8590μM in mouse liver for 33 detected amino acids; 0.61-1241 μM in mouse kidney for 37 detected amino acids; and 1.39-1,681 μM in rat urine for 34 detected amino acids. The utility of the assay was further demonstrated by measuring and comparing plasma amino acid levels between pre-diabetic Zucker diabetic fatty rats (ZDF/Gmi fa/fa) and their lean littermates (ZDF/Gmi fa/?). Significant differences (P<0.001) in 9 amino acid concentrations were observed, with the majority ranging from a 2- to 5-fold increase in pre-diabetic ZDF rats on comparison with ZDF lean rats, consistent with previous literature reports. Copyright © 2014 Elsevier B.V. All rights reserved.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes*

PubMed Central

Mosley, Amber L.; Sardiu, Mihaela E.; Pattenden, Samantha G.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

2011-01-01

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports. PMID:21048197

Quantitative proteomic analysis of microdissected oral epithelium for cancer biomarker discovery.

PubMed

Xiao, Hua; Langerman, Alexander; Zhang, Yan; Khalid, Omar; Hu, Shen; Cao, Cheng-Xi; Lingen, Mark W; Wong, David T W

2015-11-01

Specific biomarkers are urgently needed for the detection and progression of oral cancer. The objective of this study was to discover cancer biomarkers from oral epithelium through utilizing high throughput quantitative proteomics approaches. Morphologically malignant, epithelial dysplasia, and adjacent normal epithelial tissues were laser capture microdissected (LCM) from 19 patients and used for proteomics analysis. Total proteins from each group were extracted, digested and then labelled with corresponding isobaric tags for relative and absolute quantitation (iTRAQ). Labelled peptides from each sample were combined and analyzed by liquid chromatography-mass spectrometry (LC-MS/MS) for protein identification and quantification. In total, 500 proteins were identified and 425 of them were quantified. When compared with adjacent normal oral epithelium, 17 and 15 proteins were consistently up-regulated or down-regulated in malignant and epithelial dysplasia, respectively. Half of these candidate biomarkers were discovered for oral cancer for the first time. Cornulin was initially confirmed in tissue protein extracts and was further validated in tissue microarray. Its presence in the saliva of oral cancer patients was also explored. Myoglobin and S100A8 were pre-validated by tissue microarray. These data demonstrated that the proteomic biomarkers discovered through this strategy are potential targets for oral cancer detection and salivary diagnostics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Markov blanket-based approach for learning multi-dimensional Bayesian network classifiers: an application to predict the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39).

PubMed

Borchani, Hanen; Bielza, Concha; Martı Nez-Martı N, Pablo; Larrañaga, Pedro

2012-12-01

Multi-dimensional Bayesian network classifiers (MBCs) are probabilistic graphical models recently proposed to deal with multi-dimensional classification problems, where each instance in the data set has to be assigned to more than one class variable. In this paper, we propose a Markov blanket-based approach for learning MBCs from data. Basically, it consists of determining the Markov blanket around each class variable using the HITON algorithm, then specifying the directionality over the MBC subgraphs. Our approach is applied to the prediction problem of the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39) in order to estimate the health-related quality of life of Parkinson's patients. Fivefold cross-validation experiments were carried out on randomly generated synthetic data sets, Yeast data set, as well as on a real-world Parkinson's disease data set containing 488 patients. The experimental study, including comparison with additional Bayesian network-based approaches, back propagation for multi-label learning, multi-label k-nearest neighbor, multinomial logistic regression, ordinary least squares, and censored least absolute deviations, shows encouraging results in terms of predictive accuracy as well as the identification of dependence relationships among class and feature variables. Copyright © 2012 Elsevier Inc. All rights reserved.

Classification of holter registers by dynamic clustering using multi-dimensional particle swarm optimization.

PubMed

Kiranyaz, Serkan; Ince, Turker; Pulkkinen, Jenni; Gabbouj, Moncef

2010-01-01

In this paper, we address dynamic clustering in high dimensional data or feature spaces as an optimization problem where multi-dimensional particle swarm optimization (MD PSO) is used to find out the true number of clusters, while fractional global best formation (FGBF) is applied to avoid local optima. Based on these techniques we then present a novel and personalized long-term ECG classification system, which addresses the problem of labeling the beats within a long-term ECG signal, known as Holter register, recorded from an individual patient. Due to the massive amount of ECG beats in a Holter register, visual inspection is quite difficult and cumbersome, if not impossible. Therefore the proposed system helps professionals to quickly and accurately diagnose any latent heart disease by examining only the representative beats (the so called master key-beats) each of which is representing a cluster of homogeneous (similar) beats. We tested the system on a benchmark database where the beats of each Holter register have been manually labeled by cardiologists. The selection of the right master key-beats is the key factor for achieving a highly accurate classification and the proposed systematic approach produced results that were consistent with the manual labels with 99.5% average accuracy, which basically shows the efficiency of the system.

Proteomic Analysis of the Human Skin Proteome after In Vivo Treatment with Sodium Dodecyl Sulphate

PubMed Central

Parkinson, Erika; Skipp, Paul; Aleksic, Maja; Garrow, Andrew; Dadd, Tony; Hughes, Michael; Clough, Geraldine; O′Connor, C. David

2014-01-01

Background Skin has a variety of functions that are incompletely understood at the molecular level. As the most accessible tissue in the body it often reveals the first signs of inflammation or infection and also represents a potentially valuable source of biomarkers for several diseases. In this study we surveyed the skin proteome qualitatively using gel electrophoresis, liquid chromatography tandem mass spectrometry (GeLC-MS/MS) and quantitatively using an isobaric tagging strategy (iTRAQ) to characterise the response of human skin following exposure to sodium dodecyl sulphate (SDS). Results A total of 653 skin proteins were assigned, 159 of which were identified using GeLC-MS/MS and 616 using iTRAQ, representing the most comprehensive proteomic study in human skin tissue. Statistical analysis of the available iTRAQ data did not reveal any significant differences in the measured skin proteome after 4 hours exposure to the model irritant SDS. Conclusions This study represents the first step in defining the critical response to an irritant at the level of the proteome and provides a valuable resource for further studies at the later stages of irritant exposure. PMID:24849295

Quantitative Proteomics Analysis of Streptomyces coelicolor Development Demonstrates That Onset of Secondary Metabolism Coincides with Hypha Differentiation*

PubMed Central

Manteca, Angel; Sanchez, Jesus; Jung, Hye R.; Schwämmle, Veit; Jensen, Ole N.

2010-01-01

Streptomyces species produce many clinically important secondary metabolites, including antibiotics and antitumorals. They have a complex developmental cycle, including programmed cell death phenomena, that makes this bacterium a multicellular prokaryotic model. There are two differentiated mycelial stages: an early compartmentalized vegetative mycelium (first mycelium) and a multinucleated reproductive mycelium (second mycelium) arising after programmed cell death processes. In the present study, we made a detailed proteomics analysis of the distinct developmental stages of solid confluent Streptomyces coelicolor cultures using iTRAQ (isobaric tags for relative and absolute quantitation) labeling and LC-MS/MS. A new experimental approach was developed to obtain homogeneous samples at each developmental stage (temporal protein analysis) and also to obtain membrane and cytosolic protein fractions (spatial protein analysis). A total of 345 proteins were quantified in two biological replicates. Comparative bioinformatics analyses revealed the switch from primary to secondary metabolism between the initial compartmentalized mycelium and the multinucleated hyphae. PMID:20224110

Proteomic Profile of Unstable Atheroma Plaque: Increased Neutrophil Defensin 1, Clusterin, and Apolipoprotein E Levels in Carotid Secretome.

PubMed

Aragonès, Gemma; Auguet, Teresa; Guiu-Jurado, Esther; Berlanga, Alba; Curriu, Marta; Martinez, Salomé; Alibalic, Ajla; Aguilar, Carmen; Hernández, Esteban; Camara, María-Luisa; Canela, Núria; Herrero, Pol; Ruyra, Xavier; Martín-Paredero, Vicente; Richart, Cristóbal

2016-03-04

Because of the clinical significance of carotid atherosclerosis, the search for novel biomarkers has become a priority. The aim of the present study was to compare the protein secretion profile of the carotid atherosclerotic plaque (CAP, n = 12) and nonatherosclerotic mammary artery (MA, n = 10) secretomes. We used a nontargeted proteomic approach that incorporated tandem immunoaffinity depletion, iTRAQ labeling, and nanoflow liquid chromatography coupled to high-resolution mass spectrometry. In total, 162 proteins were quantified, of which 25 showed statistically significant differences in secretome levels between carotid atherosclerotic plaque and nondiseased mammary artery. We found increased levels of neutrophil defensin 1, apolipoprotein E, clusterin, and zinc-alpha-2-glycoprotein in CAP secretomes. Results were validated by ELISA assays. Also, differentially secreted proteins are involved in pathways such as focal adhesion and leukocyte transendothelial migration. In conclusion, this study provides a subset of identified proteins that are differently expressed in secretomes of clinical significance.

Using partially labeled data for normal mixture identification with application to class definition

NASA Technical Reports Server (NTRS)

Shahshahani, Behzad M.; Landgrebe, David A.

1992-01-01

The problem of estimating the parameters of a normal mixture density when, in addition to the unlabeled samples, sets of partially labeled samples are available is addressed. The density of the multidimensional feature space is modeled with a normal mixture. It is assumed that the set of components of the mixture can be partitioned into several classes and that training samples are available from each class. Since for any training sample the class of origin is known but the exact component of origin within the corresponding class is unknown, the training samples as considered to be partially labeled. The EM iterative equations are derived for estimating the parameters of the normal mixture in the presence of partially labeled samples. These equations can be used to combine the supervised and nonsupervised learning processes.

Condenser: a statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™.

PubMed

Knudsen, Anders Dahl; Bennike, Tue; Kjeldal, Henrik; Birkelund, Svend; Otzen, Daniel Erik; Stensballe, Allan

2014-05-30

We describe Condenser, a freely available, comprehensive open-source tool for merging multidimensional quantitative proteomics data from the Matrix Science Mascot Distiller Quantitation Toolbox into a common format ready for subsequent bioinformatic analysis. A number of different relative quantitation technologies, such as metabolic (15)N and amino acid stable isotope incorporation, label-free and chemical-label quantitation are supported. The program features multiple options for curative filtering of the quantified peptides, allowing the user to choose data quality thresholds appropriate for the current dataset, and ensure the quality of the calculated relative protein abundances. Condenser also features optional global normalization, peptide outlier removal, multiple testing and calculation of t-test statistics for highlighting and evaluating proteins with significantly altered relative protein abundances. Condenser provides an attractive addition to the gold-standard quantitative workflow of Mascot Distiller, allowing easy handling of larger multi-dimensional experiments. Source code, binaries, test data set and documentation are available at http://condenser.googlecode.com/. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of Quantitative Proteomics Using iTRAQ Based on the Immunological Response of Galleria mellonella Larvae Challenged with Fusarium oxysporum Microconidia

PubMed Central

Muñoz-Gómez, Amalia; Corredor, Mauricio; Benítez-Páez, Alfonso; Peláez, Carlos

2014-01-01

Galleria mellonella has emerged as a potential invertebrate model for scrutinizing innate immunity. Larvae are easy to handle in host-pathogen assays. We undertook proteomics research in order to understand immune response in a heterologous host when challenged with microconidia of Fusarium oxysporum. The aim of this study was to investigate hemolymph proteins that were differentially expressed between control and immunized larvae sets, tested with F. oxysporum at two temperatures. The iTRAQ approach allowed us to observe the effects of immune challenges in a lucid and robust manner, identifying more than 50 proteins, 17 of them probably involved in the immune response. Changes in protein expression were statistically significant, especially when temperature was increased because this was notoriously affected by F. oxysporum 104 or 106 microconidia/mL. Some proteins were up-regulated upon immune fungal microconidia challenge when temperature changed from 25 to 37°C. After analysis of identified proteins by bioinformatics and meta-analysis, results revealed that they were involved in transport, immune response, storage, oxide-reduction and catabolism: 20 from G. mellonella, 20 from the Lepidoptera species and 19 spread across bacteria, protista, fungi and animal species. Among these, 13 proteins and 2 peptides were examined for their immune expression, and the hypothetical 3D structures of 2 well-known proteins, unannotated for G. mellonella, i.e., actin and CREBP, were resolved using peptides matched with Bombyx mori and Danaus plexippus, respectively. The main conclusion in this study was that iTRAQ tool constitutes a consistent method to detect proteins associated with the innate immune system of G. mellonella in response to infection caused by F. oxysporum. In addition, iTRAQ was a reliable quantitative proteomic approach to detect and quantify the expression levels of immune system proteins and peptides, in particular, it was found that 104 microconidia/mL at 37°C over expressed many more proteins than other treatments. PMID:25379782

Old Wine in New Bottles: The Quality of Work Life in Schools and School Districts.

ERIC Educational Resources Information Center

Bacharach, Samuel B.; Mitchell, Stephen M.

This essay reviews quality of work life as a management technique and argues that quality-of-work-life programs, conceptualized multidimensionally, offer a unique mechanism for improving working conditions in schools and within districts. A brief analysis of major management ideologies concludes that some techniques advocated under the label of…

PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data*

PubMed Central

Mitchell, Christopher J.; Kim, Min-Sik; Na, Chan Hyun; Pandey, Akhilesh

2016-01-01

Quantitative mass spectrometry data necessitates an analytical pipeline that captures the accuracy and comprehensiveness of the experiments. Currently, data analysis is often coupled to specific software packages, which restricts the analysis to a given workflow and precludes a more thorough characterization of the data by other complementary tools. To address this, we have developed PyQuant, a cross-platform mass spectrometry data quantification application that is compatible with existing frameworks and can be used as a stand-alone quantification tool. PyQuant supports most types of quantitative mass spectrometry data including SILAC, NeuCode, 15N, 13C, or 18O and chemical methods such as iTRAQ or TMT and provides the option of adding custom labeling strategies. In addition, PyQuant can perform specialized analyses such as quantifying isotopically labeled samples where the label has been metabolized into other amino acids and targeted quantification of selected ions independent of spectral assignment. PyQuant is capable of quantifying search results from popular proteomic frameworks such as MaxQuant, Proteome Discoverer, and the Trans-Proteomic Pipeline in addition to several standalone search engines. We have found that PyQuant routinely quantifies a greater proportion of spectral assignments, with increases ranging from 25–45% in this study. Finally, PyQuant is capable of complementing spectral assignments between replicates to quantify ions missed because of lack of MS/MS fragmentation or that were omitted because of issues such as spectra quality or false discovery rates. This results in an increase of biologically useful data available for interpretation. In summary, PyQuant is a flexible mass spectrometry data quantification platform that is capable of interfacing with a variety of existing formats and is highly customizable, which permits easy configuration for custom analysis. PMID:27231314

Xray: N-dimensional, labeled arrays for analyzing physical datasets in Python

NASA Astrophysics Data System (ADS)

Hoyer, S.

2015-12-01

Efficient analysis of geophysical datasets requires tools that both preserve and utilize metadata, and that transparently scale to process large datas. Xray is such a tool, in the form of an open source Python library for analyzing the labeled, multi-dimensional array (tensor) datasets that are ubiquitous in the Earth sciences. Xray's approach pairs Python data structures based on the data model of the netCDF file format with the proven design and user interface of pandas, the popular Python data analysis library for labeled tabular data. On top of the NumPy array, xray adds labeled dimensions (e.g., "time") and coordinate values (e.g., "2015-04-10"), which it uses to enable a host of operations powered by these labels: selection, aggregation, alignment, broadcasting, split-apply-combine, interoperability with pandas and serialization to netCDF/HDF5. Many of these operations are enabled by xray's tight integration with pandas. Finally, to allow for easy parallelism and to enable its labeled data operations to scale to datasets that does not fit into memory, xray integrates with the parallel processing library dask.

Bacterial Expression and Purification of the Amyloidogenic Peptide PAPf39 for Multidimensional NMR Spectroscopy

PubMed Central

Shanmuganathan, Aranganathan; Bishop, Anthony C.; French, Kinsley C.; McCallum, Scott A.; Makhatadze, George I.

2013-01-01

PAPf39 is a 39 residue peptide fragment from human prostatic acidic phosphatase that forms amyloid fibrils in semen. These fibrils have been implicated in facilitating HIV transmission. To enable structural studies of PAPf39 by NMR spectroscopy, efficient methods allowing the production of milligram quantities of isotopically labeled peptide are essential. Here, we report the high-yield expression, as a fusion to ubiquitin at the N-terminus and an intein at the C-terminus, and purification of uniformly labeled 13C- and 15N-labeled PAPf39 peptide. This allows the study of the PAPf39 monomer conformational ensemble by NMR spectroscopy. To this end, we performed the NMR chemical shift assignment of the PAPf39 peptide in the monomeric state at low pH. PMID:23314347

Identification of cypermethrin induced protein changes in green algae by iTRAQ quantitative proteomics.

PubMed

Gao, Yan; Lim, Teck Kwang; Lin, Qingsong; Li, Sam Fong Yau

2016-04-29

Cypermethrin (CYP) is one of the most widely used pesticides in large scale for agricultural and domestic purpose and the residue often seriously affects aquatic system. Environmental pollutant-induced protein changes in organisms could be detected by proteomics, leading to discovery of potential biomarkers and understanding of mode of action. While proteomics investigations of CYP stress in some animal models have been well studied, few reports about the effects of exposure to CYP on algae proteome were published. To determine CYP effect in algae, the impact of various dosages (0.001μg/L, 0.01μg/L and 1μg/L) of CYP on green algae Chlorella vulgaris for 24h and 96h was investigated by using iTRAQ quantitative proteomics technique. A total of 162 and 198 proteins were significantly altered after CYP exposure for 24h and 96h, respectively. Overview of iTRAQ results indicated that the influence of CYP on algae protein might be dosage-dependent. Functional analysis of differentially expressed proteins showed that CYP could induce protein alterations related to photosynthesis, stress responses and carbohydrate metabolism. This study provides a comprehensive view of complex mode of action of algae under CYP stress and highlights several potential biomarkers for further investigation of pesticide-exposed plant and algae. Copyright © 2016 Elsevier B.V. All rights reserved.

An Efficient Approach to Evaluate Reporter Ion Behavior from MALDI-MS/MS Data for Quantification Studies using Isobaric Tags

PubMed Central

Cologna, Stephanie M.; Crutchfield, Christopher A.; Searle, Brian C.; Blank, Paul S.; Toth, Cynthia L.; Ely, Alexa M.; Picache, Jaqueline A.; Backlund, Peter S.; Wassif, Christopher A.; Porter, Forbes D.; Yergey, Alfred L.

2017-01-01

Protein quantification, identification and abundance determination are important aspects of proteome characterization and are crucial in understanding biological mechanisms and human diseases. Different strategies are available to quantify proteins using mass spectrometric detection, and most are performed at the peptide level and include both targeted and un-targeted methodologies. Discovery-based or un-targeted approaches oftentimes use covalent tagging strategies (i.e., iTRAQ®, TMT™) where reporter ion signals collected in the tandem MS experiment are used for quantification. Herein we investigate the behavior of the iTRAQ 8-plex chemistry using MALDI-TOF/TOF instrumentation. The experimental design and data analysis approach described is simple and straightforward, which allows researchers to optimize data collection and proper analysis within a laboratory. iTRAQ reporter ion signals were normalized within each spectrum to remove peptide biases. An advantage of this approach is that missing reporter ion values can be accepted for purposes of protein identification and quantification with the need for ANOVA analysis. We investigate the distribution of reporter ion peak areas in an equimolar system and a mock biological system and provide recommendations for establishing fold-change cutoff values at the peptide level for iTRAQ datasets. These data provide a unique dataset available to the community for informatics training and analysis. PMID:26288259

Proteome Analysis Using Isobaric Tags for Relative and Absolute Analysis Quantitation (iTRAQ) Reveals Alterations in Stress-Induced Dysfunctional Chicken Muscle.

PubMed

Xing, Tong; Wang, Chong; Zhao, Xue; Dai, Chen; Zhou, Guanghong; Xu, Xinglian

2017-04-05

The current study was designed to investigate changes in the protein profiles of pale, soft, and exudative (PSE)-like muscles of broilers subjected to transportation under high-temperature conditions, using isobaric tags for relative and absolute analysis quantitation (iTRAQ). Arbor Acres chickens (n = 112) were randomly divided into two treatments: unstressed control (CON) and 0.5 h of transport (T). Birds were transported according to a designed protocol. Pectoralis major (PM) muscle samples in the T group were collected and classified as normal (T-NOR) or PSE-like (T-PSE). Plasma activities of stress indicators, muscle microstructure, and proteome were measured. Results indicated that broilers in the T-PSE group exhibited higher activities of plasma stress indicators. The microstructure of T-PSE group showed a looser network and larger intercellular spaces in comparison to the other groups. Proteomic analysis, based on iTRAQ, revealed 29 differentially expressed proteins in the T-NOR and T-PSE groups that were involved in protein turnover, signal transduction, stress and defense, calcium handling, cell structure, and metabolism. In particular, proteins relating to the glycolysis pathway, calcium signaling, and molecular chaperones exhibited significant differences that may contribute to the inferior post-mortem meat quality. Overall, the proteomic results provide a further understanding of the mechanism of meat quality changes in response to stress.

A combined analysis of the Frost Multidimensional Perfectionism Scale (FMPS), Child and Adolescent Perfectionism Scale (CAPS), and Almost Perfect Scale-Revised (APS-R): Different perfectionist profiles in adolescent high school students.

PubMed

Sironic, Amanda; Reeve, Robert A

2015-12-01

To investigate differences and similarities in the dimensional constructs of the Frost Multidimensional Perfectionism Scale (FMPS; Frost, Marten, Lahart, & Rosenblate, 1990), Child and Adolescent Perfectionism Scale (CAPS; Flett, Hewitt, Boucher, Davidson, & Munro, 2000), and Almost Perfect Scale-Revised (APS-R; Slaney, Rice, Mobley, Trippi, & Ashby, 2001), 938 high school students completed the 3 perfectionism questionnaires, as well as the Depression Anxiety Stress Scales (DASS; Lovibond & Lovibond, 1995). Preliminary analyses revealed commonly observed factor structures for each perfectionism questionnaire. Exploratory factor analysis of item responses from the questionnaires (combined) yielded a 4-factor solution (factors were labeled High Personal Standards, Concerns, Doubts and Discrepancy, Externally Motivated Perfectionism, and Organization and Order). A latent class analysis of individuals' mean ratings on each of the 4 factors yielded a 6-class solution. Three of the 6 classes represented perfectionist subgroups (labeled adaptive perfectionist, externally motivated maladaptive perfectionist, and mixed maladaptive perfectionist), and 3 represented nonperfectionist subgroups (labeled nonperfectionist A, nonperfectionist B, and order and organization nonperfectionist). Each of the 6 subgroups was meaningfully associated with the DASS. Findings showed that 3 out of 10 students were classified as maladaptive perfectionists, and maladaptive perfectionists were more prevalent than adaptive perfectionists. In sum, it is evident that combined ratings from the FMPS, CAPS, and APS-R offer a meaningful characterization of perfectionism. (c) 2015 APA, all rights reserved).

Evaluation of different multidimensional LC-MS/MS pipelines for iTRAQ-based proteomic analysis of potato tubers in response to cold storage

USDA-ARS?s Scientific Manuscript database

Cold-induced sweetening in potato tubers is a costly problem for food industry. To systematically identify the proteins associated with this process, we employed a comparative proteomics approach using isobaric, stable isotope coded labels to compare the proteomes of potato tubers after 0 and 5 mont...

Infections with the Sexually Transmitted Pathogen Nosema apis Trigger an Immune Response in the Seminal Fluid of Honey Bees (Apis mellifera).

PubMed

Grassl, Julia; Peng, Yan; Baer-Imhoof, Barbara; Welch, Mat; Millar, A Harvey; Baer, Boris

2017-01-06

Honey bee (Apis mellifera) males are highly susceptible to infections with the sexually transmitted fungal pathogen Nosema apis. However, they are able to suppress this parasite in the ejaculate using immune molecules in the seminal fluid. We predicted that males respond to infections by altering the seminal fluid proteome to minimize the risk to sexually transmit the parasite to the queen and her colony. We used iTRAQ isotopic labeling to compare seminal fluid proteins from infected and noninfected males and found that N. apis infections resulted in significant abundance changes in 111 of the 260 seminal fluid proteins quantitated. The largest group of proteins with significantly changed abundances consisted of 15 proteins with well-known immune-related functions, which included two significantly more abundant chitinases in the seminal fluid of infected males. Chitinases were previously hypothesized to be involved in honey bee antifungal activity against N. apis. Here we show that infection with N. apis triggers a highly specific immune response in the seminal fluid of honey bee males.

Membrane protease degradomics: proteomic identification and quantification of cell surface protease substrates.

PubMed

Butler, Georgina S; Dean, Richard A; Smith, Derek; Overall, Christopher M

2009-01-01

The modification of cell surface proteins by plasma membrane and soluble proteases is important for physiological and pathological processes. Methods to identify shed and soluble substrates are crucial to further define the substrate repertoire, termed the substrate degradome, of individual proteases. Identifying protease substrates is essential to elucidate protease function and involvement in different homeostatic and disease pathways. This characterisation is also crucial for drug target identification and validation, which would then allow the rational design of specific targeted inhibitors for therapeutic intervention. We describe two methods for identifying and quantifying shed cell surface protease targets in cultured cells utilising Isotope-Coded Affinity Tags (ICAT) and Isobaric Tags for Relative and Absolute Quantification (iTRAQ). As a model system to develop these techniques, we chose a cell-membrane expressed matrix metalloproteinase, MMP-14, but the concepts can be applied to proteases of other classes. By over-expression, or conversely inhibition, of a particular protease with careful selection of control conditions (e.g. vector or inactive protease) and differential labelling, shed proteins can be identified and quantified by mass spectrometry (MS), MS/MS fragmentation and database searching.

Large scale systematic proteomic quantification from non-metastatic to metastatic colorectal cancer

NASA Astrophysics Data System (ADS)

Yin, Xuefei; Zhang, Yang; Guo, Shaowen; Jin, Hong; Wang, Wenhai; Yang, Pengyuan

2015-07-01

A systematic proteomic quantification of formalin-fixed, paraffin-embedded (FFPE) colorectal cancer tissues from stage I to stage IIIC was performed in large scale. 1017 proteins were identified with 338 proteins in quantitative changes by label free method, while 341 proteins were quantified with significant expression changes among 6294 proteins by iTRAQ method. We found that proteins related to migration expression increased and those for binding and adherent decreased during the colorectal cancer development according to the gene ontology (GO) annotation and ingenuity pathway analysis (IPA). The integrin alpha 5 (ITA5) in integrin family was focused, which was consistent with the metastasis related pathway. The expression level of ITA5 decreased in metastasis tissues and the result has been further verified by Western blotting. Another two cell migration related proteins vitronectin (VTN) and actin-related protein (ARP3) were also proved to be up-regulated by both mass spectrometry (MS) based quantification results and Western blotting. Up to now, our result shows one of the largest dataset in colorectal cancer proteomics research. Our strategy reveals a disease driven omics-pattern for the metastasis colorectal cancer.

Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics

PubMed Central

Van, Phu T.; Schmid, Amy K.; King, Nichole L.; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T.; Goo, Young-Ah; Deutsch, Eric W.; Reiss, David J.; Mallick, Parag; Baliga, Nitin S.

2009-01-01

The relatively small numbers of proteins and fewer possible posttranslational modifications in microbes provides a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a Peptide Atlas (PA) for 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636,000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has helped highlight plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics. PMID:18652504

Quantitative phosphoproteomic analysis of host responses in human lung epithelial (A549) cells during influenza virus infection.

PubMed

Dapat, Clyde; Saito, Reiko; Suzuki, Hiroshi; Horigome, Tsuneyoshi

2014-01-22

The emergence of antiviral drug-resistant influenza viruses highlights the need for alternative therapeutic strategies. Elucidation of host factors required during virus infection provides information not only on the signaling pathways involved but also on the identification of novel drug targets. RNA interference screening method had been utilized by several studies to determine these host factors; however, proteomics data on influenza host factors are currently limited. In this study, quantitative phosphoproteomic analysis of human lung cell line (A549) infected with 2009 pandemic influenza virus A (H1N1) virus was performed. Phosphopeptides were enriched from tryptic digests of total protein of infected and mock-infected cells using a titania column on an automated purification system followed by iTRAQ labeling. Identification and quantitative analysis of iTRAQ-labeled phosphopeptides were performed using LC-MS/MS. We identified 366 phosphorylation sites on 283 proteins. Of these, we detected 43 upregulated and 35 downregulated proteins during influenza virus infection. Gene ontology enrichment analysis showed that majority of the identified proteins are phosphoproteins involved in RNA processing, immune system process and response to infection. Host-virus interaction network analysis had identified 23 densely connected subnetworks. Of which, 13 subnetworks contained proteins with altered phosphorylation levels during by influenza virus infection. Our results will help to identify potential drug targets that can be pursued for influenza antiviral drug development. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantitative proteomic study of Aspergillus Fumigatus secretome revealed deamidation of secretory enzymes.

PubMed

Adav, Sunil S; Ravindran, Anita; Sze, Siu Kwan

2015-04-24

Aspergillus sp. plays an essential role in lignocellulosic biomass recycling and is also exploited as cell factories for the production of industrial enzymes. This study profiled the secretome of Aspergillus fumigatus when grown with cellulose, xylan and starch by high throughput quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ). Post translational modifications (PTMs) of proteins play a critical role in protein functions. However, our understanding of the PTMs in secretory proteins is limited. Here, we present the identification of PTMs such as deamidation of secreted proteins of A. fumigatus. This study quantified diverse groups of extracellular secreted enzymes and their functional classification revealed cellulases and glycoside hydrolases (32.9%), amylases (0.9%), hemicellulases (16.2%), lignin degrading enzymes (8.1%), peptidases and proteases (11.7%), chitinases, lipases and phosphatases (7.6%), and proteins with unknown function (22.5%). The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulates expression of specific cellulases and hemicellulases, and their abundance level as a function of substrate. In-depth data analysis revealed deamidation as a major PTM of key cellulose hydrolyzing enzymes like endoglucanases, cellobiohydrolases and glucosidases. Hemicellulose degrading endo-1,4-beta-xylanase, monosidases, xylosidases, lignin degrading laccase, isoamyl alcohol oxidase and oxidoreductases were also found to be deamidated. The filamentous fungi play an essential role in lignocellulosic biomass recycling and fungal strains belonging to Aspergillus were also exploited as cell factories for the production of organic acids, pharmaceuticals, and industrially important enzymes. In this study, extracellular proteins secreted by thermophilic A. fumigatus when grown with cellulose, xylan and starch were profiled using isobaric tags for relative and absolute quantification (iTRAQ) by adopting liquid chromatography tandem mass spectrometry. The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulate expression of specific cellulases and hemicellulases, and expression level as a function of substrate. Post translational modifications revealed deamidation of key cellulases including endoglucanases, cellobiohydrolases and glucosidases; and hemicellulases and lignin degrading enzymes. The knowledge on deamidated enzymes along with specific sites of modifications could be crucial information for further functional studies of these enzymes of A. fumigatus. Copyright © 2015 Elsevier B.V. All rights reserved.

A cluster analysis of perfectionism among competitive athletes.

PubMed

Martinent, Guillaume; Ferrand, Claude

2006-12-01

In the present study, the ways in which athletes may experience perfectionism in a sport context were examined. The question of interest was whether self-confidence, intensity, and direction of cognitive and somatic precompetitive anxiety would differ across identifiable profiles of perfectionism. Competitive athletes (N= 166) completed the Sport-Multidimensional Perfectionism Scale, the French-Canadian Hewitt Multidimensional Perfectionism Scale, and the Competitive State Anxiety Inventory-2 Revised, including a Direction scale. Results of the cluster analysis indicated that athletes could be classified into three groups labelled Nonperfectionists, Adaptive perfectionists, and Maladaptive perfectionists. Perfectionism profiles differed significantly on Cognitive and Somatic Anxiety Intensity and on Cognitive Anxiety Direction. The importance of considering all dimensions of perfectionism simultaneously when examining the functional nature of this construct in sport is discussed.

Mass Spectrometry Data Collection in Parallel at Multiple Core Facilities Operating TripleTOF 5600 and Orbitrap Elite/Velos Pro/Q Exactive Mass Spectrometers

PubMed Central

Jones, K.; Kim, K.; Patel, B.; Kelsen, S.; Braverman, A.; Swinton, D.; Gafken, P.; Jones, L.; Lane, W.; Neveu, J.; Leung, H.; Shaffer, S.; Leszyk, J.; Stanley, B.; Fox, T.; Stanley, A.; Yeung, Anthony

2013-01-01

Proteomic research can benefit from simultaneous access to multiple cutting-edge mass spectrometers. 18 core facilities responded to our investigators seeking service through the ABRF Discussion Forum. Five of the facilities selected completed four plasma proteomics experiments as routine fee-for-service. Each biological experiment entailed an iTRAQ 4-plex proteome comparison of immunodepleted plasma provided as 30 labeled-peptide fractions. Identical samples were analyzed by two AB SCIEX TripleTOF 5600 and three Thermo Orbitrap (Elite/Velos Pro/Q Exactive) instruments. 480 LC-MS/MS runs delivered >250 GB of data over two months. We compare herein routine service analyses of three peptide fractions of different peptide abundance. Data files from each instrument were studied to develop optimal analysis parameters to compare with default parameters in Mascot Distiller 2.4, ProteinPilot 4.5 beta, AB Sciex MS Data Converter 1.3 beta, and Proteome Discover 1.3. Peak-picking for TripleTOFs was best by ProteinPilot 4.5 beta while Mascot Distiller and Proteome Discoverer were comparable for the Orbitraps. We compared protein identification and quantitation in SwissProt 2012_07 database by Mascot Server 2.4.01 versus ProteinPilot. By all search methods, more proteins, up to two fold, were identified using the Q Exactive than others. Q Exactive excelled also at the number of unique significant peptide ion sequences. However, software-dependent impact on subsequent interpretation, due to peptide modifications, can be critical. These findings may have special implications for iTRAQ plasma proteomics. For the low abundance peptide ions, the slope of the dynamic range drop-off in the plasma proteome is uniquely sharp compared with cell lysates. Our study provides data for testable improvements in the operation of these mass spectrometers. More importantly, we have demonstrated a new affordable expedient workflow for investigators to perform proteomic experiments through the ABRF infrastructure. (We acknowledge John Cottrell for optimizing the peak-picking parameters for Mascot Distiller).

Comparative proteomic analysis of eggplant (Solanum melongena L.) heterostylous pistil development

PubMed Central

Li, Wenjia; Jiang, Yaqing; Song, Shiwei; Li, Yan; Chen, Riyuan

2017-01-01

Heterostyly is a common floral polymorphism, but the proteomic basis of this trait is still largely unexplored. In this study, self- and cross-pollination of L-morph and S-morph flowers and comparison of embryo sac development in eggplant (Solanum melongena L.) suggested that lower fruit set from S-morph flowers results from stigma-pollen incompatibility. To explore the molecular mechanism underlying heterostyly development, we conducted isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis of eggplant pistils for L- and S-morph flowers. A total of 5,259 distinct proteins were identified during heterostyly development. Compared S-morph flowers with L-morph, we discovered 57 and 184 differentially expressed proteins (DEPs) during flower development and maturity, respectively. Quantitative real time polymerase chain reactions were used for nine genes to verify DEPs from the iTRAQ approach. During flower development, DEPs were mainly involved in morphogenesis, biosynthetic processes, and metabolic pathways. At flower maturity, DEPs primarily participated in biosynthetic processes, metabolic pathways, and the formation of ribosomes and proteasomes. Additionally, some proteins associated with senescence and programmed cell death were found to be upregulated in S-morph pistils, which may lead to the lower fruit set in S-morph flowers. Although the exact roles of these related proteins are not yet known, this was the first attempt to use an iTRAQ approach to analyze proteomes of heterostylous eggplant flowers, and these results will provide insights into biochemical events taking place during the development of heterostyly. PMID:28586360

Rapid 3D NMR using the filter diagonalization method: application to oligosaccharides derivatized with 13C-labeled acetyl groups

NASA Astrophysics Data System (ADS)

Armstrong, Geoffrey S.; Cano, Kristin E.; Mandelshtam, Vladimir A.; Shaka, A. J.; Bendiak, Brad

2004-09-01

Rapid 3D NMR spectroscopy of oligosaccharides having isotopically labeled acetyl "isotags" was made possible with high resolution in the indirect dimensions using the filter diagonalization method (FDM). A pulse sequence was designed for the optimal correlation of acetyl methyl protons, methyl carbons, and carbonyl carbons. The multi-dimensional nature of the FDM, coupled with the advantages of constant-time evolution periods, resulted in marked improvements over Fourier transform (FT) and mirror-image linear prediction (MI-LP) processing methods. The three methods were directly compared using identical data sets. A highly resolved 3D spectrum was achieved with the FDM using a very short experimental time (28 min).

Rapid 3D NMR using the filter diagonalization method: application to oligosaccharides derivatized with 13C-labeled acetyl groups.

PubMed

Armstrong, Geoffrey S; Cano, Kristin E; Mandelshtam, Vladimir A; Shaka, A J; Bendiak, Brad

2004-09-01

Rapid 3D NMR spectroscopy of oligosaccharides having isotopically labeled acetyl "isotags" was made possible with high resolution in the indirect dimensions using the filter diagonalization method (FDM). A pulse sequence was designed for the optimal correlation of acetyl methyl protons, methyl carbons, and carbonyl carbons. The multi-dimensional nature of the FDM, coupled with the advantages of constant-time evolution periods, resulted in marked improvements over Fourier transform (FT) and mirror-image linear prediction (MI-LP) processing methods. The three methods were directly compared using identical data sets. A highly resolved 3D spectrum was achieved with the FDM using a very short experimental time (28 min).

Protein S100-A8: A potential metastasis-associated protein for breast cancer determined via iTRAQ quantitative proteomic and clinicopathological analysis.

PubMed

Zhong, Jing-Min; Li, Jing; Kang, An-Ding; Huang, San-Qian; Liu, Wen-Bin; Zhang, Yun; Liu, Zhi-Hong; Zeng, Liang

2018-04-01

Breast cancer is the most common malignancy in females, with metastasis of this type of cancer frequently proving lethal. However, there are still no effective biomarkers to predict breast cancer metastasis. The aim of the present study was, therefore, to analyze breast cancer metastasis-associated proteins and evaluate the association between protein S100-A8 and the prognosis of breast cancer. The isobaric tags for relative and absolute quantitation (iTRAQ) proteomic technique was used to analyze the differential expression of proteins between fresh primary breast tumor (PBT) tissue and fresh paired metastatic lymph nodes (PMLN) tissue. Subsequently, immunohistochemical staining was used to locate and assess the expression of protein S100-A8 in benign breast disease (n=15), primary breast cancer with (n=109) or without (n=83) metastasis, and in paired metastatic lymph nodes (n=109) formalin fixed paraffin embedded (FFPE) tissue. Staining scores were evaluated and the association between protein S100-A8 expression levels and the clinicopathological characteristics of 192 patients with breast cancer were evaluated using the χ 2 test. Kaplan-Meier and Cox hazards regression analyses were utilized to investigate the association between the expression of protein S100-A8 and the prognosis of patients with breast cancer. A total of 4,837 proteins were identified using the iTRAQ proteomic technique. Among these proteins, 643 differentially expressed proteins were revealed. Protein S100-A8 expression levels were identified to differ between PBT and PMLN tissues. Immunohistochemical staining suggested a significant difference between NMBT and PMLN (P=0.002), and also between PBT and PMLN (P<0.001). Cox hazards regression model analyses suggested that histological grade (P=0.031) and nodal status (P=0.001) were risk factors for lymph nodes metastasis of breast cancer. Kaplan-Meier analyses revealed no significant relationship between protein S100-A8 expression level and overall survival rate of patients with breast cancer. In conclusion, by using the iTRAQ proteomic technique and immunohistochemistry staining, it was identified that protein S100-A8 may be associated with lymph nodes metastasis of breast cancer and be a marker for progression of breast cancer.

RECENT ADVANCES IN QUANTITATIVE NEUROPROTEOMICS

PubMed Central

Craft, George E; Chen, Anshu; Nairn, Angus C

2014-01-01

The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson’s disease and Alzheimer’s disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders. PMID:23623823

Recent advances in quantitative neuroproteomics.

PubMed

Craft, George E; Chen, Anshu; Nairn, Angus C

2013-06-15

The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders. Copyright © 2013. Published by Elsevier Inc.

PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data.

PubMed

Mitchell, Christopher J; Kim, Min-Sik; Na, Chan Hyun; Pandey, Akhilesh

2016-08-01

Quantitative mass spectrometry data necessitates an analytical pipeline that captures the accuracy and comprehensiveness of the experiments. Currently, data analysis is often coupled to specific software packages, which restricts the analysis to a given workflow and precludes a more thorough characterization of the data by other complementary tools. To address this, we have developed PyQuant, a cross-platform mass spectrometry data quantification application that is compatible with existing frameworks and can be used as a stand-alone quantification tool. PyQuant supports most types of quantitative mass spectrometry data including SILAC, NeuCode, (15)N, (13)C, or (18)O and chemical methods such as iTRAQ or TMT and provides the option of adding custom labeling strategies. In addition, PyQuant can perform specialized analyses such as quantifying isotopically labeled samples where the label has been metabolized into other amino acids and targeted quantification of selected ions independent of spectral assignment. PyQuant is capable of quantifying search results from popular proteomic frameworks such as MaxQuant, Proteome Discoverer, and the Trans-Proteomic Pipeline in addition to several standalone search engines. We have found that PyQuant routinely quantifies a greater proportion of spectral assignments, with increases ranging from 25-45% in this study. Finally, PyQuant is capable of complementing spectral assignments between replicates to quantify ions missed because of lack of MS/MS fragmentation or that were omitted because of issues such as spectra quality or false discovery rates. This results in an increase of biologically useful data available for interpretation. In summary, PyQuant is a flexible mass spectrometry data quantification platform that is capable of interfacing with a variety of existing formats and is highly customizable, which permits easy configuration for custom analysis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Multidimensional daily diary of fatigue-fibromyalgia-17 items (MDF-fibro-17). part 1: development and content validity.

PubMed

Morris, S; Li, Y; Smith, J A M; Dube', S; Burbridge, C; Symonds, T

2017-05-16

Fibromyalgia (FM), a disorder characterized by chronic widespread pain and tenderness, affects greater than five million individuals in the United States alone. Patients experience multiple symptoms in addition to pain, and among them, fatigue is one of the most bothersome and disabling. There is a growing body of literature suggesting that fatigue is a multidimensional concept. Currently, to our knowledge, no multidimensional Patient Reported Outcome (PRO) measure of FM-related fatigue meets Food and Drug Administration (FDA) requirements to support a product label claim. Therefore, the objective of this research was to evaluate qualitative and quantitative data previously gathered to inform the development of a comprehensive, multidimensional, PRO measure to assess FM-related fatigue in FM clinical trials. Existing qualitative and quantitative data from three previously conducted studies in patients with FM were reviewed to inform the initial development of a multidimensional PRO measure of FM-related fatigue: 1) a concept elicitation study involving in-depth, open-ended interviews with patients with FM in the United States (US) (N = 20), Germany (N = 10), and France (N = 10); 2) a cognitive debriefing and pilot study of a preliminary pool of 23 items (N = 20 US patients with FM); and 3) a methodology study that explored initial psychometrics of the item pool (N = 145 US patients with FM). Five domains were identified that intend to capture the broad experience of FM-related fatigue reported in the qualitative research: the Global Fatigue Experience, Cognitive Fatigue, Physical Fatigue, Motivation, and Impact on Function. Seventeen of the original pool of 23 items were selected to best capture these five dimensions. These 17 items formed the basis of a newly developed multidimensional PRO measure to assess FM-related fatigue in clinical trials: the Multidimensional Daily Diary of Fatigue-Fibromyalgia-17 (MDF-Fibro-17). Qualitative analysis, and preliminary quantitative item level data, confirmed that FM-related fatigue is multidimensional and provided strong support for the content validity of the MDF-Fibro-17. The next stage was to quantitatively evaluate the measure to confirm the factor structure, psychometric properties, sensitivity to change, and meaningful change. This has been conducted and is being reported separately.

Multi-dimensional classification of GABAergic interneurons with Bayesian network-modeled label uncertainty.

PubMed

Mihaljević, Bojan; Bielza, Concha; Benavides-Piccione, Ruth; DeFelipe, Javier; Larrañaga, Pedro

2014-01-01

Interneuron classification is an important and long-debated topic in neuroscience. A recent study provided a data set of digitally reconstructed interneurons classified by 42 leading neuroscientists according to a pragmatic classification scheme composed of five categorical variables, namely, of the interneuron type and four features of axonal morphology. From this data set we now learned a model which can classify interneurons, on the basis of their axonal morphometric parameters, into these five descriptive variables simultaneously. Because of differences in opinion among the neuroscientists, especially regarding neuronal type, for many interneurons we lacked a unique, agreed-upon classification, which we could use to guide model learning. Instead, we guided model learning with a probability distribution over the neuronal type and the axonal features, obtained, for each interneuron, from the neuroscientists' classification choices. We conveniently encoded such probability distributions with Bayesian networks, calling them label Bayesian networks (LBNs), and developed a method to predict them. This method predicts an LBN by forming a probabilistic consensus among the LBNs of the interneurons most similar to the one being classified. We used 18 axonal morphometric parameters as predictor variables, 13 of which we introduce in this paper as quantitative counterparts to the categorical axonal features. We were able to accurately predict interneuronal LBNs. Furthermore, when extracting crisp (i.e., non-probabilistic) predictions from the predicted LBNs, our method outperformed related work on interneuron classification. Our results indicate that our method is adequate for multi-dimensional classification of interneurons with probabilistic labels. Moreover, the introduced morphometric parameters are good predictors of interneuron type and the four features of axonal morphology and thus may serve as objective counterparts to the subjective, categorical axonal features.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2014-01-01

pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Glycoproteomic analysis of bronchoalveolar lavage (BAL) fluid identifies tumor-associated glycoproteins from lung adenocarcinoma.

PubMed

Li, Qing Kay; Shah, Punit; Li, Yan; Aiyetan, Paul O; Chen, Jing; Yung, Rex; Molena, Daniela; Gabrielson, Edward; Askin, Frederic; Chan, Daniel W; Zhang, Hui

2013-08-02

Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis of lung cancer. Proteins released from lung cancer cells into BAL may serve as biomarkers for cancer detection. In this study, N-glycoproteins in eight cases of BAL fluid, as well as eight lung adenocarcinoma tissues and eight tumor-matched normal lung tissues, were analyzed using the solid-phase extraction of N-glycoprotein (SPEG), iTRAQ labeling, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Of 80 glycoproteins found in BAL specimens, 32 were identified in both cancer BAL and cancer tissues, with levels of 25 glycoproteins showing at least a 2-fold difference between cancer and benign BAL. Among them, eight glycoproteins showed greater than 2-fold elevations in cancer BAL, including Neutrophil elastase (NE), Integrin alpha-M, Cullin-4B, Napsin A, lysosome-associated membrane protein 2 (LAMP2), Cathepsin D, BPI fold-containing family B member 2, and Neutrophil gelatinase-associated lipocalin. The levels of Napsin A in cancer BAL were further verified in independently collected 39 BAL specimens using an ELISA assay. Our study demonstrates that potential protein biomarkers in BAL fluid can be detected and quantified.

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

PubMed

Van, Phu T; Schmid, Amy K; King, Nichole L; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T; Goo, Young Ah; Deutsch, Eric W; Reiss, David J; Mallick, Parag; Baliga, Nitin S

2008-09-01

The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

Multidimensional Interactive Radiology Report and Analysis: standardization of workflow and reporting for renal mass tracking and quantification

NASA Astrophysics Data System (ADS)

Hwang, Darryl H.; Ma, Kevin; Yepes, Fernando; Nadamuni, Mridula; Nayyar, Megha; Liu, Brent; Duddalwar, Vinay; Lepore, Natasha

2015-12-01

A conventional radiology report primarily consists of a large amount of unstructured text, and lacks clear, concise, consistent and content-rich information. Hence, an area of unmet clinical need consists of developing better ways to communicate radiology findings and information specific to each patient. Here, we design a new workflow and reporting system that combines and integrates advances in engineering technology with those from the medical sciences, the Multidimensional Interactive Radiology Report and Analysis (MIRRA). Until recently, clinical standards have primarily relied on 2D images for the purpose of measurement, but with the advent of 3D processing, many of the manually measured metrics can be automated, leading to better reproducibility and less subjective measurement placement. Hence, we make use this newly available 3D processing in our workflow. Our pipeline is used here to standardize the labeling, tracking, and quantifying of metrics for renal masses.

Urdu Nasta'liq text recognition using implicit segmentation based on multi-dimensional long short term memory neural networks.

PubMed

Naz, Saeeda; Umar, Arif Iqbal; Ahmed, Riaz; Razzak, Muhammad Imran; Rashid, Sheikh Faisal; Shafait, Faisal

2016-01-01

The recognition of Arabic script and its derivatives such as Urdu, Persian, Pashto etc. is a difficult task due to complexity of this script. Particularly, Urdu text recognition is more difficult due to its Nasta'liq writing style. Nasta'liq writing style inherits complex calligraphic nature, which presents major issues to recognition of Urdu text owing to diagonality in writing, high cursiveness, context sensitivity and overlapping of characters. Therefore, the work done for recognition of Arabic script cannot be directly applied to Urdu recognition. We present Multi-dimensional Long Short Term Memory (MDLSTM) Recurrent Neural Networks with an output layer designed for sequence labeling for recognition of printed Urdu text-lines written in the Nasta'liq writing style. Experiments show that MDLSTM attained a recognition accuracy of 98% for the unconstrained Urdu Nasta'liq printed text, which significantly outperforms the state-of-the-art techniques.

iTRAQ protein profile analysis of Citrus sinensis roots in response to long-term boron-deficiency.

PubMed

Yang, Lin-Tong; Qi, Yi-Ping; Lu, Yi-Bin; Guo, Peng; Sang, Wen; Feng, Hui; Zhang, Hong-Xing; Chen, Li-Song

2013-11-20

Seedlings of Citrus sinensis were fertilized with boron (B)-deficient (0μM H3BO3) or -sufficient (10μM H3BO3) nutrient solution for 15weeks. Thereafter, iTRAQ analysis was employed to compare the abundances of proteins from B-deficient and -sufficient roots. In B-deficient roots, 164 up-regulated and 225 down-regulated proteins were identified. These proteins were grouped into the following functional categories: protein metabolism, nucleic acid metabolism, stress responses, carbohydrate and energy metabolism, cell transport, cell wall and cytoskeleton metabolism, biological regulation and signal transduction, and lipid metabolism. The adaptive responses of roots to B-deficiency might include following several aspects: (a) decreasing root respiration; (b) improving the total ability to scavenge reactive oxygen species (ROS); and (c) enhancing cell transport. The differentially expressed proteins identified by iTRAQ are much larger than those detected using 2D gel electrophoresis, and many novel B-deficiency-responsive proteins involved in cell transport, biological regulation and signal transduction, stress responses and other metabolic processes were identified in this work. Our results indicate remarkable metabolic flexibility of citrus roots, which may contribute to the survival of B-deficient plants. This represents the most comprehensive analysis of protein profiles in response to B-deficiency. In this study, we identified many new proteins involved in cell transport, biological regulation and signal transduction, stress responses and other metabolic processes that were not previously known to be associated with root B-deficiency responses. Therefore, our manuscript represents the most comprehensive analysis of protein profiles in response to B-deficiency and provides new information about the plant response to B-deficiency. This article is part of a Special Issue entitled: Translational Plant Proteomics. Copyright © 2013 Elsevier B.V. All rights reserved.

Changes in proteomic profiles in different prostate lobes of male rats throughout growth and development and aging stages of the life span

PubMed Central

Das, Arunangshu; Bortner, James D.; Aliaga, Cesar A.; Baker, Aaron; Stanley, Anne; Stanley, Bruce A.; Kaag, Mathew; Richie, John P.; El-Bayoumy, Karam

2012-01-01

Background Aging-related changes in important cellular pathways in the prostate may promote a permissive environment for an increased risk for prostatic disease development such as prostate cancer. Our objectives were to examine for such changes, by systematically determining the effects of growth and development and aging on proteomic profiles in different lobes of the rat prostate. Methods Prostate lobes (dorsolateral lobe, DL and ventral lobe, VL) were obtained from male Fisher rats of various ages representing young (4 months), mature (12 months), old (18 months), and very old (24 months). Differentially expressed proteins between age groups in each lobe were identified using a proteomic approach, isobaric Tags for Relative and Absolute Quantitation (iTRAQ). Select changes in the DL and VL were verified by immunoblot analysis. Results iTRAQ identified 317 proteins with high confidence. iTRAQ discovered 12 and 6 proteins significantly modulated in response to growth and development in the DL and VL, respectively, and 42 and 29 proteins significantly modulated in response to aging in the DL and VL, respectively. Proteins modulated during growth and development in the DL and VL are involved in a variety of biological processes including cell communication and development, whereas proteins modulated during aging were predominantly related to antioxidant activity and immunity. Immunoblot analysis verified age-related changes for α-1 antitrypsin, annexin A1, hypoxia up-regulated protein 1, and 78 kDa glucose-regulated protein. Conclusions Aging results in changes in numerous prostatic proteins and pathways which are mainly linked to inflammation and may lead to prostatic disease development. PMID:22911278

Quantitative phosphoproteomic analysis of neuronal intermediate filament proteins (NF-M/H) in Alzheimer's disease by iTRAQ.

PubMed

Rudrabhatla, Parvathi; Grant, Philip; Jaffe, Howard; Strong, Michael J; Pant, Harish C

2010-11-01

Aberrant hyperphosphorylation of neuronal cytoskeletal proteins is one of the major pathological hallmarks of neurodegenerative disorders such as Alzheimer disease (AD), amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD). Human NF-M/H display a large number of multiple KSP repeats in the carboxy-terminal tail domain, which are phosphorylation sites of proline-directed serine/threonine (pSer/Thr-Pro, KS/T-P) kinases. The phosphorylation sites of NF-M/H have not been characterized in AD brain. Here, we use quantitative phosphoproteomic methodology, isobaric tag for relative and absolute quantitation (iTRAQ), for the characterization of NF-M/H phosphorylation sites in AD brain. We identified 13 hyperphosphorylated sites of NF-M; 9 Lys-Ser-Pro (KSP) sites; 2 variant motifs, Glu-Ser-Pro (ESP) Ser-736 and Leu-Ser-Pro (LSP) Ser-837; and 2 non-S/T-P motifs, Ser-783 and Ser-788. All the Ser/Thr residues are phosphorylated at significantly greater abundance in AD brain compared with control brain. Ten hyperphosphorylated KSP sites have been identified on the C-terminal tail domain of NF-H, with greater abundance of phosphorylation in AD brain compared with control brain. Our data provide the direct evidence that NF-M/H are hyperphosphorylated in AD compared with control brain and suggest the role of both proline-directed and non-proline-directed protein kinases in AD. This study represents the first comprehensive iTRAQ analyses and quantification of phosphorylation sites of human NF-M and NF-H from AD brain and suggests that aberrant hyperphosphorylation of neuronal intermediate filament proteins is involved in AD.

iTRAQ Protein Profile Differential Analysis of Dormant and Germinated Grassbur Twin Seeds Reveals that Ribosomal Synthesis and Carbohydrate Metabolism Promote Germination Possibly Through the PI3K Pathway.

PubMed

Zhang, Guo-Liang; Zhu, Yue; Fu, Wei-Dong; Wang, Peng; Zhang, Rui-Hai; Zhang, Yan-Lei; Song, Zhen; Xia, Gui-Xian; Wu, Jia-He

2016-06-01

Grassbur is a destructive and invasive weed in pastures, and its burs can cause gastric damage to animals. The strong adaptability and reproductive potential of grassbur are partly due to a unique germination mechanism whereby twin seeds develop in a single bur: one seed germinates, but the other remains dormant. To investigate the molecular mechanism of seed germination in twin seeds, we used isobaric tags for relative and absolute quantitation (iTRAQ) to perform a dynamic proteomic analysis of germination and dormancy. A total of 1,984 proteins were identified, 161 of which were considered to be differentially accumulated. The differentially accumulated proteins comprised 102 up-regulated and 59 down-regulated proteins. These proteins were grouped into seven functional categories, ribosomal proteins being the predominant group. The authenticity and accuracy of the results were confirmed by enzyme-linked immunosorbent assay (ELISA) and quantitative real-time reverse transcription-PCR (qPCR). A dynamic proteomic analysis revealed that ribosome synthesis and carbohydrate metabolism affect seed germination possibly through the phosphoinositide 3-kinase (PI3K) pathway. As the PI3K pathway is generally activated by insulin, analyses of seeds treated with exogenous insulin by qPCR, ELISA and iTRAQ confirmed that the PI3K pathway can be activated, which suppresses dormancy and promotes germination in twin grassbur seeds. Together, these results show that the PI3K pathway may play roles in stimulating seed germination in grassbur by modulating ribosomal synthesis and carbohydrate metabolism. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Changes in proteomic profiles in different prostate lobes of male rats throughout growth and development and aging stages of the life span.

PubMed

Das, Arunangshu; Bortner, James D; Aliaga, Cesar A; Baker, Aaron; Stanley, Anne; Stanley, Bruce A; Kaag, Matthew; Richie, John P; El-Bayoumy, Karam

2013-03-01

Aging-related changes in important cellular pathways in the prostate may promote a permissive environment for an increased risk for prostatic disease development such as prostate cancer. Our objectives were to examine for such changes, by systematically determining the effects of growth and development and aging on proteomic profiles in different lobes of the rat prostate. Prostate lobes (dorsolateral lobe, DL and ventral lobe, VL) were obtained from male Fisher rats of various ages representing young (4 months), mature (12 months), old (18 months), and very old (24 months). Differentially expressed proteins between age groups in each lobe were identified using a proteomic approach, isobaric Tags for Relative and Absolute Quantitation (iTRAQ). Select changes in the DL and VL were verified by immunoblot analysis. iTRAQ identified 317 proteins with high confidence. iTRAQ discovered 12 and 6 proteins significantly modulated in response to growth and development in the DL and VL, respectively, and 42 and 29 proteins significantly modulated in response to aging in the DL and VL, respectively. Proteins modulated during growth and development in the DL and VL are involved in a variety of biological processes including cell communication and development, whereas proteins modulated during aging were predominantly related to antioxidant activity and immunity. Immunoblot analysis verified age-related changes for α-1 antitrypsin, annexin A1, hypoxia up-regulated protein 1, and 78 kDa glucose-regulated protein. Aging results in changes in numerous prostatic proteins and pathways which are mainly linked to inflammation and may lead to prostatic disease development. Copyright © 2012 Wiley Periodicals, Inc.

An R package for analyzing and modeling ranking data

PubMed Central

2013-01-01

Background In medical informatics, psychology, market research and many other fields, researchers often need to analyze and model ranking data. However, there is no statistical software that provides tools for the comprehensive analysis of ranking data. Here, we present pmr, an R package for analyzing and modeling ranking data with a bundle of tools. The pmr package enables descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty’s and Koczkodaj’s inconsistencies), probability models (Luce model, distance-based model, and rank-ordered logit model), and the visualization of ranking data with multidimensional preference analysis. Results Examples of the use of package pmr are given using a real ranking dataset from medical informatics, in which 566 Hong Kong physicians ranked the top five incentives (1: competitive pressures; 2: increased savings; 3: government regulation; 4: improved efficiency; 5: improved quality care; 6: patient demand; 7: financial incentives) to the computerization of clinical practice. The mean rank showed that item 4 is the most preferred item and item 3 is the least preferred item, and significance difference was found between physicians’ preferences with respect to their monthly income. A multidimensional preference analysis identified two dimensions that explain 42% of the total variance. The first can be interpreted as the overall preference of the seven items (labeled as “internal/external”), and the second dimension can be interpreted as their overall variance of (labeled as “push/pull factors”). Various statistical models were fitted, and the best were found to be weighted distance-based models with Spearman’s footrule distance. Conclusions In this paper, we presented the R package pmr, the first package for analyzing and modeling ranking data. The package provides insight to users through descriptive statistics of ranking data. Users can also visualize ranking data by applying a thought multidimensional preference analysis. Various probability models for ranking data are also included, allowing users to choose that which is most suitable to their specific situations. PMID:23672645

An R package for analyzing and modeling ranking data.

PubMed

Lee, Paul H; Yu, Philip L H

2013-05-14

In medical informatics, psychology, market research and many other fields, researchers often need to analyze and model ranking data. However, there is no statistical software that provides tools for the comprehensive analysis of ranking data. Here, we present pmr, an R package for analyzing and modeling ranking data with a bundle of tools. The pmr package enables descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty's and Koczkodaj's inconsistencies), probability models (Luce model, distance-based model, and rank-ordered logit model), and the visualization of ranking data with multidimensional preference analysis. Examples of the use of package pmr are given using a real ranking dataset from medical informatics, in which 566 Hong Kong physicians ranked the top five incentives (1: competitive pressures; 2: increased savings; 3: government regulation; 4: improved efficiency; 5: improved quality care; 6: patient demand; 7: financial incentives) to the computerization of clinical practice. The mean rank showed that item 4 is the most preferred item and item 3 is the least preferred item, and significance difference was found between physicians' preferences with respect to their monthly income. A multidimensional preference analysis identified two dimensions that explain 42% of the total variance. The first can be interpreted as the overall preference of the seven items (labeled as "internal/external"), and the second dimension can be interpreted as their overall variance of (labeled as "push/pull factors"). Various statistical models were fitted, and the best were found to be weighted distance-based models with Spearman's footrule distance. In this paper, we presented the R package pmr, the first package for analyzing and modeling ranking data. The package provides insight to users through descriptive statistics of ranking data. Users can also visualize ranking data by applying a thought multidimensional preference analysis. Various probability models for ranking data are also included, allowing users to choose that which is most suitable to their specific situations.

When health policy and empirical evidence collide: the case of cigarette package warning labels and economic consumer surplus.

PubMed

Song, Anna V; Brown, Paul; Glantz, Stanton A

2014-02-01

In its graphic warning label regulations on cigarette packages, the Food and Drug Administration severely discounts the benefits of reduced smoking because of the lost "pleasure" smokers experience when they stop smoking; this is quantified as lost "consumer surplus." Consumer surplus is grounded in rational choice theory. However, empirical evidence from psychological cognitive science and behavioral economics demonstrates that the assumptions of rational choice are inconsistent with complex multidimensional decisions, particularly smoking. Rational choice does not account for the roles of emotions, misperceptions, optimistic bias, regret, and cognitive inefficiency that are germane to smoking, particularly because most smokers begin smoking in their youth. Continued application of a consumer surplus discount will undermine sensible policies to reduce tobacco use and other policies to promote public health.

A multi-dimensional Smolyak collocation method in curvilinear coordinates for computing vibrational spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Avila, Gustavo, E-mail: Gustavo-Avila@telefonica.net; Carrington, Tucker, E-mail: Tucker.Carrington@queensu.ca

In this paper, we improve the collocation method for computing vibrational spectra that was presented in Avila and Carrington, Jr. [J. Chem. Phys. 139, 134114 (2013)]. Using an iterative eigensolver, energy levels and wavefunctions are determined from values of the potential on a Smolyak grid. The kinetic energy matrix-vector product is evaluated by transforming a vector labelled with (nondirect product) grid indices to a vector labelled by (nondirect product) basis indices. Both the transformation and application of the kinetic energy operator (KEO) scale favorably. Collocation facilitates dealing with complicated KEOs because it obviates the need to calculate integrals of coordinatemore » dependent coefficients of differential operators. The ideas are tested by computing energy levels of HONO using a KEO in bond coordinates.« less

ITRAQ-based quantitative proteomic analysis of Cynops orientalis limb regeneration.

PubMed

Tang, Jie; Yu, Yuan; Zheng, Hanxue; Yin, Lu; Sun, Mei; Wang, Wenjun; Cui, Jihong; Liu, Wenguang; Xie, Xin; Chen, Fulin

2017-09-22

Salamanders regenerate their limbs after amputation. However, the molecular mechanism of this unique regeneration remains unclear. In this study, isobaric tags for relative and absolute quantification (iTRAQ) coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) was employed to quantitatively identify differentially expressed proteins in regenerating limbs 3, 7, 14, 30 and 42 days post amputation (dpa). Of 2636 proteins detected in total, 253 proteins were differentially expressed during different regeneration stages. Among these proteins, Asporin, Cadherin-13, Keratin, Collagen alpha-1(XI) and Titin were down-regulated. CAPG, Coronin-1A, AnnexinA1, Cathepsin B were up-regulated compared with the control. The identified proteins were further analyzed to obtain information about their expression patterns and functions in limb regeneration. Functional analysis indicated that the differentially expressed proteins were associated with wound healing, immune response, cellular process, metabolism and binding. This work indicated that significant proteome alternations occurred during salamander limb regeneration. The results may provide fundamental knowledge to understand the mechanism of limb regeneration.

Plant iTRAQ-based proteomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Handakumbura, Pubudu; Hixson, Kim K.; Purvine, Samuel O.

We present a simple one-­pot extraction protocol, which rapidly isolates hydrophyllic metabolites, lipids, and proteins from the same pulverized plant sample. Also detailed is a global plant proteomics sample preparation method utilizing iTRAQ multiplexing reagents that enables deep proteome coverage due to the use of HPLC fractionation of the peptides prior to mass spectrometric analysis. We have successfully used this protocol on several different plant tissues (e.g., roots, stems, leaves) from different plants (e.g., sorghum, poplar, Arabidopsis, soybean), and have been able to successfully detect and quantify thousands of proteins. Multiplexing strategies such as iTRAQ and the bioinformatics strategy outlinedmore » here, ultimately provide insight into which proteins are significantly changed in abundance between two or more groups (e.g., control, perturbation). Our bioinformatics strategy yields z-­score values, which normalize the expression data into a format that can easily be cross-­compared with other expression data (i.e., metabolomics, transcriptomics) obtained from different analytical methods and instrumentation.« less

2-DE Compared with iTRAQ-based Proteomic Analysis of the Functional Regulation of Proteins in Rhodococcus sp. BAP-1 Response to Fluoranthene

NASA Astrophysics Data System (ADS)

Xu, Jie; Wang, Hongqi; Kong, Dekang

2018-01-01

Although the degradation pathways of Polycyclic aromatic hydrocarbons (PAHs) have been extensively studied in many bacteria, the variations in the expression levels of the key functional regulation of proteins during catabolism are still not quantitatively understood. In this study, we compared two proteomic methods, that one is two-dimensional gel electrophoresis (2-DE), a traditional widely used way and the other is isobaric tags for relative and absolute quantization (iTRAQ), an innovative approach, in order to analyze the functional regulation at the protein level in high effective fluoranthene-degrading bacteria named Rhodococcus sp. BAP-1. The number of differentially expressed proteins identified using iTRAQ is much larger than employing 2-DE. Response to fluoranthene, the key over expressed proteins in BAP-1 were NADPH-dependent FMN reductase, 30S ribosomal protein S2, S-ribosylhomocysteinase, etc.; the significant down-regulated proteins were cytochrome ubiquinol oxidase subunit, NAD(P) transhydrogenase subunit alpha, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, et al.

Comparative proteomics analysis of Spodoptera frugiperda cells during Autographa californica multiple nucleopolyhedrovirus infection.

PubMed

Yu, Qian; Xiong, Youhua; Gao, Hang; Liu, Jianliang; Chen, Zhiqiang; Wang, Qin; Wen, Dongling

2015-08-04

Increasing evidence sugggest that in addition of balculovirus controling insect host, host cells also responds to balculovirus infection. However, compared to existing knowledge on virus gene, host cell responses are relatively poorly understood. In this study, Spodoptera frugiperda (Sf9) cells were infected with Autographa californica multiple nucleopolyhedrovirus (AcMNPV). The protein composition and protein changes of Spodoptera frugiperda (Sf9) cells of different infection stages were analysed by isobaric tag for relative and absolute quantification (iTRAQ) techniques. A total of 4004 Sf9 proteins were identified by iTRAQ and 413 proteins were found as more than 1.5-fold changes in abundance. The 413 proteins were categorised according to GO classification for insects and were categorised into: biological process, molecular function and cellular component. The determination of the protein changes in infected Sf9 cells would help to better understanding of host cell responses and facilitate better design of this virus-host cell interaction in pest insect control and other related fields.

iTRAQ reveals proteomic changes during intestine regeneration in the sea cucumber Apostichopus japonicus.

PubMed

Sun, Lina; Xu, Dongxue; Xu, Qinzeng; Sun, Jingchun; Xing, Lili; Zhang, Libin; Yang, Hongsheng

2017-06-01

Sea cucumbers have a striking capacity to regenerate most of their viscera after evisceration, which has drawn the interest of many researchers. In this study, the isobaric tag for relative and absolute quantitation (iTRAQ) was utilized to investigate protein abundance changes during intestine regeneration in sea cucumbers. A total of 4073 proteins were identified, and 2321 proteins exhibited significantly differential expressions, with 1100 upregulated and 1221 downregulated proteins. Our results suggest that intestine regeneration constitutes a complex life activity regulated by the cooperation of various biological processes, including cytoskeletal changes, extracellular matrix (ECM) remodeling and ECM-receptor interactions, protein synthesis, signal recognition and transduction, energy production and conversion, and substance transport and metabolism. Additionally, real-time PCR showed mRNA expression of differentially expressed genes correlated positively with their protein levels. Our results provided a basis for studying the regulatory mechanisms associated with sea cucumber regeneration. Copyright © 2017 Elsevier Inc. All rights reserved.

Non-gel Based Proteomics to Study Steroid Receptor Agonists in the Fathead Minnow

EPA Science Inventory

Toxicoproteomics is an emerging field that is greatly enabled by non-gel based methods using LC MS/MS for biomarker discovery and characterization for endocrine disrupting chemicals. Using iTRAQ (isobaric tagging for relative and absolute quantitation), we quantified a diverse r...

Proteomic analysis of PSD-93 knockout mice following the induction of ischemic cerebral injury.

PubMed

Rong, Rong; Yang, Hui; Rong, Liangqun; Wei, Xiue; Li, Qingjie; Liu, Xiaomei; Gao, Hong; Xu, Yun; Zhang, Qingxiu

2016-03-01

Postsynaptic density protein-93 (PSD-93) is enriched in the postsynaptic density and is involved in N-methyl-d-aspartate receptor (NMDAR) triggered neurotoxicity through PSD-93/NMDAR/nNOS signaling pathway. In the present study, we found that PSD-93 deficiency reduced infarcted volume and neurological deficits induced by transient middle cerebral artery occlusion (tMCAO) in the mice. To identify novel targets of PSD-93 related neurotoxicity, we applied isobaric tags for relative and absolute quantitative (iTRAQ) labeling and combined this labeling with on-line two-dimensional LC/MS/MS technology to elucidate the changes in protein expression in PSD-93 knockout mice following tMCAO. The proteomic data set consisted of 1892 proteins. Compared to control group, differences in expression levels in ischemic group >1.5-fold and <0.66-fold were considered as differential expression. A total of 104 unique proteins with differential abundance levels were identified, among which 17 proteins were selected for further validation. Gene ontology analysis using UniProt database revealed that these differentially expressed proteins are involved in diverse function such as synaptic transmission, neuronal neurotransmitter and ion transport, modification of organelle membrane components. Moreover, network analysis revealed that the interacting proteins were involved in the transport of synaptic vesicles, the integrity of synaptic membranes and the activation of the ionotropic glutamate receptors NMDAR1 and NMDAR2B. Finally, RT-PCR and Western blot analysis showed that SynGAP, syntaxin-1A, protein kinase C β, and voltage-dependent L-type calcium channels were inhibited by ischemia-reperfusion. Identification of these proteins provides valuable clues to elucidate the mechanisms underlying the actions of PSD-93 in ischemia-reperfusion induced neurotoxicity. Copyright © 2015 Elsevier Inc. All rights reserved.

SWATH™- and iTRAQ-based quantitative proteomic analyses reveal an overexpression and biological relevance of CD109 in advanced NSCLC.

PubMed

Zhang, Fanglin; Lin, Hechun; Gu, Aiqin; Li, Jing; Liu, Lei; Yu, Tao; Cui, Yongqi; Deng, Wei; Yan, Mingxia; Li, Jinjun; Yao, Ming

2014-05-06

To identify cancer-related proteins, we used isobaric tags in a relative and absolute quantitation (iTRAQ) proteomic approach and SWATH™ quantification approach to analyze the secretome of an isogenic pair of highly metastatic and low metastatic non-small-cell lung cancer (NSCLC) cell lines. In addition, we compared two groups of pooled serum samples (12 early-stage and 12 late-stage patients) to mine data for candidates screened by iTRAQ-labeled proteomic analysis. A total of 110 proteins and 71 proteins were observed to be significantly differentially expressed in the cell line secretome and NSCLC sera, respectively. Among these proteins, CD109 was found to be highly expressed in both the highly metastatic cell line secretome and the group of late-stage patients. A sandwich ELISA assay also demonstrated an elevation of serum CD109 levels in individual NSCLC patients (n=30) compared with healthy subjects (n=19). Furthermore, CD109 displayed higher expression in lung cancer tissues compared with their matched noncancerous lung tissues (n=72). In addition, the knockdown of CD109 influenced several NSCLC cell bio-functions, for instance, depressing cell growth, affecting cell cycle phases. These phenomena suggest that CD109 plays a critical role in NSCLC progression. We simultaneously applied two quantitative proteomic approaches-iTRAQ-labeling and SWATH™-to analyze the secretome of metastatic cell lines, in order to explore the cancer-associated proteins in conditioned media. In this study, our results indicate that CD109 plays a critical role in non-small-cell lung cancer (NSCLC) progression, and is overexpressed in advanced NSCLC. Copyright © 2014 Elsevier B.V. All rights reserved.

Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Enrichment and Isobaric Labeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Dian; Gaffrey, Matthew J.; Guo, Jia

2014-02-11

Protein S-glutathionylation (SSG) is an important regulatory posttranslational modification of protein cysteine (Cys) thiol redox switches, yet the role of specific cysteine residues as targets of modification is poorly understood. We report a novel quantitative mass spectrometry (MS)-based proteomic method for site-specific identification and quantification of S-glutathionylation across different conditions. Briefly, this approach consists of initial blocking of free thiols by alkylation, selective reduction of glutathionylated thiols and enrichment using thiol affinity resins, followed by on-resin tryptic digestion and isobaric labeling with iTRAQ (isobaric tags for relative and absolute quantitation) for MS-based identification and quantification. The overall approach was validatedmore » by application to RAW 264.7 mouse macrophages treated with different doses of diamide to induce glutathionylation. A total of 1071 Cys-sites from 690 proteins were identified in response to diamide treatment, with ~90% of the sites displaying >2-fold increases in SSG-modification compared to controls.. This approach was extended to identify potential SSG modified Cys-sites in response to H2O2, an endogenous oxidant produced by activated macrophages and many pathophysiological stimuli. The results revealed 364 Cys-sites from 265 proteins that were sensitive to S-glutathionylation in response to H2O2 treatment. These proteins covered a range of molecular types and molecular functions with free radical scavenging, and cell death and survival included as the most significantly enriched functional categories. Overall the results demonstrate that our approach is effective for site-specific identification and quantification of S-glutathionylated proteins. The analytical strategy also provides a unique approach to determining the major pathways and cell processes most susceptible to glutathionylation at a proteome-wide scale.« less

Textual emotion recognition for enhancing enterprise computing

NASA Astrophysics Data System (ADS)

Quan, Changqin; Ren, Fuji

2016-05-01

The growing interest in affective computing (AC) brings a lot of valuable research topics that can meet different application demands in enterprise systems. The present study explores a sub area of AC techniques - textual emotion recognition for enhancing enterprise computing. Multi-label emotion recognition in text is able to provide a more comprehensive understanding of emotions than single label emotion recognition. A representation of 'emotion state in text' is proposed to encompass the multidimensional emotions in text. It ensures the description in a formal way of the configurations of basic emotions as well as of the relations between them. Our method allows recognition of the emotions for the words bear indirect emotions, emotion ambiguity and multiple emotions. We further investigate the effect of word order for emotional expression by comparing the performances of bag-of-words model and sequence model for multi-label sentence emotion recognition. The experiments show that the classification results under sequence model are better than under bag-of-words model. And homogeneous Markov model showed promising results of multi-label sentence emotion recognition. This emotion recognition system is able to provide a convenient way to acquire valuable emotion information and to improve enterprise competitive ability in many aspects.

ITRAQ MASS SPECTROMETRIC PROTEOMIC APPLICATIONS FOR IN VIVO TOXICOLOGY STUDIES OF AMPHIBIAN SPECIES: DATA HANDLING AND INTERPRETATION USING PEPTIDE-TAGGING SOFTWARE

EPA Science Inventory

This addresses the USEPA's need for a cost effective, non-mammalian screening assay for thyroid axis disrupting chemicals; a multi-endpoint strategy combining molecular and in vivo protocols in an amphibian model is being applied at MED Duluth.

Live-Cell Imaging of Filoviruses.

PubMed

Schudt, Gordian; Dolnik, Olga; Becker, Stephan

2017-01-01

Observation of molecular processes inside living cells is fundamental to a deeper understanding of virus-host interactions in filoviral-infected cells. These observations can provide spatiotemporal insights into protein synthesis, protein-protein interaction dynamics, and transport processes of these highly pathogenic viruses. Thus, live-cell imaging provides the possibility for antiviral screening in real time and gives mechanistic insights into understanding filovirus assembly steps that are dependent on cellular factors, which then represent potential targets against this highly fatal disease. Here we describe analysis of living filovirus-infected cells under maximum biosafety (i.e., BSL4) conditions using plasmid-driven expression of fluorescently labeled viral and cellular proteins and/or viral genome-encoded expression of fluorescently labeled proteins. Such multiple-color and multidimensional time-lapse live-cell imaging analyses are a powerful method to gain a better understanding of the filovirus infection cycle.

When Health Policy and Empirical Evidence Collide: The Case of Cigarette Package Warning Labels and Economic Consumer Surplus

PubMed Central

Song, Anna V.; Brown, Paul

2014-01-01

In its graphic warning label regulations on cigarette packages, the Food and Drug Administration severely discounts the benefits of reduced smoking because of the lost “pleasure” smokers experience when they stop smoking; this is quantified as lost “consumer surplus.” Consumer surplus is grounded in rational choice theory. However, empirical evidence from psychological cognitive science and behavioral economics demonstrates that the assumptions of rational choice are inconsistent with complex multidimensional decisions, particularly smoking. Rational choice does not account for the roles of emotions, misperceptions, optimistic bias, regret, and cognitive inefficiency that are germane to smoking, particularly because most smokers begin smoking in their youth. Continued application of a consumer surplus discount will undermine sensible policies to reduce tobacco use and other policies to promote public health. PMID:24328661

Genome-wide proteomics analysis on longissimus muscles in Qinchuan beef cattle.

PubMed

He, Hua; Chen, Si; Liang, Wei; Liu, Xiaolin

2017-04-01

To gain further insight into the molecular mechanism of bovine muscle development, we combined mass spectrometry characterization of proteins with Illumina deep sequencing of RNAs obtained from bovine longissimus muscle (LD) at prenatal and postnatal stages. For the proteomic study, each group of LD proteins was extracted and labeled using isobaric tags for relative and absolute quantitation (iTRAQ) method. Among the 1321 proteins identified from six samples, 390 proteins were differentially expressed in embryos at day 135 post-fertilization (Emb135d) vs. 30-month-old adult cattle (Emb135d vs. 30M) samples. Gene Ontology, Cluster of Orthologous Groups and Kyoto Encyclopedia of Genes and Genomes analyses were further conducted to better understand the different functions. Furthermore, we analyzed the relationship between transcript and protein regulation between samples by direct comparison of expression levels from transcriptomic and iTRAQ-based proteomics. Association results indicated that 1295 of 1321 proteins could be mapped to transcriptome sequencing data. This study provides the most comprehensive, targeted survey of bovine LD proteins to date and has shown the power of combining transcriptomic and proteomic approaches to provide molecular insights for understanding the developmental characteristics in bovine muscle, and even in other mammals. © 2016 Stichting International Foundation for Animal Genetics.

Quantitative Proteomic Profiling of Low-Dose Ionizing Radiation Effects in a Human Skin Model

PubMed Central

Hengel, Shawna M.; Aldrich, Joshua T.; Waters, Katrina M.; Pasa-Tolic, Ljiljana; Stenoien, David L.

2014-01-01

To assess responses to low-dose ionizing radiation (LD-IR) exposures potentially encountered during medical diagnostic procedures, nuclear accidents or terrorist acts, a quantitative proteomic approach was used to identify changes in protein abundance in a reconstituted human skin tissue model treated with 0.1 Gy of ionizing radiation. To improve the dynamic range of the assay, subcellular fractionation was employed to remove highly abundant structural proteins and to provide insight into radiation-induced alterations in protein localization. Relative peptide quantification across cellular fractions, control and irradiated samples was performing using 8-plex iTRAQ labeling followed by online two-dimensional nano-scale liquid chromatography and high resolution MS/MS analysis. A total of 107 proteins were detected with statistically significant radiation-induced change in abundance (>1.5 fold) and/or subcellular localization compared to controls. The top biological pathways identified using bioinformatics include organ development, anatomical structure formation and the regulation of actin cytoskeleton. From the proteomic data, a change in proteolytic processing and subcellular localization of the skin barrier protein, filaggrin, was identified, and the results were confirmed by western blotting. This data indicate post-transcriptional regulation of protein abundance, localization and proteolytic processing playing an important role in regulating radiation response in human tissues. PMID:28250387

High-Resolution Enabled 12-Plex DiLeu Isobaric Tags for Quantitative Proteomics

PubMed Central

2015-01-01

Multiplex isobaric tags (e.g., tandem mass tags (TMT) and isobaric tags for relative and absolute quantification (iTRAQ)) are a valuable tool for high-throughput mass spectrometry based quantitative proteomics. We have developed our own multiplex isobaric tags, DiLeu, that feature quantitative performance on par with commercial offerings but can be readily synthesized in-house as a cost-effective alternative. In this work, we achieve a 3-fold increase in the multiplexing capacity of the DiLeu reagent without increasing structural complexity by exploiting mass defects that arise from selective incorporation of 13C, 15N, and 2H stable isotopes in the reporter group. The inclusion of eight new reporter isotopologues that differ in mass from the existing four reporters by intervals of 6 mDa yields a 12-plex isobaric set that preserves the synthetic simplicity and quantitative performance of the original implementation. We show that the new reporter variants can be baseline-resolved in high-resolution higher-energy C-trap dissociation (HCD) spectra, and we demonstrate accurate 12-plex quantitation of a DiLeu-labeled Saccharomyces cerevisiae lysate digest via high-resolution nano liquid chromatography–tandem mass spectrometry (nanoLC–MS2) analysis on an Orbitrap Elite mass spectrometer. PMID:25405479

Secretome profiles of immortalized dental follicle cells using iTRAQ-based proteomic analysis.

PubMed

Dou, Lei; Wu, Yan; Yan, Qifang; Wang, Jinhua; Zhang, Yan; Ji, Ping

2017-08-04

Secretomes produced by mesenchymal stromal cells (MSCs) were considered to be therapeutic potential. However, harvesting enough primary MSCs from tissue was time-consuming and costly, which impeded the application of MSCs secretomes. This study was to immortalize MSCs and compare the secretomes profile of immortalized and original MSCs. Human dental follicle cells (DFCs) were isolated and immortalized using pMPH86. The secretome profile of immortalized DFCs (iDFCs) was investigated and compared using iTRAQ labeling combined with mass spectrometry (MS) quantitative proteomics. The MS data was analyzed using ProteinPilotTM software, and then bioinformatic analysis of identified proteins was done. A total of 2092 secreted proteins were detected in conditioned media of iDFCs. Compared with primary DFCs, 253 differently expressed proteins were found in iDFCs secretome (142 up-regulated and 111 down-regulated). Intensive bioinformatic analysis revealed that the majority of secreted proteins were involved in cellular process, metabolic process, biological regulation, cellular component organization or biogenesis, immune system process, developmental process, response to stimulus and signaling. Proteomic profile of cell secretome wasn't largely affected after immortalization converted by this piggyBac immortalization system. The secretome of iDFCs may be a good candidate of primary DFCs for regenerative medicine.

Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration

PubMed Central

Voss, Bradley J.; Loh, John T.; Hill, Salisha; Rose, Kristie L.; McDonald, W. Hayes; Cover, Timothy L.

2015-01-01

Purpose Helicobacter pylori infection and a high dietary salt intake are each risk factors for the development of gastric cancer. We hypothesize that changes in environmental salt concentrations lead to alterations in the H. pylori membrane proteome. Experimental Design Label-free and iTRAQ methods were used to identify H. pylori proteins that change in abundance in response to alterations in environmental salt concentrations. In addition, we biotinylated intact bacteria that were grown under high- or low-salt conditions, and thereby analyzed salt-induced changes in the abundance of surface-exposed proteins. Results Proteins with increased abundance in response to high salt conditions included CagA, the outer membrane protein HopQ, and fibronectin domain-containing protein HP0746. Proteins with increased abundance in response to low salt conditions included VacA, two VacA-like proteins (ImaA and FaaA), outer-membrane iron transporter FecA3, and several proteins involved in flagellar activity. Consistent with the proteomic data, bacteria grown in high salt conditions exhibited decreased motility compared to bacteria grown in lower salt conditions. Conclusions and clinical relevance Alterations in the H. pylori membrane proteome in response to high salt conditions may contribute to the increased risk of gastric cancer associated with a high salt diet. PMID:26109032

Comparative Proteomics Provides Insights into Metabolic Responses in Rat Liver to Isolated Soy and Meat Proteins.

PubMed

Song, Shangxin; Hooiveld, Guido J; Zhang, Wei; Li, Mengjie; Zhao, Fan; Zhu, Jing; Xu, Xinglian; Muller, Michael; Li, Chunbao; Zhou, Guanghong

2016-04-01

It has been reported that isolated dietary soy and meat proteins have distinct effects on physiology and liver gene expression, but the impact on protein expression responses are unknown. Because these may differ from gene expression responses, we investigated dietary protein-induced changes in liver proteome. Rats were fed for 1 week semisynthetic diets that differed only regarding protein source; casein (reference) was fully replaced by isolated soy, chicken, fish, or pork protein. Changes in liver proteome were measured by iTRAQ labeling and LC-ESI-MS/MS. A robust set totaling 1437 unique proteins was identified and subjected to differential protein analysis and biological interpretation. Compared with casein, all other protein sources reduced the abundance of proteins involved in fatty acid metabolism and Pparα signaling pathway. All dietary proteins, except chicken, increased oxidoreductive transformation reactions but reduced energy and essential amino acid metabolic pathways. Only soy protein increased the metabolism of sulfur-containing and nonessential amino acids. Soy and fish proteins increased translation and mRNA processing, whereas only chicken protein increased TCA cycle but reduced immune responses. These findings were partially in line with previously reported transcriptome results. This study further shows the distinct effects of soy and meat proteins on liver metabolism in rats.

Characterization and comparison of proteomes of albino sea cucumber Apostichopus japonicus (Selenka) by iTRAQ analysis.

PubMed

Xia, Chang-Ge; Zhang, Dijun; Ma, Chengnv; Zhou, Jun; He, Shan; Su, Xiu-Rong

2016-04-01

Sea cucumber is a commercially important marine organism in China. Of the different colored varieties sold in China, albino sea cucumber has the greatest appeal among consumers. Identification of factors contributing to albinism in sea cucumber is therefore likely to provide a scientific basis for improving the cultivability of these strains. In this study, two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification labeling was used for the first time to quantitatively define the proteome of sea cucumbers and reveal proteomic characteristics unique to albino sea cucumbers. A total of 549 proteins were identified and quantified in albino sea cucumber and the functional annotations of 485 proteins have been exhibited based on COG database. Compared with green sea cucumber, 12 proteins were identified as differentially expressed in the intestine and 16 proteins in the body wall of albino sea cucumber. Among them, 5 proteins were up-regulated in the intestine and 8 proteins were down-regulated in body wall. Gene ontology annotations of these differentially expressed proteins consisted mostly of 'biological process'. The large number of differentially expressed proteins identified here should be highly useful in further elucidating the mechanisms underlying albinism in sea cucumber. Copyright © 2015 Elsevier Ltd. All rights reserved.

Meta-modelling, visualization and emulation of multi-dimensional data for virtual production intelligence

NASA Astrophysics Data System (ADS)

Schulz, Wolfgang; Hermanns, Torsten; Al Khawli, Toufik

2017-07-01

Decision making for competitive production in high-wage countries is a daily challenge where rational and irrational methods are used. The design of decision making processes is an intriguing, discipline spanning science. However, there are gaps in understanding the impact of the known mathematical and procedural methods on the usage of rational choice theory. Following Benjamin Franklin's rule for decision making formulated in London 1772, he called "Prudential Algebra" with the meaning of prudential reasons, one of the major ingredients of Meta-Modelling can be identified finally leading to one algebraic value labelling the results (criteria settings) of alternative decisions (parameter settings). This work describes the advances in Meta-Modelling techniques applied to multi-dimensional and multi-criterial optimization by identifying the persistence level of the corresponding Morse-Smale Complex. Implementations for laser cutting and laser drilling are presented, including the generation of fast and frugal Meta-Models with controlled error based on mathematical model reduction Reduced Models are derived to avoid any unnecessary complexity. Both, model reduction and analysis of multi-dimensional parameter space are used to enable interactive communication between Discovery Finders and Invention Makers. Emulators and visualizations of a metamodel are introduced as components of Virtual Production Intelligence making applicable the methods of Scientific Design Thinking and getting the developer as well as the operator more skilled.

Identification of potential bladder cancer markers in urine by abundant-protein depletion coupled with quantitative proteomics.

PubMed

Chen, Chien-Lun; Lin, Tsung-Shih; Tsai, Cheng-Han; Wu, Chih-Ching; Chung, Ting; Chien, Kun-Yi; Wu, Maureen; Chang, Yu-Sun; Yu, Jau-Song; Chen, Yi-Ting

2013-06-24

In this study, we evaluated the reproducibility of abundant urine protein depletion by hexapeptide-based library beads and an antibody-based affinity column using the iTRAQ technique. The antibody-based affinity-depletion approach, which proved superior, was then applied in conjunction with iTRAQ to discover proteins that were differentially expressed between pooled urine samples from hernia and bladder cancer patients. Several proteins, including seven apolipoproteins, TIM, SAA4, and proEGF were further verified in 111 to 203 individual urine samples from patients with hernia, bladder cancer, or kidney cancer. Six apolipoproteins (APOA1, APOA2, APOB, APOC2, APOC3, and APOE) were able to differentiate bladder cancer from hernia. SAA4 was significantly increased in bladder cancer subgroups, whereas ProEGF was significantly decreased in bladder cancer subgroups. Additionally, the combination of SAA4 and ProEGF exhibited higher diagnostic capacity (AUC=0.80 and p<0.001) in discriminating bladder cancer from hernia than either marker alone. Using MetaCore software to interpret global changes of the urine proteome caused by bladder cancer, we found that the most notable alterations were in immune-response/alternative complement and blood-coagulation pathways. This study confirmed the clinical significance of the urine proteome in the development of non-invasive biomarkers for the detection of bladder cancer. In this study, we evaluated the reproducibility of abundant urine protein depletion by hexapeptide-based library beads and an antibody-based affinity column using the iTRAQ technique. The antibody-based affinity-depletion approach, which proved superior, was then applied in conjunction with iTRAQ to discover proteins that were differentially expressed between pooled urine samples from hernia and bladder cancer patients. Several proteins, including seven apolipoproteins, TIM, SAA4, and proEGF were further verified in 111 to 203 individual urine samples from patients with hernia, bladder cancer, or kidney cancer. SAA4 was significantly increased in bladder cancer subgroups, whereas ProEGF was significantly decreased in bladder cancer subgroups. Additionally, the combination of SAA4 and ProEGF exhibited higher diagnostic capacity in discriminating bladder cancer from hernia than either marker alone. A marker panel composed by two novel biomarker candidates, SAA4 and proEGF, was first discovered and verified successfully using Western blotting. To the best of our knowledge, the associations of urinary SAA4 and proEGF with bladder tumor and kidney cancer have not been mentioned before. In the present study, we discovered and verified SAA4 and proEGF as potential bladder cancer biomarker for the first time. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

The effects of context on multidimensional spatial cognitive models. Ph.D. Thesis - Arizona Univ.

NASA Technical Reports Server (NTRS)

Dupnick, E. G.

1979-01-01

Spatial cognitive models obtained by multidimensional scaling represent cognitive structure by defining alternatives as points in a coordinate space based on relevant dimensions such that interstimulus dissimilarities perceived by the individual correspond to distances between the respective alternatives. The dependence of spatial models on the context of the judgments required of the individual was investigated. Context, which is defined as a perceptual interpretation and cognitive understanding of a judgment situation, was analyzed and classified with respect to five characteristics: physical environment, social environment, task definition, individual perspective, and temporal setting. Four experiments designed to produce changes in the characteristics of context and to test the effects of these changes upon individual cognitive spaces are described with focus on experiment design, objectives, statistical analysis, results, and conclusions. The hypothesis is advanced that an individual can be characterized as having a master cognitive space for a set of alternatives. When the context changes, the individual appears to change the dimension weights to give a new spatial configuration. Factor analysis was used in the interpretation and labeling of cognitive space dimensions.

Structure and Membrane Interactions of the Antibiotic Peptide Dermadistinctin K by Multidimensional Solution and Oriented 15N and 31P Solid-State NMR Spectroscopy

PubMed Central

Verly, Rodrigo M.; Moraes, Cléria Mendonça de; Resende, Jarbas M.; Aisenbrey, Christopher; Bemquerer, Marcelo Porto; Piló-Veloso, Dorila; Valente, Ana Paula; Almeida, Fábio C.L.; Bechinger, Burkhard

2009-01-01

DD K, a peptide first isolated from the skin secretion of the Phyllomedusa distincta frog, has been prepared by solid-phase chemical peptide synthesis and its conformation was studied in trifluoroethanol/water as well as in the presence of sodium dodecyl sulfate and dodecylphosphocholine micelles or small unilamellar vesicles. Multidimensional solution NMR spectroscopy indicates an α-helical conformation in membrane environments starting at residue 7 and extending to the C-terminal carboxyamide. Furthermore, DD K has been labeled with 15N at a single alanine position that is located within the helical core region of the sequence. When reconstituted into oriented phosphatidylcholine membranes the resulting 15N solid-state NMR spectrum shows a well-defined helix alignment parallel to the membrane surface in excellent agreement with the amphipathic character of DD K. Proton-decoupled 31P solid-state NMR spectroscopy indicates that the peptide creates a high level of disorder at the level of the phospholipid headgroup suggesting that DD K partitions into the bilayer where it severely disrupts membrane packing. PMID:19289046

Automatic construction of a recurrent neural network based classifier for vehicle passage detection

NASA Astrophysics Data System (ADS)

Burnaev, Evgeny; Koptelov, Ivan; Novikov, German; Khanipov, Timur

2017-03-01

Recurrent Neural Networks (RNNs) are extensively used for time-series modeling and prediction. We propose an approach for automatic construction of a binary classifier based on Long Short-Term Memory RNNs (LSTM-RNNs) for detection of a vehicle passage through a checkpoint. As an input to the classifier we use multidimensional signals of various sensors that are installed on the checkpoint. Obtained results demonstrate that the previous approach to handcrafting a classifier, consisting of a set of deterministic rules, can be successfully replaced by an automatic RNN training on an appropriately labelled data.

Identification of Biomarkers Associated with the Healing of Chronic Wounds

DTIC Science & Technology

2010-06-01

and iTRAQ findings and the final set of custom antibody arrays included calreticulin, ENO1, Gelsolin, Progranulin , sRAGE. S100A12/ENRAGE, S100A6...Gelsolin 29.47 .0872 -13.04 .5660 .20 .7444 -.40 .6368 Progranulin 3.67 .0282 -1.80 .4151 .068 .2398 -.019 .8153 sRAGE 3.10 .2720 .44 .9052 -.01 .8842

Proteomic analysis by iTRAQ in red claw crayfish, Cherax quadricarinatus, hematopoietic tissue cells post white spot syndrome virus infection.

PubMed

Jeswin, Joseph; Xie, Xiao-lu; Ji, Qiao-lin; Wang, Ke-jian; Liu, Hai-peng

2016-03-01

To elucidate proteomic changes of Hpt cells from red claw crayfish, Cherax quadricarinatus, we have carried out isobaric tags for relative and absolute quantitation (iTRAQ) of cellular proteins at both early (1 hpi) and late stage (12 hpi) post white spot syndrome virus (WSSV) infection. Protein database search revealed 594 protein hits by Mascot, in which 17 and 30 proteins were present as differentially expressed proteins at early and late viral infection, respectively. Generally, these differentially expressed proteins include: 1) the metabolic process related proteins in glycolysis and glucogenesis, DNA replication, nucleotide/amino acid/fatty acid metabolism and protein biosynthesis; 2) the signal transduction related proteins like small GTPases, G-protein-alpha stimulatory subunit, proteins bearing PDZ- or 14-3-3-domains that help holding together and organize signaling complexes, casein kinase I and proteins of the MAP-kinase signal transduction pathway; 3) the immune defense related proteins such as α-2 macroglobulin, transglutaminase and trans-activation response RNA-binding protein 1. Taken together, these protein information shed new light on the host cellular response against WSSV infection in a crustacean cell culture. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative proteomic analysis of Cronobacter sakazakii by iTRAQ provides insights into response to desiccation.

PubMed

Hu, Shuangfang; Yu, Yigang; Wu, Xinwei; Xia, Xingzhou; Xiao, Xinglong; Wu, Hui

2017-10-01

Cronobacter sakazakii is a foodborne pathogen throughout the world and survives extremely desiccation stress. However, the molecular basis involved in desiccation resistance of C. sakazakii is still unknown. In this study, the potential desiccation resistance factors of C. sakazakii ATCC 29544 were determined using iTRAQ-based quantitative proteomic analysis. A total of 2775 proteins were identified by iTRAQ, of which 233 showed a different protein expression between control group and desiccation stress group. Among these 233 proteins identified as desiccation resistance proteins, there were 146 proteins downregulated and 87 proteins upregulated. According to the comprehensive proteome coverage analysis, C. sakazakii increased its resistance to desiccation by reducing the gene involved with unnecessary survival functions such as those used for virulence, adhesion, invasion and flagella assembly, while increasing gene expression of genes used in withstanding osmotic stress such as those genes involved in trehalose and betaine uptake. However, the mechanism involved in amino acid metabolism in an osmotic stress response, including the producing of γ-aminobutyric acid in C. sakazakii is still uncertain. This is the first report to determine the potential desiccation resistant factors of C. sakazakii at the proteomic levels. Copyright © 2017. Published by Elsevier Ltd.

Differential proteomic analysis of cancer stem cell properties in hepatocellular carcinomas by isobaric tag labeling and mass spectrometry.

PubMed

Ko, Ching-Huai; Cheng, Chieh-Fang; Lai, Chin-Pen; Tzu, Te-Hui; Chiu, Chih-Wei; Lin, Mei-Wei; Wu, Si-Yuan; Sun, Chung-Yuan; Tseng, Hsiang-Wen; Wang, Chun-Chung; Kuo, Zong-Keng; Wang, Ling-Mei; Chen, Sung-Fang

2013-08-02

Malignant tumors are relatively resistant to treatment due to their heterogeneous nature, drug resistance, and tendency for metastasis. Recent studies suggest that a subpopulation of cancer cells is responsible for the malignant outcomes. These cells are considered as cancer stem cells (CSC). Although a number of molecules have been identified in different cancer cells as markers for cancer stem cells, no promising markers are currently available for hepatocellular carcinoma cells. In this study, two clones of Hep3B cell lines were functionally characterized as control or CSC-like cells, based on properties including spheroid formation, drug resistance, and tumor initiation. Furthermore, their protein expression profiles were investigated by isobaric tags for relative and absolute quantitation (iTRAQ), and a total of 1,127 proteins were identified and quantified from the combined fractions; 50 proteins exhibited at least 2-fold differences between these two clones. These 50 proteins were analyzed by GeneGo and were found to be associated with liver neoplasms, hepatocellular carcinoma (HCC), and liver diseases. They were also components of metabolic pathways, immune responses, and cytoskeleton remodeling. Among these proteins, the expressions of S100P, S100A14, and vimentin were verified in several HCC cell lines, and their expressions were correlated with tumorigenicity in HCC cell lines. The functional significance of vimentin and S100A14 were also investigated and verified.

Plasma proteomic changes during hypothermic and normothermic cardiopulmonary bypass in aortic surgeries

PubMed Central

ODA, TEIJI; YAMAGUCHI, AKANE; YOKOYAMA, MASAO; SHIMIZU, KOJI; TOYOTA, KOSAKU; NIKAI, TETSURO; MATSUMOTO, KEN-ICHI

2014-01-01

Deep hypothermic circulatory arrest (DHCA) is a protective method against brain ischemia in aortic surgery. However, the possible effects of DHCA on the plasma proteins remain to be determined. In the present study, we used novel high-throughput technology to compare the plasma proteomes during DHCA (22°C) with selective cerebral perfusion (SCP, n=7) to those during normothermic cardiopulmonary bypass (CPB, n=7). Three plasma samples per patient were obtained during CPB: T1, prior to cooling; T2, during hypothermia; T3, after rewarming for the DHCA group and three corresponding points for the normothermic group. A proteomic analysis was performed using isobaric tag for relative and absolute quantification (iTRAQ) labeling tandem mass spectrometry to assess quantitative protein changes. In total, the analysis identified 262 proteins. The bioinformatics analysis revealed a significant upregulation of complement activation at T2 in normothermic CPB, which was suppressed in DHCA. These findings were confirmed by the changes of the terminal complement complex (SC5b-9) levels. At T3, however, the level of SC5b-9 showed a greater increase in DHCA compared to normothermic CPB, while 48 proteins were significantly downregulated in DHCA. The results demonstrated that DHCA and rewarming potentially exert a significant effect on the plasma proteome in patients undergoing aortic surgery. PMID:25050567

Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant.

PubMed

Kramer, Annemarie; Beck, Hans Christian; Kumar, Abhishek; Kristensen, Lars Peter; Imhoff, Johannes F; Labes, Antje

2015-01-01

The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.

Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant

PubMed Central

Kramer, Annemarie; Beck, Hans Christian; Kumar, Abhishek; Kristensen, Lars Peter; Imhoff, Johannes F.; Labes, Antje

2015-01-01

The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum. PMID:26460745

A multiplexed quantitative proteomics approach for investigating protein expression in the developing central nervous system.

PubMed

Orme, Rowan P; Gates, Monte A; Fricker-Gates, Rosemary A

2010-08-15

Cell transplantation using stem cell-derived neurons is commonly viewed as a candidate therapy for neurodegenerative diseases. However, methods for differentiating stem cells into homogenous populations of neurons suitable for transplant remain elusive. This suggests that there are as yet unknown signalling factors working in vivo to specify neuronal cell fate during development. These factors could be manipulated to better differentiate stem cells into neural populations useful for therapeutic transplantation. Here a quantitative proteomics approach is described for investigating cell signalling in the developing central nervous system (CNS), using the embryonic ventral mesencephalon as a model. Briefly, total protein was extracted from embryonic ventral midbrain tissue before, during and after the birth of dopaminergic neurons, and digested using trypsin. Two-dimensional liquid chromatography, coupled with tandem mass spectrometry, was then used to identify proteins from the tryptic peptides. Isobaric tagging for relative and absolute quantification (iTRAQ) reagents were used to label the tryptic peptides and facilitate relative quantitative analysis. The success of the experiment was confirmed by the identification of proteins known to be expressed in the developing ventral midbrain, as well as by Western blotting, and immunolabelling of embryonic tissue sections. This method of protein discovery improves upon previous attempts to identify novel signalling factors through microarray analysis. Importantly, the methods described here could be applied to virtually any aspect of development. (c) 2010 Elsevier B.V. All rights reserved.

Differential Protein Expressions in Virus-Infected and Uninfected Trichomonas vaginalis.

PubMed

He, Ding; Pengtao, Gong; Ju, Yang; Jianhua, Li; He, Li; Guocai, Zhang; Xichen, Zhang

2017-04-01

Protozoan viruses may influence the function and pathogenicity of the protozoa. Trichomonas vaginalis is a parasitic protozoan that could contain a double stranded RNA (dsRNA) virus, T. vaginalis virus (TVV). However, there are few reports on the properties of the virus. To further determine variations in protein expression of T. vaginalis , we detected 2 strains of T. vaginalis ; the virus-infected (V + ) and uninfected (V - ) isolates to examine differentially expressed proteins upon TVV infection. Using a stable isotope N-terminal labeling strategy (iTRAQ) on soluble fractions to analyze proteomes, we identified 293 proteins, of which 50 were altered in V + compared with V - isolates. The results showed that the expression of 29 proteins was increased, and 21 proteins decreased in V + isolates. These differentially expressed proteins can be classified into 4 categories: ribosomal proteins, metabolic enzymes, heat shock proteins, and putative uncharacterized proteins. Quantitative PCR was used to detect 4 metabolic processes proteins: glycogen phosphorylase, malate dehydrogenase, triosephosphate isomerase, and glucose-6-phosphate isomerase, which were differentially expressed in V + and V - isolates. Our findings suggest that mRNA levels of these genes were consistent with protein expression levels. This study was the first which analyzed protein expression variations upon TVV infection. These observations will provide a basis for future studies concerning the possible roles of these proteins in host-parasite interactions.

Changes in the Plasma Proteome Follows Chronic Opiate Administration In Simian Immunodeficiency Virus Infected Rhesus Macaques*

PubMed Central

Wiederin, Jayme L.; Yu, Fang; Donahoe, Robert M.; Fox, Howard S.; Ciborowski, Pawel; Gendelman, Howard E.

2011-01-01

Background Substantive plasma proteomic changes follow lentiviral infection and disease pathobiology. We posit that such protein alterations are modified during drug abuse, further serving to affect the disease. To this end, we investigated the effect of opiate administration on the plasma proteome of Indian-strain rhesus monkeys infected with simian immunodeficiency virus (SIV) strain smm9. Methods Whole blood was collected at 7 weeks prior to and 1.4 and 49 weeks after viral infection. Viral load, CD4+ T cell subsets, and plasma protein content were measured from monkeys that did or did not receive continuous opiate administrations. The plasma proteome was identified and quantified by isobaric tags for relative and absolute quantitation labeling (iTRAQ) and mass spectrometry. Results While substantive changes in plasma proteins were seen during SIV infection, the addition of opiates led to suppression of these changes as well as increased variance of the proteome. These changes demonstrate that opiates induce broad but variant immune suppression in SIV-infected monkeys. Conclusion The broad suppressive changes seen in plasma of SIV-infected monkeys likely reflect reduced multisystem immune homeostatic responses induced by opiates. Such occur as a consequence of complex cell-to-cell interactions operative between the virus and the host. We conclude that such changes in plasma proteomic profiling may be underappreciated and as such supports the need for improved clinical definitions. PMID:21821369

Comparative quantitative proteomics analysis of the ABA response of roots of drought-sensitive and drought-tolerant wheat varieties identifies proteomic signatures of drought adaptability.

PubMed

Alvarez, Sophie; Roy Choudhury, Swarup; Pandey, Sona

2014-03-07

Wheat is one of the most highly cultivated cereals in the world. Like other cultivated crops, wheat production is significantly affected by abiotic stresses such as drought. Multiple wheat varieties suitable for different geographical regions of the world have been developed that are adapted to different environmental conditions; however, the molecular basis of such adaptations remains unknown in most cases. We have compared the quantitative proteomics profile of the roots of two different wheat varieties, Nesser (drought-tolerant) and Opata (drought-sensitive), in the absence and presence of abscisic acid (ABA, as a proxy for drought). A labeling LC-based quantitative proteomics approach using iTRAQ was applied to elucidate the changes in protein abundance levels. Quantitative differences in protein levels were analyzed for the evaluation of inherent differences between the two varieties as well as the overall and variety-specific effect of ABA on the root proteome. This study reveals the most elaborate ABA-responsive root proteome identified to date in wheat. A large number of proteins exhibited inherently different expression levels between Nesser and Opata. Additionally, significantly higher numbers of proteins were ABA-responsive in Nesser roots compared with Opata roots. Furthermore, several proteins showed variety-specific regulation by ABA, suggesting their role in drought adaptation.

Implementing Connected Component Labeling as a User Defined Operator for SciDB

NASA Technical Reports Server (NTRS)

Oloso, Amidu; Kuo, Kwo-Sen; Clune, Thomas; Brown, Paul; Poliakov, Alex; Yu, Hongfeng

2016-01-01

We have implemented a flexible User Defined Operator (UDO) for labeling connected components of a binary mask expressed as an array in SciDB, a parallel distributed database management system based on the array data model. This UDO is able to process very large multidimensional arrays by exploiting SciDB's memory management mechanism that efficiently manipulates arrays whose memory requirements far exceed available physical memory. The UDO takes as primary inputs a binary mask array and a binary stencil array that specifies the connectivity of a given cell to its neighbors. The UDO returns an array of the same shape as the input mask array with each foreground cell containing the label of the component it belongs to. By default, dimensions are treated as non-periodic, but the UDO also accepts optional input parameters to specify periodicity in any of the array dimensions. The UDO requires four stages to completely label connected components. In the first stage, labels are computed for each subarray or chunk of the mask array in parallel across SciDB instances using the weighted quick union (WQU) with half-path compression algorithm. In the second stage, labels around chunk boundaries from the first stage are stored in a temporary SciDB array that is then replicated across all SciDB instances. Equivalences are resolved by again applying the WQU algorithm to these boundary labels. In the third stage, relabeling is done for each chunk using the resolved equivalences. In the fourth stage, the resolved labels, which so far are "flattened" coordinates of the original binary mask array, are renamed with sequential integers for legibility. The UDO is demonstrated on a 3-D mask of O(1011) elements, with O(108) foreground cells and O(106) connected components. The operator completes in 19 minutes using 84 SciDB instances.

Integration of isoelectric focusing with parallel sodium dodecyl sulfate gel electrophoresis for multidimensional protein separations in a plastic microfluidic [correction of microfludic] network.

PubMed

Li, Yan; Buch, Jesse S; Rosenberger, Frederick; DeVoe, Don L; Lee, Cheng S

2004-02-01

An integrated protein concentration/separation system, combining non-native isoelectric focusing (IEF) with sodium dodecyl sulfate (SDS) gel electrophoresis on a polymer microfluidic chip, is reported. The system provides significant analyte concentration and extremely high resolving power for separated protein mixtures. The ability to introduce and isolate multiple separation media in a plastic microfluidic network is one of two key requirements for achieving multidimensional protein separations. The second requirement lies in the quantitative transfer of focused proteins from the first to second separation dimensions without significant loss in the resolution acquired from the first dimension. Rather than sequentially sampling protein analytes eluted from IEF, focused proteins are electrokinetically transferred into an array of orthogonal microchannels and further resolved by SDS gel electrophoresis in a parallel and high-throughput format. Resolved protein analytes are monitored using noncovalent, environment-sensitive, fluorescent probes such as Sypro Red. In comparison with covalently labeling proteins, the use of Sypro staining during electrophoretic separations not only presents a generic detection approach for the analysis of complex protein mixtures such as cell lysates but also avoids additional introduction of protein microheterogeneity as the result of labeling reaction. A comprehensive 2-D protein separation is completed in less than 10 min with an overall peak capacity of approximately 1700 using a chip with planar dimensions of as small as 2 cm x 3 cm. Significant enhancement in the peak capacity can be realized by simply raising the density of microchannels in the array, thereby increasing the number of IEF fractions further analyzed in the size-based separation dimension.

Identification of Novel Molecular Targets for Endometrial Cancer Using a Drill-Down LC-MS/MS Approach with iTRAQ

PubMed Central

Voisin, Sébastien N.; Krakovska, Olga; Matta, Ajay; DeSouza, Leroi V.; Romaschin, Alexander D.; Colgan, Terence J.; Siu, K. W. Michael

2011-01-01

Background The number of patients with endometrial carcinoma (EmCa) with advanced stage or high histological grade is increasing and prognosis has not improved for over the last decade. There is an urgent need for the discovery of novel molecular targets for diagnosis, prognosis and treatment of EmCa, which will have the potential to improve the clinical strategy and outcome of this disease. Methodology and Results We used a “drill-down” proteomics approach to facilitate the identification of novel molecular targets for diagnosis, prognosis and/or therapeutic intervention for EmCa. Based on peptide ions identified and their retention times in the first LC-MS/MS analysis, an exclusion list was generated for subsequent iterations. A total of 1529 proteins have been identified below the Proteinpilot® 5% error threshold from the seven sets of iTRAQ experiments performed. On average, the second iteration added 78% new peptides to those identified after the first run, while the third iteration added 36% additional peptides. Of the 1529 proteins identified, only 40 satisfied our criteria for significant differential expression in EmCa in comparison to normal proliferative tissues. These proteins included metabolic enzymes (pyruvate kinase M2 and lactate dehydrogenase A); calcium binding proteins (S100A6, calcyphosine and calumenin), and proteins involved in regulating inflammation, proliferation and invasion (annexin A1, interleukin enhancer-binding factor 3, alpha-1-antitrypsin, macrophage capping protein and cathepsin B). Network analyses revealed regulation of these molecular targets by c-myc, Her2/neu and TNF alpha, suggesting intervention with these pathways may be a promising strategy for the development of novel molecular targeted therapies for EmCa. Conclusions Our analyses revealed the significance of drill-down proteomics approach in combination with iTRAQ to overcome some of the limitations of current proteomics strategies. This study led to the identification of a number of novel molecular targets having therapeutic potential for targeted molecular therapies for endometrial carcinoma. PMID:21305022

Orphan spin operators enable the acquisition of multiple 2D and 3D magic angle spinning solid-state NMR spectra

NASA Astrophysics Data System (ADS)

Gopinath, T.; Veglia, Gianluigi

2013-05-01

We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.

Structure of the Complex between a Heparan Sulfate Octasaccharide and Mycobacterial Heparin-Binding Hemagglutinin.

PubMed

Huang, Teng-Yi; Irene, Deli; Zulueta, Medel Manuel L; Tai, Tzu-Jui; Lain, Shih-Han; Cheng, Cheng-Po; Tsai, Ping-Xi; Lin, Shu-Yi; Chen, Zhi-Geng; Ku, Chiao-Chu; Hsiao, Chwan-Deng; Chyan, Chia-Lin; Hung, Shang-Cheng

2017-04-03

Heparin-binding hemagglutinin (HBHA) is a 199 amino acid virulence factor at the envelope of Mycobacterium tuberculosis that contributes to latent tuberculosis. The binding of HBHA to respiratory epithelial cells, which leads to extrapulmonary dissemination of the pathogen, is mediated by cell-surface heparan sulfate (HS). We report the structural characterization of the HBHA/HS complex by NMR spectroscopy. To develop a model for the molecular recognition, the first chemically synthesized uniformly 13 C- and 15 N-labeled HS octasaccharide and a uniformly 13 C- and 15 N-labeled form of HBHA were prepared. Residues 180-195 at the C-terminal region of HBHA show large chemical shift perturbation upon association with the octasaccharide. Molecular dynamics simulations conforming to the multidimensional NMR data revealed key electrostatic and even hydrophobic interactions between the binding partners that may aid in the development of agents targeting the binding event. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Noninvasive diagnosis of intraamniotic infection: proteomic biomarkers in vaginal fluid.

PubMed

Hitti, Jane; Lapidus, Jodi A; Lu, Xinfang; Reddy, Ashok P; Jacob, Thomas; Dasari, Surendra; Eschenbach, David A; Gravett, Michael G; Nagalla, Srinivasa R

2010-07-01

We analyzed the vaginal fluid proteome to identify biomarkers of intraamniotic infection among women in preterm labor. Proteome analysis was performed on vaginal fluid specimens from women with preterm labor, using multidimensional liquid chromatography, tandem mass spectrometry, and label-free quantification. Enzyme immunoassays were used to quantify candidate proteins. Classification accuracy for intraamniotic infection (positive amniotic fluid bacterial culture and/or interleukin-6 >2 ng/mL) was evaluated using receiver-operator characteristic curves obtained by logistic regression. Of 170 subjects, 30 (18%) had intraamniotic infection. Vaginal fluid proteome analysis revealed 338 unique proteins. Label-free quantification identified 15 proteins differentially expressed in intraamniotic infection, including acute-phase reactants, immune modulators, high-abundance amniotic fluid proteins and extracellular matrix-signaling factors; these findings were confirmed by enzyme immunoassay. A multi-analyte algorithm showed accurate classification of intraamniotic infection. Vaginal fluid proteome analyses identified proteins capable of discriminating between patients with and without intraamniotic infection. Copyright (c) 2010 Mosby, Inc. All rights reserved.

Off-Line Multidimensional Liquid Chromatography and Auto Sampling Result in Sample Loss in LC/LC–MS/MS

PubMed Central

2015-01-01

Large-scale proteomics often employs two orthogonal separation methods to fractionate complex peptide mixtures. Fractionation can involve ion exchange separation coupled to reversed-phase separation or, more recently, two reversed-phase separations performed at different pH values. When multidimensional separations are combined with tandem mass spectrometry for protein identification, the strategy is often referred to as multidimensional protein identification technology (MudPIT). MudPIT has been used in either an automated (online) or manual (offline) format. In this study, we evaluated the performance of different MudPIT strategies by both label-free and tandem mass tag (TMT) isobaric tagging. Our findings revealed that online MudPIT provided more peptide/protein identifications and higher sequence coverage than offline platforms. When employing an off-line fractionation method with direct loading of samples onto the column from an eppendorf tube via a high-pressure device, a 5.3% loss in protein identifications is observed. When off-line fractionated samples are loaded via an autosampler, a 44.5% loss in protein identifications is observed compared with direct loading of samples onto a triphasic capillary column. Moreover, peptide recovery was significantly lower after offline fractionation than in online fractionation. Signal-to-noise (S/N) ratio, however, was not significantly altered between experimental groups. It is likely that offline sample collection results in stochastic peptide loss due to noncovalent adsorption to solid surfaces. Therefore, the use of the offline approaches should be considered carefully when processing minute quantities of valuable samples. PMID:25040086

Carbonylation of Mitochondrial Aconitase with 4-Hydroxy-2-(E)-nonenal: Localization and Relative Reactivity of Addition Sites

PubMed Central

Liu, Qingyuan; Simpson, David C.; Gronert, Scott

2013-01-01

Mass spectrometry was used to investigate the effects of exposing mitochondrial aconitase (ACO2) to the membrane lipid peroxidation product, 4-hydroxy-2-(E)-nonenal (HNE). ACO2 was selected for this study because (1) it is known to be inactivated by HNE, (2) elevated concentrations of HNE-adducted ACO2 have been associated with disease states, (3) extensive structural information is available, and (4) the iron-sulfur cluster in ACO2 offers a critical target for HNE adduction. The aim of this study was to relate the inactivation of ACO2 by HNE to structural features. Initially, western blotting and an enzyme activity assay were used to assess aggregate effects and then gel electrophoresis, in-gel digestion, and tandem mass spectrometry were used to identify HNE addition sites. HNE addition reaction rates were determined for the most significant sites using the iTRAQ approach. The most reactive sites were Cys358, Cys421, and Cys424, the three iron-sulfur cluster-coordinating cysteines, Cys99, the closest non-ligated cysteine to the cluster, and Cys565, which is located in the cleft leading to the active site. Interestingly, both enzyme activity assay and iTRAQ relative abundance plots appeared to be trending toward horizontal asymptotes, rather than completion. PMID:23518448

Differential proteomics profiling of the ova between healthy and Rice stripe virus-infected female insects of Laodelphax striatellus.

PubMed

Liu, Beibei; Qin, Faliang; Liu, Wenwen; Wang, Xifeng

2016-06-09

Rice stripe virus-infected females of the small brown planthopper (SBPH, Laodelphax striatellus) usually lay fewer eggs with a longer hatch period, low hatchability, malformation and retarded or defective development compared with healthy females. To explore the molecular mechanism of those phenomena, we analyzed the differential proteomics profiling of the ova between viruliferous and healthy female insects using an isobaric tag for relative and absolute quantitation (iTRAQ) approach. We obtained 147 differentially accumulated proteins: 98 (66.7%) proteins increased, but 49 (33.3%) decreased in the ova of the viruliferous females. RT-qPCR was used to verify the 12 differential expressed proteins from iTRAQ, finding that trends in the transcriptional change for the 12 genes were consistent with those at the proteomic level. Differentially expressed proteins that were associated with meiosis (serine/threonine-protein phosphatase 2B and cyclin B3) and mitosis (cyclin B3 and dynein heavy chain) in viruliferous ova may contribute to low hatchability and defective or retarded development. Alterations in the abundance of proteins involved in the respiratory chain and nutrition metabolism may affect embryonic development. Our study begins to explain macroscopical developmental phenomena and explore the mechanisms by which Rice stripe virus impacts the development of SBPH.

Differential proteomics profiling of the ova between healthy and Rice stripe virus-infected female insects of Laodelphax striatellus

PubMed Central

Liu, Beibei; Qin, Faliang; Liu, Wenwen; Wang, Xifeng

2016-01-01

Rice stripe virus-infected females of the small brown planthopper (SBPH, Laodelphax striatellus) usually lay fewer eggs with a longer hatch period, low hatchability, malformation and retarded or defective development compared with healthy females. To explore the molecular mechanism of those phenomena, we analyzed the differential proteomics profiling of the ova between viruliferous and healthy female insects using an isobaric tag for relative and absolute quantitation (iTRAQ) approach. We obtained 147 differentially accumulated proteins: 98 (66.7%) proteins increased, but 49 (33.3%) decreased in the ova of the viruliferous females. RT-qPCR was used to verify the 12 differential expressed proteins from iTRAQ, finding that trends in the transcriptional change for the 12 genes were consistent with those at the proteomic level. Differentially expressed proteins that were associated with meiosis (serine/threonine-protein phosphatase 2B and cyclin B3) and mitosis (cyclin B3 and dynein heavy chain) in viruliferous ova may contribute to low hatchability and defective or retarded development. Alterations in the abundance of proteins involved in the respiratory chain and nutrition metabolism may affect embryonic development. Our study begins to explain macroscopical developmental phenomena and explore the mechanisms by which Rice stripe virus impacts the development of SBPH. PMID:27277140

The response of growth and patulin production of postharvest pathogen Penicillium expansum to exogenous potassium phosphite treatment.

PubMed

Lai, Tongfei; Wang, Ying; Fan, Yaya; Zhou, Yingying; Bao, Ying; Zhou, Ting

2017-03-06

In this study, the effects of exogenous potassium phosphite (Phi) on growth and patulin production of postharvest pathogen Penicillium expansum were assessed. The results indicated that P. expansum under 5mmol/L Phi stress presented obvious development retardation, yield reduction of patulin and lower infectivity to apple fruit. Meanwhile, expression analysis of 15 genes related to patulin biosynthesis suggested that Phi mainly affected the early steps of patulin synthetic route at transcriptional level. Furthermore, a global view of proteome and transcriptome alteration of P. expansum spores during 6h of Phi stress was evaluated by iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq (RNA sequencing) approaches. A total of 582 differentially expressed proteins (DEPs) and 177 differentially expressed genes (DEGs) were acquired, most of which participated in carbohydrate metabolism, amino acid metabolism, lipid metabolism, genetic information processing and biosynthesis of secondary metabolites. Finally, 39 overlapped candidates were screened out through correlational analysis between iTRAQ and RNA-seq datasets. These findings will afford more precise and directional clues to explore the inhibitory mechanism of Phi on growth and patulin biosynthesis of P. expansum, and be beneficial to develop effective controlling approaches based on Phi. Copyright © 2016 Elsevier B.V. All rights reserved.

Inhalation of Roman chamomile essential oil attenuates depressive-like behaviors in Wistar Kyoto rats.

PubMed

Kong, Yingying; Wang, Ting; Wang, Rong; Ma, Yichuan; Song, Shanshan; Liu, Juan; Hu, Weiwei; Li, Shengtian

2017-06-01

The idea of aromatherapy, using essential oils, has been considered as an alternative antidepressant treatment. In the present study, we investigated the effect of Roman chamomile essential oil inhalation for two weeks on depressive-like behaviors in Wistar-Kyoto (WKY) rats. We found that inhalation of either Roman chamomile or one of its main components α-pinene, attenuated depressive-like behavior in WKY rats in the forced swim test. Using isobaric tags for relative and absolute quantitation analysis (iTRAQ), we found that inhalation of α-pinene increased expression of proteins that are involved in oxidative phosphorylation, such as cytochrome c oxidase subunit 6C-2, cytochrome c oxidase subunit 7A2, ATPase inhibitor in the hippocampus, and cytochrome c oxidase subunit 6C-2, ATP synthase subunit e, Acyl carrier protein, and Cytochrome b-c1 complex subunit 6 in the PFC (prefrontal cortex). In addition, using the quantitative real-time polymerase chain reaction technique, we confirmed an increase of parvalbumin mRNA expression in the hippocampus, which was shown to be upregulated by 2.8-fold in iTRAQ analysis, in α-pinene treated WKY rats. These findings collectively suggest the involvement of mitochondrial functions and parvalbumin-related signaling in the antidepressant effect of α-pinene inhalation.

Integrative proteomics to understand the transmission mechanism of Barley yellow dwarf virus-GPV by its insect vector Rhopalosiphum padi

PubMed Central

Wang, Hui; Wu, Keke; Liu, Yan; Wu, Yunfeng; Wang, Xifeng

2015-01-01

Barley yellow dwarf virus-GPV (BYDV-GPV) is transmitted by Rhopalosiphum padi and Schizaphis graminum in a persistent nonpropagative manner. To improve our understanding of its transmission mechanism by aphid vectors, we used two approaches, isobaric tags for relative and absolute quantitation (iTRAQ) and yeast two-hybrid (YTH) system, to identify proteins in R. padi that may interact with or direct the spread of BYDV-GPV along the circulative transmission pathway. Thirty-three differential aphid proteins in viruliferous and nonviruliferous insects were identified using iTRAQ coupled to 2DLC-MS/MS. With the yeast two-hybrid system, 25 prey proteins were identified as interacting with the readthrough protein (RTP) and eight with the coat protein (CP), which are encoded by BYDV-GPV. Among the aphid proteins identified, most were involved in primary energy metabolism, synaptic vesicle cycle, the proteasome pathway and the cell cytoskeleton organization pathway. In a systematic comparison of the two methods, we found that the information generated by the two methods was complementary. Taken together, our findings provide useful information on the interactions between BYDV-GPV and its vector R. padi to further our understanding of the mechanisms regulating circulative transmission in aphid vectors. PMID:26161807

Proteomic comparison by iTRAQ combined with mass spectrometry of egg white proteins in laying hens (Gallus gallus) fed with soybean meal and cottonseed meal

PubMed Central

He, Tao; Zhang, Haijun; Wang, Jing; Wu, Shugeng; Yue, Hongyuan; Qi, Guanghai

2017-01-01

Cottonseed meal (CSM) is commonly used in hens’ diets to replace soybean meal (SBM). However, the molecular consequences of this substitution remains unclear. To investigate the impact of this substitution at the molecular level, iTRAQ combined with biochemical analysis was performed in Hy-Line W-36 hens supplemented with a mixed diet of CSM and SBM. Egg weight, albumen height, and Haugh unit were significantly reduced in the CSM100 group (100% crude protein of SBM replaced by CSM) compared with the SBM group (P<0.05). A total of 15 proteins, accounting for 75% of egg white proteins with various biological functions of egg whites, were found to be reduced. This finding may relate to the decrease of albumen quality in the CSM100 group. Oviduct magnum morphology and hormone analysis indicated that a reduced level of plasma progesterone caused reduced growth of the tubular gland and epithelial cells in the magnum, further decreasing egg white protein synthesis in the magnum. These findings help demonstrate the molecular mechanisms of a CSM diet that cause adverse effects on albumen quality, while also showing that SBM should not be totally replaced with CSM in a hen diet. PMID:28813468

Comparative proteomic exploration of whey proteins in human and bovine colostrum and mature milk using iTRAQ-coupled LC-MS/MS.

PubMed

Yang, Mei; Cao, Xueyan; Wu, Rina; Liu, Biao; Ye, Wenhui; Yue, Xiqing; Wu, Junrui

2017-09-01

Whey, an essential source of dietary nutrients, is widely used in dairy foods for infants. A total of 584 whey proteins in human and bovine colostrum and mature milk were identified and quantified by the isobaric tag for relative and absolute quantification (iTRAQ) proteomic method. The 424 differentially expressed whey proteins were identified and analyzed according to gene ontology (GO) annotation, Kyoto encyclopedia of genes and genomes (KEGG) pathway, and multivariate statistical analysis. Biological processes principally involved biological regulation and response to stimulus. Major cellular components were extracellular region part and extracellular space. The most prevalent molecular function was protein binding. Twenty immune-related proteins and 13 proteins related to enzyme regulatory activity were differentially expressed in human and bovine milk. Differentially expressed whey proteins participated in many KEGG pathways, including major complement and coagulation cascades and in phagosomes. Whey proteins show obvious differences in expression in human and bovine colostrum and mature milk, with consequences for biological function. The results here increase our understanding of different whey proteomes, which could provide useful information for the development and manufacture of dairy products and nutrient food for infants. The advanced iTRAQ proteomic approach was used to analyze differentially expressed whey proteins in human and bovine colostrum and mature milk.

Role of the Tomato Non-Ripening Mutation in Regulating Fruit Quality Elucidated Using iTRAQ Protein Profile Analysis

PubMed Central

Yuan, Xin-Yu; Wang, Rui-Heng; Zhao, Xiao-Dan; Luo, Yun-Bo; Fu, Da-Qi

2016-01-01

Natural mutants of the Non-ripening (Nor) gene repress the normal ripening of tomato fruit. The molecular mechanism of fruit ripening regulation by the Nor gene is unclear. To elucidate how the Nor gene can affect ripening and fruit quality at the protein level, we used the fruits of Nor mutants and wild-type Ailsa Craig (AC) to perform iTRAQ (isobaric tags for relative and absolute quantitation) analysis. The Nor mutation altered tomato fruit ripening and affected quality in various respects, including ethylene biosynthesis by down-regulating the abundance of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), pigment biosynthesis by repressing phytoene synthase 1 (PSY1), ζ-carotene isomerase (Z-ISO), chalcone synthase 1 (CHS1) and other proteins, enhancing fruit firmness by increasing the abundance of cellulose synthase protein, while reducing those of polygalacturonase 2 (PG2) and pectate lyase (PL), altering biosynthesis of nutrients such as carbohydrates, amino acids, and anthocyanins. Conversely, Nor mutation also enhanced the fruit’s resistance to some pathogens by up-regulating the expression of several genes associated with stress and defense. Therefore, the Nor gene is involved in the regulation of fruit ripening and quality. It is useful in the future as a means to improve fruit quality in tomato. PMID:27732677

Investigating fast enzyme-DNA kinetics using multidimensional fluorescence imaging and microfluidics

NASA Astrophysics Data System (ADS)

Robinson, Tom; Manning, Hugh B.; Dunsby, Christopher; Neil, Mark A. A.; Baldwin, Geoff S.; de Mello, Andrew J.; French, Paul M. W.

2010-02-01

We have developed a rapid microfluidic mixing device to image fast kinetics. To verify the performance of the device it was simulated using computational fluid dynamics (CFD) and the results were directly compared to experimental fluorescence lifetime imaging (FLIM) measurements. The theoretical and measured mixing times of the device were found to be in agreement over a range of flow rates. This mixing device is being developed with the aim of analysing fast enzyme kinetics in the sub-millisecond time domain, which cannot be achieved with conventional macro-stopped flow devices. Here we have studied the binding of a DNA repair enzyme, uracil DNA glycosylase (UDG), to a fluorescently labelled DNA substrate. Bulk phase fluorescence measurements have been used to measure changes on binding: it was found that the fluorescence lifetime increased along with an increase in the polarisation anisotropy and rotational correlation time. Analysis of the same reaction in the microfluidic mixer by CFD enabled us to predict the mixing time of the device to be 46 μs, more than 20 times faster than current stopped-flow techniques. We also demonstrate that it is possible to image UDG-DNA interactions within the micromixer using the signal changes observed from the multidimensional spectrofluorometer.

The development of a multi-dimensional gambling accessibility scale.

PubMed

Hing, Nerilee; Haw, John

2009-12-01

The aim of the current study was to develop a scale of gambling accessibility that would have theoretical significance to exposure theory and also serve to highlight the accessibility risk factors for problem gambling. Scale items were generated from the Productivity Commission's (Australia's Gambling Industries: Report No. 10. AusInfo, Canberra, 1999) recommendations and tested on a group with high exposure to the gambling environment. In total, 533 gaming venue employees (aged 18-70 years; 67% women) completed a questionnaire that included six 13-item scales measuring accessibility across a range of gambling forms (gaming machines, keno, casino table games, lotteries, horse and dog racing, sports betting). Also included in the questionnaire was the Problem Gambling Severity Index (PGSI) along with measures of gambling frequency and expenditure. Principal components analysis indicated that a common three factor structure existed across all forms of gambling and these were labelled social accessibility, physical accessibility and cognitive accessibility. However, convergent validity was not demonstrated with inconsistent correlations between each subscale and measures of gambling behaviour. These results are discussed in light of exposure theory and the further development of a multi-dimensional measure of gambling accessibility.

Investigation of Pokemon-regulated proteins in hepatocellular carcinoma using mass spectrometry-based multiplex quantitative proteomics.

PubMed

Bi, Xin; Jin, Yibao; Gao, Xiang; Liu, Feng; Gao, Dan; Jiang, Yuyang; Liu, Hongxia

2013-01-01

Pokemon is a transcription regulator involved in embryonic development, cellular differentiation and oncogenesis. It is aberrantly overexpressed in multiple human cancers including Hepatocellular carcinoma (HCC) and is considered as a promising biomarker for HCC. In this work, the isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy was used to investigate the proteomic profile associated with Pokemon in human HCC cell line QGY7703 and human hepatocyte line HL7702. Samples were labeled with four-plex iTRAQ reagents followed by two-dimensional liquid chromatography coupled with tandem mass spectrometry analysis. A total of 24 differentially expressed proteins were selected as significant. Nine proteins were potentially up-regulated by Pokemon while 15 proteins were potentially down-regulated and many proteins were previously identified as potential biomarkers for HCC. Gene ontology (GO) term enrichment revealed that the listed proteins were mainly involved in DNA metabolism and biosynthesis process. The changes of glucose-6-phosphate 1-dehydrogenase (G6PD, up-regulated) and ribonucleoside-diphosphate reductase large sub-unit (RIM1, down-regulated) were validated by Western blotting analysis and denoted as Pokemon's function of oncogenesis. We also found that Pokemon potentially repressed the expression of highly clustered proteins (MCM3, MCM5, MCM6, MCM7) which played key roles in promoting DNA replication. Altogether, our results may help better understand the role of Pokemon in HCC and promote the clinical applications.

Type conversion of secretomes in a 3D TAM2 and HCC cell co-culture system and functional importance of CXCL2 in HCC

PubMed Central

Lu, Yu; Li, Shan; Ma, Liping; Li, Yan; Zhang, Xiaolian; Peng, Qiliu; Mo, Cuiju; Huang, Li; Qin, Xue; Liu, Yinkun

2016-01-01

Macrophages play important roles in the tumor microenvironment, driving cancer progression and metastasis, particularly in hepatocellular carcinoma (HCC). However, few studies have assessed the exact secretome composition in HCC. In the present study, the impact of different phenotype of macrophages on HCC cells was investigated. Alternatively activated macrophages (M2) were found to significantly increase the proliferation, migration, and invasion abilities of SMMC7721 cells (all P < 0.05). M2 were then co-cultured with SMMC7721 cells to reconstruct the tumor microenvironment. Conditioned medium from 3D single cultures of M2, SMMC7721 cells, and their co-culture system were analyzed using quantitative proteomics via iTRAQ labeling combined with mass spectrometric analysis. Secretome analysis revealed a total of 159 differential secreted proteins in the co-culture system compared to the single culture systems, with 63 being up-regulated (>1.3-fold) and 96 down-regulated (<0.7-fold). CXCL2 was confirmed to have higher expression in the co-culture system and HCC tissues, and was selected for further investigation. Functional effects data suggested that recombinant human CXCL2 significantly enhanced the migration, invasion ability of SMMC7721 cells, and weakened adhesion ability. While CXCL2 neutralization and CXCR2 blockage significantly inhibited the effects of CXCL2 on SMMC7721 cells, indicating that CXCL2 may play pivotal role in HCC metastasis. PMID:27117207

Proteomic Comparison and MRM-Based Comparative Analysis of Metabolites Reveal Metabolic Shift in Human Prostate Cancer Cell Lines.

PubMed

Shu, Qingbo; Cai, Tanxi; Chen, Xiulan; Zhu, Helen He; Xue, Peng; Zhu, Nali; Xie, Zhensheng; Wei, Shasha; Zhang, Qing; Niu, Lili; Gao, Wei-Qiang; Yang, Fuquan

2015-08-07

One of the major challenges in prostate cancer therapy remains the development of effective treatments for castration-resistant prostate cancer (CRPC), as the underlying mechanisms for its progression remain elusive. Previous studies showed that androgen receptor (AR) is crucially involved in regulation of metabolism in prostate cancer (PCa) cells throughout the transition from early stage, androgen-sensitive PCa to androgen-independent CRPC. AR achieves such metabolic rewiring directively either via its transcriptional activity or via interactions with AMP-activated protein kinase (AMPK). However, due to the heterogeneous expression and activity status of AR in PCa cells, it remains a challenge to investigate the links between AR status and metabolic alterations. To this end, we compared the proteomes of three pairs of androgen-sensitive (AS) and androgen-independent (AI) PCa cell lines, namely, PC3-AR(+)/PC3, 22Rv1/Du145, and LNCaP/C42B, using an iTRAQ labeling approach. Our results revealed that most of the differentially expressed proteins between each pair function in metabolism, indicating a metabolic shift between AS and AI cells, as further validated by multiple reaction monitoring (MRM)-based quantification of nucleotides and relative comparison of fatty acids between these cell lines. Furthermore, increased adenylate kinase isoenzyme 1 (AK1) in AS relative to AI cells may result in activation of AMPK, representing a major regulatory factor involved in the observed metabolic shift in PCa cells.

Proteomic and phosphoproteomic analysis of renal cortex in a salt-load rat model of advanced kidney damage

PubMed Central

Jiang, Shaoling; He, Hanchang; Tan, Lishan; Wang, Liangliang; Su, Zhengxiu; Liu, Yufeng; Zhu, Hongguo; Zhang, Menghuan; Hou, Fan Fan; Li, Aiqing

2016-01-01

Salt plays an essential role in the progression of chronic kidney disease and hypertension. However, the mechanisms underlying pathogenesis of salt-induced kidney damage remain largely unknown. Here, Sprague-Dawley rats, that underwent 5/6 nephrectomy (5/6Nx, a model of advanced kidney damage) or sham operation, were treated for 2 weeks with a normal or high-salt diet. We employed aTiO2 enrichment, iTRAQ labeling and liquid-chromatography tandem mass spectrometry strategy for proteomic and phosphoproteomic profiling of the renal cortex. We found 318 proteins differentially expressed in 5/6Nx group relative to sham group, and 310 proteins significantly changed in response to salt load in 5/6Nx animals. Totally, 1810 unique phosphopeptides corresponding to 550 phosphoproteins were identified. We identified 113 upregulated and 84 downregulated phosphopeptides in 5/6Nx animals relative to sham animals. Salt load induced 78 upregulated and 91 downregulated phosphopeptides in 5/6Nx rats. The differentially expressed phospholproteins are important transporters, structural molecules, and receptors. Protein-protein interaction analysis revealed that the differentially phosphorylated proteins in 5/6Nx group, Polr2a, Srrm1, Gsta2 and Pxn were the most linked. Salt-induced differential phosphoproteins, Myh6, Lmna and Des were the most linked. Altered phosphorylation levels of lamin A and phospholamban were validated. This study will provide new insight into pathogenetic mechanisms of chronic kidney disease and salt sensitivity. PMID:27775022

Type conversion of secretomes in a 3D TAM2 and HCC cell co-culture system and functional importance of CXCL2 in HCC.

PubMed

Lu, Yu; Li, Shan; Ma, Liping; Li, Yan; Zhang, Xiaolian; Peng, Qiliu; Mo, Cuiju; Huang, Li; Qin, Xue; Liu, Yinkun

2016-04-27

Macrophages play important roles in the tumor microenvironment, driving cancer progression and metastasis, particularly in hepatocellular carcinoma (HCC). However, few studies have assessed the exact secretome composition in HCC. In the present study, the impact of different phenotype of macrophages on HCC cells was investigated. Alternatively activated macrophages (M2) were found to significantly increase the proliferation, migration, and invasion abilities of SMMC7721 cells (all P < 0.05). M2 were then co-cultured with SMMC7721 cells to reconstruct the tumor microenvironment. Conditioned medium from 3D single cultures of M2, SMMC7721 cells, and their co-culture system were analyzed using quantitative proteomics via iTRAQ labeling combined with mass spectrometric analysis. Secretome analysis revealed a total of 159 differential secreted proteins in the co-culture system compared to the single culture systems, with 63 being up-regulated (>1.3-fold) and 96 down-regulated (<0.7-fold). CXCL2 was confirmed to have higher expression in the co-culture system and HCC tissues, and was selected for further investigation. Functional effects data suggested that recombinant human CXCL2 significantly enhanced the migration, invasion ability of SMMC7721 cells, and weakened adhesion ability. While CXCL2 neutralization and CXCR2 blockage significantly inhibited the effects of CXCL2 on SMMC7721 cells, indicating that CXCL2 may play pivotal role in HCC metastasis.

Criteria used to judge obese persons in the workplace.

PubMed

Popovich, P M; Everton, W J; Campbell, K L; Godinho, R M; Kramer, K M; Mangan, M R

1997-12-01

Researchers have speculated that employers are less likely to hire obese persons for more publicly visible jobs, although this hypothesis remains untested. In the present study, 54 undergraduate students rated 40 jobs on several items, including the likelihood they would hire an obese person for each job. Multidimensional scaling showed a one-dimensional solution, labeled as physical activity, with participants less likely to hire obese persons for more active jobs. For hiring likelihood ratings for jobs at either end of the dimension appear to be most similar for men and individuals with more positive attitudes toward obese persons versus women and individuals with more negative attitudes toward obese persons. Implications for both theory and practice are discussed.

Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bingol, Kerem; Brüschweiler, Rafael

Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexitymore » of these tasks.« less

Integrated Multi-process Microfluidic Systems for Automating Analysis

PubMed Central

Yang, Weichun; Woolley, Adam T.

2010-01-01

Microfluidic technologies have been applied extensively in rapid sample analysis. Some current challenges for standard microfluidic systems are relatively high detection limits, and reduced resolving power and peak capacity compared to conventional approaches. The integration of multiple functions and components onto a single platform can overcome these separation and detection limitations of microfluidics. Multiplexed systems can greatly increase peak capacity in multidimensional separations and can increase sample throughput by analyzing many samples simultaneously. On-chip sample preparation, including labeling, preconcentration, cleanup and amplification, can all serve to speed up and automate processes in integrated microfluidic systems. This paper summarizes advances in integrated multi-process microfluidic systems for automated analysis, their benefits and areas for needed improvement. PMID:20514343

Evaluation of mobility impacts of advanced information systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peeta, S.; Poonuru, K.; Sinha, K.

2000-06-01

Advanced technologies under the aegis of advanced traveler information systems and advanced traffic management systems are being employed to address the debilitating traffic congestion problem. Broadly identified under the label intelligent transportation systems (ITS), they focus on enhancing the efficiency of the existing roadway utilization. Though ITS has transitioned from the conceptual framework stage to the operational test phase that analyzes real-world feasibility, studies that systematically quantify the multidimensional real-world impacts of these technologies in terms of mobility, safety, and air quality, are lacking. This paper proposes a simulation-based framework to address the mobility impacts of these technologies through themore » provision of information to travelers. The information provision technologies are labeled as advanced information systems (AIS), and include pretrip information, en route information, variable message signs, and combinations thereof. The primary focus of the paper is to evaluate alternative AIS technologies using the heavily traveled Borman Expressway corridor in northwestern Indiana as a case study. Simulation results provide insights into the mobility impacts of AIS technologies, and contrast the effectiveness of alternative information provision sources and strategies.« less

Identification of Proteins Involved in Carbohydrate Metabolism and Energy Metabolism Pathways and Their Regulation of Cytoplasmic Male Sterility in Wheat.

PubMed

Geng, Xingxia; Ye, Jiali; Yang, Xuetong; Li, Sha; Zhang, Lingli; Song, Xiyue

2018-01-23

Cytoplasmic male sterility (CMS) where no functional pollen is produced has important roles in wheat breeding. The anther is a unique organ for male gametogenesis and its abnormal development can cause male sterility. However, the mechanisms and regulatory networks related to plant male sterility are poorly understood. In this study, we conducted comparative analyses using isobaric tags for relative and absolute quantification (iTRAQ) of the pollen proteins in a CMS line and its wheat maintainer. Differentially abundant proteins (DAPs) were analyzed based on Gene Ontology classifications, metabolic pathways and transcriptional regulation networks using Blast2GO. We identified 5570 proteins based on 23,277 peptides, which matched with 73,688 spectra, including proteins in key pathways such as glyceraldehyde-3-phosphate dehydrogenase, pyruvate kinase and 6-phosphofructokinase 1 in the glycolysis pathway, isocitrate dehydrogenase and citrate synthase in the tricarboxylic acid cycle and nicotinamide adenine dinucleotide (NADH)-dehydrogenase and adenosine-triphosphate (ATP) synthases in the oxidative phosphorylation pathway. These proteins may comprise a network that regulates male sterility in wheat. Quantitative real time polymerase chain reaction (qRT-PCR) analysis, ATP assays and total sugar assays validated the iTRAQ results. These DAPs could be associated with abnormal pollen grain formation and male sterility. Our findings provide insights into the molecular mechanism related to male sterility in wheat.

Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes.

PubMed

Adav, Sunil S; Li, An A; Manavalan, Arulmani; Punt, Peter; Sze, Siu Kwan

2010-08-06

The natural lifestyle of Aspergillus niger made them more effective secretors of hydrolytic proteins and becomes critical when this species were exploited as hosts for the commercial secretion of heterologous proteins. The protein secretion profile of A. niger and its mutant at different pH was explored using iTRAQ-based quantitative proteomics approach coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). This study characterized 102 highly confident unique proteins in the secretome with zero false discovery rate based on decoy strategy. The iTRAQ technique identified and relatively quantified many hydrolyzing enzymes such as cellulases, hemicellulases, glycoside hydrolases, proteases, peroxidases, and protein translocating transporter proteins during fermentation. The enzymes have potential application in lignocellulosic biomass hydrolysis for biofuel production, for example, the cellulolytic and hemicellulolytic enzymes glucan 1,4-alpha-glucosidase, alpha-glucosidase C, endoglucanase, alpha l-arabinofuranosidase, beta-mannosidase, glycosyl hydrolase; proteases such as tripeptidyl-peptidase, aspergillopepsin, and other enzymes including cytochrome c oxidase, cytochrome c oxidase, glucose oxidase were highly expressed in A. niger and its mutant secretion. In addition, specific enzyme production can be stimulated by controlling pH of the culture medium. Our results showed comprehensive unique secretory protein profile of A. niger, its regulation at different pH, and the potential application of iTRAQ-based quantitative proteomics for the microbial secretome analysis.

A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef.

PubMed

Kamies, Rizqah; Farrant, Jill M; Tadele, Zerihun; Cannarozzi, Gina; Rafudeen, Mohammed Suhail

2017-11-15

The orphan crop, Eragrostis tef , was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef downregulated proteins.

Profound Impact of Hfq on Nutrient Acquisition, Metabolism and Motility in the Plant Pathogen Agrobacterium tumefaciens

PubMed Central

Möller, Philip; Overlöper, Aaron; Förstner, Konrad U.; Wen, Tuan-Nan; Sharma, Cynthia M.; Lai, Erh-Min; Narberhaus, Franz

2014-01-01

As matchmaker between mRNA and sRNA interactions, the RNA chaperone Hfq plays a key role in riboregulation of many bacteria. Often, the global influence of Hfq on the transcriptome is reflected by substantially altered proteomes and pleiotropic phenotypes in hfq mutants. Using quantitative proteomics and co-immunoprecipitation combined with RNA-sequencing (RIP-seq) of Hfq-bound RNAs, we demonstrate the pervasive role of Hfq in nutrient acquisition, metabolism and motility of the plant pathogen Agrobacterium tumefaciens. 136 of 2544 proteins identified by iTRAQ (isobaric tags for relative and absolute quantitation) were affected in the absence of Hfq. Most of them were associated with ABC transporters, general metabolism and motility. RIP-seq of chromosomally encoded Hfq3xFlag revealed 1697 mRNAs and 209 non-coding RNAs (ncRNAs) associated with Hfq. 56 ncRNAs were previously undescribed. Interestingly, 55% of the Hfq-bound ncRNAs were encoded antisense (as) to a protein-coding sequence suggesting that A. tumefaciens Hfq plays an important role in asRNA-target interactions. The exclusive enrichment of 296 mRNAs and 31 ncRNAs under virulence conditions further indicates a role for post-transcriptional regulation in A. tumefaciens-mediated plant infection. On the basis of the iTRAQ and RIP-seq data, we assembled a comprehensive model of the Hfq core regulon in A. tumefaciens. PMID:25330313

Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens.

PubMed

Möller, Philip; Overlöper, Aaron; Förstner, Konrad U; Wen, Tuan-Nan; Sharma, Cynthia M; Lai, Erh-Min; Narberhaus, Franz

2014-01-01

As matchmaker between mRNA and sRNA interactions, the RNA chaperone Hfq plays a key role in riboregulation of many bacteria. Often, the global influence of Hfq on the transcriptome is reflected by substantially altered proteomes and pleiotropic phenotypes in hfq mutants. Using quantitative proteomics and co-immunoprecipitation combined with RNA-sequencing (RIP-seq) of Hfq-bound RNAs, we demonstrate the pervasive role of Hfq in nutrient acquisition, metabolism and motility of the plant pathogen Agrobacterium tumefaciens. 136 of 2544 proteins identified by iTRAQ (isobaric tags for relative and absolute quantitation) were affected in the absence of Hfq. Most of them were associated with ABC transporters, general metabolism and motility. RIP-seq of chromosomally encoded Hfq3xFlag revealed 1697 mRNAs and 209 non-coding RNAs (ncRNAs) associated with Hfq. 56 ncRNAs were previously undescribed. Interestingly, 55% of the Hfq-bound ncRNAs were encoded antisense (as) to a protein-coding sequence suggesting that A. tumefaciens Hfq plays an important role in asRNA-target interactions. The exclusive enrichment of 296 mRNAs and 31 ncRNAs under virulence conditions further indicates a role for post-transcriptional regulation in A. tumefaciens-mediated plant infection. On the basis of the iTRAQ and RIP-seq data, we assembled a comprehensive model of the Hfq core regulon in A. tumefaciens.

Quantitative Proteomic Analysis of Mouse Embryonic Fibroblasts and Induced Pluripotent Stem Cells Using 16O /18O labeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Xin; Tian, Changhai; Liu, Miao

2012-04-06

Induced pluripotent stem cells (iPSC) hold great promise for regenerative medicine as well as for investigations into the pathogenesis and treatment of various diseases. Understanding of key intracellular signaling pathways and protein targets that control development of iPSC from somatic cells is essential for designing new approaches to improve reprogramming efficiency. Here we report the development and application of an integrated quantitative proteomics platform for investigating differences in protein expressions between mouse embryonic fibroblasts (MEF) and MEF-derived iPSC. This platform consists of 16O/18O labeling, multidimensional peptide separation coupled with tandem mass spectrometry, and data analysis with UNiquant software. Using thismore » platform a total of 2,481 proteins were identified and quantified from the 16O/18O-labeled MEF-iPSC proteome mixtures with a false discovery rate of 0.01. Among them, 218 proteins were significantly upregulated, while 247 proteins were significantly downregulated in iPSC compared to MEF. Many nuclear proteins, including Hdac1, Dnmt1, Pcna, Ccnd1, Smarcc1, and subunits in DNA replication and RNA polymerase II complex were found to be enhanced in iPSC. Protein network analysis revealed that Pcna functions as a hub orchestrating complicated mechanisms including DNA replication, epigenetic inheritance (Dnmt1) and chromatin remodeling (Smarcc1) to reprogram MEF and maintain stemness of iPSC.« less

Multidimensional Patterns of Sexual Risk Behavior and Psychiatric Disorders in Men with Substance Use Disorders.

PubMed

Villalobos-Gallegos, Luis; Medina-Mora, María Elena; Benjet, Corina; Ruiz-Velasco, Silvia; Magis-Rodriguez, Carlos; Marín-Navarrete, Rodrigo

2018-05-29

Previous evidence links substance use disorders (SUD) to STI/HIV risk and suggests that comorbid psychiatric disorders increase the probability to engage in sexual risk behaviors. This study had two aims: (1) to identify subgroups based on sexual risk behavior using a person-centered approach in a sample of substance users and (2) to measure the association of psychiatric and SUD with subgroup membership. We assessed 402 male adults with SUD, reporting sexual intercourse in the previous 12 months using the HIV-Risk Behavior Scale and the Mini International Neuropsychiatric Interview. Latent class analysis was performed to determine multidimensional patterns of sexual risk behaviors and multinomial logistic regression was utilized to associate classes with disorders. The three-class model showed the best fit, and the classes were labeled: Relationship-Based (31.34% of the sample), Condom-Based (39.55%), and Multiple Risks (29.10%). Controlling for age and marital status, major depressive disorders, antisocial personality disorder, and any psychiatric disorder were associated with the Multiple Risks class. Results stress the importance of developing a personalized assessment and counseling for sexual risk behaviors in individuals with SUD, particularly when they endorse criteria for comorbid psychiatric disorders. Future studies should focus on evaluating differential response to preventive interventions.

Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry.

PubMed

Keshishian, Hasmik; Burgess, Michael W; Specht, Harrison; Wallace, Luke; Clauser, Karl R; Gillette, Michael A; Carr, Steven A

2017-08-01

Proteomic characterization of blood plasma is of central importance to clinical proteomics and particularly to biomarker discovery studies. The vast dynamic range and high complexity of the plasma proteome have, however, proven to be serious challenges and have often led to unacceptable tradeoffs between depth of coverage and sample throughput. We present an optimized sample-processing pipeline for analysis of the human plasma proteome that provides greatly increased depth of detection, improved quantitative precision and much higher sample analysis throughput as compared with prior methods. The process includes abundant protein depletion, isobaric labeling at the peptide level for multiplexed relative quantification and ultra-high-performance liquid chromatography coupled to accurate-mass, high-resolution tandem mass spectrometry analysis of peptides fractionated off-line by basic pH reversed-phase (bRP) chromatography. The overall reproducibility of the process, including immunoaffinity depletion, is high, with a process replicate coefficient of variation (CV) of <12%. Using isobaric tags for relative and absolute quantitation (iTRAQ) 4-plex, >4,500 proteins are detected and quantified per patient sample on average, with two or more peptides per protein and starting from as little as 200 μl of plasma. The approach can be multiplexed up to 10-plex using tandem mass tags (TMT) reagents, further increasing throughput, albeit with some decrease in the number of proteins quantified. In addition, we provide a rapid protocol for analysis of nonfractionated depleted plasma samples analyzed in 10-plex. This provides ∼600 quantified proteins for each of the ten samples in ∼5 h of instrument time.

Androgen-induced alterations in endometrial proteins crucial in recurrent miscarriages.

PubMed

Rahman, Tanzil Ur; Ullah, Kamran; Guo, Meng-Xi; Pan, Hai-Tao; Liu, Juan; Ren, Jun; Jin, Lu-Yang; Zhou, Yu-Zhong; Cheng, Yi; Sheng, Jian-Zhong; Huang, He-Feng

2018-05-15

High androgen level impairs endometrial receptivity in women experiences the recurrent miscarriage. The mechanism of androgen actions on endometrium is still uncertain. We hypothesized that androgen has a direct effect on the endometrium in women with recurrent miscarriage. In the present study, we assess the impact of androgen (A 2 ) at high concentration (10 -7 M) on Ishikawa cells compared with the physiological concentration of androgen (10 -9 M). To go into deeper analysis, we use global stable isotopes labeled profiling tactic using iTRAQ reagents, followed by 2D LC-MS/MS. We determine 175 non-redundant proteins, and 18 of these were quantified. The analysis of differentially expressed proteins (DEPs) identified 8 up-regulated proteins and 10 down-regulated in the high androgen group. These DEPs were examined by ingenuity pathway (IPA) analysis and established that these proteins might play vital roles in recurrent miscarriage and endometrium receptivity. In addition, proteins cyclin-dependent kinase inhibitor 2a (CDKN2a), endothelial protein C receptor (EPCR), armadillo repeat for velocardiofacial (ARVCF) were independently confirmed using western blot. Knockdown of CDKN2a significantly decreased the expression level of CDKN2a protein in ishikawa cells, and decreased migration ( p < 0.01), invasion ( p < 0.05), proliferation ( p < 0.05), and the rate of Jar spheroid attachment ( p < 0.05) to Ishikawa cell monolayer. The present results suggest that androgen at high concentration could alter the expression levels of proteins related to endometrium development and embryo implantation, which might be a cause of the impaired endometrial receptivity and miscarriage.

Treatment with Cefotaxime Affects Expression of Conjugation Associated Proteins and Conjugation Transfer Frequency of an IncI1 Plasmid in Escherichia coli

PubMed Central

Møller, Thea S. B.; Liu, Gang; Boysen, Anders; Thomsen, Line E.; Lüthje, Freja L.; Mortensen, Sisse; Møller-Jensen, Jakob; Olsen, John E.

2017-01-01

Horizontal gene transfer (HGT) is the major mechanism responsible for spread of antibiotic resistance. Antibiotic treatment has been suggested to promote HGT, either by directly affecting the conjugation process itself or by selecting for conjugations subsequent to DNA transfer. However, recent research suggests that the effect of antibiotic treatment on plasmid conjugation frequencies, and hence the spread of resistance plasmids, may have been overestimated. We addressed the question by quantifying transfer proteins and conjugation frequencies of a blaCTX−M−1 encoding IncI1 resistance plasmid in Escherichia coli MG1655 in the presence and absence of therapeutically relevant concentrations of cefotaxime (CTX). Analysis of the proteome by iTRAQ labeling and liquid chromatography tandem mass spectrometry revealed that Tra proteins were significantly up-regulated in the presence of CTX. The up-regulation of the transfer machinery was confirmed at the transcriptional level for five selected genes. The CTX treatment did not cause induction of the SOS-response as revealed by absence of significantly regulated SOS associated proteins in the proteome and no significant up-regulation of recA and sfiA genes. The frequency of plasmid conjugation, measured in an antibiotic free environment, increased significantly when the donor was pre-grown in broth containing CTX compared to growth without this drug, regardless of whether blaCTX-M-1 was located on the plasmid or in trans on the chromosome. The results shows that antibiotic treatment can affect expression of a plasmid conjugation machinery and subsequent DNA transfer. PMID:29238335

Proteomic analysis of a NAP1 Clostridium difficile clinical isolate resistant to metronidazole.

PubMed

Chong, Patrick M; Lynch, Tarah; McCorrister, Stuart; Kibsey, Pamela; Miller, Mark; Gravel, Denise; Westmacott, Garrett R; Mulvey, Michael R

2014-01-01

Clostridium difficile is an anaerobic, Gram-positive bacterium that has been implicated as the leading cause of antibiotic-associated diarrhea. Metronidazole is currently the first-line treatment for mild to moderate C. difficile infections. Our laboratory isolated a strain of C. difficile with a stable resistance phenotype to metronidazole. A shotgun proteomics approach was used to compare differences in the proteomes of metronidazole-resistant and -susceptible isolates. NAP1 C. difficile strains CD26A54_R (Met-resistant), CD26A54_S (reduced- susceptibility), and VLOO13 (Met-susceptible) were grown to mid-log phase, and spiked with metronidazole at concentrations 2 doubling dilutions below the MIC. Peptides from each sample were labeled with iTRAQ and subjected to 2D-LC-MS/MS analysis. In the absence of metronidazole, higher expression was observed of some proteins in C. difficile strains CD26A54_S and CD26A54_R that may be involved with reduced susceptibility or resistance to metronidazole, including DNA repair proteins, putative nitroreductases, and the ferric uptake regulator (Fur). After treatment with metronidazole, moderate increases were seen in the expression of stress-related proteins in all strains. A moderate increase was also observed in the expression of the DNA repair protein RecA in CD26A54_R. This study provided an in-depth proteomic analysis of a stable, metronidazole-resistant C. difficile isolate. The results suggested that a multi-factorial response may be associated with high level metronidazole-resistance in C. difficile, including the possible roles of altered iron metabolism and/or DNA repair.

Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis.

PubMed

Milewski, Robert J; Kumagai, Yutaro; Fujita, Katsumasa; Standley, Daron M; Smith, Nicholas I

2010-11-19

Macrophages represent the front lines of our immune system; they recognize and engulf pathogens or foreign particles thus initiating the immune response. Imaging macrophages presents unique challenges, as most optical techniques require labeling or staining of the cellular compartments in order to resolve organelles, and such stains or labels have the potential to perturb the cell, particularly in cases where incomplete information exists regarding the precise cellular reaction under observation. Label-free imaging techniques such as Raman microscopy are thus valuable tools for studying the transformations that occur in immune cells upon activation, both on the molecular and organelle levels. Due to extremely low signal levels, however, Raman microscopy requires sophisticated image processing techniques for noise reduction and signal extraction. To date, efficient, automated algorithms for resolving sub-cellular features in noisy, multi-dimensional image sets have not been explored extensively. We show that hybrid z-score normalization and standard regression (Z-LSR) can highlight the spectral differences within the cell and provide image contrast dependent on spectral content. In contrast to typical Raman imaging processing methods using multivariate analysis, such as single value decomposition (SVD), our implementation of the Z-LSR method can operate nearly in real-time. In spite of its computational simplicity, Z-LSR can automatically remove background and bias in the signal, improve the resolution of spatially distributed spectral differences and enable sub-cellular features to be resolved in Raman microscopy images of mouse macrophage cells. Significantly, the Z-LSR processed images automatically exhibited subcellular architectures whereas SVD, in general, requires human assistance in selecting the components of interest. The computational efficiency of Z-LSR enables automated resolution of sub-cellular features in large Raman microscopy data sets without compromise in image quality or information loss in associated spectra. These results motivate further use of label free microscopy techniques in real-time imaging of live immune cells.

Looking for prosocial genes: ITRAQ analysis of proteins involved in MDMA-induced sociability in mice.

PubMed

Kuteykin-Teplyakov, Konstantin; Maldonado, Rafael

2014-11-01

Social behavior plays a fundamental role in life of many animal species, allowing the interaction between individuals and sharing of experiences, needs, and goals across them. In humans, some neuropsychiatric diseases, including anxiety, posttraumatic stress disorder and autism spectrum disorders, are often characterized by impaired sociability. Here we report that N-Methyl-3,4-methylenedioxyamphetamine (MDMA, "Ecstasy") at low dose (3mg/kg) has differential effects on mouse social behavior. In some animals, MDMA promotes sociability without hyperlocomotion, whereas in other mice it elevates locomotor activity without affecting sociability. Both WAY-100635, a selective antagonist of 5-HT1A receptor, and L-368899, a selective oxytocin receptor antagonist, abolish prosocial effects of MDMA. Differential quantitative analysis of brain proteome by isobaric tag for relative and absolute quantification technology (iTRAQ) revealed 21 specific proteins that were highly correlated with sociability, and allowed to distinguish between entactogenic prosocial and hyperlocomotor effects of MDMA on proteome level. Our data suggest particular relevance of neurotransmission mediated by GABA B receptor, as well as proteins involved in energy maintenance for MDMA-induced sociability. Functional association network for differentially expressed proteins in cerebral cortex, hippocampus and amygdala were identified. These results provide new information for understanding the neurobiological substrate of sociability and may help to discover new therapeutic approaches to modulate social behavior in patients suffering from social fear and low sociability. Copyright © 2014 Elsevier B.V. and ECNP. All rights reserved.

iTRAQ proteomics analysis reveals that PI3K is highly associated with bupivacaine-induced neurotoxicity pathways.

PubMed

Zhao, Wei; Liu, Zhongjie; Yu, Xujiao; Lai, Luying; Li, Haobo; Liu, Zipeng; Li, Le; Jiang, Shan; Xia, Zhengyuan; Xu, Shi-yuan

2016-02-01

Bupivacaine, a commonly used local anesthetic, has potential neurotoxicity through diverse signaling pathways. However, the key mechanism of bupivacaine-induced neurotoxicity remains unclear. Cultured human SH-SY5Y neuroblastoma cells were treated (bupivacaine) or untreated (control) with bupivacaine for 24 h. Compared to the control group, bupivacaine significantly increased cyto-inhibition, cellular reactive oxygen species, DNA damage, mitochondrial injury, apoptosis (increased TUNEL-positive cells, cleaved caspase 3, and Bcl-2/Bax), and activated autophagy (enhanced LC3II/LC3I ratio). To explore changes in protein expression and intercommunication among the pathways involved in bupivacaine-induced neurotoxicity, an 8-plex iTRAQ proteomic technique and bioinformatics analysis were performed. Compared to the control group, 241 differentially expressed proteins were identified, of which, 145 were up-regulated and 96 were down-regulated. Bioinformatics analysis of the cross-talk between the significant proteins with altered expression in bupivacaine-induced neurotoxicity indicated that phosphatidyl-3-kinase (PI3K) was the most frequently targeted protein in each of the interactions. We further confirmed these results by determining the downstream targets of the identified signaling pathways (PI3K, Akt, FoxO1, Erk, and JNK). In conclusion, our study demonstrated that PI3K may play a central role in contacting and regulating the signaling pathways that contribute to bupivacaine-induced neurotoxicity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomic analysis of grapevine resistance induced by Trichoderma harzianum T39 reveals specific defence pathways activated against downy mildew

PubMed Central

Perazzolli, Michele

2012-01-01

Downy mildew is caused by the oomycete Plasmopara viticola and is one of the most serious diseases of grapevine. The beneficial microorganism Trichoderma harzianum T39 (T39) has previously been shown to induce plant-mediated resistance and to reduce the severity of downy mildew in susceptible grapevines. In order to better understand the cellular processes associated with T39-induced resistance, the proteomic and histochemical changes activated by T39 in grapevine were investigated before and 1 day after P. viticola inoculation. A comprehensive proteomic analysis of T39-induced resistance in grapevine was performed using an eight-plex iTRAQ protocol, resulting in the identification and quantification of a total of 800 proteins. Most of the proteins directly affected by T39 were found to be involved in signal transduction, indicating activation of a complete microbial recognition machinery. Moreover, T39-induced resistance was associated with rapid accumulation of reactive oxygen species and callose at infection sites, as well as changes in abundance of proteins involved in response to stress and redox balance, indicating an active defence response to downy mildew. On the other hand, proteins affected by P. viticola in control plants mainly decreased in abundance, possibly reflecting the establishment of a compatible interaction. Finally, the high-throughput iTRAQ protocol allowed de novo peptide sequencing, which will be used to improve annotation of the Vitis vinifera cv. Pinot Noir proteome. PMID:23105132

Proteomics analysis of maize (Zea mays L.) grain based on iTRAQ reveals molecular mechanisms of poor grain filling in inferior grains.

PubMed

Yu, Tao; Li, Geng; Liu, Peng; Dong, Shuting; Zhang, Jiwang; Zhao, Bin

2017-06-01

In maize, inferior grains (IG) located on the upper part of the ear have poor grain filling process compared to superior grains (SG) located on the middle and lower parts of the ear. This difference limits satisfactory yield and quality; however, the underlying molecular mechanisms remain unknown. Here, using the isobaric tag for relative and absolute quantification (iTRAQ) technology, the proteomes of IG and SG during early and middle grain filling stages were investigated. In total, 4720 proteins were identified in maize grain and 305 differentially accumulated proteins (DiAPs) were detected between IG and SG. These DiAPs were involved in diverse cellular and metabolic processes with preferred distribution in protein synthesis/destination and metabolism. Compared to SG, DiAPs related to cell growth/division and starch synthesis were lag-accumulated and down-regulated in IG, respectively, resulting in smaller sink sizes and lower sink activities in IG. Meanwhile, impediment of the glycolysis pathway in IG may lead to reduce energy supply and building materials for substance synthesis. Additionally, reactive oxygen species (ROS) homeostasis and the defense system were disturbed in IG, which might lead to reduce protection against various environmental stresses. The present study provides new information on the proteomic differences between IG and SG, and explains possible molecular mechanisms for poor grain filling in IG. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Quantitative proteomics analysis with iTRAQ in human lenses with nuclear cataracts of different axial lengths.

PubMed

Zhou, Haiyan; Yan, Hong; Yan, Weijia; Wang, Xinchuan; Ma, Yong; Wang, Jianping

2016-01-01

The goal of this study was to identify and quantify the differentially expressed proteins in human nuclear cataract with different axial lengths. Thirty-six samples of human lens nuclei with hardness grade III or IV were obtained during cataract surgery with extracapsular cataract extraction (ECCE). Six healthy transparent human lens nuclei were obtained from fresh healthy cadaver eyes during corneal transplantation surgery. The lens nuclei were divided into seven groups (six lenses in each group) according to the optic axis: Group A (mean axial length 28.7±1.5 mm; average age 59.8±1.9 years), Group B (mean axial length 23.0±0.4 mm; average age 60.3±2.5 years), Group C (mean axial length 19.9±0.5 mm; average age 55.1±2.5 years), Group D (mean axial length 28.7±1.4 mm; average age 58.0±4.0 years), Group E (mean axial length 23.0±0.3 mm; average age 56.9±4.2 years), and Group F (mean axial length 20.7±0.6 mm; average age 57.6±5.3 years). The six healthy transparent human lenses were included in a younger group with standard optic axes, Group G (mean axial length 23.0±0.5 mm; average age 34.7±4.2 years).Water-soluble, water-insoluble, and water-insoluble-urea-soluble protein fractions were extracted from the samples. The three-part protein fractions from the individual lenses were combined to form the total proteins of each sample. The proteomic profiles of each group were analyzed using 8-plex isobaric tagging for relative and absolute protein quantification (iTRAQ) labeling combined with two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS). The data were analyzed with ProteinPilot software for peptide matching, protein identification, and quantification. Differentially expressed proteins were validated with western blotting. We employed biological and technical replicates and selected the intersection of the two sets of results, which included 40 proteins. From the 40 proteins identified, six were selected as differentially expressed proteins closely related to axial length. The six proteins were gap junction alpha-3 protein, beta-crystallin B2, T-complex protein 1 subunit beta, gamma-enolase, pyruvate kinase isozymes M1/M2, and sorbitol dehydrogenase. Levels of beta-crystallin B2 expression were decreased in nuclear cataracts with longer axial length. The results of the mass spectrometric analysis were consistent with the western blot validation. The discovery of these differentially expressed proteins provides valuable clues for understanding the pathogenesis of axial-related nuclear cataract. The results indicate that beta-crystallin B2 (CRBB2) may be involved in axial-related nuclear cataract pathogenesis. Further studies are needed to investigate the correlation between CRBB2 and axial-related nuclear cataract.

Reproducible, high-throughput synthesis of colloidal nanocrystals for optimization in multidimensional parameter space.

PubMed

Chan, Emory M; Xu, Chenxu; Mao, Alvin W; Han, Gang; Owen, Jonathan S; Cohen, Bruce E; Milliron, Delia J

2010-05-12

While colloidal nanocrystals hold tremendous potential for both enhancing fundamental understanding of materials scaling and enabling advanced technologies, progress in both realms can be inhibited by the limited reproducibility of traditional synthetic methods and by the difficulty of optimizing syntheses over a large number of synthetic parameters. Here, we describe an automated platform for the reproducible synthesis of colloidal nanocrystals and for the high-throughput optimization of physical properties relevant to emerging applications of nanomaterials. This robotic platform enables precise control over reaction conditions while performing workflows analogous to those of traditional flask syntheses. We demonstrate control over the size, size distribution, kinetics, and concentration of reactions by synthesizing CdSe nanocrystals with 0.2% coefficient of variation in the mean diameters across an array of batch reactors and over multiple runs. Leveraging this precise control along with high-throughput optical and diffraction characterization, we effectively map multidimensional parameter space to tune the size and polydispersity of CdSe nanocrystals, to maximize the photoluminescence efficiency of CdTe nanocrystals, and to control the crystal phase and maximize the upconverted luminescence of lanthanide-doped NaYF(4) nanocrystals. On the basis of these demonstrative examples, we conclude that this automated synthesis approach will be of great utility for the development of diverse colloidal nanomaterials for electronic assemblies, luminescent biological labels, electroluminescent devices, and other emerging applications.

Visualizing Science Dissections in 3D: Contextualizing Student Responses to Multidimensional Learning Materials in Science Dissections

NASA Astrophysics Data System (ADS)

Walker, Robin Annette

A series of dissection tasks was developed in this mixed-methods study of student self-explanations of their learning using actual and virtual multidimensional science dissections and visuo-spatial instruction. Thirty-five seventh-grade students from a science classroom (N = 20 Female/15 Male, Age =13 years) were assigned to three dissection environments instructing them to: (a) construct static paper designs of frogs, (b) perform active dissections with formaldehyde specimens, and (c) engage with interactive 3D frog visualizations and virtual simulations. This multi-methods analysis of student engagement with anchored dissection materials found learning gains on labeling exercises and lab assessments among most students. Data revealed that students who correctly utilized multimedia text and diagrams, individually and collaboratively, manipulated 3D tools more effectively and were better able to self-explain and complete their dissection work. Student questionnaire responses corroborated that they preferred learning how to dissect a frog using 3D multimedia instruction. The data were used to discuss the impact of 3D technologies, programs, and activities on student learning, spatial reasoning, and their interest in science. Implications were drawn regarding how to best integrate 3D visualizations into science curricula as innovative learning options for students, as instructional alternatives for teachers, and as mandated dissection choices for those who object to physical dissections in schools.

CPTAC Evaluates Long-Term Reproducibility of Quantitative Proteomics Using Breast Cancer Xenografts | Office of Cancer Clinical Proteomics Research

Cancer.gov

Liquid chromatography tandem-mass spectrometry (LC-MS/MS)- based methods such as isobaric tags for relative and absolute quantification (iTRAQ) and tandem mass tags (TMT) have been shown to provide overall better quantification accuracy and reproducibility over other LC-MS/MS techniques. However, large scale projects like the Clinical Proteomic Tumor Analysis Consortium (CPTAC) require comparisons across many genomically characterized clinical specimens in a single study and often exceed the capability of traditional iTRAQ-based quantification.

Wound Status Early Outcome Sensor and 3D Construct Development

DTIC Science & Technology

2015-03-01

1.35 Fyn  94 83 0.11 0.04 0.74 0.99 Milk   Fat  Globule Membrane  Protein 1.35 Milk   Fat  Globule Membrane  Protein 1413 1240 0.02 0.03 11.06 14.94 PGP9.5...reproducible in biological replicates, which indicates the possibility of random bias for certain proteins with iTRAQ channel specificity. Raw spectrum...public release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Early identification of the specific proteins , which indicate delayed

Multidimensional poverty, household environment and short-term morbidity in India.

PubMed

Dehury, Bidyadhar; Mohanty, Sanjay K

2017-01-01

Using the unit data from the second round of the Indian Human Development Survey (IHDS-II), 2011-2012, which covered 42,152 households, this paper examines the association between multidimensional poverty, household environmental deprivation and short-term morbidities (fever, cough and diarrhoea) in India. Poverty is measured in a multidimensional framework that includes the dimensions of education, health and income, while household environmental deprivation is defined as lack of access to improved sanitation, drinking water and cooking fuel. A composite index combining multidimensional poverty and household environmental deprivation has been computed, and households are classified as follows: multidimensional poor and living in a poor household environment, multidimensional non-poor and living in a poor household environment, multidimensional poor and living in a good household environment and multidimensional non-poor and living in a good household environment. Results suggest that about 23% of the population belonging to multidimensional poor households and living in a poor household environment had experienced short-term morbidities in a reference period of 30 days compared to 20% of the population belonging to multidimensional non-poor households and living in a poor household environment, 19% of the population belonging to multidimensional poor households and living in a good household environment and 15% of the population belonging to multidimensional non-poor households and living in a good household environment. Controlling for socioeconomic covariates, the odds of short-term morbidity was 1.47 [CI 1.40-1.53] among the multidimensional poor and living in a poor household environment, 1.28 [CI 1.21-1.37] among the multidimensional non-poor and living in a poor household environment and 1.21 [CI 1.64-1.28] among the multidimensional poor and living in a good household environment compared to the multidimensional non-poor and living in a good household environment. Results are robust across states and hold good for each of the three morbidities: fever, cough and diarrhoea. This establishes that along with poverty, household environmental conditions have a significant bearing on short-term morbidities in India. Public investment in sanitation, drinking water and cooking fuel can reduce the morbidity and improve the health of the population.

Proteomic analysis in type 2 diabetes patients before and after a very low calorie diet reveals potential disease state and intervention specific biomarkers.

PubMed

Sleddering, Maria A; Markvoort, Albert J; Dharuri, Harish K; Jeyakar, Skhandhan; Snel, Marieke; Juhasz, Peter; Lynch, Moira; Hines, Wade; Li, Xiaohong; Jazet, Ingrid M; Adourian, Aram; Hilbers, Peter A J; Smit, Johannes W A; Van Dijk, Ko Willems

2014-01-01

Very low calorie diets (VLCD) with and without exercise programs lead to major metabolic improvements in obese type 2 diabetes patients. The mechanisms underlying these improvements have so far not been elucidated fully. To further investigate the mechanisms of a VLCD with or without exercise and to uncover possible biomarkers associated with these interventions, blood samples were collected from 27 obese type 2 diabetes patients before and after a 16-week VLCD (Modifast ∼ 450 kcal/day). Thirteen of these patients followed an exercise program in addition to the VCLD. Plasma was obtained from 27 lean and 27 obese controls as well. Proteomic analysis was performed using mass spectrometry (MS) and targeted multiple reaction monitoring (MRM) and a large scale isobaric tags for relative and absolute quantitation (iTRAQ) approach. After the 16-week VLCD, there was a significant decrease in body weight and HbA1c in all patients, without differences between the two intervention groups. Targeted MRM analysis revealed differences in several proteins, which could be divided in diabetes-associated (fibrinogen, transthyretin), obesity-associated (complement C3), and diet-associated markers (apolipoproteins, especially apolipoprotein A-IV). To further investigate the effects of exercise, large scale iTRAQ analysis was performed. However, no proteins were found showing an exercise effect. Thus, in this study, specific proteins were found to be differentially expressed in type 2 diabetes patients versus controls and before and after a VLCD. These proteins are potential disease state and intervention specific biomarkers. Controlled-Trials.com ISRCTN76920690.

Proteomic Analysis in Type 2 Diabetes Patients before and after a Very Low Calorie Diet Reveals Potential Disease State and Intervention Specific Biomarkers

PubMed Central

Dharuri, Harish K.; Jeyakar, Skhandhan; Snel, Marieke; Juhasz, Peter; Lynch, Moira; Hines, Wade; Li, Xiaohong; Jazet, Ingrid M.; Adourian, Aram; Hilbers, Peter A. J.; Smit, Johannes W. A.; Van Dijk, Ko Willems

2014-01-01

Very low calorie diets (VLCD) with and without exercise programs lead to major metabolic improvements in obese type 2 diabetes patients. The mechanisms underlying these improvements have so far not been elucidated fully. To further investigate the mechanisms of a VLCD with or without exercise and to uncover possible biomarkers associated with these interventions, blood samples were collected from 27 obese type 2 diabetes patients before and after a 16-week VLCD (Modifast ∼450 kcal/day). Thirteen of these patients followed an exercise program in addition to the VCLD. Plasma was obtained from 27 lean and 27 obese controls as well. Proteomic analysis was performed using mass spectrometry (MS) and targeted multiple reaction monitoring (MRM) and a large scale isobaric tags for relative and absolute quantitation (iTRAQ) approach. After the 16-week VLCD, there was a significant decrease in body weight and HbA1c in all patients, without differences between the two intervention groups. Targeted MRM analysis revealed differences in several proteins, which could be divided in diabetes-associated (fibrinogen, transthyretin), obesity-associated (complement C3), and diet-associated markers (apolipoproteins, especially apolipoprotein A-IV). To further investigate the effects of exercise, large scale iTRAQ analysis was performed. However, no proteins were found showing an exercise effect. Thus, in this study, specific proteins were found to be differentially expressed in type 2 diabetes patients versus controls and before and after a VLCD. These proteins are potential disease state and intervention specific biomarkers. Trial Registration Controlled-Trials.com ISRCTN76920690 PMID:25415563

Quantitative iTRAQ LC-MS/MS proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis sp. PCC 6803.

PubMed

Qiao, Jianjun; Wang, Jiangxin; Chen, Lei; Tian, Xiaoxu; Huang, Siqiang; Ren, Xiaoyue; Zhang, Weiwen

2012-11-02

Recent progress in metabolic engineering has led to autotrophic production of ethanol in various cyanobacterial hosts. However, cyanobacteria are known to be sensitive to ethanol, which restricts further efforts to increase ethanol production levels in these renewable host systems. To understand the mechanisms of ethanol tolerance so that engineering more robust cyanobacterial hosts can be possible, in this study, the responses of model cyanobacterial Synechocystis sp. PCC 6803 to ethanol were determined using a quantitative proteomics approach with iTRAQ LC-MS/MS technologies. The resulting high-quality proteomic data set consisted of 24,887 unique peptides corresponding to 1509 identified proteins, a coverage of approximately 42% of the predicted proteins in the Synechocystis genome. Using a cutoff of 1.5-fold change and a p-value less than 0.05, 135 and 293 unique proteins with differential abundance levels were identified between control and ethanol-treated samples at 24 and 48 h, respectively. Functional analysis showed that the Synechocystis cells employed a combination of induced common stress response, modifications of cell membrane and envelope, and induction of multiple transporters and cell mobility-related proteins as protection mechanisms against ethanol toxicity. Interestingly, our proteomic analysis revealed that proteins related to multiple aspects of photosynthesis were up-regulated in the ethanol-treated Synechocystis cells, consistent with increased chlorophyll a concentration in the cells upon ethanol exposure. The study provided the first comprehensive view of the complicated molecular mechanisms against ethanol stress and also provided a list of potential gene targets for further engineering ethanol tolerance in Synechocystis PCC 6803.

Combined serum and EPS-urine proteomic analysis using iTRAQ technology for discovery of potential prostate cancer biomarkers.

PubMed

Zhang, Mo; Chen, Lizhu; Yuan, Zhengwei; Yang, Zeyu; Li, Yue; Shan, Liping; Yin, Bo; Fei, Xiang; Miao, Jianing; Song, Yongsheng

2016-11-01

Prostate cancer (PCa) is one of the most common malignant tumors and a major cause of cancer-related death for men worldwide. The aim of our study was to identify potential non-invasive serum and expressed prostatic secretion (EPS)-urine biomarkers for accurate diagnosis of PCa. Here, we performed a combined isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis to compare protein profiles using pooled serum and EPS-urine samples from 4 groups of patients: benign prostate hyperplasia (BPH), high grade prostatic intraepithelial neoplasia (HGPIN), localized PCa and metastatic PCa. The differentially expressed proteins were rigorously selected and further validated in a large and independent cohort using classical ELISA and Western blot assays. Finally, we established a multiplex biomarker panel consisting of 3 proteins (serum PF4V1, PSA, and urinary CRISP3) with an excellent diagnostic capacity to differentiate PCa from BPH [area under the receiver operating characteristic curve (AUC) of 0.941], which showed an evidently greater discriminatory ability than PSA alone (AUC, 0.757) (P<0.001). Importantly, even when PSA level was in the gray zone (4-10 ng/mL), a combination of PF4V1 and CRISP3 could achieve a relatively high diagnostic efficacy (AUC, 0.895). Furthermore, their combination also had the potential to distinguish PCa from HGPIN (AUC, 0.934). Our results demonstrated that the combined application of serum and EPS-urine biomarkers can improve the diagnosis of PCa and provide a new prospect for non-invasive PCa detection.

Comparative proteomics analysis of apoptotic Spodoptera frugiperda cells during p35 knockout Autographa californica multiple nucleopolyhedrovirus infection.

PubMed

Yu, Qian; Xiong, Youhua; Liu, Jianliang; Wang, Qin; Qiu, Yuanxin; Wen, Dongling

2016-06-01

Infection with Autographa californica multiple nucleopolyhedrovirus (AcMNPV) mutants lacking a functional p35 gene can induce host cell apoptosis, which provides the possibility to use the potential of these viruses in the biological control of pest insects. Nonetheless, the proteomics or the protein changes of Spodoptera frugiperda (Sf9) cells infected with p35 knockout AcMNPV have not yet been studied. To further improve the use of AcMNPV, we set out to analyze the protein composition and protein changes of Sf9 cells of different infection stages by isobaric tag for relative and absolute quantification (iTRAQ) techniques. A total of 4004 sf9 proteins were identified by iTRAQ. After comparation of the significantly expressed 483 proteins from p35koAcMNPV-infected Sf9 cells and the significantly expressed 413 proteins from wtAcMNPV-infected Sf9 cells, we found that 226 proteins were specific to p35koAcMNPV-infected Sf9 cells. The 226 proteins were categorized according to GO classification for insects and were categorized into: biological processes, molecular functions and cellular components. Of interest, the most up-regulated proteins related to Epstein-Barr virus infection, RNA transport, Calcium signaling pathway, cGMP-PKG signaling pathway, oxidative phosphorylation and N-Glycan biosynthesis. Determination of the protein changes in p35 knockout AcMNPV-infected Sf9 cells would facilitate the better use of this virus-host cell interaction in pest insect control and other related fields. Copyright © 2016 Elsevier Inc. All rights reserved.

iTRAQ Analysis Reveals Mechanisms of Growth Defects Due to Excess Zinc in Arabidopsis1[W][OA

PubMed Central

Fukao, Yoichiro; Ferjani, Ali; Tomioka, Rie; Nagasaki, Nahoko; Kurata, Rie; Nishimori, Yuka; Fujiwara, Masayuki; Maeshima, Masayoshi

2011-01-01

The micronutrient zinc is essential for all living organisms, but it is toxic at high concentrations. Here, to understand the effects of excess zinc on plant cells, we performed an iTRAQ (for isobaric tags for relative and absolute quantification)-based quantitative proteomics approach to analyze microsomal proteins from Arabidopsis (Arabidopsis thaliana) roots. Our approach was sensitive enough to identify 521 proteins, including several membrane proteins. Among them, IRT1, an iron and zinc transporter, and FRO2, a ferric-chelate reductase, increased greatly in response to excess zinc. The expression of these two genes has been previously reported to increase under iron-deficient conditions. Indeed, the concentration of iron was significantly decreased in roots and shoots under excess zinc. Also, seven subunits of the vacuolar H+-ATPase (V-ATPase), a proton pump on the tonoplast and endosome, were identified, and three of them decreased significantly in response to excess zinc. In addition, excess zinc in the wild type decreased V-ATPase activity and length of roots and cells to levels comparable to those of the untreated de-etiolated3-1 mutant, which bears a mutation in V-ATPase subunit C. Interestingly, excess zinc led to the formation of branched and abnormally shaped root hairs, a phenotype that correlates with decreased levels of proteins of several root hair-defective mutants. Our results point out mechanisms of growth defects caused by excess zinc in which cross talk between iron and zinc homeostasis and V-ATPase activity might play a central role. PMID:21325567

Multidimensional chromatography in food analysis.

PubMed

Herrero, Miguel; Ibáñez, Elena; Cifuentes, Alejandro; Bernal, Jose

2009-10-23

In this work, the main developments and applications of multidimensional chromatographic techniques in food analysis are reviewed. Different aspects related to the existing couplings involving chromatographic techniques are examined. These couplings include multidimensional GC, multidimensional LC, multidimensional SFC as well as all their possible combinations. Main advantages and drawbacks of each coupling are critically discussed and their key applications in food analysis described.

Multidimensional Riemann problem with self-similar internal structure - part III - a multidimensional analogue of the HLLI Riemann solver for conservative hyperbolic systems

NASA Astrophysics Data System (ADS)

Balsara, Dinshaw S.; Nkonga, Boniface

2017-10-01

Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The fastest way of endowing such sub-structure consists of making a multidimensional extension of the HLLI Riemann solver for hyperbolic conservation laws. Presenting such a multidimensional analogue of the HLLI Riemann solver with linear sub-structure for use on structured meshes is the goal of this work. The multidimensional MuSIC Riemann solver documented here is universal in the sense that it can be applied to any hyperbolic conservation law. The multidimensional Riemann solver is made to be consistent with constraints that emerge naturally from the Galerkin projection of the self-similar states within the wave model. When the full eigenstructure in both directions is used in the present Riemann solver, it becomes a complete Riemann solver in a multidimensional sense. I.e., all the intermediate waves are represented in the multidimensional wave model. The work also presents, for the very first time, an important analysis of the dissipation characteristics of multidimensional Riemann solvers. The present Riemann solver results in the most efficient implementation of a multidimensional Riemann solver with sub-structure. Because it preserves stationary linearly degenerate waves, it might also help with well-balancing. Implementation-related details are presented in pointwise fashion for the one-dimensional HLLI Riemann solver as well as the multidimensional MuSIC Riemann solver.

Fibrotic-like changes in degenerate human intervertebral discs revealed by quantitative proteomic analysis.

PubMed

Yee, A; Lam, M P Y; Tam, V; Chan, W C W; Chu, I K; Cheah, K S E; Cheung, K M C; Chan, D

2016-03-01

Intervertebral disc degeneration (IDD) can lead to symptomatic conditions including sciatica and back pain. The purpose of this study is to understand the extracellular matrix (ECM) changes in disc biology through comparative proteomic analysis of degenerated and non-degenerated human intervertebral disc (IVD) tissues of different ages. Seven non-degenerated (11-46 years of age) and seven degenerated (16-53 years of age) annulus fibrosus (AF) and nucleus pulposus (NP) samples were used. Proteins were extracted using guanidine hydrochloride, separated from large proteoglycans (PGs) by caesium chloride (CsCl) density gradient ultracentrifugation, and identified using liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). For quantitative comparison, proteins were labeled with iTRAQ reagents. Collagen fibrils in the NP were assessed using scanning electron microscopy (SEM). In the AF, quantitative analysis revealed increased levels of HTRA1, COMP and CILP in degeneration when compared with samples from older individuals. Fibronectin showed increment with age and degeneration. In the NP, more CILP and CILP2 were present in degenerated samples of younger individuals. Reduced protein solubility was observed in degenerated and older non-degenerated samples correlated with an accumulation of type I collagen in the insoluble fibers. Characterization of collagen fibrils in the NP revealed smaller mean fibril diameters and decreased porosity in the degenerated samples. Our study identified distinct matrix changes associated with aging and degeneration in the intervertebral discs (IVDs). The nature of the ECM changes, together with observed decreased in solubility and changes in fibril diameter is consistent with a fibrotic-like environment. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Quantitative proteomic analysis reveals novel mitochondrial targets of estrogen deficiency in the aged female rat heart.

PubMed

Lancaster, T S; Jefferson, S J; Hunter, J Craig; Lopez, Veronica; Van Eyk, J E; Lakatta, E G; Korzick, D H

2012-10-17

The incidence of myocardial infarction rises sharply at menopause, implicating a potential role for estrogen (E(2)) loss in age-related increases in ischemic injury. We aimed to identify quantitative changes to the cardiac mitochondrial proteome of aging females, based on the hypothesis that E(2) deficiency exacerbates age-dependent disruptions in mitochondrial proteins. Mitochondria isolated from left ventricles of adult (6 mo) and aged (24 mo) F344 ovary-intact or ovariectomized (OVX) rats were labeled with 8plex isobaric tags for relative and absolute quantification (iTRAQ; n = 5-6/group). Groups studied were adult, adult OVX, aged, and aged OVX. In vivo coronary artery ligation and in vitro mitochondrial respiration studies were also performed in a subset of rats. We identified 965 proteins across groups and significant directional changes in 67 proteins of aged and/or aged OVX; 32 proteins were unique to aged OVX. Notably, only six proteins were similarly altered in adult OVX (voltage-dependent ion channel 1, adenine nucleotide translocator 1, cytochrome c oxidase subunits VIIc and VIc, catalase, and myosin binding protein C). Proteins affected by aging were primarily related to cellular metabolism, oxidative stress, and cell death. The largest change occurred in monoamine oxidase-A (MAO-A), a source of oxidative stress. While acute MAO-A inhibition induced mild uncoupling in aged mitochondria, reductions in infarct size were not observed. Age-dependent alterations in mitochondrial signaling indicate a highly selective myocardial response to E(2) deficiency. The combined proteomic and functional approaches described here offer possibility of new protein targets for experimentation and therapeutic intervention in the aged female population.

Local delivery of a PKCε-activating peptide limits ischemia reperfusion injury in the aged female rat heart.

PubMed

Lancaster, T S; Jefferson, S J; Korzick, D H

2011-11-01

Reduced efficacy of cardioprotective interventions in the aged female heart, including estrogen replacement, highlights the need for alternative therapeutics to reduce myocardial ischemia-reperfusion (I/R) injury in postmenopausal women. Here, we sought to determine the efficacy of protein kinase-Cε (PKCε)-mediated cardioprotection in the aged, estradiol-deficient rat heart. Infarct size and functional recovery were assessed in Langendorff-perfused hearts from adult (5 mo) or aged (23 mo) female Fisher 344 ovary-intact or ovariectomized (OVX) rats administered a PKCε-activator, receptor for activated C kinase (ψεRACK) prior to 47-min ischemia and 60-min reperfusion. Proteomic analysis was conducted on left ventricular mitochondrial fractions treated with ψεRACK prior to I/R, utilizing isobaric tags for relative and absolute quantitation (iTRAQ) 8plex labeling and tandem mass spectrometry. Real-time PCR was utilized to assess connexin 43 (Cx43) and RACK2 mRNA post-I/R. Greater infarct size in aged OVX (78%) vs. adult (37%) was reduced by ψεRACK (35%, P < 0.0001) and associated with greater mitochondrial PKCε localization (P < 0.0003). Proteomic analysis revealed three novel mitochondrial targets of PKCε-mediated cardioprotection with aging (P < 0.05): the antioxidant enzymes glutathione peroxidase (GPX) and MnSOD2, and heat shock protein 10. Finally, decreased levels of Cx43 and RACK2 mRNA seen with age were partially abrogated by administration of ψεRACK (P < 0.05). The mechanisms described here may represent important therapeutic candidates for the treatment of acute myocardial infarction in postmenopausal women and age-associated estradiol deficiency.

Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liberton, Michelle; Saha, Rajib; Jacobs, Jon M.

2016-04-07

Cyanobacteria are photosynthetic microbes with highly differentiated membrane systems. These organisms contain an outer membrane, plasma membrane, and an internal system of thylakoid membranes where the photosynthetic and respiratory machinery are found. This existence of compartmentalization and differentiation of membrane systems poses a number of challenges for cyanobacterial cells in terms of organization and distribution of proteins to the correct membrane system. Proteomics studies have long sought to identify the components of the different membrane systems, and to date about 450 different proteins have been attributed to either the plasma membrane or thylakoid membrane. Given the complexity of these membranes,more » many more proteins remain to be identified in these membrane systems, and a comprehensive catalog of plasma membrane and thylakoid membrane proteins is needed. Here we describe the identification of 635 proteins in Synechocystis sp. PCC 6803 by quantitative iTRAQ isobaric labeling; of these, 459 proteins were localized to the plasma membrane and 176 were localized to the thylakoid membrane. Surprisingly, we found over 2.5 times the number of unique proteins identified in the plasma membrane compared to the thylakoid membrane. This suggests that the protein composition of the thylakoid membrane is more homogeneous than the plasma membrane, consistent with the role of the plasma membrane in diverse cellular processes including protein trafficking and nutrient import, compared to a more specialized role for the thylakoid membrane in cellular energetics. Overall, the protein composition of the Synechocystis 6803 plasma membrane and thylakoid membrane is quite similar to the E.coli plasma membrane and Arabidopsis thylakoid membrane, respectively. Synechocystis 6803 can therefore be described as a gram-negative bacterium that has an additional internal membrane system that fulfils the energetic requirements of the cell.« less

Quantitative chemical proteomics profiling of de novo protein synthesis during starvation-mediated autophagy

PubMed Central

Wang, Jigang; Zhang, Jianbin; Lee, Yew-Mun; Koh, Pin-Lang; Ng, Shukie; Bao, Feichao; Lin, Qingsong; Shen, Han-Ming

2016-01-01

ABSTRACT Autophagy is an intracellular degradation mechanism in response to nutrient starvation. Via autophagy, some nonessential cellular constituents are degraded in a lysosome-dependent manner to generate biomolecules that can be utilized for maintaining the metabolic homeostasis. Although it is known that under starvation the global protein synthesis is significantly reduced mainly due to suppression of MTOR (mechanistic target of rapamycin serine/threonine kinase), emerging evidence demonstrates that de novo protein synthesis is involved in the autophagic process. However, characterizing these de novo proteins has been an issue with current techniques. Here, we developed a novel method to identify newly synthesized proteins during starvation-mediated autophagy by combining bio-orthogonal noncanonical amino acid tagging (BONCAT) and isobaric tags for relative and absolute quantitation (iTRAQTM). Using bio-orthogonal metabolic tagging, L-azidohomoalanine (AHA) was incorporated into newly synthesized proteins which were then enriched with avidin beads after a click reaction between alkyne-bearing biotin and AHA's bio-orthogonal azide moiety. The enriched proteins were subjected to iTRAQ labeling for protein identification and quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Via the above approach, we identified and quantified a total of 1176 proteins and among them 711 proteins were found to meet our defined criteria as de novo synthesized proteins during starvation-mediated autophagy. The characterized functional profiles of the 711 newly synthesized proteins by bioinformatics analysis suggest their roles in ensuring the prosurvival outcome of autophagy. Finally, we performed validation assays for some selected proteins and found that knockdown of some genes has a significant impact on starvation-induced autophagy. Thus, we think that the BONCAT-iTRAQ approach is effective in the identification of newly synthesized proteins and provides useful insights to the molecular mechanisms and biological functions of autophagy. PMID:27463841

Altered protein networks and cellular pathways in severe west nile disease in mice.

PubMed

Fraisier, Christophe; Camoin, Luc; Lim, Stephanie M; Lim, Stéphanie; Bakli, Mahfoud; Belghazi, Maya; Fourquet, Patrick; Granjeaud, Samuel; Osterhaus, Ab D M E; Koraka, Penelope; Martina, Byron; Almeras, Lionel

2013-01-01

The recent West Nile virus (WNV) outbreaks in developed countries, including Europe and the United States, have been associated with significantly higher neuropathology incidence and mortality rate than previously documented. The changing epidemiology, the constant risk of (re-)emergence of more virulent WNV strains, and the lack of effective human antiviral therapy or vaccines makes understanding the pathogenesis of severe disease a priority. Thus, to gain insight into the pathophysiological processes in severe WNV infection, a kinetic analysis of protein expression profiles in the brain of WNV-infected mice was conducted using samples prior to and after the onset of clinical symptoms. To this end, 2D-DIGE and gel-free iTRAQ labeling approaches were combined, followed by protein identification by mass spectrometry. Using these quantitative proteomic approaches, a set of 148 proteins with modified abundance was identified. The bioinformatics analysis (Ingenuity Pathway Analysis) of each protein dataset originating from the different time-point comparisons revealed that four major functions were altered during the course of WNV-infection in mouse brain tissue: i) modification of cytoskeleton maintenance associated with virus circulation; ii) deregulation of the protein ubiquitination pathway; iii) modulation of the inflammatory response; and iv) alteration of neurological development and neuronal cell death. The differential regulation of selected host protein candidates as being representative of these biological processes were validated by western blotting using an original fluorescence-based method. This study provides novel insights into the in vivo kinetic host reactions against WNV infection and the pathophysiologic processes involved, according to clinical symptoms. This work offers useful clues for anti-viral research and further evaluation of early biomarkers for the diagnosis and prevention of severe neurological disease caused by WNV.

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.

PubMed

Rudnick, Paul A; Markey, Sanford P; Roth, Jeri; Mirokhin, Yuri; Yan, Xinjian; Tchekhovskoi, Dmitrii V; Edwards, Nathan J; Thangudu, Ratna R; Ketchum, Karen A; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Stein, Stephen E

2016-03-04

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics data sets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and nonreference markers of cancer. The CPTAC laboratories have focused on colon, breast, and ovarian tissues in the first round of analyses; spectra from these data sets were produced from 2D liquid chromatography-tandem mass spectrometry analyses and represent deep coverage. To reduce the variability introduced by disparate data analysis platforms (e.g., software packages, versions, parameters, sequence databases, etc.), the CPTAC Common Data Analysis Platform (CDAP) was created. The CDAP produces both peptide-spectrum-match (PSM) reports and gene-level reports. The pipeline processes raw mass spectrometry data according to the following: (1) peak-picking and quantitative data extraction, (2) database searching, (3) gene-based protein parsimony, and (4) false-discovery rate-based filtering. The pipeline also produces localization scores for the phosphopeptide enrichment studies using the PhosphoRS program. Quantitative information for each of the data sets is specific to the sample processing, with PSM and protein reports containing the spectrum-level or gene-level ("rolled-up") precursor peak areas and spectral counts for label-free or reporter ion log-ratios for 4plex iTRAQ. The reports are available in simple tab-delimited formats and, for the PSM-reports, in mzIdentML. The goal of the CDAP is to provide standard, uniform reports for all of the CPTAC data to enable comparisons between different samples and cancer types as well as across the major omics fields.

Proteomic Analysis of a NAP1 Clostridium difficile Clinical Isolate Resistant to Metronidazole

PubMed Central

Chong, Patrick M.; Lynch, Tarah; McCorrister, Stuart; Kibsey, Pamela; Miller, Mark; Gravel, Denise; Westmacott, Garrett R.; Mulvey, Michael R.

2014-01-01

Background Clostridium difficile is an anaerobic, Gram-positive bacterium that has been implicated as the leading cause of antibiotic-associated diarrhea. Metronidazole is currently the first-line treatment for mild to moderate C. difficile infections. Our laboratory isolated a strain of C. difficile with a stable resistance phenotype to metronidazole. A shotgun proteomics approach was used to compare differences in the proteomes of metronidazole-resistant and -susceptible isolates. Methodology/Principal Findings NAP1 C. difficile strains CD26A54_R (Met-resistant), CD26A54_S (reduced- susceptibility), and VLOO13 (Met-susceptible) were grown to mid-log phase, and spiked with metronidazole at concentrations 2 doubling dilutions below the MIC. Peptides from each sample were labeled with iTRAQ and subjected to 2D-LC-MS/MS analysis. In the absence of metronidazole, higher expression was observed of some proteins in C. difficile strains CD26A54_S and CD26A54_R that may be involved with reduced susceptibility or resistance to metronidazole, including DNA repair proteins, putative nitroreductases, and the ferric uptake regulator (Fur). After treatment with metronidazole, moderate increases were seen in the expression of stress-related proteins in all strains. A moderate increase was also observed in the expression of the DNA repair protein RecA in CD26A54_R. Conclusions/Significance This study provided an in-depth proteomic analysis of a stable, metronidazole-resistant C. difficile isolate. The results suggested that a multi-factorial response may be associated with high level metronidazole-resistance in C. difficile, including the possible roles of altered iron metabolism and/or DNA repair. PMID:24400070

Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome.

PubMed

Marimuthu, Arivusudar; Chavan, Sandip; Sathe, Gajanan; Sahasrabuddhe, Nandini A; Srikanth, Srinivas M; Renuse, Santosh; Ahmad, Sartaj; Radhakrishnan, Aneesha; Barbhuiya, Mustafa A; Kumar, Rekha V; Harsha, H C; Sidransky, David; Califano, Joseph; Pandey, Akhilesh; Chatterjee, Aditi

2013-11-01

Protein biomarker discovery for early detection of head and neck squamous cell carcinoma (HNSCC) is a crucial unmet need to improve patient outcomes. Mass spectrometry-based proteomics has emerged as a promising tool for identification of biomarkers in different cancer types. Proteins secreted from cancer cells can serve as potential biomarkers for early diagnosis. In the current study, we have used isobaric tag for relative and absolute quantitation (iTRAQ) labeling methodology coupled with high resolution mass spectrometry to identify and quantitate secreted proteins from a panel of head and neck carcinoma cell lines. In all, we identified 2,472 proteins, of which 225 proteins were secreted at higher or lower abundance in HNSCC-derived cell lines. Of these, 148 were present in higher abundance and 77 were present in lower abundance in the cancer-cell derived secretome. We detected a higher abundance of some previously known markers for HNSCC including insulin like growth factor binding protein 3, IGFBP3 (11-fold) and opioid growth factor receptor, OGFR (10-fold) demonstrating the validity of our approach. We also identified several novel secreted proteins in HNSCC including olfactomedin-4, OLFM4 (12-fold) and hepatocyte growth factor activator, HGFA (5-fold). IHC-based validation was conducted in HNSCC using tissue microarrays which revealed overexpression of IGFBP3 and OLFM4 in 70% and 75% of the tested cases, respectively. Our study illustrates quantitative proteomics of secretome as a robust approach for identification of potential HNSCC biomarkers. This article is part of a Special Issue entitled: An Updated Secretome. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantitative Proteomic Profiling of Low Dose Ionizing Radiation Effects in a Human Skin Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hengel, Shawna; Aldrich, Joshua T.; Waters, Katrina M.

2014-07-29

To assess molecular responses to low doses of radiation that may be encountered during medical diagnostic procedures, nuclear accidents, or terrorist acts, a quantitative global proteomic approach was used to identify protein alterations in a reconstituted human skin tissue treated with 10 cGy of ionizing radiation. Subcellular fractionation was employed to remove highly abundant structural proteins and provide insight on radiation induced alterations in protein abundance and localization. In addition, peptides were post-fractionated using high resolution 2-dimensional liquid chromatography to increase the dynamic range of detection of protein abundance and translocation changes. Quantitative data was obtained by labeling peptides withmore » 8-plex isobaric iTRAQ tags. A total of 207 proteins were detected with statistically significant alterations in abundance and/or subcellular localization compared to sham irradiated tissues. Bioinformatics analysis of the data indicated that the top canonical pathways affected by low dose radiation are related to cellular metabolism. Among the proteins showing alterations in abundance, localization and proteolytic processing was the skin barrier protein filaggrin which is consistent with our previous observation that ionizing radiation alters profilaggrin processing with potential effects on skin barrier functions. In addition, a large number of proteases and protease regulators were affected by low dose radiation exposure indicating that altered proteolytic activity may be a hallmark of low dose radiation exposure. While several studies have demonstrated altered transcriptional regulation occurs following low dose radiation exposures, the data presented here indicates post-transcriptional regulation of protein abundance, localization, and proteolytic processing play an important role in regulating radiation responses in complex human tissues.« less

Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Tran H.; Brechenmacher, Laurent; Aldrich, Joshua T.

2012-11-11

Root hairs are single hair-forming cells on roots that function to increase root surface area, enhancing water and nutrient uptake. In leguminous plants, root hairs also play a critical role as the site of infection by symbiotic nitrogen fixing rhizobia, leading to the formation of a novel organ, the nodule. The initial steps in the rhizobia-root hair infection process are known to involve specific receptor kinases and subsequent kinase cascades. Here, we characterize the phosphoproteome of the root hairs and the corresponding stripped roots (i.e., roots from which root hairs were removed) during rhizobial colonization and infection to gain insightmore » into the molecular mechanism of root hair cell biology. We chose soybean (Glycine max L.), one of the most important crop plants in the legume family, for this study because of its larger root size, which permits isolation of sufficient root hair material for phosphoproteomic analysis. Phosphopeptides derived from root hairs and stripped roots, mock inoculated or inoculated with the soybean-specific rhizobium Bradyrhizobium japonicum, were labeled with the isobaric tag 8-plex ITRAQ, enriched using Ni-NTA magnetic beads and subjected to nRPLC-MS/MS analysis using HCD and decision tree guided CID/ETD strategy. A total of 1,625 unique phosphopeptides, spanning 1,659 non-redundant phosphorylation sites, were detected from 1,126 soybean phosphoproteins. Among them, 273 phosphopeptides corresponding to 240 phosphoproteins were found to be significantly regulated (>1.5 fold abundance change) in response to inoculation with B. japonicum. The data reveal unique features of the soybean root hair phosphoproteome, including root hair and stripped root-specific phosphorylation suggesting a complex network of kinase-substrate and phosphatase-substrate interactions in response to rhizobial inoculation.« less

Multidimensional spectrometer

DOEpatents

Zanni, Martin Thomas; Damrauer, Niels H.

2010-07-20

A multidimensional spectrometer for the infrared, visible, and ultraviolet regions of the electromagnetic spectrum, and a method for making multidimensional spectroscopic measurements in the infrared, visible, and ultraviolet regions of the electromagnetic spectrum. The multidimensional spectrometer facilitates measurements of inter- and intra-molecular interactions.

Automation of sample preparation for mass cytometry barcoding in support of clinical research: protocol optimization.

PubMed

Nassar, Ala F; Wisnewski, Adam V; Raddassi, Khadir

2017-03-01

Analysis of multiplexed assays is highly important for clinical diagnostics and other analytical applications. Mass cytometry enables multi-dimensional, single-cell analysis of cell type and state. In mass cytometry, the rare earth metals used as reporters on antibodies allow determination of marker expression in individual cells. Barcode-based bioassays for CyTOF are able to encode and decode for different experimental conditions or samples within the same experiment, facilitating progress in producing straightforward and consistent results. Herein, an integrated protocol for automated sample preparation for barcoding used in conjunction with mass cytometry for clinical bioanalysis samples is described; we offer results of our work with barcoding protocol optimization. In addition, we present some points to be considered in order to minimize the variability of quantitative mass cytometry measurements. For example, we discuss the importance of having multiple populations during titration of the antibodies and effect of storage and shipping of labelled samples on the stability of staining for purposes of CyTOF analysis. Data quality is not affected when labelled samples are stored either frozen or at 4 °C and used within 10 days; we observed that cell loss is greater if cells are washed with deionized water prior to shipment or are shipped in lower concentration. Once the labelled samples for CyTOF are suspended in deionized water, the analysis should be performed expeditiously, preferably within the first hour. Damage can be minimized if the cells are resuspended in phosphate-buffered saline (PBS) rather than deionized water while waiting for data acquisition.

Optimizing area under the ROC curve using semi-supervised learning

PubMed Central

Wang, Shijun; Li, Diana; Petrick, Nicholas; Sahiner, Berkman; Linguraru, Marius George; Summers, Ronald M.

2014-01-01

Receiver operating characteristic (ROC) analysis is a standard methodology to evaluate the performance of a binary classification system. The area under the ROC curve (AUC) is a performance metric that summarizes how well a classifier separates two classes. Traditional AUC optimization techniques are supervised learning methods that utilize only labeled data (i.e., the true class is known for all data) to train the classifiers. In this work, inspired by semi-supervised and transductive learning, we propose two new AUC optimization algorithms hereby referred to as semi-supervised learning receiver operating characteristic (SSLROC) algorithms, which utilize unlabeled test samples in classifier training to maximize AUC. Unlabeled samples are incorporated into the AUC optimization process, and their ranking relationships to labeled positive and negative training samples are considered as optimization constraints. The introduced test samples will cause the learned decision boundary in a multidimensional feature space to adapt not only to the distribution of labeled training data, but also to the distribution of unlabeled test data. We formulate the semi-supervised AUC optimization problem as a semi-definite programming problem based on the margin maximization theory. The proposed methods SSLROC1 (1-norm) and SSLROC2 (2-norm) were evaluated using 34 (determined by power analysis) randomly selected datasets from the University of California, Irvine machine learning repository. Wilcoxon signed rank tests showed that the proposed methods achieved significant improvement compared with state-of-the-art methods. The proposed methods were also applied to a CT colonography dataset for colonic polyp classification and showed promising results.1 PMID:25395692

Optimizing area under the ROC curve using semi-supervised learning.

PubMed

Wang, Shijun; Li, Diana; Petrick, Nicholas; Sahiner, Berkman; Linguraru, Marius George; Summers, Ronald M

2015-01-01

Receiver operating characteristic (ROC) analysis is a standard methodology to evaluate the performance of a binary classification system. The area under the ROC curve (AUC) is a performance metric that summarizes how well a classifier separates two classes. Traditional AUC optimization techniques are supervised learning methods that utilize only labeled data (i.e., the true class is known for all data) to train the classifiers. In this work, inspired by semi-supervised and transductive learning, we propose two new AUC optimization algorithms hereby referred to as semi-supervised learning receiver operating characteristic (SSLROC) algorithms, which utilize unlabeled test samples in classifier training to maximize AUC. Unlabeled samples are incorporated into the AUC optimization process, and their ranking relationships to labeled positive and negative training samples are considered as optimization constraints. The introduced test samples will cause the learned decision boundary in a multidimensional feature space to adapt not only to the distribution of labeled training data, but also to the distribution of unlabeled test data. We formulate the semi-supervised AUC optimization problem as a semi-definite programming problem based on the margin maximization theory. The proposed methods SSLROC1 (1-norm) and SSLROC2 (2-norm) were evaluated using 34 (determined by power analysis) randomly selected datasets from the University of California, Irvine machine learning repository. Wilcoxon signed rank tests showed that the proposed methods achieved significant improvement compared with state-of-the-art methods. The proposed methods were also applied to a CT colonography dataset for colonic polyp classification and showed promising results.

Experimental Aspects of Polarization Optimized Experiments (POE) for Magic Angle Spinning Solid-State NMR of Microcrystalline and Membrane-Bound Proteins.

PubMed

Gopinath, T; Veglia, Gianluigi

2018-01-01

Conventional NMR pulse sequences record one spectrum per experiment, while spending most of the time waiting for the spin system to return to the equilibrium. As a result, a full set of multidimensional NMR experiments for biological macromolecules may take up to several months to complete. Here, we present a practical guide for setting up a new class of MAS solid-state NMR experiments (POE or polarization optimized experiments) that enable the simultaneous acquisition of multiple spectra of proteins, accelerating data acquisition. POE exploit the long-lived 15 N polarization of isotopically labeled proteins and enable one to obtain up to eight spectra, by concatenating classical NMR pulse sequences. This new strategy propels data throughput of solid-state NMR spectroscopy of fibers, microcrystalline preparations, as well as membrane proteins.

Large scale preparation of high mannose and paucimannose N-glycans from soybean proteins by oxidative release of natural glycans (ORNG).

PubMed

Zhu, Yuyang; Yan, Maomao; Lasanajak, Yi; Smith, David F; Song, Xuezheng

2018-07-15

Despite the important advances in chemical and chemoenzymatic synthesis of glycans, access to large quantities of complex natural glycans remains a major impediment to progress in Glycoscience. Here we report a large-scale preparation of N-glycans from a kilogram of commercial soy proteins using oxidative release of natural glycans (ORNG). The high mannose and paucimannose N-glycans were labeled with a fluorescent tag and purified by size exclusion and multidimensional preparative HPLC. Side products are identified and potential mechanisms for the oxidative release of natural N-glycans from glycoproteins are proposed. This study demonstrates the potential for using the ORNG approach as a complementary route to synthetic approaches for the preparation of multi-milligram quantities of biomedically relevant complex glycans. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mechanisms of Surface-Mediated DNA Hybridization

PubMed Central

2015-01-01

Single-molecule total internal reflection fluorescence microscopy was employed in conjunction with resonance energy transfer (RET) to observe the dynamic behavior of donor-labeled ssDNA at the interface between aqueous solution and a solid surface decorated with complementary acceptor-labeled ssDNA. At least 100 000 molecular trajectories were determined for both complementary strands and negative control ssDNA. RET was used to identify trajectory segments corresponding to the hybridized state. The vast majority of molecules from solution adsorbed nonspecifically to the surface, where a brief two-dimensional search was performed with a 7% chance of hybridization. Successful hybridization events occurred with a characteristic search time of ∼0.1 s, and unsuccessful searches resulted in desorption from the surface, ultimately repeating the adsorption and search process. Hybridization was reversible, and two distinct modes of melting (i.e., dehybridization) were observed, corresponding to long-lived (∼15 s) and short-lived (∼1.4 s) hybridized time intervals. A strand that melted back onto the surface could rehybridize after a brief search or desorb from the interface. These mechanistic observations provide guidance for technologies that involve DNA interactions in the near-surface region, suggesting a need to design surfaces that both enhance the complex multidimensional search process and stabilize the hybridized state. PMID:24708278

Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose

PubMed Central

Mori, Tetsuya; Tsuboi, Yuuri; Ishida, Nobuhiro; Nishikubo, Nobuyuki; Demura, Taku; Kikuchi, Jun

2015-01-01

Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components. PMID:26143886

Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways

PubMed Central

Chikayama, Eisuke; Suto, Michitaka; Nishihara, Takashi; Shinozaki, Kazuo; Hirayama, Takashi; Kikuchi, Jun

2008-01-01

Background Metabolic phenotyping has become an important ‘bird's-eye-view’ technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of ‘top-down’ chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. Methodology/Principal Findings The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 1H and 13C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each 13C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient 13C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. Conclusions/Significance Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of 13C atoms of given metabolites on development-dependent changes in the 56 identified 13C-HSQC signals, we have determined the changes in metabolic networks that are associated with energy and nitrogen metabolism. PMID:19030231

Numeric invariants from multidimensional persistence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skryzalin, Jacek; Carlsson, Gunnar

2017-05-19

In this paper, we analyze the space of multidimensional persistence modules from the perspectives of algebraic geometry. We first build a moduli space of a certain subclass of easily analyzed multidimensional persistence modules, which we construct specifically to capture much of the information which can be gained by using multidimensional persistence over one-dimensional persistence. We argue that the global sections of this space provide interesting numeric invariants when evaluated against our subclass of multidimensional persistence modules. Lastly, we extend these global sections to the space of all multidimensional persistence modules and discuss how the resulting numeric invariants might be usedmore » to study data.« less

Factor Structure of the Brief Multidimensional Measure of Religiousness/Spirituality in US and Indian Samples with Traumatic Brain Injury.

PubMed

Johnstone, Brick; Bhushan, Braj; Hanks, Robin; Yoon, Dong Pil; Cohen, Daniel

2016-04-01

The aim of this paper was to determine the factor structure of the Brief Multidimensional Measure of Religiousness/Spirituality (BMMRS) based on a sample of individuals from diverse cultures (i.e., USA, India), ethnicities (i.e., Caucasian, African-American, South Asian), and religions (i.e., Christian, Muslim, Hindu). A total of 109 individuals with traumatic brain injury (TBI) were included. Participants completed the BMMRS as part of a broader study on spirituality, religion, prosocial behaviors, and neuropsychological function. A principal components factor analysis with varimax rotation and Kaiser normalization identified a six-factor solution accounting for 72% of the variance in scores. Five of the factors were deemed to be interpretable and were labeled based on face validity as: (1) Positive Spirituality/Religious Practices; (2) Positive Congregational Support; (3) Negative Spirituality/Negative Congregational Support; (4) Organizational Religion; and (5) Forgiveness. The results were generally consistent with previous studies, suggesting the existence of universal religious, spiritual, and congregational support factors across different cultures and faith traditions. For health outcomes research, it is suggested that the BMMRS factors may be best conceptualized as measuring the following general domains: (a) emotional connectedness with a higher power (i.e., spirituality, positive/negative); (b) culturally based behavioral practices (i.e., religion); and (c) social support (i.e., positive/negative). The results indicate that factor relationships may differ among spiritual, religious, and congregational support variables according to culture and/or religious tradition.

Using Explanatory Item Response Models to Evaluate Complex Scientific Tasks Designed for the Next Generation Science Standards

NASA Astrophysics Data System (ADS)

Chiu, Tina

This dissertation includes three studies that analyze a new set of assessment tasks developed by the Learning Progressions in Middle School Science (LPS) Project. These assessment tasks were designed to measure science content knowledge on the structure of matter domain and scientific argumentation, while following the goals from the Next Generation Science Standards (NGSS). The three studies focus on the evidence available for the success of this design and its implementation, generally labelled as "validity" evidence. I use explanatory item response models (EIRMs) as the overarching framework to investigate these assessment tasks. These models can be useful when gathering validity evidence for assessments as they can help explain student learning and group differences. In the first study, I explore the dimensionality of the LPS assessment by comparing the fit of unidimensional, between-item multidimensional, and Rasch testlet models to see which is most appropriate for this data. By applying multidimensional item response models, multiple relationships can be investigated, and in turn, allow for a more substantive look into the assessment tasks. The second study focuses on person predictors through latent regression and differential item functioning (DIF) models. Latent regression models show the influence of certain person characteristics on item responses, while DIF models test whether one group is differentially affected by specific assessment items, after conditioning on latent ability. Finally, the last study applies the linear logistic test model (LLTM) to investigate whether item features can help explain differences in item difficulties.

A theoretical framework for the associations between identity and psychopathology.

PubMed

Klimstra, Theo A; Denissen, Jaap J A

2017-11-01

Identity research largely emerged from clinical observations. Decades of empirical work advanced the field in refining existing approaches and adding new approaches. Furthermore, the existence of linkages of identity with psychopathology is now well established. Unfortunately, both the directionality of effects between identity aspects and psychopathology symptoms, and the mechanisms underlying associations are unclear. In the present paper, we present a new framework to inspire hypothesis-driven empirical research to overcome this limitation. The framework has a basic resemblance to theoretical models for the study of personality and psychopathology, so we provide examples of how these might apply to the study of identity. Next, we explain that unique features of identity may come into play in individuals suffering from psychopathology that are mostly related to the content of one's identity. These include pros and cons of identifying with one's diagnostic label. Finally, inspired by Hermans' dialogical self theory and principles derived from Piaget's, Swann's and Kelly's work, we delineate a framework with identity at the core of an individual multidimensional space. In this space, psychopathology symptoms have a known distance (representing relevance) to one's identity, and individual multidimensional spaces are connected to those of other individuals in one's social network. We discuss methodological (quantitative and qualitative, idiographic and nomothetic) and statistical procedures (multilevel models and network models) to test the framework. Resulting evidence can boost the field of identity research in demonstrating its high practical relevance for the emergence and conservation of psychopathology. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A Comparative Study of Online Item Calibration Methods in Multidimensional Computerized Adaptive Testing

ERIC Educational Resources Information Center

Chen, Ping

2017-01-01

Calibration of new items online has been an important topic in item replenishment for multidimensional computerized adaptive testing (MCAT). Several online calibration methods have been proposed for MCAT, such as multidimensional "one expectation-maximization (EM) cycle" (M-OEM) and multidimensional "multiple EM cycles"…

Best Design for Multidimensional Computerized Adaptive Testing with the Bifactor Model

ERIC Educational Resources Information Center

Seo, Dong Gi; Weiss, David J.

2015-01-01

Most computerized adaptive tests (CATs) have been studied using the framework of unidimensional item response theory. However, many psychological variables are multidimensional and might benefit from using a multidimensional approach to CATs. This study investigated the accuracy, fidelity, and efficiency of a fully multidimensional CAT algorithm…

Multidimensional Measurement of Poverty among Women in Sub-Saharan Africa

ERIC Educational Resources Information Center

Batana, Yele Maweki

2013-01-01

Since the seminal work of Sen, poverty has been recognized as a multidimensional phenomenon. The recent availability of relevant databases renewed the interest in this approach. This paper estimates multidimensional poverty among women in fourteen Sub-Saharan African countries using the Alkire and Foster multidimensional poverty measures, whose…

The Efficacy of Multidimensional Constraint Keys in Database Query Performance

ERIC Educational Resources Information Center

Cardwell, Leslie K.

2012-01-01

This work is intended to introduce a database design method to resolve the two-dimensional complexities inherent in the relational data model and its resulting performance challenges through abstract multidimensional constructs. A multidimensional constraint is derived and utilized to implement an indexed Multidimensional Key (MK) to abstract a…

A Comprehensive Analysis of Chromoplast Differentiation Reveals Complex Protein Changes Associated with Plastoglobule Biogenesis and Remodeling of Protein Systems in Sweet Orange Flesh1[OPEN

PubMed Central

Wang, Lun; Deng, Xiuxin

2015-01-01

Globular and crystalloid chromoplasts were observed to be region specifically formed in sweet orange (Citrus sinensis) flesh and converted from amyloplasts during fruit maturation, which was associated with the composition of specific carotenoids and the expression of carotenogenic genes. Subsequent isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analyses of purified plastids from the flesh during chromoplast differentiation and senescence identified 1,386 putative plastid-localized proteins, 1,016 of which were quantified by spectral counting. The iTRAQ values reflecting the expression abundance of three identified proteins were validated by immunoblotting. Based on iTRAQ data, chromoplastogenesis appeared to be associated with three major protein expression patterns: (1) marked decrease in abundance of the proteins participating in the translation machinery through ribosome assembly; (2) increase in abundance of the proteins involved in terpenoid biosynthesis (including carotenoids), stress responses (redox, ascorbate, and glutathione), and development; and (3) maintenance of the proteins for signaling and DNA and RNA. Interestingly, a strong increase in abundance of several plastoglobule-localized proteins coincided with the formation of plastoglobules in the chromoplast. The proteomic data also showed that stable functioning of protein import, suppression of ribosome assembly, and accumulation of chromoplast proteases are correlated with the amyloplast-to-chromoplast transition; thus, these processes may play a collective role in chromoplast biogenesis and differentiation. By contrast, the chromoplast senescence process was inferred to be associated with significant increases in stress response and energy supply. In conclusion, this comprehensive proteomic study identified many potentially new plastid-localized proteins and provides insights into the potential developmental and molecular mechanisms underlying chromoplast biogenesis, differentiation, and senescence in sweet orange flesh. PMID:26056088

Comparative analysis of two femtosecond LASIK platforms using iTRAQ quantitative proteomics.

PubMed

D'Souza, Sharon; Petznick, Andrea; Tong, Louis; Hall, Reece C; Rosman, Mohamad; Chan, Cordelia; Koh, Siew Kwan; Beuerman, Roger W; Zhou, Lei; Mehta, Jodhbir S

2014-05-06

New femtosecond laser platforms may reduce ocular surface interference and LASIK-associated dry eye. This study investigated tear protein profiles in subjects who underwent LASIK using two femtosecond lasers to assess differences in protein expression. This was a randomized interventional clinical trial involving 22 patients who underwent femtosecond laser refractive surgery with a contralateral paired eye design. Corneal flaps of 22 subjects were created by either Visumax or Intralase laser. Tear samples were collected preoperatively, and at 1 week and 3 months postoperatively using Schirmer's strips. Tear protein ratios were calculated relative to preoperative protein levels at baseline. The main outcome measures were the levels of a panel of dry eye protein markers analyzed using isobaric tagging for relative and absolute quantitation (iTRAQ) mass spectrometry. A total of 824 unique proteins were quantifiable. Tear protein ratios were differentially regulated between the eyes treated with different lasers. The secretoglobulins Lipophilin A (1.80-fold) and Lipophilin C (1.77) were significantly upregulated (P < 0.05) at 1 week postoperatively in Visumax but not in Intralase-treated eyes. At 1 week, orosomucoid1 was upregulated (1.78) in Intralase but not Visumax-treated eyes. In the same eyes, lysozyme, cathepsin B, and lipo-oxygenase were downregulated at 0.44-, 0.64-, and 0.64-folds, respectively. Transglutaminase-2 was downregulated in both groups of eyes. Different laser platforms induce distinct biological responses in the cornea and ocular surface, which manifests as different levels of tear proteins. This study has implications for surgical technology and modulation of wound healing responses. (ClinicalTrials.gov number, NCT01252654.). Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

Identification of diverse defense mechanisms in rainbow trout red blood cells in response to halted replication of VHS virus.

PubMed

Nombela, Ivan; Puente-Marin, Sara; Chico, Veronica; Villena, Alberto J; Carracedo, Begoña; Ciordia, Sergio; Mena, Maria Carmen; Mercado, Luis; Perez, Luis; Coll, Julio; Estepa, Amparo; Ortega-Villaizan, Maria Del Mar

2017-01-01

Background: It has been described that fish nucleated red blood cells (RBCs) generate a wide variety of immune-related gene transcripts when viruses highly replicate inside them and are their main target cell. The immune response and mechanisms of fish RBCs against viruses targeting other cells or tissues has not yet been explored and is the objective of our study. Methods: Rainbow trout RBCs were obtained from peripheral blood, ficoll purified and exposed to Viral Haemorrhagic Septicaemia virus (VHSV). Immune response was evaluated by means of RT-qPCR, flow cytometry, immunofluorescence and isobaric tag for relative and absolute quantification (iTRAQ) protein profiling. Results: VHSV N gene transcripts incremented early postexposure and were drastically decreased after 6 hours postexposure (hpe). The expression of type I interferon ( ifn1 ) gene was significantly downregulated at early postexposure (3 hpe), together with a gradual downregulation of interferon-inducible mx and pkr genes until 72 hpe. Type I IFN protein was downregulated and interferon-inducible Mx protein was maintained at basal levels. Co-culture assays of RBCs, previously exposed to UV-inactivated VHSV, and TSS (stromal cell line from spleen) revealed IFN crosstalk between both cell types. On the other hand, anti-microbial peptide β-defensin 1 and neutrophil chemotactic factor interleukin 8 were slightly upregulated in VHSV-exposed RBCs. iTRAQ profiling revealed that VHSV exposure can induce a global protein downregulation in rainbow trout RBCs, mainly related to RNA stability and proteasome pathways. Antioxidant/antiviral response is also suggested to be involved in the response of rainbow trout RBCs to VHSV. Conclusions: A variety of mechanisms are proposed to be implicated in the antiviral response of rainbow trout RBCs against VHSV halted infection. Ongoing research is focused on understanding the mechanisms in detail.

Investigation of serum biomarkers in primary gout patients using iTRAQ-based screening.

PubMed

Ying, Ying; Chen, Yong; Zhang, Shun; Huang, Haiyan; Zou, Rouxin; Li, Xiaoke; Chu, Zanbo; Huang, Xianqian; Peng, Yong; Gan, Minzhi; Geng, Baoqing; Zhu, Mengya; Ying, Yinyan; Huang, Zuoan

2018-03-21

Primary gout is a major disease that affects human health; however, its pathogenesis is not well known. The purpose of this study was to identify biomarkers to explore the underlying mechanisms of primary gout. We used the isobaric tags for relative and absolute quantitation (iTRAQ) technique combined with liquid chromatography-tandem mass spectrometry to screen differentially expressed proteins between gout patients and controls. We also identified proteins potentially involved in gout pathogenesis by analysing biological processes, cellular components, molecular functions, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and protein-protein interactions. We further verified some samples using enzyme-linked immunosorbent assay (ELISA). Statistical analyses were carried out using SPSS v. 20.0 and ROC (receiver operating characterstic) curve analyses were carried out using Medcalc software. Two-sided p-values <0.05 were deemed to be statistically significant for all analyses. We identified 95 differentially expressed proteins (50 up-regulated and 45 down-regulated), and selected nine proteins (α-enolase (ENOA), glyceraldehyde-3-phosphate dehydrogenase (G3P), complement component C9 (CO9), profilin-1 (PROF1), lipopolysaccharide-binding protein (LBP), tubulin beta-4A chain (TBB4A), phosphoglycerate kinase (PGK1), glucose-6-phosphate isomerase (G6PI), and transketolase (TKT)) for verification. This showed that the level of TBB4A was significantly higher in primary gout than in controls (p=0.023). iTRAQ technology was useful in the selection of differentially expressed proteins from proteomes, and provides a strong theoretical basis for the study of biomarkers and mechanisms in primary gout. In addition, TBB4A protein may be associated with primary gout.

Insight into Enzymatic Degradation of Corn, Wheat, and Soybean Cell Wall Cellulose Using Quantitative Secretome Analysis of Aspergillus fumigatus.

PubMed

Sharma Ghimire, Prakriti; Ouyang, Haomiao; Wang, Qian; Luo, Yuanming; Shi, Bo; Yang, Jinghua; Lü, Yang; Jin, Cheng

2016-12-02

Lignocelluloses contained in animal forage cannot be digested by pigs or poultry with 100% efficiency. On contrary, Aspergillus fumigatus, a saprophytic filamentous fungus, is known to harbor 263 glycoside hydrolase encoding genes, suggesting that A. fumigatus is an efficient lignocellulose degrader. Hence the present study uses corn, wheat, or soybean as a sole carbon source to culture A. fumigatus under animal physiological condition to understand how cellulolytic enzymes work together to achieve an efficient degradation of lignocellulose. Our results showed that A. fumigatus produced different sets of enzymes to degrade lignocelluloses derived from corn, wheat, or soybean cell wall. In addition, the cellulolytic enzymes produced by A. fumigatus were stable under acidic condition or at higher temperatures. Using isobaric tags for a relative and absolute quantification (iTRAQ) approach, a total of ∼600 extracellular proteins were identified and quantified, in which ∼50 proteins were involved in lignocellulolysis, including cellulases, hemicellulases, lignin-degrading enzymes, and some hypothetical proteins. Data are available via ProteomeXchange with identifier PXD004670. On the basis of quantitative iTRAQ results, 14 genes were selected for further confirmation by RT-PCR. Taken together, our results indicated that the expression and regulation of lignocellulolytic proteins in the secretome of A. fumigatus were dependent on both nature and complexity of cellulose, thus suggesting that a different enzyme system is required for degradation of different lignocelluloses derived from plant cells. Although A. fumigatus is a pathogenic fungus and cannot be directly used as an enzyme source, as an efficient lignocellulose degrader its strategy to synergistically degrade various lignocelluloses with different enzymes can be used to design enzyme combination for optimal digestion and absorption of corn, wheat, or soybean that are used as forage of pig and poultry.

Biochemical and proteomic analyses of the physiological response induced by individual housing in gilts provide new potential stress markers.

PubMed

Marco-Ramell, Anna; Arroyo, Laura; Peña, Raquel; Pato, Raquel; Saco, Yolanda; Fraile, Lorenzo; Bendixen, Emøke; Bassols, Anna

2016-11-25

The objective assessment of animal stress and welfare requires proper laboratory biomarkers. In this work, we have analyzed the changes in serum composition in gilts after switching their housing, from pen to individual stalls, which is generally accepted to cause animal discomfort. Blood and saliva samples were collected a day before and up to four days after changing the housing system. Biochemical analyses showed adaptive changes in lipid and protein metabolism after the housing switch, whereas cortisol and muscular markers showed a large variability between animals. 2D-DIGE and iTRAQ proteomic approaches revealed variations in serum protein composition after changing housing and diet of gilts. Both techniques showed alterations in two main homeostatic mechanisms: the innate immune and redox systems. The acute phase proteins haptoglobin, apolipoprotein A-I and α1-antichymotrypsin 3, and the antioxidant enzyme peroxiredoxin 2 were found differentially expressed by 2D-DIGE. Other proteins related to the innate immune system, including lactotransferrin, protegrin 3 and galectin 1 were also identified by iTRAQ, as well as oxidative stress enzymes such as peroxiredoxin 2 and glutathione peroxidase 3. Proteomics also revealed the decrease of apolipoproteins, and the presence of intracellular proteins in serum, which may indicate physical injury to tissues. Housing of gilts in individual stalls and diet change increase lipid and protein catabolism, oxidative stress, activate the innate immune system and cause a certain degree of tissue damage. We propose that valuable assays for stress assessment in gilts may be based on a score composed by a combination of salivary cortisol, lipid metabolites, innate immunity and oxidative stress markers and intracellular proteins.

Differential proteomic analysis reveals sequential heat stress-responsive regulatory network in radish (Raphanus sativus L.) taproot.

PubMed

Wang, Ronghua; Mei, Yi; Xu, Liang; Zhu, Xianwen; Wang, Yan; Guo, Jun; Liu, Liwang

2018-05-01

Differential abundance protein species (DAPS) involved in reducing damage and enhancing thermotolerance in radish were firstly identified. Proteomic analysis and omics association analysis revealed a HS-responsive regulatory network in radish. Heat stress (HS) is a major destructive factor influencing radish production and supply in summer, for radish is a cool season vegetable crop being susceptible to high temperature. In this study, the proteome changes of radish taproots under 40 °C treatment at 0 h (Control), 12 h (Heat12) and 24 h (Heat24) were analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification) approach. In total, 2258 DAPS representing 1542 differentially accumulated uniprotein species which respond to HS were identified. A total of 604, 910 and 744 DAPS was detected in comparison of Control vs. Heat12, Control vs. Heat24, and Heat12 vs. Heat24, respectively. Gene ontology and pathway analysis showed that annexin, ubiquitin-conjugating enzyme, ATP synthase, heat shock protein (HSP) and other stress-related proteins were predominately enriched in signal transduction, stress and defense pathways, photosynthesis and energy metabolic pathways, working cooperatively to reduce stress-induced damage in radish. Based on iTRAQ combined with the transcriptomics analysis, a schematic model of a sequential HS-responsive regulatory network was proposed. The initial sensing of HS occurred at the plasma membrane, and then key components of stress signal transduction triggered heat-responsive genes in the plant protective metabolism to re-establish homeostasis and enhance thermotolerance. These results provide new insights into characteristics of HS-responsive DAPS and facilitate dissecting the molecular mechanisms underlying heat tolerance in radish and other root crops.

Comparative proteomic study on Brassica hexaploid and its parents provides new insights into the effects of polyploidization.

PubMed

Shen, Yanyue; Zhang, Yu; Zou, Jun; Meng, Jinling; Wang, Jianbo

2015-01-01

Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. Although genomic and transcriptomic changes have been observed in polyploids, the effects of polyploidization on proteomic divergence are poorly understood. In this study, we reported quantitative analysis of proteomic changes in leaves of Brassica hexaploid and its parents using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with mass spectrometry. A total of 2044 reproducible proteins were quantified by at least two unique peptides. We detected 452 proteins differentially expressed between Brassica hexaploid and its parents, and 100 proteins were non-additively expressed in Brassica hexaploid, which suggested a trend of non-additive protein regulation following genomic merger and doubling. Functional categories of cellular component biogenesis, immune system process, and response to stimulus, were significantly enriched in non-additive proteins, probably providing a driving force for variation and adaptation in allopolyploids. In particular, majority of the total 452 differentially expressed proteins showed expression level dominance of one parental expression, and there was an expression level dominance bias toward the tetraploid progenitor. In addition, the percentage of differentially expressed proteins that matched previously reported differentially genes were relatively low. This study aimed to get new insights into the effects of polyploidization on proteomic divergence. Using iTRAQ LC-MS/MS technology, we identified 452 differentially expressed proteins between allopolyploid and its parents which involved in response to stimulus, multi-organism process, and immune system process, much more than previous studies using 2-DE coupled with mass spectrometry technology. Therefore, our manuscript represents the most comprehensive analysis of protein profiles in allopolyploid and its parents, which will lead to a better understanding of novelty and plasticity of the allopolyploid genomes. Copyright © 2014 Elsevier B.V. All rights reserved.

iTRAQ-based proteomic profile analysis of ISKNV-infected CPB cells with emphasizing on glucose metabolism, apoptosis and autophagy pathways.

PubMed

Wu, Shiwei; Yu, Lujun; Fu, Xiaozhe; Yan, Xi; Lin, Qiang; Liu, Lihui; Liang, Hongru; Li, Ningqiu

2018-05-04

Infectious spleen and kidney necrosis virus (ISKNV) has caused significant losses in the cultured mandarin fish (Siniperca chuatsi) industry. The molecular mechanisms that underlie interaction between ISKNV and hosts are not fully understood. In this study, the proteomic profile of CPB cells at progressive time points after ISKNV infection was analyzed by isobaric tags for relative and absolute quantitation (iTRAQ). A total of 2731 proteins corresponding to 6363 novel peptides (false discovery rate <0.01) were identified. In the samples harvested 24 h (early-stage) and 72 h (late-stage) post-infection, 232 and 199 differentially expressed proteins were identified comparing with mock-infected cells, respectively. Western-blotting analysis of several proteins as G6PDH, β-tubulin and RPL11 were done to validate iTRAQ data. Among those differentially expressed proteins, several glucose metabolism-related enzymes, including glucose-6-phosphate dehydrogenase (G6PDH), pyruvate dehydrogenase phosphatase (PDP) and fumarate hydratase (FH), were up-regulated, while pyruvate dehydrogenase kinase (PDK) and enolase (ENO) were down-regulated at 24 h poi, suggesting that ISKNV enhanced glucose metabolism in CPB cells in early-stage infection. Simultaneously, expression of apoptosis-related proteins including Caspase 8, phosphoinositide 3-kinases (PI3Ks), and regulatory-associated protein of mTOR-like isoform X3 changed upon ISKNV infection, indicating that ISKNV induced apoptosis of CPB cells. Autophagy-related proteins including LC3 and PI3Ks were up-regulated at 24 h poi, indicating that ISKNV induced autophagy of CPB cells in early-stage infection. These findings may improve the understanding of ISKNV and host interaction and help clarify its pathogenesis mechanisms. Copyright © 2018. Published by Elsevier Ltd.

The depressed central carbon and energy metabolisms is associated to the acquisition of levofloxacin resistance in Vibrio alginolyticus.

PubMed

Cheng, Zhi-Xue; Yang, Man-Jun; Peng, Bo; Peng, Xuan-Xian; Lin, Xiang-Min; Li, Hui

2018-06-15

The overuse and misuse of antibiotics lead to bacterial antibiotic resistance, challenging human health and intensive cultivation. It is especially required to understand for the mechanism of antibiotic resistance to control antibiotic-resistant pathogens. The present study characterized the differential proteome of levofloxacin-resistant Vibrio alginolyticus with the most advanced iTRAQ quantitative proteomics technology. A total of 160 proteins of differential abundance were identified, where 70 were decreased and 90 were increased. Further analysis demonstrated that crucial metabolic pathways like TCA cycle were significantly down-regulated. qRT-PCR analysis demonstrated the decreased gene expression of glycolysis/gluconeogenesis, the TCA cycle, and fatty acid biosynthesis. Moreover, Na(+)-NQR complex gene expression, membrane potential and the adenylate energy charge ratio were decreased, indicating that the decreased central carbon metabolism is associated to the acquisition of levofloxacin resistance. Therefore, the reduced central carbon and energy metabolisms form a characteristic feature as fitness costs of V. alginolyticus in resistance to levofloxacin. The overuse and misuse of antibiotics lead to bacterial antibiotic resistance, challenging human health and intensive cultivation. Understanding for the antibiotic resistance mechanisms is especially required to control these antibiotic-resistant pathogens. The present study characterized the differential proteome of levofloxacin-resistant Vibrio alginolyticus using the most advanced iTRAQ quantitative proteomics technology. A total of 160 differential abundance of proteins were identified with 70 decreases and 90 increases by liquid chromatography matrix assisted laser desorption ionization mass spectrometry. Most interestingly, crucial metabolic pathways such as the TCA cycle sharply fluctuated. This is the first report that the reduced central carbon and energy metabolisms form a characteristic feature as a mechanism of V. alginolyticus in resistance to levofloxacin. Copyright © 2018 Elsevier B.V. All rights reserved.

Proteomic Markers of Functional Sperm Population in Bovines: Comparison of Low- and High-Density Spermatozoa Following Cryopreservation.

PubMed

D'Amours, Olivier; Frenette, Gilles; Bourassa, Sylvie; Calvo, Ézéchiel; Blondin, Patrick; Sullivan, Robert

2018-01-05

Mammalian semen contains a heterogeneous population of sperm cells. This heterogeneity results from variability in the complex processes of cell differentiation in the testis, biochemical modifications undergone by spermatozoa during transit along the male reproductive tract, interactions with secretions from accessory sex glands at ejaculation, and, in the context of reproductive technologies, in the ability of ejaculated spermatozoa to resist damage associated with freeze-thaw procedures. When submitted to density gradient centrifugation, ejaculated spermatozoa distribute themselves into two distinct populations: a low-density population characterized by low motility parameters, and a high-density population with high motility characteristics. To understand the origin of ejaculated spermatozoa heterogeneity, cryopreserved semen samples from bulls used by the artificial insemination (A.I.) industry were submitted to Percoll gradient centrifugation. Proteins from low and high density spermatozoa were then extracted with sodium deoxycholate and submitted to proteomic analysis using iTRAQ (isobaric tag for relative and absolute quantitation) methodologies. Quantification of selected sperm proteins was confirmed by multiple reaction monitoring (MRM). Overall, 31 different proteins were more abundant in low-density spermatozoa, while 80 different proteins were more abundant in the high-density subpopulation. Proteins enriched in high-density spermatozoa were markers of sperm functionality such as the glycolytic process, binding to the egg zona pellucida, and motility. Low-density spermatozoa were not solely characterized by loss of proteins and their associated functions. Chaperonin-containing TCP1s and chaperones are hallmarks of the low-density subpopulation. iTRAQ analysis revealed that other proteins such as binder of sperm proteins, histone, GPX5, ELSPBP1, and clusterin are overexpressed in low-density spermatozoa suggesting that these proteins represent defects occurring at different steps during the sperm journey. These differences contribute to the sperm cell heterogeneity present in mammalian semen.

Quantitative Proteomic Profiling of Early and Late Responses to Salicylic Acid in Cucumber Leaves

PubMed Central

Li, Liang; Shang, Qing-Mao

2016-01-01

Salicylic acid (SA) is an important phytohormone that plays vital regulatory roles in plant growth, development, and stress responses. However, studies on the molecular mechanism of SA, especially during the early SA responses, are lagging behind. In this study, we initiated a comprehensive isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis to explore the early and late SA-responsive proteins in leaves of cucumber (Cucumis sativus L.) seedlings. Upon SA application through the roots, endogenous SA accumulated in cucumber leaves. By assaying the changes in marker gene expression and photosynthetic rate, we collected samples at 12 h and 72 h post treatment (hpt) to profile the early and late SA responsiveness, respectively. The iTRAQ assay followed by tandem mass spectrometry revealed 135 differentially expressed proteins (DEPs) at 12 hpt and 301 DEPs at 72 hpt. The functional categories for these SA-responsive proteins included in a variety of biochemical processes, including photosynthesis, redox homeostasis, carbohydrate and energy metabolism, lipid metabolism, transport, protein folding and modification, proteolysis, cell wall organization, and the secondary phenylpropanoid pathway. Conclusively, based on the abundant changes of these DEPs, together with their putative functions, we proposed a possible SA-responsive protein network. It appears that SA could elicit reactive oxygen species (ROS) production via enhancing the photosynthetic electron transferring, and then confer some growth-promoting and stress-priming effects on cells during the late phase, including enhanced photosynthesis and ROS scavenging, altered carbon metabolic flux for the biosynthesis of amino acids and nucleotides, and cell wall reorganization. Overall, the present iTRAQ assay provides higher proteome coverage and deepened our understanding of the molecular basis of SA-responses. PMID:27551830

Identification of p90 Ribosomal S6 Kinase 2 as a Novel Host Protein in HBx Augmenting HBV Replication by iTRAQ-Based Quantitative Comparative Proteomics.

PubMed

Yan, Li-Bo; Yu, You-Jia; Zhang, Qing-Bo; Tang, Xiao-Qiong; Bai, Lang; Huang, FeiJun; Tang, Hong

2018-05-01

The aim of this study was to screen for novel host proteins that play a role in HBx augmenting Hepatitis B virus (HBV) replication. Three HepG2 cell lines stably harboring different functional domains of HBx (HBx, HBx-Cm6, and HBx-Cm16) were cultured. ITRAQ technology integrated with LC-MS/MS analysis was applied to identify the proteome differences among these three cell lines. In brief, a total of 70 different proteins were identified among HepG2-HBx, HepG2-HBx-Cm6, and HepG2-HBx-Cm16 by double repetition. Several differentially expressed proteins, including p90 ribosomal S6 kinase 2 (RSK2), were further validated. RSK2 was expressed at higher levels in HepG2-HBx and HepG2-HBx-Cm6 compared with HepG2-HBx-Cm16. Furthermore, levels of HBV replication intermediates were decreased after silencing RSK2 in HepG2.2.15. An HBx-minus HBV mutant genome led to decreased levels of HBV replication intermediates and these decreases were restored to levels similar to wild-type HBV by transient ectopic expression of HBx. After silencing RSK2 expression, the levels of HBV replication intermediates synthesized from the HBx-minus HBV mutant genome were not restored to levels that were observed with wild-type HBV by transient HBx expression. Based on iTRAQ quantitative comparative proteomics, RSK2 was identified as a novel host protein that plays a role in HBx augmenting HBV replication. © 2018 The Authors. Proteomics - Clinical Application Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integration of Transcriptome, Proteome and Metabolism Data Reveals the Alkaloids Biosynthesis in Macleaya cordata and Macleaya microcarpa

PubMed Central

Liu, Fuqing; Huang, Peng; Zhu, Pengcheng; Chen, Jinjun; Shi, Mingming; Guo, Fang; Cheng, Pi; Zeng, Jing; Liao, Yifang; Gong, Jing; Zhang, Hong-Mei; Wang, Depeng; Guo, An-Yuan; Xiong, Xingyao

2013-01-01

Background The Macleaya spp., including Macleaya cordata and Macleaya microcarpa, are traditional anti-virus, inflammation eliminating, and insecticide herb medicines for their isoquinoline alkaloids. They are also known as the basis of the popular natural animal food addictive in Europe. However, few studies especially at genomics level were conducted on them. Hence, we performed the Macleaya spp. transcriptome and integrated it with iTRAQ proteome analysis in order to identify potential genes involved in alkaloids biosynthesis. Methodology and Principal Findings We elaborately designed the transcriptome, proteome and metabolism profiling for 10 samples of both species to explore their alkaloids biosynthesis. From the transcriptome data, we obtained 69367 and 78255 unigenes for M. cordata and M. microcarpa, in which about two thirds of them were similar to sequences in public databases. By metabolism profiling, reverse patterns for alkaloids sanguinarine, chelerythrine, protopine, and allocryptopine were observed in different organs of two species. We characterized the expressions of enzymes in alkaloid biosynthesis pathways. We also identified more than 1000 proteins from iTRAQ proteome data. Our results strongly suggest that the root maybe the organ for major alkaloids biosynthesis of Macleaya spp. Except for biosynthesis, the alkaloids storage and transport were also important for their accumulation. The ultrastructure of laticifers by SEM helps us to prove the alkaloids maybe accumulated in the mature roots. Conclusions/Significance To our knowledge this is the first study to elucidate the genetic makeup of Macleaya spp. This work provides clues to the identification of the potential modulate genes involved in alkaloids biosynthesis in Macleaya spp., and sheds light on researches for non-model medicinal plants by integrating different high-throughput technologies. PMID:23326424

Accessing Multi-Dimensional Images and Data Cubes in the Virtual Observatory

NASA Astrophysics Data System (ADS)

Tody, Douglas; Plante, R. L.; Berriman, G. B.; Cresitello-Dittmar, M.; Good, J.; Graham, M.; Greene, G.; Hanisch, R. J.; Jenness, T.; Lazio, J.; Norris, P.; Pevunova, O.; Rots, A. H.

2014-01-01

Telescopes across the spectrum are routinely producing multi-dimensional images and datasets, such as Doppler velocity cubes, polarization datasets, and time-resolved “movies.” Examples of current telescopes producing such multi-dimensional images include the JVLA, ALMA, and the IFU instruments on large optical and near-infrared wavelength telescopes. In the near future, both the LSST and JWST will also produce such multi-dimensional images routinely. High-energy instruments such as Chandra produce event datasets that are also a form of multi-dimensional data, in effect being a very sparse multi-dimensional image. Ensuring that the data sets produced by these telescopes can be both discovered and accessed by the community is essential and is part of the mission of the Virtual Observatory (VO). The Virtual Astronomical Observatory (VAO, http://www.usvao.org/), in conjunction with its international partners in the International Virtual Observatory Alliance (IVOA), has developed a protocol and an initial demonstration service designed for the publication, discovery, and access of arbitrarily large multi-dimensional images. The protocol describing multi-dimensional images is the Simple Image Access Protocol, version 2, which provides the minimal set of metadata required to characterize a multi-dimensional image for its discovery and access. A companion Image Data Model formally defines the semantics and structure of multi-dimensional images independently of how they are serialized, while providing capabilities such as support for sparse data that are essential to deal effectively with large cubes. A prototype data access service has been deployed and tested, using a suite of multi-dimensional images from a variety of telescopes. The prototype has demonstrated the capability to discover and remotely access multi-dimensional data via standard VO protocols. The prototype informs the specification of a protocol that will be submitted to the IVOA for approval, with an operational data cube service to be delivered in mid-2014. An associated user-installable VO data service framework will provide the capabilities required to publish VO-compatible multi-dimensional images or data cubes.

Multidimensional Unfolding by Nonmetric Multidimensional Scaling of Spearman Distances in the Extended Permutation Polytope

ERIC Educational Resources Information Center

Van Deun, Katrijn; Heiser, Willem J.; Delbeke, Luc

2007-01-01

A multidimensional unfolding technique that is not prone to degenerate solutions and is based on multidimensional scaling of a complete data matrix is proposed: distance information about the unfolding data and about the distances both among judges and among objects is included in the complete matrix. The latter information is derived from the…

Psychological profiling of offender characteristics from crime behaviors in serial rape offences.

PubMed

Kocsis, Richard N; Cooksey, Ray W; Irwin, Harvey J

2002-04-01

Criminal psychological profiling has progressively been incorporated into police procedures despite a dearth of empirical research. Indeed, in the study of serial violent crimes for the purpose of psychological profiling, very few original, quantitative, academically reviewed studies actually exist. This article reports on the analysis of 62 incidents of serial sexual assault. The statistical procedure of multidimensional scaling was employed in the analysis of this data, which in turn produced a five-cluster model of serial rapist behavior. First, a central cluster of behaviors were identified that represent common behaviors to all patterns of serial rape. Second, four distinct outlying patterns were identified as demonstrating distinct offence styles, these being assigned the following descriptive labels brutality, intercourse, chaotic, and ritual. Furthermore, analysis of these patterns also identified distinct offender characteristics that allow for the use of empirically robust offender profiles in future serial rape investigations.

Mediastinal lymph node detection and station mapping on chest CT using spatial priors and random forest

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Jiamin; Hoffman, Joanne; Zhao, Jocelyn

2016-07-15

Purpose: To develop an automated system for mediastinal lymph node detection and station mapping for chest CT. Methods: The contextual organs, trachea, lungs, and spine are first automatically identified to locate the region of interest (ROI) (mediastinum). The authors employ shape features derived from Hessian analysis, local object scale, and circular transformation that are computed per voxel in the ROI. Eight more anatomical structures are simultaneously segmented by multiatlas label fusion. Spatial priors are defined as the relative multidimensional distance vectors corresponding to each structure. Intensity, shape, and spatial prior features are integrated and parsed by a random forest classifiermore » for lymph node detection. The detected candidates are then segmented by the following curve evolution process. Texture features are computed on the segmented lymph nodes and a support vector machine committee is used for final classification. For lymph node station labeling, based on the segmentation results of the above anatomical structures, the textual definitions of mediastinal lymph node map according to the International Association for the Study of Lung Cancer are converted into patient-specific color-coded CT image, where the lymph node station can be automatically assigned for each detected node. Results: The chest CT volumes from 70 patients with 316 enlarged mediastinal lymph nodes are used for validation. For lymph node detection, their system achieves 88% sensitivity at eight false positives per patient. For lymph node station labeling, 84.5% of lymph nodes are correctly assigned to their stations. Conclusions: Multiple-channel shape, intensity, and spatial prior features aggregated by a random forest classifier improve mediastinal lymph node detection on chest CT. Using the location information of segmented anatomic structures from the multiatlas formulation enables accurate identification of lymph node stations.« less

Multidimensional effects in nonadiabatic statistical theories of spin- forbidden kinetics. A case study of 3O + CO → CO 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jasper, Ahren

2015-04-14

The appropriateness of treating crossing seams of electronic states of different spins as nonadiabatic transition states in statistical calculations of spin-forbidden reaction rates is considered. We show that the spin-forbidden reaction coordinate, the nuclear coordinate perpendicular to the crossing seam, is coupled to the remaining nuclear degrees of freedom. We found that this coupling gives rise to multidimensional effects that are not typically included in statistical treatments of spin-forbidden kinetics. Three qualitative categories of multidimensional effects may be identified: static multidimensional effects due to the geometry-dependence of the local shape of the crossing seam and of the spin–orbit coupling, dynamicalmore » multidimensional effects due to energy exchange with the reaction coordinate during the seam crossing, and nonlocal(history-dependent) multidimensional effects due to interference of the electronic variables at second, third, and later seam crossings. Nonlocal multidimensional effects are intimately related to electronic decoherence, where electronic dephasing acts to erase the history of the system. A semiclassical model based on short-time full-dimensional trajectories that includes all three multidimensional effects as well as a model for electronic decoherence is presented. The results of this multidimensional nonadiabatic statistical theory (MNST) for the 3O + CO → CO 2 reaction are compared with the results of statistical theories employing one-dimensional (Landau–Zener and weak coupling) models for the transition probability and with those calculated previously using multistate trajectories. The MNST method is shown to accurately reproduce the multistate decay-of-mixing trajectory results, so long as consistent thresholds are used. Furthermore, the MNST approach has several advantages over multistate trajectory approaches and is more suitable in chemical kinetics calculations at low temperatures and for complex systems. The error in statistical calculations that neglect multidimensional effects is shown to be as large as a factor of 2 for this system, with static multidimensional effects identified as the largest source of error.« less

On the Need for Multidimensional Stirling Simulations

NASA Technical Reports Server (NTRS)

Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.; Demko, Rikako

2005-01-01

Given the cost and complication of simulating Stirling convertors, do we really need multidimensional modeling when one-dimensional capabilities exist? This paper provides a comprehensive description of when and why multidimensional simulation is needed.

Multidimensional Scaling in the Poincare Disk

DTIC Science & Technology

2011-05-01

REPORT Multidimensional Scaling in the Poincare Dis 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: Multidimensional scaling (MDS) is a class of projective...DATES COVERED (From - To) Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 - Multidimensional Scaling in the Poincare Dis Report Title... plane . Our construction is based on an approximate hyperbolic line search and exempli?es some of the particulars that need to be addressed when

Scaling Laws for the Multidimensional Burgers Equation with Quadratic External Potential

NASA Astrophysics Data System (ADS)

Leonenko, N. N.; Ruiz-Medina, M. D.

2006-07-01

The reordering of the multidimensional exponential quadratic operator in coordinate-momentum space (see X. Wang, C.H. Oh and L.C. Kwek (1998). J. Phys. A.: Math. Gen. 31:4329-4336) is applied to derive an explicit formulation of the solution to the multidimensional heat equation with quadratic external potential and random initial conditions. The solution to the multidimensional Burgers equation with quadratic external potential under Gaussian strongly dependent scenarios is also obtained via the Hopf-Cole transformation. The limiting distributions of scaling solutions to the multidimensional heat and Burgers equations with quadratic external potential are then obtained under such scenarios.

Models of multidimensional discrete distribution of probabilities of random variables in information systems

NASA Astrophysics Data System (ADS)

Gromov, Yu Yu; Minin, Yu V.; Ivanova, O. G.; Morozova, O. N.

2018-03-01

Multidimensional discrete distributions of probabilities of independent random values were received. Their one-dimensional distribution is widely used in probability theory. Producing functions of those multidimensional distributions were also received.

A New Time-varying Concept of Risk in a Changing Climate.

PubMed

Sarhadi, Ali; Ausín, María Concepción; Wiper, Michael P

2016-10-20

In a changing climate arising from anthropogenic global warming, the nature of extreme climatic events is changing over time. Existing analytical stationary-based risk methods, however, assume multi-dimensional extreme climate phenomena will not significantly vary over time. To strengthen the reliability of infrastructure designs and the management of water systems in the changing environment, multidimensional stationary risk studies should be replaced with a new adaptive perspective. The results of a comparison indicate that current multi-dimensional stationary risk frameworks are no longer applicable to projecting the changing behaviour of multi-dimensional extreme climate processes. Using static stationary-based multivariate risk methods may lead to undesirable consequences in designing water system infrastructures. The static stationary concept should be replaced with a flexible multi-dimensional time-varying risk framework. The present study introduces a new multi-dimensional time-varying risk concept to be incorporated in updating infrastructure design strategies under changing environments arising from human-induced climate change. The proposed generalized time-varying risk concept can be applied for all stochastic multi-dimensional systems that are under the influence of changing environments.

The Application of SILAC Mouse in Human Body Fluid Proteomics Analysis Reveals Protein Patterns Associated with IgA Nephropathy.

PubMed

Zhao, Shilin; Li, Rongxia; Cai, Xiaofan; Chen, Wanjia; Li, Qingrun; Xing, Tao; Zhu, Wenjie; Chen, Y Eugene; Zeng, Rong; Deng, Yueyi

2013-01-01

Body fluid proteome is the most informative proteome from a medical viewpoint. But the lack of accurate quantitation method for complicated body fluid limited its application in disease research and biomarker discovery. To address this problem, we introduced a novel strategy, in which SILAC-labeled mouse serum was used as internal standard for human serum and urine proteome analysis. The SILAC-labeled mouse serum was mixed with human serum and urine, and multidimensional separation coupled with tandem mass spectrometry (IEF-LC-MS/MS) analysis was performed. The shared peptides between two species were quantified by their SILAC pairs, and the human-only peptides were quantified by mouse peptides with coelution. The comparison for the results from two replicate experiments indicated the high repeatability of our strategy. Then the urine from Immunoglobulin A nephropathy patients treated and untreated was compared by this quantitation strategy. Fifty-three peptides were found to be significantly changed between two groups, including both known diagnostic markers for IgAN and novel candidates, such as Complement C3, Albumin, VDBP, ApoA,1 and IGFBP7. In conclusion, we have developed a practical and accurate quantitation strategy for comparison of complicated human body fluid proteome. The results from such strategy could provide potential disease-related biomarkers for evaluation of treatment.

Multidimensional Knowledge Structures.

ERIC Educational Resources Information Center

Schuh, Kathy L.

Multidimensional knowledge structures, described from a constructivist perspective and aligned with the "Mind as Rhizome" metaphor, provide support for constructivist learning strategies. This qualitative study was conducted to seek empirical support for a description of multidimensional knowledge structures, focusing on the…

Multidimensional quantum entanglement with large-scale integrated optics.

PubMed

Wang, Jianwei; Paesani, Stefano; Ding, Yunhong; Santagati, Raffaele; Skrzypczyk, Paul; Salavrakos, Alexia; Tura, Jordi; Augusiak, Remigiusz; Mančinska, Laura; Bacco, Davide; Bonneau, Damien; Silverstone, Joshua W; Gong, Qihuang; Acín, Antonio; Rottwitt, Karsten; Oxenløwe, Leif K; O'Brien, Jeremy L; Laing, Anthony; Thompson, Mark G

2018-04-20

The ability to control multidimensional quantum systems is central to the development of advanced quantum technologies. We demonstrate a multidimensional integrated quantum photonic platform able to generate, control, and analyze high-dimensional entanglement. A programmable bipartite entangled system is realized with dimensions up to 15 × 15 on a large-scale silicon photonics quantum circuit. The device integrates more than 550 photonic components on a single chip, including 16 identical photon-pair sources. We verify the high precision, generality, and controllability of our multidimensional technology, and further exploit these abilities to demonstrate previously unexplored quantum applications, such as quantum randomness expansion and self-testing on multidimensional states. Our work provides an experimental platform for the development of multidimensional quantum technologies. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Multidimensional Perfectionism and the Self

ERIC Educational Resources Information Center

Ward, Andrew M.; Ashby, Jeffrey S.

2008-01-01

This study examined multidimensional perfectionism and self-development. Two hundred seventy-one undergraduates completed a measure of multidimensional perfectionism and two Kohutian measures designed to measure aspects of self-development including social connectedness, social assurance, goal instability (idealization), and grandiosity. The…

Chemical space visualization: transforming multidimensional chemical spaces into similarity-based molecular networks.

PubMed

de la Vega de León, Antonio; Bajorath, Jürgen

2016-09-01

The concept of chemical space is of fundamental relevance for medicinal chemistry and chemical informatics. Multidimensional chemical space representations are coordinate-based. Chemical space networks (CSNs) have been introduced as a coordinate-free representation. A computational approach is presented for the transformation of multidimensional chemical space into CSNs. The design of transformation CSNs (TRANS-CSNs) is based upon a similarity function that directly reflects distance relationships in original multidimensional space. TRANS-CSNs provide an immediate visualization of coordinate-based chemical space and do not require the use of dimensionality reduction techniques. At low network density, TRANS-CSNs are readily interpretable and make it possible to evaluate structure-activity relationship information originating from multidimensional chemical space.

Multidimensional poverty and catastrophic health spending in the mountainous regions of Myanmar, Nepal and India.

PubMed

Mohanty, Sanjay K; Agrawal, Nand Kishor; Mahapatra, Bidhubhusan; Choudhury, Dhrupad; Tuladhar, Sabarnee; Holmgren, E Valdemar

2017-01-18

Economic burden to households due to out-of-pocket expenditure (OOPE) is large in many Asian countries. Though studies suggest increasing household poverty due to high OOPE in developing countries, studies on association of multidimensional poverty and household health spending is limited. This paper tests the hypothesis that the multidimensionally poor are more likely to incur catastrophic health spending cutting across countries. Data from the Poverty and Vulnerability Assessment (PVA) Survey carried out by the International Center for Integrated Mountain Development (ICIMOD) has been used in the analyses. The PVA survey was a comprehensive household survey that covered the mountainous regions of India, Nepal and Myanmar. A total of 2647 households from India, 2310 households in Nepal and 4290 households in Myanmar covered under the PVA survey. Poverty is measured in a multidimensional framework by including the dimensions of education, income and energy, water and sanitation using the Alkire and Foster method. Health shock is measured using the frequency of illness, family sickness and death of any family member in a reference period of one year. Catastrophic health expenditure is defined as 40% above the household's capacity to pay. Results suggest that about three-fifths of the population in Myanmar, two-fifths of the population in Nepal and one-third of the population in India are multidimensionally poor. About 47% of the multidimensionally poor in India had incurred catastrophic health spending compared to 35% of the multidimensionally non-poor and the pattern was similar in both Nepal and Myanmar. The odds of incurring catastrophic health spending was 56% more among the multidimensionally poor than among the multidimensionally non-poor [95% CI: 1.35-1.76]. While health shocks to households are consistently significant predictors of catastrophic health spending cutting across country of residence, the educational attainment of the head of the household is not significant. The multidimensionally poor in the poorer regions are more likely to face health shocks and are less likely to afford professional health services. Increasing government spending on health and increasing households' access to health insurance can reduce catastrophic health spending and multidimensional poverty.

An introduction to multidimensional measurement using Rasch models.

PubMed

Briggs, Derek C; Wilson, Mark

2003-01-01

The act of constructing a measure requires a number of important assumptions. Principle among these assumptions is that the construct is unidimensional. In practice there are many instances when the assumption of unidimensionality does not hold, and where the application of a multidimensional measurement model is both technically appropriate and substantively advantageous. In this paper we illustrate the usefulness of a multidimensional approach to measurement with the Multidimensional Random Coefficient Multinomial Logit (MRCML) model, an extension of the unidimensional Rasch model. An empirical example is taken from a collection of embedded assessments administered to 541 students enrolled in middle school science classes with a hands-on science curriculum. Student achievement on these assessments are multidimensional in nature, but can also be treated as consecutive unidimensional estimates, or as is most common, as a composite unidimensional estimate. Structural parameters are estimated for each model using ConQuest, and model fit is compared. Student achievement in science is also compared across models. The multidimensional approach has the best fit to the data, and provides more reliable estimates of student achievement than under the consecutive unidimensional approach. Finally, at an interpretational level, the multidimensional approach may well provide richer information to the classroom teacher about the nature of student achievement.

The Tunneling Method for Global Optimization in Multidimensional Scaling.

ERIC Educational Resources Information Center

Groenen, Patrick J. F.; Heiser, Willem J.

1996-01-01

A tunneling method for global minimization in multidimensional scaling is introduced and adjusted for multidimensional scaling with general Minkowski distances. The method alternates a local search step with a tunneling step in which a different configuration is sought with the same STRESS implementation. (SLD)

Multidimensional Poverty and Health Status as a Predictor of Chronic Income Poverty.

PubMed

Callander, Emily J; Schofield, Deborah J

2015-12-01

Longitudinal analysis of Wave 5 to 10 of the nationally representative Household, Income and Labour Dynamics in Australia dataset was undertaken to assess whether multidimensional poverty status can predict chronic income poverty. Of those who were multidimensionally poor (low income plus poor health or poor health and insufficient education attainment) in 2007, and those who were in income poverty only (no other forms of disadvantage) in 2007, a greater proportion of those in multidimensional poverty continued to be in income poverty for the subsequent 5 years through to 2012. People who were multidimensionally poor in 2007 had 2.17 times the odds of being in income poverty each year through to 2012 than those who were in income poverty only in 2005 (95% CI: 1.23-3.83). Multidimensional poverty measures are a useful tool for policymakers to identify target populations for policies aiming to improve equity and reduce chronic disadvantage. Copyright © 2014 John Wiley & Sons, Ltd.

Multidimensional upwind hydrodynamics on unstructured meshes using graphics processing units - I. Two-dimensional uniform meshes

NASA Astrophysics Data System (ADS)

Paardekooper, S.-J.

2017-08-01

We present a new method for numerical hydrodynamics which uses a multidimensional generalization of the Roe solver and operates on an unstructured triangular mesh. The main advantage over traditional methods based on Riemann solvers, which commonly use one-dimensional flux estimates as building blocks for a multidimensional integration, is its inherently multidimensional nature, and as a consequence its ability to recognize multidimensional stationary states that are not hydrostatic. A second novelty is the focus on graphics processing units (GPUs). By tailoring the algorithms specifically to GPUs, we are able to get speedups of 100-250 compared to a desktop machine. We compare the multidimensional upwind scheme to a traditional, dimensionally split implementation of the Roe solver on several test problems, and we find that the new method significantly outperforms the Roe solver in almost all cases. This comes with increased computational costs per time-step, which makes the new method approximately a factor of 2 slower than a dimensionally split scheme acting on a structured grid.

Enhancing Student Motivation and Engagement: The Effects of a Multidimensional Intervention

ERIC Educational Resources Information Center

Martin, Andrew J.

2008-01-01

The present study sought to investigate the effects of a multidimensional educational intervention on high school students' motivation and engagement. The intervention incorporated: (a) multidimensional targets of motivation and engagement, (b) empirically derived intervention methodology, (c) research-based risk and protective factors, (d)…

Heteronuclear Multidimensional Protein NMR in a Teaching Laboratory

ERIC Educational Resources Information Center

Wright, Nathan T.

2016-01-01

Heteronuclear multidimensional NMR techniques are commonly used to study protein structure, function, and dynamics, yet they are rarely taught at the undergraduate level. Here, we describe a senior undergraduate laboratory where students collect, process, and analyze heteronuclear multidimensional NMR experiments using an unstudied Ig domain (Ig2…

Compressed Continuous Computation v. 12/20/2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorodetsky, Alex

2017-02-17

A library for performing numerical computation with low-rank functions. The (C3) library enables performing continuous linear and multilinear algebra with multidimensional functions. Common tasks include taking "matrix" decompositions of vector- or matrix-valued functions, approximating multidimensional functions in low-rank format, adding or multiplying functions together, integrating multidimensional functions.

The Discriminating Power of Items that Measure More than One Dimension.

ERIC Educational Resources Information Center

Reckase, Mark D.

The work presented in this paper defined conceptually the concepts of multidimensional discrimination and information, derived mathematical expressions for the concepts for a particular multidimensional item response theory (IRT) model, and applied the concepts to actual test data. Multidimensional discrimination was defined as a function of the…

Multidimensional Computerized Adaptive Testing for Indonesia Junior High School Biology

ERIC Educational Resources Information Center

Kuo, Bor-Chen; Daud, Muslem; Yang, Chih-Wei

2015-01-01

This paper describes a curriculum-based multidimensional computerized adaptive test that was developed for Indonesia junior high school Biology. In adherence to the Indonesian curriculum of different Biology dimensions, 300 items was constructed, and then tested to 2238 students. A multidimensional random coefficients multinomial logit model was…

Supervised and Unsupervised Learning of Multidimensional Acoustic Categories

ERIC Educational Resources Information Center

Goudbeek, Martijn; Swingley, Daniel; Smits, Roel

2009-01-01

Learning to recognize the contrasts of a language-specific phonemic repertoire can be viewed as forming categories in a multidimensional psychophysical space. Research on the learning of distributionally defined visual categories has shown that categories defined over 1 dimension are easy to learn and that learning multidimensional categories is…

Health, Wealth and Wisdom: Exploring Multidimensional Inequality in a Developing Country

ERIC Educational Resources Information Center

Nilsson, Therese

2010-01-01

Despite a broad theoretical literature on multidimensional inequality and a widespread belief that welfare is not synonymous to income--not the least in a developing context--empirical inequality examinations rarely includes several welfare attributes. We explore three techniques on how to evaluate multidimensional inequality using Zambian…

Multidimensional Physical Self-Concept of Athletes with Physical Disabilities

ERIC Educational Resources Information Center

Shapiro, Deborah R.; Martin, Jeffrey J.

2010-01-01

The purposes of this investigation were first to predict reported PA (physical activity) behavior and self-esteem using a multidimensional physical self-concept model and second to describe perceptions of multidimensional physical self-concept (e.g., strength, endurance, sport competence) among athletes with physical disabilities. Athletes (N =…

Method of data mining including determining multidimensional coordinates of each item using a predetermined scalar similarity value for each item pair

DOEpatents

Meyers, Charles E.; Davidson, George S.; Johnson, David K.; Hendrickson, Bruce A.; Wylie, Brian N.

1999-01-01

A method of data mining represents related items in a multidimensional space. Distance between items in the multidimensional space corresponds to the extent of relationship between the items. The user can select portions of the space to perceive. The user also can interact with and control the communication of the space, focusing attention on aspects of the space of most interest. The multidimensional spatial representation allows more ready comprehension of the structure of the relationships among the items.

A Conceptual Model for Multidimensional Analysis of Documents

NASA Astrophysics Data System (ADS)

Ravat, Franck; Teste, Olivier; Tournier, Ronan; Zurlfluh, Gilles

Data warehousing and OLAP are mainly used for the analysis of transactional data. Nowadays, with the evolution of Internet, and the development of semi-structured data exchange format (such as XML), it is possible to consider entire fragments of data such as documents as analysis sources. As a consequence, an adapted multidimensional analysis framework needs to be provided. In this paper, we introduce an OLAP multidimensional conceptual model without facts. This model is based on the unique concept of dimensions and is adapted for multidimensional document analysis. We also provide a set of manipulation operations.

A review of snapshot multidimensional optical imaging: measuring photon tags in parallel

PubMed Central

Gao, Liang; Wang, Lihong V.

2015-01-01

Multidimensional optical imaging has seen remarkable growth in the past decade. Rather than measuring only the two-dimensional spatial distribution of light, as in conventional photography, multidimensional optical imaging captures light in up to nine dimensions, providing unprecedented information about incident photons’ spatial coordinates, emittance angles, wavelength, time, and polarization. Multidimensional optical imaging can be accomplished either by scanning or parallel acquisition. Compared with scanning-based imagers, parallel acquisition—also dubbed snapshot imaging—has a prominent advantage in maximizing optical throughput, particularly when measuring a datacube of high dimensions. Here, we first categorize snapshot multidimensional imagers based on their acquisition and image reconstruction strategies, then highlight the snapshot advantage in the context of optical throughput, and finally we discuss their state-of-the-art implementations and applications. PMID:27134340

A multidimensional subdiffusion model: An arbitrage-free market

NASA Astrophysics Data System (ADS)

Li, Guo-Hua; Zhang, Hong; Luo, Mao-Kang

2012-12-01

To capture the subdiffusive characteristics of financial markets, the subordinated process, directed by the inverse α-stale subordinator Sα(t) for 0 < α < 1, has been employed as the model of asset prices. In this article, we introduce a multidimensional subdiffusion model that has a bond and K correlated stocks. The stock price process is a multidimensional subdiffusion process directed by the inverse α-stable subordinator. This model describes the period of stagnation for each stock and the behavior of the dependency between multiple stocks. Moreover, we derive the multidimensional fractional backward Kolmogorov equation for the subordinated process using the Laplace transform technique. Finally, using a martingale approach, we prove that the multidimensional subdiffusion model is arbitrage-free, and also gives an arbitrage-free pricing rule for contingent claims associated with the martingale measure.

Progress in multi-dimensional upwind differencing

NASA Technical Reports Server (NTRS)

Vanleer, Bram

1992-01-01

Multi-dimensional upwind-differencing schemes for the Euler equations are reviewed. On the basis of the first-order upwind scheme for a one-dimensional convection equation, the two approaches to upwind differencing are discussed: the fluctuation approach and the finite-volume approach. The usual extension of the finite-volume method to the multi-dimensional Euler equations is not entirely satisfactory, because the direction of wave propagation is always assumed to be normal to the cell faces. This leads to smearing of shock and shear waves when these are not grid-aligned. Multi-directional methods, in which upwind-biased fluxes are computed in a frame aligned with a dominant wave, overcome this problem, but at the expense of robustness. The same is true for the schemes incorporating a multi-dimensional wave model not based on multi-dimensional data but on an 'educated guess' of what they could be. The fluctuation approach offers the best possibilities for the development of genuinely multi-dimensional upwind schemes. Three building blocks are needed for such schemes: a wave model, a way to achieve conservation, and a compact convection scheme. Recent advances in each of these components are discussed; putting them all together is the present focus of a worldwide research effort. Some numerical results are presented, illustrating the potential of the new multi-dimensional schemes.

Quantitative Profiling Identifies Potential Regulatory Proteins Involved in Development from Dauer Stage to L4 Stage in Caenorhabditis elegans.

PubMed

Kim, Sunhee; Lee, Hyoung-Joo; Hahm, Jeong-Hoon; Jeong, Seul-Ki; Park, Don-Ha; Hancock, William S; Paik, Young-Ki

2016-02-05

When Caenorhabditis elegans encounters unfavorable growth conditions, it enters the dauer stage, an alternative L3 developmental period. A dauer larva resumes larval development to the normal L4 stage by uncharacterized postdauer reprogramming (PDR) when growth conditions become more favorable. During this transition period, certain heterochronic genes involved in controlling the proper sequence of developmental events are known to act, with their mutations suppressing the Muv (multivulva) phenotype in C. elegans. To identify the specific proteins in which the Muv phenotype is highly suppressed, quantitative proteomic analysis with iTRAQ labeling of samples obtained from worms at L1 + 30 h (for continuous development [CD]) and dauer recovery +3 h (for postdauer development [PD]) was carried out to detect changes in protein abundance in the CD and PD states of both N2 and lin-28(n719). Of the 1661 unique proteins identified with a < 1% false discovery rate at the peptide level, we selected 58 proteins exhibiting ≥2-fold up-regulation or ≥2-fold down-regulation in the PD state and analyzed the Gene Ontology terms. RNAi assays against 15 selected up-regulated genes showed that seven genes were predicted to be involved in higher Muv phenotype (p < 0.05) in lin-28(n791), which is not seen in N2. Specifically, two genes, K08H10.1 and W05H9.1, displayed not only the highest rate (%) of Muv phenotype in the RNAi assay but also the dauer-specific mRNA expression, indicating that these genes may be required for PDR, leading to the very early onset of dauer recovery. Thus, our proteomic approach identifies and quantitates the regulatory proteins potentially involved in PDR in C. elegans, which safeguards the overall lifecycle in response to environmental changes.

Profilin-1 overexpression in MDA-MB-231 breast cancer cells is associated with alterations in proteomics biomarkers of cell proliferation, survival, and motility as revealed by global proteomics analyses.

PubMed

Coumans, Joëlle V F; Gau, David; Poljak, Anne; Wasinger, Valerie; Roy, Partha; Moens, Pierre D J

2014-12-01

Despite early screening programs and new therapeutic strategies, metastatic breast cancer is still the leading cause of cancer death in women in industrialized countries and regions. There is a need for novel biomarkers of susceptibility, progression, and therapeutic response. Global analyses or systems science approaches with omics technologies offer concrete ways forward in biomarker discovery for breast cancer. Previous studies have shown that expression of profilin-1 (PFN1), a ubiquitously expressed actin-binding protein, is downregulated in invasive and metastatic breast cancer. It has also been reported that PFN1 overexpression can suppress tumorigenic ability and motility/invasiveness of breast cancer cells. To obtain insights into the underlying molecular mechanisms of how elevating PFN1 level induces these phenotypic changes in breast cancer cells, we investigated the alteration in global protein expression profiles of breast cancer cells upon stable overexpression of PFN1 by a combination of three different proteome analysis methods (2-DE, iTRAQ, label-free). Using MDA-MB-231 as a model breast cancer cell line, we provide evidence that PFN1 overexpression is associated with alterations in the expression of proteins that have been functionally linked to cell proliferation (FKPB1A, HDGF, MIF, PRDX1, TXNRD1, LGALS1, STMN1, LASP1, S100A11, S100A6), survival (HSPE1, HSPB1, HSPD1, HSPA5 and PPIA, YWHAZ, CFL1, NME1) and motility (CFL1, CORO1B, PFN2, PLS3, FLNA, FLNB, NME2, ARHGDIB). In view of the pleotropic effects of PFN1 overexpression in breast cancer cells as suggested by these new findings, we propose that PFN1-induced phenotypic changes in cancer cells involve multiple mechanisms. Our data reported here might also offer innovative strategies for identification and validation of novel therapeutic targets and companion diagnostics for persons with, or susceptibility to, breast cancer.

Quantitative proteomic analysis of host--pathogen interactions: a study of Acinetobacter baumannii responses to host airways.

PubMed

Méndez, Jose Antonio; Mateos, Jesús; Beceiro, Alejandro; Lopez, María; Tomás, María; Poza, Margarita; Bou, Germán

2015-05-30

Acinetobacter baumannii is a major health problem. The most common infection caused by A. baumannii is hospital acquired pneumonia, and the associated mortality rate is approximately 50%. Neither in vivo nor ex vivo expression profiling has been performed at the proteomic or transcriptomic level for pneumonia caused by A. baumannii. In this study, we characterized the proteome of A. baumannii under conditions that simulate those found in the airways, to gain some insight into how A. baumannii adapts to the host and to improve knowledge about the pathogenesis and virulence of this bacterium. A clinical strain of A. baumannii was grown under different conditions: in the presence of bronchoalveolar lavage fluid from infected rats, of RAW 264.7 cells to simulate conditions in the respiratory tract and in control conditions. We used iTRAQ labelling and LC-MALDI-TOF/TOF to investigate how A. baumannii responds on exposure to macrophages/BALF. 179 proteins showed differential expression. In both models, proteins involved in the following processes were over-expressed: (i) pathogenesis and virulence (OmpA, YjjK); (ii) cell wall/membrane/envelope biogenesis (MurC); (iii) energy production and conversion (acetyl-CoA hydrolase); and (iv) translation (50S ribosomal protein L9). Proteins involved in the following were under-expressed: (i) lipid metabolism (short-chain dehydrogenase); (ii) amino acid metabolism and transport (aspartate aminotransferase); (iii) unknown function (DNA-binding protein); and (iv) inorganic ion transport and metabolism (hydroperoxidase). We observed alterations in cell wall synthesis and identified 2 upregulated virulence-associated proteins with >15 peptides/protein in both ex vivo models (OmpA and YjjK), suggesting that these proteins are fundamental for pathogenesis and virulence in the airways. This study is the first comprehensive overview of the ex vivo proteome of A. baumannii and is an important step towards identification of diagnostic biomarkers, novel drug targets and potential vaccine candidates in the fight against pneumonia caused by A. baumannii.

Modulation of Protein Phosphorylation, N-Glycosylation and Lys-Acetylation in Grape (Vitis vinifera) Mesocarp and Exocarp Owing to Lobesia botrana Infection*

PubMed Central

Melo-Braga, Marcella N.; Verano-Braga, Thiago; León, Ileana R.; Antonacci, Donato; Nogueira, Fábio C. S.; Thelen, Jay J.; Larsen, Martin R.; Palmisano, Giuseppe

2012-01-01

Grapevine (Vitis vinifera) is an economically important fruit crop that is subject to many types of insect and pathogen attack. To better elucidate the plant response to Lobesia botrana pathogen infection, we initiated a global comparative proteomic study monitoring steady-state protein expression as well as changes in N-glycosylation, phosphorylation, and Lys-acetylation in control and infected mesocarp and exocarp from V. vinifera cv Italia. A multi-parallel, large-scale proteomic approach employing iTRAQ labeling prior to three peptide enrichment techniques followed by tandem mass spectrometry led to the identification of a total of 3059 proteins, 1135 phosphorylation sites, 323 N-linked glycosylation sites and 138 Lys-acetylation sites. Of these, we could identify changes in abundance of 899 proteins. The occupancy of 110 phosphorylation sites, 10 N-glycosylation sites and 20 Lys-acetylation sites differentially changed during L. botrana infection. Sequence consensus analysis for phosphorylation sites showed eight significant motifs, two of which containing up-regulated phosphopeptides (X-G-S-X and S-X-X-D) and two containing down-regulated phosphopeptides (R-X-X-S and S-D-X-E) in response to pathogen infection. Topographical distribution of phosphorylation sites within primary sequences reveal preferential phosphorylation at both the N- and C termini, and a clear preference for C-terminal phosphorylation in response to pathogen infection suggesting induction of region-specific kinase(s). Lys-acetylation analysis confirmed the consensus X-K-Y-X motif previously detected in mammals and revealed the importance of this modification in plant defense. The importance of N-linked protein glycosylation in plant response to biotic stimulus was evident by an up-regulated glycopeptide belonging to the disease resistance response protein 206. This study represents a substantial step toward the understanding of protein and PTMs-mediated plant-pathogen interaction shedding light on the mechanisms underlying the grape infection. PMID:22778145

[Analysis of virulence factors of Porphyromonas endodontalis based on comparative proteomics technique].

PubMed

Li, H; Ji, H; Wu, S S; Hou, B X

2016-12-09

Objective: To analyze the protein expression profile and the potential virulence factors of Porphyromonas endodontalis (Pe) via comparison with that of two strains of Porphyromonas gingivalis (Pg) with high and low virulences, respectively. Methods: Whole cell comparative proteomics of Pe ATCC35406 was examined and compared with that of high virulent strain Pg W83 andlow virulent strain Pg ATCC33277, respectively. Isobaric tags for relative and absolute quantitation (iTRAQ) combined with nano liquid chromatography-tandem mass spectrometry (Nano-LC-MS/MS) were adopted to identify and quantitate the proteins of Pe and two strains of Pg with various virulences by using the methods of isotopically labeled peptides, mass spectrometric detection and bioinformatics analysis. The biological functions of similar proteins expressed by Pe ATCC35406 and two strains of Pg were quantified and analyzed. Results: Totally 1 210 proteins were identified while Pe compared with Pg W83. There were 130 proteins (10.74% of the total proteins) expressed similarly, including 89 known functional proteins and 41 proteins of unknown functions. Totally 1 223 proteins were identified when Pe compared with Pg ATCC33277. There were 110 proteins (8.99% of the total proteins) expressed similarly, including 72 known functional proteins and 38 proteins of unknown functions. The similarly expressed proteins in Pe and Pg strains with various virulences mainly focused on catalytic activity and binding function, including recombination activation gene (RagA), lipoprotein, chaperonin Dnak, Clp family proteins (ClpC and ClpX) and various iron-binding proteins. They were involved in metabolism and cellular processes. In addition, the type and number of similar virulence proteins between Pe and high virulence Pg were higher than those between Pe and low virulence Pg. Conclusions: Lipoprotein, oxygen resistance protein, iron binding protein were probably the potential virulence factors of Pe ATCC35406. It was speculated that pathogenicity of Pe was more similar to high virulence Pg than that to low virulence strain.

Transcriptomic and Proteomic Analysis of Oenococcus oeni Adaptation to Wine Stress Conditions

PubMed Central

Margalef-Català, Mar; Araque, Isabel; Bordons, Albert; Reguant, Cristina; Bautista-Gallego, Joaquín

2016-01-01

Oenococcus oeni, the main lactic acid bacteria responsible for malolactic fermentation in wine, has to adapt to stressful conditions, such as low pH and high ethanol content. In this study, the changes in the transcriptome and the proteome of O. oeni PSU-1 during the adaptation period before MLF start have been studied. DNA microarrays were used for the transcriptomic analysis and two complementary proteomic techniques, 2-D DIGE and iTRAQ labeling were used to analyze the proteomic response. One of the most influenced functions in PSU-1 due to inoculation into wine-like medium (WLM) was translation, showing the over-expression of certain ribosomal genes and the corresponding proteins. Amino acid metabolism and transport was also altered and several peptidases were up regulated both at gene and protein level. Certain proteins involved in glutamine and glutamate metabolism showed an increased abundance revealing the key role of nitrogen uptake under stressful conditions. A strong transcriptional inhibition of carbohydrate metabolism related genes was observed. On the other hand, the transcriptional up-regulation of malate transport and citrate consumption was indicative of the use of L-malate and citrate associated to stress response and as an alternative energy source to sugar metabolism. Regarding the stress mechanisms, our results support the relevance of the thioredoxin and glutathione systems in the adaptation of O. oeni to wine related stress. Genes and proteins related to cell wall showed also significant changes indicating the relevance of the cell envelop as protective barrier to environmental stress. The differences found between transcriptomic and proteomic data suggested the relevance of post-transcriptional mechanisms and the complexity of the stress response in O. oeni adaptation. Further research should deepen into the metabolisms mostly altered due to wine conditions to elucidate the role of each mechanism in the O. oeni ability to develop MLF. PMID:27746771

Decreased Serum Thrombospondin-1 Levels in Pancreatic Cancer Patients Up to 24 Months Prior to Clinical Diagnosis: Association with Diabetes Mellitus.

PubMed

Jenkinson, Claire; Elliott, Victoria L; Evans, Anthony; Oldfield, Lucy; Jenkins, Rosalind E; O'Brien, Darragh P; Apostolidou, Sophia; Gentry-Maharaj, Aleksandra; Fourkala, Evangelia-O; Jacobs, Ian J; Menon, Usha; Cox, Trevor; Campbell, Fiona; Pereira, Stephen P; Tuveson, David A; Park, B Kevin; Greenhalf, William; Sutton, Robert; Timms, John F; Neoptolemos, John P; Costello, Eithne

2016-04-01

Identification of serum biomarkers enabling earlier diagnosis of pancreatic ductal adenocarcinoma (PDAC) could improve outcome. Serum protein profiles in patients with preclinical disease and at diagnosis were investigated. Serum from cases up to 4 years prior to PDAC diagnosis and controls (UKCTOCS,n= 174) were studied, alongside samples from patients diagnosed with PDAC, chronic pancreatitis, benign biliary disease, type 2 diabetes mellitus, and healthy subjects (n= 298). Isobaric tags for relative and absolute quantification (iTRAQ) enabled comparisons of pooled serum from a test set (n= 150). Validation was undertaken using multiple reaction monitoring (MRM) and/or Western blotting in all 472 human samples and samples from a KPC mouse model. iTRAQ identified thrombospondin-1 (TSP-1) as reduced preclinically and in diagnosed samples. MRM confirmed significant reduction in levels of TSP-1 up to 24 months prior to diagnosis. A combination of TSP-1 and CA19-9 gave an AUC of 0.86, significantly outperforming both markers alone (0.69 and 0.77, respectively;P< 0.01). TSP-1 was also decreased in PDAC patients compared with healthy controls (P< 0.05) and patients with benign biliary obstruction (P< 0.01). Low levels of TSP-1 correlated with poorer survival, preclinically (P< 0.05) and at clinical diagnosis (P< 0.02). In PDAC patients, reduced TSP-1 levels were more frequently observed in those with confirmed diabetes mellitus (P< 0.01). Significantly lower levels were also observed in PDAC patients with diabetes compared with individuals with type 2 diabetes mellitus (P= 0.01). Circulating TSP-1 levels decrease up to 24 months prior to diagnosis of PDAC and significantly enhance the diagnostic performance of CA19-9. The influence of diabetes mellitus on biomarker behavior should be considered in future studies. ©2015 American Association for Cancer Research.

Describing the Diapause-Preparatory Proteome of the Beetle Colaphellus bowringi and Identifying Candidates Affecting Lipid Accumulation Using Isobaric Tags for Mass Spectrometry-Based Proteome Quantification (iTRAQ)

PubMed Central

Tan, Qian-Qian; Liu, Wen; Zhu, Fen; Lei, Chao-Liang; Hahn, Daniel A.; Wang, Xiao-Ping

2017-01-01

Prior to entering diapause, insects must prepare themselves physiologically to withstand the stresses of arresting their development for a lengthy period. While studies describing the biochemical and cellular milieu of the maintenance phase of diapause are accumulating, few studies have taken an “omics” approach to describing molecular events during the diapause preparatory phase. We used isobaric tags and mass spectrometry (iTRAQ) to quantitatively compare the expression profiles of proteins identified during the onset of diapause preparation phase in the heads of adult female cabbage beetles, Colaphellus bowringi. A total of 3,175 proteins were identified, 297 of which were differentially expressed between diapause-destined and non-diapause-destined female adults and could therefore be involved in diapause preparation in this species. Comparison of identified proteins with protein function databases shows that many of these differentially expressed proteins enhanced in diapause destined beetles are involved in energy production and conversion, carbohydrate metabolism and transport, and lipid metabolism. Further hand annotation of differentially abundant peptides nominates several associated with stress hardiness, including HSPs and antioxidants, as well as neural development. In contrast, non-diapause destined beetles show substantial increases in cuticle proteins, suggesting additional post-emergence growth. Using RNA interference to silence a fatty acid-binding protein (FABP) that was highly abundant in the head of diapause-destined females prevented the accumulation of lipids in the fat body, a common product of diapause preparation in this species and others. Surprisingly, RNAi against the FABP also affected the transcript abundance of several heat shock proteins. These results suggest that the identified differentially expressed proteins that play vital roles in lipid metabolism may also contribute somehow to enhanced hardiness to environmental stress that is characteristic of diapause. PMID:28491041

Comparative transcriptional and translational analysis of leptospiral outer membrane protein expression in response to temperature.

PubMed

Lo, Miranda; Cordwell, Stuart J; Bulach, Dieter M; Adler, Ben

2009-12-08

Leptospirosis is a global zoonosis affecting millions of people annually. Transcriptional changes in response to temperature were previously investigated using microarrays to identify genes potentially expressed upon host entry. Past studies found that various leptospiral outer membrane proteins are differentially expressed at different temperatures. However, our microarray studies highlighted a divergence between protein abundance and transcript levels for some proteins. Given the abundance of post-transcriptional expression control mechanisms, this finding highlighted the importance of global protein analysis systems. To complement our previous transcription study, we evaluated differences in the proteins of the leptospiral outer membrane fraction in response to temperature upshift. Outer membrane protein-enriched fractions from Leptospira interrogans grown at 30 degrees C or overnight upshift to 37 degrees C were isolated and the relative abundance of each protein was determined by iTRAQ analysis coupled with two-dimensional liquid chromatography and tandem mass spectrometry (2-DLC/MS-MS). We identified 1026 proteins with 99% confidence; 27 and 66 were present at elevated and reduced abundance respectively. Protein abundance changes were compared with transcriptional differences determined from the microarray studies. While there was some correlation between the microarray and iTRAQ data, a subset of genes that showed no differential expression by microarray was found to encode temperature-regulated proteins. This set of genes is of particular interest as it is likely that regulation of their expression occurs post-transcriptionally, providing an opportunity to develop hypotheses about the molecular dynamics of the outer membrane of Leptospira in response to changing environments. This is the first study to compare transcriptional and translational responses to temperature shift in L. interrogans. The results thus provide an insight into the mechanisms used by L. interrogans to adapt to conditions encountered in the host and to cause disease. Our results suggest down-regulation of protein expression in response to temperature, and decreased expression of outer membrane proteins may facilitate minimal interaction with host immune mechanisms.

Identification of diverse defense mechanisms in rainbow trout red blood cells in response to halted replication of VHS virus

PubMed Central

Nombela, Ivan; Puente-Marin, Sara; Chico, Veronica; Villena, Alberto J.; Carracedo, Begoña; Ciordia, Sergio; Mena, Maria Carmen; Mercado, Luis; Perez, Luis; Coll, Julio; Ortega-Villaizan, Maria del Mar

2018-01-01

Background: It has been described that fish nucleated red blood cells (RBCs) generate a wide variety of immune-related gene transcripts when viruses highly replicate inside them and are their main target cell. The immune response and mechanisms of fish RBCs against viruses targeting other cells or tissues has not yet been explored and is the objective of our study. Methods: Rainbow trout RBCs were obtained from peripheral blood, ficoll purified and exposed to Viral Haemorrhagic Septicaemia virus (VHSV). Immune response was evaluated by means of RT-qPCR, flow cytometry, immunofluorescence and isobaric tag for relative and absolute quantification (iTRAQ) protein profiling. Results: VHSV N gene transcripts incremented early postexposure and were drastically decreased after 6 hours postexposure (hpe). The expression of type I interferon ( ifn1) gene was significantly downregulated at early postexposure (3 hpe), together with a gradual downregulation of interferon-inducible mx and pkr genes until 72 hpe. Type I IFN protein was downregulated and interferon-inducible Mx protein was maintained at basal levels. Co-culture assays of RBCs, previously exposed to UV-inactivated VHSV, and TSS (stromal cell line from spleen) revealed IFN crosstalk between both cell types. On the other hand, anti-microbial peptide β-defensin 1 and neutrophil chemotactic factor interleukin 8 were slightly upregulated in VHSV-exposed RBCs. iTRAQ profiling revealed that VHSV exposure can induce a global protein downregulation in rainbow trout RBCs, mainly related to RNA stability and proteasome pathways. Antioxidant/antiviral response is also suggested to be involved in the response of rainbow trout RBCs to VHSV. Conclusions: A variety of mechanisms are proposed to be implicated in the antiviral response of rainbow trout RBCs against VHSV halted infection. Ongoing research is focused on understanding the mechanisms in detail. PMID:29527292

Global iTRAQ-based proteomic profiling of Toxoplasma gondii oocysts during sporulation.

PubMed

Zhou, Chun-Xue; Zhu, Xing-Quan; Elsheikha, Hany M; He, Shuai; Li, Qian; Zhou, Dong-Hui; Suo, Xun

2016-10-04

Toxoplasma gondii is a medically and economically important protozoan parasite. However, the molecular mechanisms of its sporulation remain largely unknown. Here, we applied iTRAQ coupled with 2D LC-MS/MS proteomic analysis to investigate the proteomic expression profile of T. gondii oocysts during sporulation. Of the 2095 non-redundant proteins identified, 587 were identified as differentially expressed proteins (DEPs). Based on Gene Ontology enrichment and KEGG pathway analyses the majority of these DEPs were found related to the metabolism of amino acids, carbon and energy. Protein interaction network analysis generated by STRING identified ATP-citrate lyase (ACL), GMP synthase, IMP dehydrogenase (IMPDH), poly (ADP-ribose) glycohydrolase (PARG), and bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) as the top five hubs. We also identified 25 parasite virulence factors that were expressed at relatively high levels in sporulated oocysts compared to non-sporulated oocysts, which might contribute to the infectivity of mature oocysts. Considering the importance of oocysts in the dissemination of toxoplasmosis these findings may help in the search of protein targets with a key role in infectiousness and ecological success of oocysts, creating new opportunities for the development of better means for disease prevention. The development of new preventative interventions against T. gondii infection relies on an improved understanding of the proteome and chemical pathways of this parasite. To identify proteins required for the development of environmentally resistant and infective T. gondii oocysts, we compared the proteome of non-sporulated (immature) oocysts with the proteome of sporulated (mature, infective) oocysts. iTRAQ 2D-LC-MS/MS analysis revealed proteomic changes that distinguish non-sporulated from sporulated oocysts. Many of the differentially expressed proteins were involved in metabolic pathways and 25 virulence factors were identified upregulated in the sporulated oocysts. This work provides the first quantitative characterization of the proteomic variations that occur in T. gondii oocyst stage during sporulation. Copyright © 2016. Published by Elsevier B.V.

Maternal serum proteome changes between the first and third trimester of pregnancy in rural southern Nepal.

PubMed

Scholl, P F; Cole, R N; Ruczinski, I; Gucek, M; Diez, R; Rennie, A; Nathasingh, C; Schulze, K; Christian, P; Yager, J D; Groopman, J D; West, K P

2012-05-01

Characterization of normal changes in the serum proteome during pregnancy may enhance understanding of maternal physiology and lead to the development of new gestational biomarkers. In 23 Nepalese pregnant women who delivered at term, two-dimensional difference in-gel electrophoresis (DIGE) was used to assess changes in relative protein abundance between paired serum samples collected in the first and third trimesters. One-hundred and forty-five of over 700 protein spots in DIGE gels (pI 4.2-6.8) exhibited nominally significant (p < 0.05) differences in abundance across trimesters. Additional filtering using a Bonferroni correction reduced the number of significant (p < 0.00019) spots to 61. Mass spectrometric analysis detected 38 proteins associated with gestational age, cytoskeletal remodeling, blood pressure regulation, lipid and nutrient transport, and inflammation. One new protein, pregnancy-specific β-glycoprotein 4 was detected. A follow-up isotope tagging for relative and absolute quantitation (iTRAQ) experiment of six mothers from the DIGE study revealed 111 proteins, of which 11 exhibited significant (p < 0.05) differences between trimesters. Four of these proteins: gelsolin, complement C1r subcomponent, α-1-acid glycoprotein, and α-1B-glycoprotein also changed in the DIGE analysis. Although not previously associated with normal pregnancy, gelsolin decreased in abundance by the third trimester (p < 0.01) in DIGE, iTRAQ and Western analyses. Changes in abundance of proteins in serum that are associated with syncytiotrophoblasts (gelsolin, pregnancy-specific β-1 glycoprotein 1 and β-2-glycoprotein I) probably reflect dynamics of a placental proteome shed into maternal circulation during pregnancy. Measurement of changes in the maternal serum proteome, when linked with birth outcomes, may yield biomarkers for tracking reproductive health in resource poor settings in future studies. Published by Elsevier Ltd.

Proteomic Analysis of Detergent Resistant Membrane Domains during Early Interaction of Macrophages with Rough and Smooth Brucella melitensis

PubMed Central

Lauer, Sabine A.; Iyer, Srinivas; Sanchez, Timothy; Forst, Christian V.; Bowden, Brent; Carlson, Kay; Sriranganathan, Nammalwar; Boyle, Stephen M.

2014-01-01

The plasma membrane contains discrete nanometer-sized domains that are resistant to non-ionic detergents, and which are called detergent resistant membrane domains (DRMDs) or lipid rafts. Exposure of host cells to pathogenic bacteria has been shown to induce the re-distribution of specific host proteins between DRMDs and detergent soluble membranes, which leads to the initiation of cell signaling that enable pathogens to access host cells. DRMDs have been shown to play a role in the invasion of Brucella into host macrophages and the formation of replicative phagosomes called Brucella-containing vacuoles (BCVs). In this study we sought to characterize changes to the protein expression profiles in DRMDs and to respective cellular pathways and networks of Mono Mac 6 cells in response to the adherence of rough VTRM1 and smooth 16 M B. melitensis strains. DRMDs were extracted from Mono Mac 6 cells exposed for 2 minutes at 4°C to Brucella (no infection occurs) and from unexposed control cells. Protein expression was determined using the non-gel based quantitative iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) mass spectrometry technique. Using the identified iTRAQ proteins we performed enrichment analyses and probed constructed human biochemical networks for interactions and metabolic reactions. We identified 149 proteins, which either became enriched, depleted or whose amounts did not change in DRMDs upon Brucella exposure. Several of these proteins were distinctly enriched or depleted in DRMDs upon exposure to rough and smooth B. melitensis strains which results in the differential engagement of cellular pathways and networks immediately upon Brucella encounter. For some of the proteins such as myosin 9, small G protein signaling modulator 3, lysine-specific demethylase 5D, erlin-2, and voltage-dependent anion-selective channel protein 2, we observed extreme differential depletion or enrichment in DRMDs. The identified proteins and pathways could provide the basis for novel ways of treating or diagnosing Brucellosis. PMID:24643124

Proteomics and bioinformatics analysis of altered protein expression in the placental villous tissue from early recurrent miscarriage patients.

PubMed

Pan, Hai-Tao; Ding, Hai-Gang; Fang, Min; Yu, Bin; Cheng, Yi; Tan, Ya-Jing; Fu, Qi-Qin; Lu, Bo; Cai, Hong-Guang; Jin, Xin; Xia, Xian-Qing; Zhang, Tao

2018-01-01

Recurrent miscarriage (RM) affects 5% of women, it has an adverse emotional impact on women. Because of the complexities of early development, the mechanism of recurrent miscarriage is still unclear. We hypothesized that abnormal placenta leads to early recurrent miscarriage (ERM). The aim of this study was to identify ERM associated factors in human placenta villous tissue using proteomics. Investigation of these differences in protein expression in parallel profiling is essential to understand the comprehensive pathophysiological mechanism underlying recurrent miscarriage (RM). To gain more insight into mechanisms of recurrent miscarriage (RM), a comparative proteome profile of the human placenta villous tissue in normal and RM pregnancies was analyzed using iTRAQ technology and bioinformatics analysis used by Ingenuity Pathway Analysis (IPA) software. In this study, we employed an iTRAQ based proteomics analysis of four placental villous tissues from patients with early recurrent miscarriage (ERM) and four from normal pregnant women. Finally, we identified 2805 proteins and 79,998 peptides between patients with RM and normal matched group. Further analysis identified 314 differentially expressed proteins in placental villous tissue (≥1.3-fold, Student's t-test, p < 0.05); 209 proteins showed the increased expression while 105 proteins showed decreased expression. These 314 proteins were analyzed by Ingenuity Pathway Analysis (IPA) and were found to play important roles in the growth of embryo. Furthermore, network analysis show that Angiotensinogen (AGT), MAPK14 and Prothrombin (F2) are core factors in early embryonic development. We used another 8 independent samples (4 cases and 4 controls) to cross validation of the proteomic data. This study has identified several proteins that are associated with early development, these results may supply new insight into mechanisms behind recurrent miscarriage. Copyright © 2017 Elsevier Ltd. All rights reserved.

A proteomic approach reveals the variation in human platelet protein composition after storage at different temperatures.

PubMed

Wang, Shichun; Jiang, Tianlun; Fan, Yahan; Zhao, Shuming

2018-03-29

Cryopreservation can slow down the metabolism and decrease the risk of bacterial contamination. But, chilled platelets (PLTs) show a reduced period in circulation due to the rapid clearance by hepatic cells or spleen macrophages after transfusion. The deleterious changes that PLTs undergo are mainly considered the result of PLT protein variation. However, the basis for proteomic variation of stored PLTs remains poorly understood. Besides count, activation markers (CD62P and Annexin V), and aggregation, we used quantitative mass spectrometry to create the first comprehensive and quantitative human PLT proteome of samples stored at different temperatures (22°C, 10°C and -80°C). We found different conditions caused different platelet storage lesion (PSL). PLT count was decreased no matter at what temperature stored. PLTs viability at low temperature dropped by 21.78% and 11.21%, respectively, as compared 10.26% at room temperature, there were no significant differences between the storage methods. Membrane expression of CD62P gradually increased in all groups especially stored at 22°C up to 40% and 10°C up to 30%. However, exposure of PS on the PLT membrane was below 1% in every group. The PLT proteome showed there were 575 and 454 potential proteins identified by general iTRAQ analysis and phosphorylation iTRAQ a nalysis, respectively, among them, 33 common differentially expressed proteins caused by storage time and 44 caused by storage temperature Especially, membrane-bound proteins (such as FERMT3, STX4, MYL9 and TAGLN2) played key roles in PLT storage lesion. The pathways "Endocytosis", "Fc gamma R-mediated phagocytosis" and "Regulation of actin cytoskeleton" were affected predominantly by storage time. And the pathways "SNARE interactions in vesicular transport" and "Vasopressin-regulated water reabsorption" were affected by cold storage in our study. Proteomic results can help us to understand PLT biochemistry and physiology and thus unravel the mechanisms of PSL in time and space for more successful PLT transfusion therapy.

Proteome-wide analysis of Anopheles culicifacies mosquito midgut: new insights into the mechanism of refractoriness.

PubMed

Vijay, Sonam; Rawal, Ritu; Kadian, Kavita; Singh, Jagbir; Adak, Tridibesh; Sharma, Arun

2018-05-08

Midgut invasion, a major bottleneck for malaria parasites transmission is considered as a potential target for vector-parasite interaction studies. New intervention strategies are required to explore the midgut proteins and their potential role in refractoriness for malaria control in Anopheles mosquitoes. To better understand the midgut functional proteins of An. culicifacies susceptible and refractory species, proteomic approaches coupled with bioinformatics analysis is an effective means in order to understand the mechanism of refractoriness. In the present study, an integrated in solution- in gel trypsin digestion approach, along with Isobaric tag for relative and absolute quantitation (iTRAQ)-Liquid chromatography/Mass spectrometry (LC/MS/MS) and data mining were performed to identify the proteomic profile and differentially expressed proteins in Anopheles culicifacies susceptible species A and refractory species B. Shot gun proteomics approaches led to the identification of 80 proteins in An. culicifacies susceptible species A and 92 in refractory species B and catalogue was prepared. iTRAQ based proteomic analysis identified 48 differentially expressed proteins from total 130 proteins. Of these, 41 were downregulated and 7 were upregulated in refractory species B in comparison to susceptible species A. We report that the altered midgut proteins identified in naturally refractory mosquitoes are involved in oxidative phosphorylation, antioxidant and proteolysis process that may suggest their role in parasite growth inhibition. Furthermore, real time polymerase chain reaction (PCR) analysis of few proteins indicated higher expression of iTRAQ upregulated protein in refractory species than susceptible species. This study elucidates the first proteome of the midguts of An. culicifacies sibling species that attempts to analyze unique proteogenomic interactions to provide insights for better understanding of the mechanism of refractoriness. Functional implications of these upregulated proteins in refractory species may reflect the phenotypic characteristics of the mosquitoes and will improve our understandings of blood meal digestion process, parasite vector interactions and proteomes of other vectors of human diseases for development of novel vector control strategies.

Proteomic analysis of maize grain development using iTRAQ reveals temporal programs of diverse metabolic processes.

PubMed

Yu, Tao; Li, Geng; Dong, Shuting; Liu, Peng; Zhang, Jiwang; Zhao, Bin

2016-11-04

Grain development in maize is an essential process in the plant's life cycle and is vital for use of the plant as a crop for animals and humans. However, little is known regarding the protein regulatory networks that control grain development. Here, isobaric tag for relative and absolute quantification (iTRAQ) technology was used to analyze temporal changes in protein expression during maize grain development. Maize grain proteins and changes in protein expression at eight developmental stages from 3 to 50 d after pollination (DAP) were performed using iTRAQ-based proteomics. Overall, 4751 proteins were identified; 2639 of these were quantified and 1235 showed at least 1.5-fold changes in expression levels at different developmental stages and were identified as differentially expressed proteins (DEPs). The DEPs were involved in different cellular and metabolic processes with a preferential distribution to protein synthesis/destination and metabolism categories. A K-means clustering analysis revealed coordinated protein expression associated with different functional categories/subcategories at different development stages. Our results revealed developing maize grain display different proteomic characteristics at distinct stages, such as numerous DEPs for cell growth/division were highly expressed during early stages, whereas those for starch biosynthesis and defense/stress accumulated in middle and late stages, respectively. We also observed coordinated expression of multiple proteins of the antioxidant system, which are essential for the maintenance of reactive oxygen species (ROS) homeostasis during grain development. Particularly, some DEPs, such as zinc metallothionein class II, pyruvate orthophosphate dikinase (PPDK) and 14-3-3 proteins, undergo major changes in expression at specific developmental stages, suggesting their roles in maize grain development. These results provide a valuable resource for analyzing protein function on a global scale and also provide new insights into the potential protein regulatory networks that control grain yield and quality.

Integrated transcriptomic and proteomic analysis of the bile stress response in probiotic Lactobacillus salivarius LI01.

PubMed

Lv, Long-Xian; Yan, Ren; Shi, Hai-Yan; Shi, Ding; Fang, Dai-Qiong; Jiang, Hui-Yong; Wu, Wen-Rui; Guo, Fei-Fei; Jiang, Xia-Wei; Gu, Si-Lan; Chen, Yun-Bo; Yao, Jian; Li, Lan-Juan

2017-01-06

Lactobacillus salivarius LI01, isolated from healthy humans, has demonstrated probiotic properties in the prevention and treatment of liver failure. Tolerance to bile stress is crucial to allow lactobacilli to survive in the gastrointestinal tract and exert their benefits. In this work, we used a Digital Gene Expression transcriptomic and iTRAQ LC-MS/MS proteomic approach to examine the characteristics of LI01 in response to bile stress. Using culture medium with or without 0.15% ox bile, 591 differentially transcribed genes and 347 differentially expressed proteins were detected in LI01. Overall, we found the bile resistance of LI01 to be based on a highly remodeled cell envelope and a reinforced bile efflux system rather than on the activity of bile salt hydrolases. Additionally, some differentially expressed genes related to regulatory systems, the general stress response and central metabolism processes, also play roles in stress sensing, bile-induced damage prevention and energy efficiency. Moreover, bile salts appear to enhance proteolysis and amino acid uptake (especially aromatic amino acids) by LI01, which may support the liver protection properties of this strain. Altogether, this study establishes a model of global response mechanism to bile stress in L. salivarius LI01. L. salivarius strain LI01 exhibits not only antibacterial and antifungal properties but also exerts a good health-promoting effect in acute liver failure. As a potential probiotic strain, the bile-tolerance trait of strain LI01 is important, though this has not yet been explored. In this study, an analysis based on DGE and iTRAQ was performed to investigate the gene expression in strain LI01 under bile stress at the mRNA and protein levels, respectively. To our knowledge, this work also represents the first combined transcriptomic and proteomic analysis of the bile stress response mechanism in L. salivarius. Copyright © 2016. Published by Elsevier B.V.

Equating Multidimensional Tests under a Random Groups Design: A Comparison of Various Equating Procedures

ERIC Educational Resources Information Center

Lee, Eunjung

2013-01-01

The purpose of this research was to compare the equating performance of various equating procedures for the multidimensional tests. To examine the various equating procedures, simulated data sets were used that were generated based on a multidimensional item response theory (MIRT) framework. Various equating procedures were examined, including…

Effect Size Measures for Differential Item Functioning in a Multidimensional IRT Model

ERIC Educational Resources Information Center

Suh, Youngsuk

2016-01-01

This study adapted an effect size measure used for studying differential item functioning (DIF) in unidimensional tests and extended the measure to multidimensional tests. Two effect size measures were considered in a multidimensional item response theory model: signed weighted P-difference and unsigned weighted P-difference. The performance of…

On Multidimensional Item Response Theory: A Coordinate-Free Approach. Research Report. ETS RR-07-30

ERIC Educational Resources Information Center

Antal, Tamás

2007-01-01

A coordinate-free definition of complex-structure multidimensional item response theory (MIRT) for dichotomously scored items is presented. The point of view taken emphasizes the possibilities and subtleties of understanding MIRT as a multidimensional extension of the classical unidimensional item response theory models. The main theorem of the…

The Definition of Difficulty and Discrimination for Multidimensional Item Response Theory Models.

ERIC Educational Resources Information Center

Reckase, Mark D.; McKinley, Robert L.

A study was undertaken to develop guidelines for the interpretation of the parameters of three multidimensional item response theory models and to determine the relationship between the parameters and traditional concepts of item difficulty and discrimination. The three models considered were multidimensional extensions of the one-, two-, and…

Bifactor Approach to Modeling Multidimensionality of Physical Self-Perception Profile

ERIC Educational Resources Information Center

Chung, ChihMing; Liao, Xiaolan; Song, Hairong; Lee, Taehun

2016-01-01

The multi-dimensionality of Physical Self-Perception Profile (PSPP) has been acknowledged by the use of correlated-factor model and second-order model. In this study, the authors critically endorse the bifactor model, as a substitute to address the multi-dimensionality of PSPP. To cross-validate the models, analyses are conducted first in…

Item Vector Plots for the Multidimensional Three-Parameter Logistic Model

ERIC Educational Resources Information Center

Bryant, Damon; Davis, Larry

2011-01-01

This brief technical note describes how to construct item vector plots for dichotomously scored items fitting the multidimensional three-parameter logistic model (M3PLM). As multidimensional item response theory (MIRT) shows promise of being a very useful framework in the test development life cycle, graphical tools that facilitate understanding…

Deriving Multidimensional Poverty Indicators: Methodological Issues and an Empirical Analysis for Italy

ERIC Educational Resources Information Center

Coromaldi, Manuela; Zoli, Mariangela

2012-01-01

Theoretical and empirical studies have recently adopted a multidimensional concept of poverty. There is considerable debate about the most appropriate degree of multidimensionality to retain in the analysis. In this work we add to the received literature in two ways. First, we derive indicators of multiple deprivation by applying a particular…

Evaluating Item Fit for Multidimensional Item Response Models

ERIC Educational Resources Information Center

Zhang, Bo; Stone, Clement A.

2008-01-01

This research examines the utility of the s-x[superscript 2] statistic proposed by Orlando and Thissen (2000) in evaluating item fit for multidimensional item response models. Monte Carlo simulation was conducted to investigate both the Type I error and statistical power of this fit statistic in analyzing two kinds of multidimensional test…

A Multidimensional Scaling Approach to Dimensionality Assessment for Measurement Instruments Modeled by Multidimensional Item Response Theory

ERIC Educational Resources Information Center

Toro, Maritsa

2011-01-01

The statistical assessment of dimensionality provides evidence of the underlying constructs measured by a survey or test instrument. This study focuses on educational measurement, specifically tests comprised of items described as multidimensional. That is, items that require examinee proficiency in multiple content areas and/or multiple cognitive…

Perceptual Salience and Children's Multidimensional Problem Solving

ERIC Educational Resources Information Center

Odom, Richard D.; Corbin, David W.

1973-01-01

Uni- and multidimensional processing of 6- to 9-year olds was studied using recall tasks in which an array of stimuli was reconstructed to match a model array. Results indicated that both age groups were able to solve multidimensional problems, but that solution rate was retarded by the unidimensional processing of highly salient dimensions.…

The Multidimensional Attitudes Scale toward Persons with Disabilities (MAS): Construction and Validation

ERIC Educational Resources Information Center

Findler, Liora; Vilchinsky, Noa; Werner, Shirli

2007-01-01

This study presents the development of a new instrument, the "Multidimensional Attitudes Scale Toward Persons With Disabilities" (MAS). Based on the multidimensional approach, it posits that attitudes are composed of three dimensions: affect, cognition, and behavior. The scale was distributed to a sample of 132 people along with a…

Multidimensional immunolabeling and 4D time-lapse imaging of vital ex vivo lung tissue

PubMed Central

Vierkotten, Sarah; Lindner, Michael; Königshoff, Melanie; Eickelberg, Oliver

2015-01-01

During the last decades, the study of cell behavior was largely accomplished in uncoated or extracellular matrix (ECM)-coated plastic dishes. To date, considerable cell biological efforts have tried to model in vitro the natural microenvironment found in vivo. For the lung, explants cultured ex vivo as lung tissue cultures (LTCs) provide a three-dimensional (3D) tissue model containing all cells in their natural microenvironment. Techniques for assessing the dynamic live interaction between ECM and cellular tissue components, however, are still missing. Here, we describe specific multidimensional immunolabeling of living 3D-LTCs, derived from healthy and fibrotic mouse lungs, as well as patient-derived 3D-LTCs, and concomitant real-time four-dimensional multichannel imaging thereof. This approach allowed the evaluation of dynamic interactions between mesenchymal cells and macrophages with their ECM. Furthermore, fibroblasts transiently expressing focal adhesions markers incorporated into the 3D-LTCs, paving new ways for studying the dynamic interaction between cellular adhesions and their natural-derived ECM. A novel protein transfer technology (FuseIt/Ibidi) shuttled fluorescently labeled α-smooth muscle actin antibodies into the native cells of living 3D-LTCs, enabling live monitoring of α-smooth muscle actin-positive stress fibers in native tissue myofibroblasts residing in fibrotic lesions of 3D-LTCs. Finally, this technique can be applied to healthy and diseased human lung tissue, as well as to adherent cells in conventional two-dimensional cell culture. This novel method will provide valuable new insights into the dynamics of ECM (patho)biology, studying in detail the interaction between ECM and cellular tissue components in their natural microenvironment. PMID:26092995

HIV serostatus disclosure: development and validation of indicators considering target and modality. Results from a community-based research in 5 countries.

PubMed

Préau, Marie; Beaulieu-Prévost, Dominic; Henry, Emilie; Bernier, Adeline; Veillette-Bourbeau, Ludivine; Otis, Joanne

2015-12-01

HIV serostatus disclosure is a complex challenge for persons living with HIV (PLHIV). Despite its beneficial effects, it can also lead to stigmatization and rejection. The current lack of multi-dimensional measurement tools impede an in-depth understanding of the dynamic of disclosure. To develop and validate complex measures of serostatus disclosure. This international community based research study was performed by joint research teams (researchers/community based organizations (CBO)) in five countries (Democratic Republic of the Congo, Ecuador, Mali, Morocco and Romania). A convenience sample of 1500 people living with HIV (PLHIV) in contact with local CBO were recruited in 2011 (300 in each country). Face-to-face interviews were performed using a 125-item questionnaire covering HIV status disclosure to 23 potential disclosure targets and related issues (including personal history with HIV, people's reaction to disclosure, sexuality). A principal component analysis and a hierarchical cluster analysis were performed, in order to identify the main components of HIV disclosure, create measures and classify participants into profiles. Patterns of disclosure were summarized using two main measures: direct and indirect disclosure. Disclosure to sexual partners, whether steady or not, was different from patterns of disclosure to other targets. Among the participants, three profiles emerged - labelled Restricted disclosure, Mainly indirect disclosure and Mainly direct disclosure, respectively representing 61%, 13% and 26% of the total sample. The profiles were associated with different aspects of PLHIV's lives, including self-efficacy, functional limitations and social exclusion. Patterns varied across the five studied countries. Results suggest that multi-dimensional constructs should be used to measure disclosure in order to improve understanding of the disclosure process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Consumer preference of fertilizer in West Java using multi-dimensional scaling approach

NASA Astrophysics Data System (ADS)

Utami, Hesty Nurul; Sadeli, Agriani Hermita; Perdana, Tomy; Renaldy, Eddy; Mahra Arari, H.; Ajeng Sesy N., P.; Fernianda Rahayu, H.; Ginanjar, Tetep; Sanjaya, Sonny

2018-02-01

There are various fertilizer products in the markets for farmers to be used for farming activities. Fertilizers are a supplements supply to soil nutrients, build up soil fertility in order to support plant nutrients and increase plants productivity. Fertilizers consists of nitrogen, phosphorous, potassium, micro vitamins and other complex nutrient in farming systems that commonly used in agricultural activities to improve quantity and quality of harvest. Recently, market demand for fertilizer has been increased dramatically; furthermore, fertilizer companies are required to develop strategies to know about consumer preferences towards several issues. Consumer preference depends on consumer needs selected by subject (individual) that is measured by utilization from several things that market offered and as final decision on purchase process. West Java is one of province as the main producer of agricultural products and automatically is one of the potential consumer's fertilizers on farming activities. This research is a case study in nine districts in West Java province, i.e., Bandung, West Bandung, Bogor, Depok, Garut, Indramayu, Majalengka, Cirebon and Cianjur. The purpose of this research is to describe the attributes on consumer preference for fertilizers. The multi-dimensional scaling method is used as quantitative method to help visualize the level of similarity of individual cases on a dataset, to describe and mapping the information system and to accept the goal. The attributes in this research are availability, nutrients content, price, form of fertilizer, decomposition speed, easy to use, label, packaging type, color, design and size of packaging, hardening process and promotion. There are tendency towards two fertilizer brand have similarity on availability of products, price, speed of decomposition and hardening process.

The Extraction of One-Dimensional Flow Properties from Multi-Dimensional Data Sets

NASA Technical Reports Server (NTRS)

Baurle, Robert A.; Gaffney, Richard L., Jr.

2007-01-01

The engineering design and analysis of air-breathing propulsion systems relies heavily on zero- or one-dimensional properties (e.g. thrust, total pressure recovery, mixing and combustion efficiency, etc.) for figures of merit. The extraction of these parameters from experimental data sets and/or multi-dimensional computational data sets is therefore an important aspect of the design process. A variety of methods exist for extracting performance measures from multi-dimensional data sets. Some of the information contained in the multi-dimensional flow is inevitably lost when any one-dimensionalization technique is applied. Hence, the unique assumptions associated with a given approach may result in one-dimensional properties that are significantly different than those extracted using alternative approaches. The purpose of this effort is to examine some of the more popular methods used for the extraction of performance measures from multi-dimensional data sets, reveal the strengths and weaknesses of each approach, and highlight various numerical issues that result when mapping data from a multi-dimensional space to a space of one dimension.

The Art of Extracting One-Dimensional Flow Properties from Multi-Dimensional Data Sets

NASA Technical Reports Server (NTRS)

Baurle, R. A.; Gaffney, R. L.

2007-01-01

The engineering design and analysis of air-breathing propulsion systems relies heavily on zero- or one-dimensional properties (e:g: thrust, total pressure recovery, mixing and combustion efficiency, etc.) for figures of merit. The extraction of these parameters from experimental data sets and/or multi-dimensional computational data sets is therefore an important aspect of the design process. A variety of methods exist for extracting performance measures from multi-dimensional data sets. Some of the information contained in the multi-dimensional flow is inevitably lost when any one-dimensionalization technique is applied. Hence, the unique assumptions associated with a given approach may result in one-dimensional properties that are significantly different than those extracted using alternative approaches. The purpose of this effort is to examine some of the more popular methods used for the extraction of performance measures from multi-dimensional data sets, reveal the strengths and weaknesses of each approach, and highlight various numerical issues that result when mapping data from a multi-dimensional space to a space of one dimension.

The Cognitive Visualization System with the Dynamic Projection of Multidimensional Data

NASA Astrophysics Data System (ADS)

Gorohov, V.; Vitkovskiy, V.

2008-08-01

The phenomenon of cognitive machine drawing consists in the generation on the screen the special graphic representations, which create in the brain of human operator entertainment means. These means seem man by aesthetically attractive and, thus, they stimulate its descriptive imagination, closely related to the intuitive mechanisms of thinking. The essence of cognitive effect lies in the fact that man receives the moving projection as pseudo-three-dimensional object characterizing multidimensional means in the multidimensional space. After the thorough qualitative study of the visual aspects of multidimensional means with the aid of the enumerated algorithms appears the possibility, using algorithms of standard machine drawing to paint the interesting user separate objects or the groups of objects. Then it is possible to again return to the dynamic behavior of the rotation of means for the purpose of checking the intuitive ideas of user about the clusters and the connections in multidimensional data. Is possible the development of the methods of cognitive machine drawing in combination with other information technologies, first of all with the packets of digital processing of images and multidimensional statistical analysis.

Multidimensional motion measurement of a bimorph-type piezoelectric actuator using a diffraction grating target

NASA Astrophysics Data System (ADS)

Kim, Jong-Ahn; Bae, Eui Won; Kim, Soo Hyun; Kwak, Yoon Keun

2001-09-01

Precision actuators, such as pick-up actuators for HDDs or CD-ROMs, mostly show multidimensional motion. So, to evaluate them more completely, multidimensional measurement is required. Through structural variation and optimization of the design index, the performance of a measurement system can be improved to satisfy the requirement of this application, and so the resolution of each axis is higher than 0.1 μm for translation and 0.5 arcsec for rotation. Using this measurement system, the multidimensional motion and frequency transfer functions of a bimorph-type piezoelectric actuator are obtained.

A generative probabilistic model and discriminative extensions for brain lesion segmentation – with application to tumor and stroke

PubMed Central

Menze, Bjoern H.; Van Leemput, Koen; Lashkari, Danial; Riklin-Raviv, Tammy; Geremia, Ezequiel; Alberts, Esther; Gruber, Philipp; Wegener, Susanne; Weber, Marc-André; Székely, Gabor; Ayache, Nicholas; Golland, Polina

2016-01-01

We introduce a generative probabilistic model for segmentation of brain lesions in multi-dimensional images that generalizes the EM segmenter, a common approach for modelling brain images using Gaussian mixtures and a probabilistic tissue atlas that employs expectation-maximization (EM) to estimate the label map for a new image. Our model augments the probabilistic atlas of the healthy tissues with a latent atlas of the lesion. We derive an estimation algorithm with closed-form EM update equations. The method extracts a latent atlas prior distribution and the lesion posterior distributions jointly from the image data. It delineates lesion areas individually in each channel, allowing for differences in lesion appearance across modalities, an important feature of many brain tumor imaging sequences. We also propose discriminative model extensions to map the output of the generative model to arbitrary labels with semantic and biological meaning, such as “tumor core” or “fluid-filled structure”, but without a one-to-one correspondence to the hypo-or hyper-intense lesion areas identified by the generative model. We test the approach in two image sets: the publicly available BRATS set of glioma patient scans, and multimodal brain images of patients with acute and subacute ischemic stroke. We find the generative model that has been designed for tumor lesions to generalize well to stroke images, and the generative-discriminative model to be one of the top ranking methods in the BRATS evaluation. PMID:26599702

A Generative Probabilistic Model and Discriminative Extensions for Brain Lesion Segmentation--With Application to Tumor and Stroke.

PubMed

Menze, Bjoern H; Van Leemput, Koen; Lashkari, Danial; Riklin-Raviv, Tammy; Geremia, Ezequiel; Alberts, Esther; Gruber, Philipp; Wegener, Susanne; Weber, Marc-Andre; Szekely, Gabor; Ayache, Nicholas; Golland, Polina

2016-04-01

We introduce a generative probabilistic model for segmentation of brain lesions in multi-dimensional images that generalizes the EM segmenter, a common approach for modelling brain images using Gaussian mixtures and a probabilistic tissue atlas that employs expectation-maximization (EM), to estimate the label map for a new image. Our model augments the probabilistic atlas of the healthy tissues with a latent atlas of the lesion. We derive an estimation algorithm with closed-form EM update equations. The method extracts a latent atlas prior distribution and the lesion posterior distributions jointly from the image data. It delineates lesion areas individually in each channel, allowing for differences in lesion appearance across modalities, an important feature of many brain tumor imaging sequences. We also propose discriminative model extensions to map the output of the generative model to arbitrary labels with semantic and biological meaning, such as "tumor core" or "fluid-filled structure", but without a one-to-one correspondence to the hypo- or hyper-intense lesion areas identified by the generative model. We test the approach in two image sets: the publicly available BRATS set of glioma patient scans, and multimodal brain images of patients with acute and subacute ischemic stroke. We find the generative model that has been designed for tumor lesions to generalize well to stroke images, and the extended discriminative -discriminative model to be one of the top ranking methods in the BRATS evaluation.

Semantic networks for odors and colors in Alzheimer's disease.

PubMed

Razani, Jill; Chan, Agnes; Nordin, Steven; Murphy, Claire

2010-05-01

Impairment in odor-naming ability and in verbal and visual semantic networks raised the hypothesis of a breakdown in the semantic network for odors in Alzheimer's disease (AD). The current study addressed this hypothesis. Twenty-four individuals, half patients with probable AD and half control participants, performed triadic-similarity judgments for odors and colors, separately, which, utilizing the multidimensional scaling (MDS) technique of individual difference scaling analysis (INDSCAL), generated two-dimensional configurations of similarity. The abilities to match odors and colors with written name labels were assessed to investigate disease-related differences in ability to identify and conceptualize the stimuli. In addition, responses on attribute-sorting tasks, requiring the odor and color perceptions to be categorized as one polarity of a certain dimension, were obtained to allow for objective interpretation of the MDS spatial maps. Whereas comparison subjects generated spatial maps based predominantly on relatively abstract characteristics, patients with AD classified odors on perceptual characteristics. The maps for patients with AD also showed disorganized groupings and loose associations between odors. Their normal configurations for colors imply that the patients were able to comprehend the task per se. The data for label matching and for attribute sorting provide further evidence for a disturbance in semantic odor memory in AD. The patients performed poorer than controls on both these odor tasks, implying that the ability to identify and/or conceptualize odors is impaired in AD. The results provide clear evidence for deterioration of the structure of semantic knowledge for odors in AD.

When Do Older Adults Become “Disabled”? Social and Health Antecedents of Perceived Disability in a Panel Study of the Oldest Old*

PubMed Central

KELLEY-MOORE, JESSICA A.; SCHUMACHER, JOHN G.; KAHANA, EVA; KAHANA, BOAZ

2007-01-01

Disability carries negative social meaning, and little is known about when (or if), in the process of health decline, persons identify themselves as “disabled” We examine the social and health criteria that older adults use to subjectively rate their own disability status. Using a panel study of older adults (ages 72+), we estimate ordered probit and growth curve models of perceived disability over time. Total prevalent morbidity, functional limitations, and cognitive impairment are predictors of perceived disability. Cessation of driving and receipt of home health care also influence older adults’ perceptions of their own disability. A dense social network slowed the rate of labeling oneself disabled, while health anxiety accelerated the process over time, independent of health status. When considering perceived disability, the oldest old use multidimensional criteria capturing function, recent changes in health status and social networks, and anxiety about their health. PMID:16821507

Prosocial behaviour in palliative nurses: psychometric evaluation of the prosociality scale.

PubMed

Biagioli, Valentina; Prandi, Cesarina; Giuliani, Lucia; Nyatanga, Brian; Frida, Roberta

2016-06-01

The aim of this study was to examine the psychometric properties of a prosociality scale within the palliative nursing context, and then examine the impact of prosocial behaviour in relation to job and educational satisfaction among palliative nurses. An online cross-sectional survey was conducted in 25 Italian palliative care centres, with a total of 107 nurses completing the prosociality scale by Caprara et al (2005) . Exploratory and confirmatory factor analyses were examined to evaluate a multidimensional model of prosociality. A three-factor solution with a second order factor fitted the data well. The three dimensions extracted were labelled as helping, empathy, and sharing. Participants reported high levels of prosociality. In addition, prosociality was positively associated with job and educational satisfaction. The prosociality scale was valid and reliable when tested with palliative nurses. Although prosociality may be embedded in nurses' personalities, this quality should be actively promoted to expand and improve the culture and the ethics of nursing.

Data Sets Representative of the Structures and Experimental Properties of FDA-Approved Drugs.

PubMed

Douguet, Dominique

2018-03-08

Presented here are several data sets that gather information collected from the labels of the FDA approved drugs: their molecular structures and those of the described active metabolites, their associated pharmacokinetics and pharmacodynamics data, and the history of their marketing authorization by the FDA. To date, 1852 chemical structures have been identified with a molecular weight less than 2000 of which 492 are or have active metabolites. To promote the sharing of data, the original web server was upgraded for browsing the database and downloading the data sets (http://chemoinfo.ipmc.cnrs.fr/edrug3d). It is believed that the multidimensional chemistry-oriented collections are an essential resource for a thorough analysis of the current drug chemical space. The data sets are envisioned as being used in a wide range of endeavors that include drug repurposing, drug design, privileged structures analyses, structure-activity relationship studies, and improving of absorption, distribution, metabolism, and elimination predictive models.

Thinking about gender types: cognitive organization of female and male types.

PubMed

Vonk, Roos; Ashmore, Richard D

2003-06-01

We examined the content and dimensional structure of a large and representative sample of gender types. In Study 1, using an open-ended procedure, participants generated 306 different labels for female types (e.g. housewife, feminist, femme fatale, secretary, slob) and 310 for male types (e.g. workaholic, family man, sissy, womanizer, labourer). In Study 2A, a multidimensional configuration of 229 of these male and female types was derived from a free sorting task among a new set of participants. In Study 2B, a subset of types was judged on several dimensions of meaning, which were then fitted into the configuration of types. The most important dimensions in describing the structure of gender types were: young-old, masculine-feminine and traditional-modern. The masculine-feminine dimension showed that the male and female types were largely separated from each other; within each gender category, the types were ordered by their position on the masculine-feminine dimension. Several other aspects of current thinking about men and women are discussed.

Quantitative multiphoton imaging

NASA Astrophysics Data System (ADS)

König, Karsten; Weinigel, Martin; Breunig, Hans Georg; Uchugonova, Aisada

2014-02-01

Certified clinical multiphoton tomographs for label-free multidimensional high-resolution in vivo imaging have been introduced to the market several years ago. Novel tomographs include a flexible 360° scan head attached to a mechanooptical arm for autofluorescence and SHG imaging as well as a CARS module. Non-fluorescent lipids and water, mitochondrial fluorescent NAD(P)H, fluorescent elastin, keratin, and melanin as well as SHG-active collagen can be imaged in vivo with submicron resolution in human skin. Sensitive and rapid detectors allow single photon counting and the construction of 3D maps where the number of detected photons per voxel is depicted. Intratissue concentration profiles from endogenous as well exogenous substances can be generated when the number of detected photons can be correlated with the number of molecules with respect to binding and scattering behavior. Furthermore, the skin ageing index SAAID based on the ratio elastin/collagen as well as the epidermis depth based on the onset of SHG generation can be determined.

Multidimensional poverty and child survival in India.

PubMed

Mohanty, Sanjay K

2011-01-01

Though the concept of multidimensional poverty has been acknowledged cutting across the disciplines (among economists, public health professionals, development thinkers, social scientists, policy makers and international organizations) and included in the development agenda, its measurement and application are still limited. OBJECTIVES AND METHODOLOGY: Using unit data from the National Family and Health Survey 3, India, this paper measures poverty in multidimensional space and examine the linkages of multidimensional poverty with child survival. The multidimensional poverty is measured in the dimension of knowledge, health and wealth and the child survival is measured with respect to infant mortality and under-five mortality. Descriptive statistics, principal component analyses and the life table methods are used in the analyses. The estimates of multidimensional poverty are robust and the inter-state differentials are large. While infant mortality rate and under-five mortality rate are disproportionately higher among the abject poor compared to the non-poor, there are no significant differences in child survival among educationally, economically and health poor at the national level. State pattern in child survival among the education, economical and health poor are mixed. Use of multidimensional poverty measures help to identify abject poor who are unlikely to come out of poverty trap. The child survival is significantly lower among abject poor compared to moderate poor and non-poor. We urge to popularize the concept of multiple deprivations in research and program so as to reduce poverty and inequality in the population.

Biodiversity as a multidimensional construct: a review, framework and case study of herbivory's impact on plant biodiversity

PubMed Central

Naeem, S.; Prager, Case; Weeks, Brian; Varga, Alex; Flynn, Dan F. B.; Griffin, Kevin; Muscarella, Robert; Palmer, Matthew; Wood, Stephen; Schuster, William

2016-01-01

Biodiversity is inherently multidimensional, encompassing taxonomic, functional, phylogenetic, genetic, landscape and many other elements of variability of life on the Earth. However, this fundamental principle of multidimensionality is rarely applied in research aimed at understanding biodiversity's value to ecosystem functions and the services they provide. This oversight means that our current understanding of the ecological and environmental consequences of biodiversity loss is limited primarily to what unidimensional studies have revealed. To address this issue, we review the literature, develop a conceptual framework for multidimensional biodiversity research based on this review and provide a case study to explore the framework. Our case study specifically examines how herbivory by whitetail deer (Odocoileus virginianus) alters the multidimensional influence of biodiversity on understory plant cover at Black Rock Forest, New York. Using three biodiversity dimensions (taxonomic, functional and phylogenetic diversity) to explore our framework, we found that herbivory alters biodiversity's multidimensional influence on plant cover; an effect not observable through a unidimensional approach. Although our review, framework and case study illustrate the advantages of multidimensional over unidimensional approaches, they also illustrate the statistical and empirical challenges such work entails. Meeting these challenges, however, where data and resources permit, will be important if we are to better understand and manage the consequences we face as biodiversity continues to decline in the foreseeable future. PMID:27928041

Biodiversity as a multidimensional construct: a review, framework and case study of herbivory's impact on plant biodiversity.

PubMed

Naeem, S; Prager, Case; Weeks, Brian; Varga, Alex; Flynn, Dan F B; Griffin, Kevin; Muscarella, Robert; Palmer, Matthew; Wood, Stephen; Schuster, William

2016-12-14

Biodiversity is inherently multidimensional, encompassing taxonomic, functional, phylogenetic, genetic, landscape and many other elements of variability of life on the Earth. However, this fundamental principle of multidimensionality is rarely applied in research aimed at understanding biodiversity's value to ecosystem functions and the services they provide. This oversight means that our current understanding of the ecological and environmental consequences of biodiversity loss is limited primarily to what unidimensional studies have revealed. To address this issue, we review the literature, develop a conceptual framework for multidimensional biodiversity research based on this review and provide a case study to explore the framework. Our case study specifically examines how herbivory by whitetail deer (Odocoileus virginianus) alters the multidimensional influence of biodiversity on understory plant cover at Black Rock Forest, New York. Using three biodiversity dimensions (taxonomic, functional and phylogenetic diversity) to explore our framework, we found that herbivory alters biodiversity's multidimensional influence on plant cover; an effect not observable through a unidimensional approach. Although our review, framework and case study illustrate the advantages of multidimensional over unidimensional approaches, they also illustrate the statistical and empirical challenges such work entails. Meeting these challenges, however, where data and resources permit, will be important if we are to better understand and manage the consequences we face as biodiversity continues to decline in the foreseeable future. © 2016 The Authors.

The reality of disability: Multidimensional poverty of people with disability and their families in Latin America.

PubMed

Pinilla-Roncancio, Mónica

2017-12-30

Disability and poverty are interconnected and although this relationship has been recognised, there is a lack of empirical evidence to support any possible causal relationship in this topic, particularly in the context of Latin America (LA). This study tests the hypothesis "Disability increases the risk of multidimensional poverty of people living with disabilities and their families". Using national census data from Brazil, Chile, Colombia, Costa Rica and Mexico, the Global Multidimensional Poverty Index (Global MPI) was calculated with the aim of measuring and comparing the levels of multidimensional poverty of people living in households with and without disabled members in the five countries. We found that in the five countries people with disabilities and their families had higher incidence, intensity and levels of multidimensional poverty compared with people living in other households. Their levels of deprivation were also higher for all the indicators included in the Global MPI and the contribution of this group to the national MPI was higher than their share of the population, thus people with disabilities and their families are overrepresented in those living in multidimensional poverty. People with disabilities and their families are in worse conditions than poor households without disabled members and social policies should aim to reduce their high levels of multidimensional poverty and deprivation. Copyright © 2017 Elsevier Inc. All rights reserved.

A Multidimensional Partial Credit Model with Associated Item and Test Statistics: An Application to Mixed-Format Tests

ERIC Educational Resources Information Center

Yao, Lihua; Schwarz, Richard D.

2006-01-01

Multidimensional item response theory (IRT) models have been proposed for better understanding the dimensional structure of data or to define diagnostic profiles of student learning. A compensatory multidimensional two-parameter partial credit model (M-2PPC) for constructed-response items is presented that is a generalization of those proposed to…

Self-Concepts in Reading, Writing, Listening, and Speaking: A Multidimensional and Hierarchical Structure and Its Generalizability across Native and Foreign Languages

ERIC Educational Resources Information Center

Arens, A. Katrin; Jansen, Malte

2016-01-01

Academic self-concept has been conceptualized as a multidimensional and hierarchical construct. Previous research has mostly focused on its multidimensionality, distinguishing between verbal and mathematical self-concept domains, and only a few studies have examined the factorial structure within specific self-concept domains. The present study…

Assessing Construct Validity Using Multidimensional Item Response Theory.

ERIC Educational Resources Information Center

Ackerman, Terry A.

The concept of a user-specified validity sector is discussed. The idea of the validity sector combines the work of M. D. Reckase (1986) and R. Shealy and W. Stout (1991). Reckase developed a methodology to represent an item in a multidimensional latent space as a vector. Item vectors are computed using multidimensional item response theory item…

Motivation and Engagement in the Workplace: Examining a Multidimensional Framework and Instrument from a Measurement and Evaluation Perspective

ERIC Educational Resources Information Center

Martin, Andrew J.

2009-01-01

This investigation conducts measurement and evaluation of a multidimensional model of workplace motivation and engagement from a construct validation perspective. Two studies were conducted, one using the multi-item multidimensional Motivation and Engagement Scale-Work (N = 637 school personnel) and one using a parallel short form (N = 574 school…

Effects of Multidimensional Concept Maps on Fourth Graders' Learning in Web-Based Computer Course

ERIC Educational Resources Information Center

Huang, Hwa-Shan; Chiou, Chei-Chang; Chiang, Heien-Kun; Lai, Sung-Hsi; Huang, Chiun-Yen; Chou, Yin-Yu

2012-01-01

This study explores the effect of multidimensional concept mapping instruction on students' learning performance in a web-based computer course. The subjects consisted of 103 fourth graders from an elementary school in central Taiwan. They were divided into three groups: multidimensional concept map (MCM) instruction group, Novak concept map (NCM)…

Evaluating the Invariance of Cognitive Profile Patterns Derived from Profile Analysis via Multidimensional Scaling (PAMS): A Bootstrapping Approach

ERIC Educational Resources Information Center

Kim, Se-Kang

2010-01-01

The aim of the current study is to validate the invariance of major profile patterns derived from multidimensional scaling (MDS) by bootstrapping. Profile Analysis via Multidimensional Scaling (PAMS) was employed to obtain profiles and bootstrapping was used to construct the sampling distributions of the profile coordinates and the empirical…

Psychometric Properties of the Frost Multidimensional Perfectionism Scale with Australian Adolescent Girls: Clarification of Multidimensionality and Perfectionist Typology

ERIC Educational Resources Information Center

Hawkins, Colleen C.; Watt, Helen M. G.; Sinclair, Kenneth E.

2006-01-01

The psychometric properties of the Frost, Marten, Lahart, and Rosenblate Multidimensional Perfectionism Scale (1990) are investigated to determine its usefulness as a measurement of perfectionism with Australian secondary school girls and to find empirical support for the existence of both healthy and unhealthy types of perfectionist students.…

PedsQL™ Multidimensional Fatigue Scale in sickle cell disease: feasibility, reliability, and validity.

PubMed

Panepinto, Julie A; Torres, Sylvia; Bendo, Cristiane B; McCavit, Timothy L; Dinu, Bogdan; Sherman-Bien, Sandra; Bemrich-Stolz, Christy; Varni, James W

2014-01-01

Sickle cell disease (SCD) is an inherited blood disorder characterized by a chronic hemolytic anemia that can contribute to fatigue and global cognitive impairment in patients. The study objective was to report on the feasibility, reliability, and validity of the PedsQL™ Multidimensional Fatigue Scale in SCD for pediatric patient self-report ages 5-18 years and parent proxy-report for ages 2-18 years. This was a cross-sectional multi-site study whereby 240 pediatric patients with SCD and 303 parents completed the 18-item PedsQL™ Multidimensional Fatigue Scale. Participants also completed the PedsQL™ 4.0 Generic Core Scales. The PedsQL™ Multidimensional Fatigue Scale evidenced excellent feasibility, excellent reliability for the Total Scale Scores (patient self-report α = 0.90; parent proxy-report α = 0.95), and acceptable reliability for the three individual scales (patient self-report α = 0.77-0.84; parent proxy-report α = 0.90-0.97). Intercorrelations of the PedsQL™ Multidimensional Fatigue Scale with the PedsQL™ Generic Core Scales were predominantly in the large (≥0.50) range, supporting construct validity. PedsQL™ Multidimensional Fatigue Scale Scores were significantly worse with large effects sizes (≥0.80) for patients with SCD than for a comparison sample of healthy children, supporting known-groups discriminant validity. Confirmatory factor analysis demonstrated an acceptable to excellent model fit in SCD. The PedsQL™ Multidimensional Fatigue Scale demonstrated acceptable to excellent measurement properties in SCD. The results demonstrate the relative severity of fatigue symptoms in pediatric patients with SCD, indicating the potential clinical utility of multidimensional assessment of fatigue in patients with SCD in clinical research and practice. © 2013 Wiley Periodicals, Inc.

PedsQL™ Multidimensional Fatigue Scale in Sickle Cell Disease: Feasibility, Reliability and Validity

PubMed Central

Panepinto, Julie A.; Torres, Sylvia; Bendo, Cristiane B.; McCavit, Timothy L.; Dinu, Bogdan; Sherman-Bien, Sandra; Bemrich-Stolz, Christy; Varni, James W.

2013-01-01

Background Sickle cell disease (SCD) is an inherited blood disorder characterized by a chronic hemolytic anemia that can contribute to fatigue and global cognitive impairment in patients. The study objective was to report on the feasibility, reliability, and validity of the PedsQL™ Multidimensional Fatigue Scale in SCD for pediatric patient self-report ages 5–18 years and parent proxy-report for ages 2–18 years. Procedure This was a cross-sectional multi-site study whereby 240 pediatric patients with SCD and 303 parents completed the 18-item PedsQL™ Multidimensional Fatigue Scale. Participants also completed the PedsQL™ 4.0 Generic Core Scales. Results The PedsQL™ Multidimensional Fatigue Scale evidenced excellent feasibility, excellent reliability for the Total Scale Scores (patient self-report α = 0.90; parent proxy-report α = 0.95), and acceptable reliability for the three individual scales (patient self-report α = 0.77–0.84; parent proxy-report α = 0.90–0.97). Intercorrelations of the PedsQL™ Multidimensional Fatigue Scale with the PedsQL™ Generic Core Scales were predominantly in the large (≥ 0.50) range, supporting construct validity. PedsQL™ Multidimensional Fatigue Scale Scores were significantly worse with large effects sizes (≥0.80) for patients with SCD than for a comparison sample of healthy children, supporting known-groups discriminant validity. Confirmatory factor analysis demonstrated an acceptable to excellent model fit in SCD. Conclusions The PedsQL™ Multidimensional Fatigue Scale demonstrated acceptable to excellent measurement properties in SCD. The results demonstrate the relative severity of fatigue symptoms in pediatric patients with SCD, indicating the potential clinical utility of multidimensional assessment of fatigue in patients with SCD in clinical research and practice. PMID:24038960

Development of multi-dimensional body image scale for malaysian female adolescents

PubMed Central

Taib, Mohd Nasir Mohd; Shariff, Zalilah Mohd; Khor, Geok Lin

2008-01-01

The present study was conducted to develop a Multi-dimensional Body Image Scale for Malaysian female adolescents. Data were collected among 328 female adolescents from a secondary school in Kuantan district, state of Pahang, Malaysia by using a self-administered questionnaire and anthropometric measurements. The self-administered questionnaire comprised multiple measures of body image, Eating Attitude Test (EAT-26; Garner & Garfinkel, 1979) and Rosenberg Self-esteem Inventory (Rosenberg, 1965). The 152 items from selected multiple measures of body image were examined through factor analysis and for internal consistency. Correlations between Multi-dimensional Body Image Scale and body mass index (BMI), risk of eating disorders and self-esteem were assessed for construct validity. A seven factor model of a 62-item Multi-dimensional Body Image Scale for Malaysian female adolescents with construct validity and good internal consistency was developed. The scale encompasses 1) preoccupation with thinness and dieting behavior, 2) appearance and body satisfaction, 3) body importance, 4) muscle increasing behavior, 5) extreme dieting behavior, 6) appearance importance, and 7) perception of size and shape dimensions. Besides, a multidimensional body image composite score was proposed to screen negative body image risk in female adolescents. The result found body image was correlated with BMI, risk of eating disorders and self-esteem in female adolescents. In short, the present study supports a multi-dimensional concept for body image and provides a new insight into its multi-dimensionality in Malaysian female adolescents with preliminary validity and reliability of the scale. The Multi-dimensional Body Image Scale can be used to identify female adolescents who are potentially at risk of developing body image disturbance through future intervention programs. PMID:20126371

Development of multi-dimensional body image scale for malaysian female adolescents.

PubMed

Chin, Yit Siew; Taib, Mohd Nasir Mohd; Shariff, Zalilah Mohd; Khor, Geok Lin

2008-01-01

The present study was conducted to develop a Multi-dimensional Body Image Scale for Malaysian female adolescents. Data were collected among 328 female adolescents from a secondary school in Kuantan district, state of Pahang, Malaysia by using a self-administered questionnaire and anthropometric measurements. The self-administered questionnaire comprised multiple measures of body image, Eating Attitude Test (EAT-26; Garner & Garfinkel, 1979) and Rosenberg Self-esteem Inventory (Rosenberg, 1965). The 152 items from selected multiple measures of body image were examined through factor analysis and for internal consistency. Correlations between Multi-dimensional Body Image Scale and body mass index (BMI), risk of eating disorders and self-esteem were assessed for construct validity. A seven factor model of a 62-item Multi-dimensional Body Image Scale for Malaysian female adolescents with construct validity and good internal consistency was developed. The scale encompasses 1) preoccupation with thinness and dieting behavior, 2) appearance and body satisfaction, 3) body importance, 4) muscle increasing behavior, 5) extreme dieting behavior, 6) appearance importance, and 7) perception of size and shape dimensions. Besides, a multidimensional body image composite score was proposed to screen negative body image risk in female adolescents. The result found body image was correlated with BMI, risk of eating disorders and self-esteem in female adolescents. In short, the present study supports a multi-dimensional concept for body image and provides a new insight into its multi-dimensionality in Malaysian female adolescents with preliminary validity and reliability of the scale. The Multi-dimensional Body Image Scale can be used to identify female adolescents who are potentially at risk of developing body image disturbance through future intervention programs.

Multi-dimensional scores to predict mortality in patients with idiopathic pulmonary fibrosis undergoing lung transplantation assessment.

PubMed

Fisher, Jolene H; Al-Hejaili, Faris; Kandel, Sonja; Hirji, Alim; Shapera, Shane; Mura, Marco

2017-04-01

The heterogeneous progression of idiopathic pulmonary fibrosis (IPF) makes prognostication difficult and contributes to high mortality on the waitlist for lung transplantation (LTx). Multi-dimensional scores (Composite Physiologic index [CPI], [Gender-Age-Physiology [GAP]; RIsk Stratification scorE [RISE]) demonstrated enhanced predictive power towards outcome in IPF. The lung allocation score (LAS) is a multi-dimensional tool commonly used to stratify patients assessed for LTx. We sought to investigate whether IPF-specific multi-dimensional scores predict mortality in patients with IPF assessed for LTx. The study included 302 patients with IPF who underwent a LTx assessment (2003-2014). Multi-dimensional scores were calculated. The primary outcome was 12-month mortality after assessment. LTx was considered as competing event in all analyses. At the end of the observation period, there were 134 transplants, 63 deaths, and 105 patients were alive without LTx. Multi-dimensional scores predicted mortality with accuracy similar to LAS, and superior to that of individual variables: area under the curve (AUC) for LAS was 0.78 (sensitivity 71%, specificity 86%); CPI 0.75 (sensitivity 67%, specificity 82%); GAP 0.67 (sensitivity 59%, specificity 74%); RISE 0.78 (sensitivity 71%, specificity 84%). A separate analysis conducted only in patients actively listed for LTx (n = 247; 50 deaths) yielded similar results. In patients with IPF assessed for LTx as well as in those actually listed, multi-dimensional scores predict mortality better than individual variables, and with accuracy similar to the LAS. If validated, multi-dimensional scores may serve as inexpensive tools to guide decisions on the timing of referral and listing for LTx. Copyright © 2017 Elsevier Ltd. All rights reserved.

Numeric invariants from multidimensional persistence

DOE PAGES

Skryzalin, Jacek; Carlsson, Gunnar

2017-05-19

Topological data analysis is the study of data using techniques from algebraic topology. Often, one begins with a finite set of points representing data and a “filter” function which assigns a real number to each datum. Using both the data and the filter function, one can construct a filtered complex for further analysis. For example, applying the homology functor to the filtered complex produces an algebraic object known as a “one-dimensional persistence module”, which can often be interpreted as a finite set of intervals representing various geometric features in the data. If one runs the above process incorporating multiple filtermore » functions simultaneously, one instead obtains a multidimensional persistence module. Unfortunately, these are much more difficult to interpret. In this article, we analyze the space of multidimensional persistence modules from the perspective of algebraic geometry. First we build a moduli space of a certain subclass of easily analyzed multidimensional persistence modules, which we construct specifically to capture much of the information which can be gained by using multidimensional persistence instead of one-dimensional persistence. Fruthermore, we argue that the global sections of this space provide interesting numeric invariants when evaluated against our subclass of multidimensional persistence modules. Finally, we extend these global sections to the space of all multidimensional persistence modules and discuss how the resulting numeric invariants might be used to study data. This paper extends the results of Adcock et al. (Homol Homotopy Appl 18(1), 381–402, 2016) by constructing numeric invariants from the computation of a multidimensional persistence module as given by Carlsson et al. (J Comput Geom 1(1), 72–100, 2010).« less

Effectiveness of Multidimensional Cancer Survivor Rehabilitation and Cost-Effectiveness of Cancer Rehabilitation in General: A Systematic Review

PubMed Central

Mewes, Janne C.; IJzerman, Maarten J.; van Harten, Wim H.

2012-01-01

Introduction. Many cancer survivors suffer from a combination of disease- and treatment-related morbidities and complaints after primary treatment. There is a growing evidence base for the effectiveness of monodimensional rehabilitation interventions; in practice, however, patients often participate in multidimensional programs. This study systematically reviews evidence regarding effectiveness of multidimensional rehabilitation programs for cancer survivors and cost-effectiveness of cancer rehabilitation in general. Methods. The published literature was systematically reviewed. Data were extracted using standardized forms and were summarized narratively. Results. Sixteen effectiveness and six cost-effectiveness studies were included. Multidimensional rehabilitation programs were found to be effective, but not more effective than monodimensional interventions, and not on all outcome measures. Effect sizes for quality of life were in the range of −0.12 (95% confidence interval [CI], −0.45–0.20) to 0.98 (95% CI, 0.69–1.29). Incremental cost-effectiveness ratios ranged from −€16,976, indicating cost savings, to €11,057 per quality-adjusted life year. Conclusions. The evidence for multidimensional interventions and the economic impact of rehabilitation studies is scarce and dominated by breast cancer studies. Studies published so far report statistically significant benefits for multidimensional interventions over usual care, most notably for the outcomes fatigue and physical functioning. An additional benefit of multidimensional over monodimensional rehabilitation was not found, but this was also sparsely reported on. Available economic evaluations assessed very different rehabilitation interventions. Yet, despite low comparability, all showed favorable cost-effectiveness ratios. Future studies should focus their designs on the comparative effectiveness and cost-effectiveness of multidimensional programs. PMID:22982580

The Multidimensional Assessment of Interoceptive Awareness (MAIA)

PubMed Central

Mehling, Wolf E.; Price, Cynthia; Daubenmier, Jennifer J.; Acree, Mike; Bartmess, Elizabeth; Stewart, Anita

2012-01-01

This paper describes the development of a multidimensional self-report measure of interoceptive body awareness. The systematic mixed-methods process involved reviewing the current literature, specifying a multidimensional conceptual framework, evaluating prior instruments, developing items, and analyzing focus group responses to scale items by instructors and patients of body awareness-enhancing therapies. Following refinement by cognitive testing, items were field-tested in students and instructors of mind-body approaches. Final item selection was achieved by submitting the field test data to an iterative process using multiple validation methods, including exploratory cluster and confirmatory factor analyses, comparison between known groups, and correlations with established measures of related constructs. The resulting 32-item multidimensional instrument assesses eight concepts. The psychometric properties of these final scales suggest that the Multidimensional Assessment of Interoceptive Awareness (MAIA) may serve as a starting point for research and further collaborative refinement. PMID:23133619

Benefits of Multidimensional Measures of Child Well Being in China

PubMed Central

Gatenio Gabel, Shirley; Zhang, Yiwei

2017-01-01

In recent decades, measures of child well-being have evolved from single dimension to multidimensional measures. Multi-dimensional measures deepen and broaden our understanding of child well-being and inform us of areas of neglect. Child well-being in China today is measured through proxy measures of household need. This paper discusses the evolution of child well-being measures more generally, explores the benefits of positive indicators and multiple dimensions in formulating policy, and then reviews efforts to date by the Chinese government, researchers, and non-governmental and intergovernmental organizations to develop comprehensive multidimensional measures of child well-being in China. The domains and their potential interactions, as well as data sources and availability, are presented. The authors believe that child well-being in China would benefit from the development of a multidimensional index and that there is sufficient data to develop such an index. PMID:29113121

Positivity-preserving numerical schemes for multidimensional advection

NASA Technical Reports Server (NTRS)

Leonard, B. P.; Macvean, M. K.; Lock, A. P.

1993-01-01

This report describes the construction of an explicit, single time-step, conservative, finite-volume method for multidimensional advective flow, based on a uniformly third-order polynomial interpolation algorithm (UTOPIA). Particular attention is paid to the problem of flow-to-grid angle-dependent, anisotropic distortion typical of one-dimensional schemes used component-wise. The third-order multidimensional scheme automatically includes certain cross-difference terms that guarantee good isotropy (and stability). However, above first-order, polynomial-based advection schemes do not preserve positivity (the multidimensional analogue of monotonicity). For this reason, a multidimensional generalization of the first author's universal flux-limiter is sought. This is a very challenging problem. A simple flux-limiter can be found; but this introduces strong anisotropic distortion. A more sophisticated technique, limiting part of the flux and then restoring the isotropy-maintaining cross-terms afterwards, gives more satisfactory results. Test cases are confined to two dimensions; three-dimensional extensions are briefly discussed.

Benefits of Multidimensional Measures of Child Well Being in China.

PubMed

Gatenio Gabel, Shirley; Zhang, Yiwei

2017-11-06

In recent decades, measures of child well-being have evolved from single dimension to multidimensional measures. Multi-dimensional measures deepen and broaden our understanding of child well-being and inform us of areas of neglect. Child well-being in China today is measured through proxy measures of household need. This paper discusses the evolution of child well-being measures more generally, explores the benefits of positive indicators and multiple dimensions in formulating policy, and then reviews efforts to date by the Chinese government, researchers, and non-governmental and intergovernmental organizations to develop comprehensive multidimensional measures of child well-being in China. The domains and their potential interactions, as well as data sources and availability, are presented. The authors believe that child well-being in China would benefit from the development of a multidimensional index and that there is sufficient data to develop such an index.

Testing the multidimensionality of the inventory of school motivation in a Dutch student sample.

PubMed

Korpershoek, Hanke; Xu, Kun; Mok, Magdalena Mo Ching; McInerney, Dennis M; van der Werf, Greetje

2015-01-01

A factor analytic and a Rasch measurement approach were applied to evaluate the multidimensional nature of the school motivation construct among more than 7,000 Dutch secondary school students. The Inventory of School Motivation (McInerney and Ali, 2006) was used, which intends to measure four motivation dimensions (mastery, performance, social, and extrinsic motivation), each comprising of two first-order factors. One unidimensional model and three multidimensional models (4-factor, 8-factor, higher order) were fit to the data. Results of both approaches showed that the multidimensional models validly represented the school motivation among Dutch secondary school pupils, whereas model fit of the unidimensional model was poor. The differences in model fit between the three multidimensional models were small, although a different model was favoured by the two approaches. The need for improvement of some of the items and the need to increase measurement precision of several first-order factors are discussed.

NMR studies of two spliced leader RNAs using isotope labeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapham, J.; Crothers, D.M.

1994-12-01

Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions betweenmore » the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.« less

Why it's important for it to stop: Examining the mental health correlates of bullying and ill-treatment at work in a cohort study.

PubMed

Butterworth, Peter; Leach, Liana S; Kiely, Kim M

2016-11-01

There is limited Australian information on the prevalence and mental health consequences of bullying and ill-treatment at work. The aims of this study were to use data from an ongoing Australian longitudinal cohort study to (1) compare different measures of workplace bullying, (2) estimate the prevalence of bullying and ill-treatment at work, (3) evaluate whether workplace bullying is distinct from other adverse work characteristics and (4) examine the unique contribution of workplace bullying to common mental disorders in mid-life. The sample comprised 1466 participants (52% women) aged 52-58 from wave four of the Personality and Total Health (PATH) through Life study. Workplace bullying was assessed by a single item of self-labelling measure of bullying and a 15-item scale of bullying-related behaviours experienced in the past 6 months. Factor analysis the identified underlying factor structure of the behavioural bullying scale. Current bullying was reported by 7.0% of respondents, while 46.4% of respondents reported that they had been bullied at some point in their working life. Person-related and work-related bullying behaviours were more common than violence and intimidation. The multi-dimensional scale of bullying behaviours had greater concordance with a single item of self-labelled bullying (Area Under the Curve = 0.88) than other adverse work characteristics (all Area Under the Curves < 0.67). Self-labelled bullying and scales reflecting person-related and work-related bullying were independent predictors of depression and/or anxiety. This study provides unique information on the prevalence and mental health impacts of workplace bullying and ill-treatment in Australia. Workplace bullying is a relatively common experience, and is associated with increased risk of depression and anxiety. Greater attention to identifying and preventing bullying and ill-treatment in the workplace is warranted. © The Royal Australian and New Zealand College of Psychiatrists 2015.

Multidimensional CAT Item Selection Methods for Domain Scores and Composite Scores with Item Exposure Control and Content Constraints

ERIC Educational Resources Information Center

Yao, Lihua

2014-01-01

The intent of this research was to find an item selection procedure in the multidimensional computer adaptive testing (CAT) framework that yielded higher precision for both the domain and composite abilities, had a higher usage of the item pool, and controlled the exposure rate. Five multidimensional CAT item selection procedures (minimum angle;…

Reliability and Validity of the Chinese Version of the Multidimensional Anxiety Scale for Children among Chinese Secondary School Students

ERIC Educational Resources Information Center

Yao, Shuqiao; Zou, Tao; Zhu, Xiongzhao; Abela, John R. Z.; Auerbach, Randy P.; Tong, Xi

2007-01-01

The objective of the current study was to develop a Chinese translation of the Multidimensional Anxiety Scale for Children (MASC) [March (1997) Multidimensional anxiety scale for children: Technical manual, Multi health systems, Toronto, ON], and to evaluate its reliability and validity. The original version of the MASC was translated into Chinese…

Self Esteem, Locus of Control and Multidimensional Perfectionism as the Predictors of Subjective Well Being

ERIC Educational Resources Information Center

Karatas, Zeynep; Tagay, Ozlem

2012-01-01

The purpose of this study is to determine whether there is a relationship between self-esteem, locus of control and multidimensional perfectionism, and the extent to which the variables of self-esteem, locus of control and multidimensional perfectionism contribute to the prediction of subjective well-being. The study was carried out with 318 final…

Pedagogical Factors Stimulating the Self-Development of Students' Multi-Dimensional Thinking in Terms of Subject-Oriented Teaching

ERIC Educational Resources Information Center

Andreev, Valentin I.

2014-01-01

The main aim of this research is to disclose the essence of students' multi-dimensional thinking, also to reveal the rating of factors which stimulate the raising of effectiveness of self-development of students' multi-dimensional thinking in terms of subject-oriented teaching. Subject-oriented learning is characterized as a type of learning where…

Applying Multidimensional Item Response Theory Models in Validating Test Dimensionality: An Example of K-12 Large-Scale Science Assessment

ERIC Educational Resources Information Center

Li, Ying; Jiao, Hong; Lissitz, Robert W.

2012-01-01

This study investigated the application of multidimensional item response theory (IRT) models to validate test structure and dimensionality. Multiple content areas or domains within a single subject often exist in large-scale achievement tests. Such areas or domains may cause multidimensionality or local item dependence, which both violate the…

A Multidimensional Ideal Point Item Response Theory Model for Binary Data

ERIC Educational Resources Information Center

Maydeu-Olivares, Albert; Hernandez, Adolfo; McDonald, Roderick P.

2006-01-01

We introduce a multidimensional item response theory (IRT) model for binary data based on a proximity response mechanism. Under the model, a respondent at the mode of the item response function (IRF) endorses the item with probability one. The mode of the IRF is the ideal point, or in the multidimensional case, an ideal hyperplane. The model…

A Canonical Correlation Analysis of the Influence of Social Comparison, Gender, and Grade Level on the Multidimensional Self-Concepts of Gifted Adolescents

ERIC Educational Resources Information Center

Rinn, Anne N.; Jamieson, Kelly M.; Gross, Candace M.; McQueen, Kand S.

2009-01-01

This study examines the effects of social comparison, gender, and grade level on gifted adolescents' multidimensional self-concept. Participants include 248 gifted adolescents who had completed the sixth through tenth grade during the previous academic year. Multidimensional self-concept was measured using the Self Description Questionnaire II…

Some applications of the multi-dimensional fractional order for the Riemann-Liouville derivative

NASA Astrophysics Data System (ADS)

Ahmood, Wasan Ajeel; Kiliçman, Adem

2017-01-01

In this paper, the aim of this work is to study theorem for the one-dimensional space-time fractional deriative, generalize some function for the one-dimensional fractional by table represents the fractional Laplace transforms of some elementary functions to be valid for the multi-dimensional fractional Laplace transform and give the definition of the multi-dimensional fractional Laplace transform. This study includes that, dedicate the one-dimensional fractional Laplace transform for functions of only one independent variable and develop of the one-dimensional fractional Laplace transform to multi-dimensional fractional Laplace transform based on the modified Riemann-Liouville derivative.

Multidimensional scaling for evolutionary algorithms--visualization of the path through search space and solution space using Sammon mapping.

PubMed

Pohlheim, Hartmut

2006-01-01

Multidimensional scaling as a technique for the presentation of high-dimensional data with standard visualization techniques is presented. The technique used is often known as Sammon mapping. We explain the mathematical foundations of multidimensional scaling and its robust calculation. We also demonstrate the use of this technique in the area of evolutionary algorithms. First, we present the visualization of the path through the search space of the best individuals during an optimization run. We then apply multidimensional scaling to the comparison of multiple runs regarding the variables of individuals and multi-criteria objective values (path through the solution space).

Best Design for Multidimensional Computerized Adaptive Testing With the Bifactor Model

PubMed Central

Seo, Dong Gi; Weiss, David J.

2015-01-01

Most computerized adaptive tests (CATs) have been studied using the framework of unidimensional item response theory. However, many psychological variables are multidimensional and might benefit from using a multidimensional approach to CATs. This study investigated the accuracy, fidelity, and efficiency of a fully multidimensional CAT algorithm (MCAT) with a bifactor model using simulated data. Four item selection methods in MCAT were examined for three bifactor pattern designs using two multidimensional item response theory models. To compare MCAT item selection and estimation methods, a fixed test length was used. The Ds-optimality item selection improved θ estimates with respect to a general factor, and either D- or A-optimality improved estimates of the group factors in three bifactor pattern designs under two multidimensional item response theory models. The MCAT model without a guessing parameter functioned better than the MCAT model with a guessing parameter. The MAP (maximum a posteriori) estimation method provided more accurate θ estimates than the EAP (expected a posteriori) method under most conditions, and MAP showed lower observed standard errors than EAP under most conditions, except for a general factor condition using Ds-optimality item selection. PMID:29795848

A Multidimensional Study of Vocal Function Following Radiation Therapy for Laryngeal Cancers.

PubMed

Angadi, Vrushali; Dressler, Emily; Stemple, Joseph

2017-06-01

Radiation therapy (XRT) has proven to be an effective curative modality in the treatment of laryngeal cancers. However, XRT also has deleterious effects on vocal function. To demonstrate the multidimensional nature of deficits in vocal function as a result of radiation therapy for laryngeal cancer. Cohort study. Vocal function parameters were chosen from the 5 domains of voice assessment to complete a multidimensional assessment battery. Adults irradiated (XRT group) for laryngeal cancers were compared to a control group of individuals with no history of head and neck cancers or radiation therapy. The control group was matched in age, sex, and pack years of smoking. Eighteen participants were recruited for the study. The XRT group demonstrated significantly worse clinical values as compared to the control group across select parameters in the each of the 5 domains of voice assessment. Radiation therapy for laryngeal cancers results in multidimensional deficits in vocal function. Notably, these deficits persist long term. In the present study sample, multidimensional deficits were persistent 2 to 7 years following completion of XRT. The observed multidimensional persistent vocal difficulties highlight the importance of vocal rehabilitation in the irradiated larynx cancer population.

The PedsQL multidimensional fatigue scale in pediatric obesity: feasibility, reliability and validity.

PubMed

Varni, James W; Limbers, Christine A; Bryant, William P; Wilson, Don P

2010-01-01

The PedsQL (Pediatric Quality of Life Inventory) is a modular instrument designed to measure health-related quality of life (HRQOL) and disease-specific symptoms in children and adolescents. The PedsQL Multidimensional Fatigue Scale was designed as a child self-report and parent proxy-report generic symptom-specific instrument to measure fatigue in pediatric patients. The objective of the present study was to determine the feasibility, reliability, and validity of the PedsQL Multidimensional Fatigue Scale in pediatric obesity. The 18-item PedsQL Multidimensional Fatigue Scale (General Fatigue, Sleep/Rest Fatigue, and Cognitive Fatigue domains) and the PedsQL 4.0 Generic Core Scales were completed by 41 pediatric patients with a physician-diagnosis of obesity and 43 parents from a hospital-based Pediatric Endocrinology Clinic. The PedsQL Multidimensional Fatigue Scale evidenced minimal missing responses (1.6%, child report; 0.5%, parent report), achieved excellent reliability for the Total Fatigue Scale Score (alpha = 0.90 child report, 0.90 parent report), distinguished between pediatric patients with obesity and healthy children, and was significantly correlated with the PedsQL 4.0 Generic Core Scales supporting construct validity. Pediatric patients with obesity experienced fatigue comparable with pediatric patients receiving cancer treatment, demonstrating the relative severity of their fatigue symptoms. The results demonstrate the measurement properties of the PedsQL Multidimensional Fatigue Scale in pediatric obesity. The findings suggest that the PedsQL Multidimensional Fatigue Scale may be utilized in the standardized evaluation of fatigue in pediatric patients with obesity.

Multidimensional Poverty and Child Survival in India

PubMed Central

Mohanty, Sanjay K.

2011-01-01

Background Though the concept of multidimensional poverty has been acknowledged cutting across the disciplines (among economists, public health professionals, development thinkers, social scientists, policy makers and international organizations) and included in the development agenda, its measurement and application are still limited. Objectives and Methodology Using unit data from the National Family and Health Survey 3, India, this paper measures poverty in multidimensional space and examine the linkages of multidimensional poverty with child survival. The multidimensional poverty is measured in the dimension of knowledge, health and wealth and the child survival is measured with respect to infant mortality and under-five mortality. Descriptive statistics, principal component analyses and the life table methods are used in the analyses. Results The estimates of multidimensional poverty are robust and the inter-state differentials are large. While infant mortality rate and under-five mortality rate are disproportionately higher among the abject poor compared to the non-poor, there are no significant differences in child survival among educationally, economically and health poor at the national level. State pattern in child survival among the education, economical and health poor are mixed. Conclusion Use of multidimensional poverty measures help to identify abject poor who are unlikely to come out of poverty trap. The child survival is significantly lower among abject poor compared to moderate poor and non-poor. We urge to popularize the concept of multiple deprivations in research and program so as to reduce poverty and inequality in the population. PMID:22046384

Psychometric Validation of a Multidimensional Schema of Substance Use Topology: Discrimination of High and Low Risk Youth and Prediction of Substance Use Disorder.

ERIC Educational Resources Information Center

Kirisci, Levent; Tarter, Ralph E.

2001-01-01

Designs and evaluates a multidimensional schema for the assessment of alcohol, tobacco and other drug use topology. Findings illustrate the value of multidimensional assessment for identifying youth at high risk for substance use disorder (SUD) as well as for elucidating the factors contributing to the transition to suprathreshold SUD. (Contains…

Development of a Computerized Adaptive Testing for Diagnosing the Cognitive Process of Grade 7 Students in Learning Algebra, Using Multidimensional Item Response Theory

ERIC Educational Resources Information Center

Senarat, Somprasong; Tayraukham, Sombat; Piyapimonsit, Chatsiri; Tongkhambanjong, Sakesan

2013-01-01

The purpose of this research is to develop a multidimensional computerized adaptive test for diagnosing the cognitive process of grade 7 students in learning algebra by applying multidimensional item response theory. The research is divided into 4 steps: 1) the development of item bank of algebra, 2) the development of the multidimensional…

Multi-dimensional quantum state sharing based on quantum Fourier transform

NASA Astrophysics Data System (ADS)

Qin, Huawang; Tso, Raylin; Dai, Yuewei

2018-03-01

A scheme of multi-dimensional quantum state sharing is proposed. The dealer performs the quantum SUM gate and the quantum Fourier transform to encode a multi-dimensional quantum state into an entanglement state. Then the dealer distributes each participant a particle of the entanglement state, to share the quantum state among n participants. In the recovery, n-1 participants measure their particles and supply their measurement results; the last participant performs the unitary operation on his particle according to these measurement results and can reconstruct the initial quantum state. The proposed scheme has two merits: It can share the multi-dimensional quantum state and it does not need the entanglement measurement.

Some theorems and properties of multi-dimensional fractional Laplace transforms

NASA Astrophysics Data System (ADS)

Ahmood, Wasan Ajeel; Kiliçman, Adem

2016-06-01

The aim of this work is to study theorems and properties for the one-dimensional fractional Laplace transform, generalize some properties for the one-dimensional fractional Lapalce transform to be valid for the multi-dimensional fractional Lapalce transform and is to give the definition of the multi-dimensional fractional Lapalce transform. This study includes: dedicate the one-dimensional fractional Laplace transform for functions of only one independent variable with some of important theorems and properties and develop of some properties for the one-dimensional fractional Laplace transform to multi-dimensional fractional Laplace transform. Also, we obtain a fractional Laplace inversion theorem after a short survey on fractional analysis based on the modified Riemann-Liouville derivative.

The Necessity-Concerns-Framework: A Multidimensional Theory Benefits from Multidimensional Analysis

PubMed Central

Phillips, L. Alison; Diefenbach, Michael; Kronish, Ian M.; Negron, Rennie M.; Horowitz, Carol R.

2014-01-01

Background Patients’ medication-related concerns and necessity-beliefs predict adherence. Evaluation of the potentially complex interplay of these two dimensions has been limited because of methods that reduce them to a single dimension (difference scores). Purpose We use polynomial regression to assess the multidimensional effect of stroke-event survivors’ medication-related concerns and necessity-beliefs on their adherence to stroke-prevention medication. Methods Survivors (n=600) rated their concerns, necessity-beliefs, and adherence to medication. Confirmatory and exploratory polynomial regression determined the best-fitting multidimensional model. Results As posited by the Necessity-Concerns Framework (NCF), the greatest and lowest adherence was reported by those with strong necessity-beliefs/weak concerns and strong concerns/weak necessity-beliefs, respectively. However, as could not be assessed using a difference-score model, patients with ambivalent beliefs were less adherent than those exhibiting indifference. Conclusions Polynomial regression allows for assessment of the multidimensional nature of the NCF. Clinicians/Researchers should be aware that concerns and necessity dimensions are not polar opposites. PMID:24500078

The necessity-concerns framework: a multidimensional theory benefits from multidimensional analysis.

PubMed

Phillips, L Alison; Diefenbach, Michael A; Kronish, Ian M; Negron, Rennie M; Horowitz, Carol R

2014-08-01

Patients' medication-related concerns and necessity-beliefs predict adherence. Evaluation of the potentially complex interplay of these two dimensions has been limited because of methods that reduce them to a single dimension (difference scores). We use polynomial regression to assess the multidimensional effect of stroke-event survivors' medication-related concerns and necessity beliefs on their adherence to stroke-prevention medication. Survivors (n = 600) rated their concerns, necessity beliefs, and adherence to medication. Confirmatory and exploratory polynomial regression determined the best-fitting multidimensional model. As posited by the necessity-concerns framework (NCF), the greatest and lowest adherence was reported by those necessity weak concerns and strong concerns/weak Necessity-Beliefs, respectively. However, as could not be assessed using a difference-score model, patients with ambivalent beliefs were less adherent than those exhibiting indifference. Polynomial regression allows for assessment of the multidimensional nature of the NCF. Clinicians/Researchers should be aware that concerns and necessity dimensions are not polar opposites.

The moderating effects of gender on the associations between multidimensional hostility and psychosomatic symptoms: a Chinese case.

PubMed

Weng, Chia-Ying; Lin, I-Mei; Jiang, Ding-Yu

2010-08-01

The purpose of this study was to examine the effects of gender on the relationship between multidimensional hostility and psychosomatic symptoms in Chinese culture. The participants in this study were 398 Chinese college students (40% female) recruited from Taiwan. Four dimensions of multidimensional hostility-hostility cognition, hostility affect, expressive hostility behavior, and suppressive hostility behavior-were measured by the Chinese Hostility Inventory. After controlling for the effects of depression and anxiety, the results of path analysis revealed that the multidimensional hostility predicted psychosomatic symptoms directly, and predicted psychosomatic symptoms indirectly through negative health behavior. Furthermore, gender moderated the relationships between multidimensional hostility and health outcomes. Expressive hostility exacerbated psychosomatic symptom in females but buffered it in males, while affective hostility exacerbated psychosomatic symptoms in males. Additionally, suppressive hostility behavior was correlated to psychosomatic symptoms indirectly through negative health behavior in females. Moreover, expressive hostility was correlated to psychosomatic symptoms indirectly through negative health behavior more in males than in females.

On new physics searches with multidimensional differential shapes

NASA Astrophysics Data System (ADS)

Ferreira, Felipe; Fichet, Sylvain; Sanz, Veronica

2018-03-01

In the context of upcoming new physics searches at the LHC, we investigate the impact of multidimensional differential rates in typical LHC analyses. We discuss the properties of shape information, and argue that multidimensional rates bring limited information in the scope of a discovery, but can have a large impact on model discrimination. We also point out subtleties about systematic uncertainties cancellations and the Cauchy-Schwarz bound on interference terms.

Measuring the Perception of the Teachers' Autonomy-Supportive Behavior in Physical Education: Development and Initial Validation of a Multi-Dimensional Instrument

ERIC Educational Resources Information Center

Tilga, Henri; Hein, Vello; Koka, Andre

2017-01-01

This research aimed to develop and validate an instrument to assess the students' perceptions of the teachers' autonomy-supportive behavior by the multi-dimensional scale (Multi-Dimensional Perceived Autonomy Support Scale for Physical Education). The participants were 1,476 students aged 12- to 15-years-old. In Study 1, a pool of 37 items was…

Multidimensional modulation for next-generation transmission systems

NASA Astrophysics Data System (ADS)

Millar, David S.; Koike-Akino, Toshiaki; Kojima, Keisuke; Parsons, Kieran

2017-01-01

Recent research in multidimensional modulation has shown great promise in long reach applications. In this work, we will investigate the origins of this gain, the different approaches to multidimensional constellation design, and different performance metrics for coded modulation. We will also discuss the reason that such coded modulation schemes seem to have limited application at shorter distances, and the potential for other coded modulation schemes in future transmission systems.

Multidimensional Data Modeling for Business Process Analysis

NASA Astrophysics Data System (ADS)

Mansmann, Svetlana; Neumuth, Thomas; Scholl, Marc H.

The emerging area of business process intelligence attempts to enhance the analytical capabilities of business process management systems by employing data warehousing and mining technologies. This paper presents an approach to re-engineering the business process modeling in conformity with the multidimensional data model. Since the business process and the multidimensional model are driven by rather different objectives and assumptions, there is no straightforward solution to converging these models.

The Psychometric Properties of an Arabic version of the PedsQL Multidimensional Fatigue Scale Tested for Children with Cancer.

PubMed

Al-Gamal, Ekhlas; Long, Tony

2017-09-01

Fatigue is considered to be one of the most reported symptoms experienced by children with cancer. A major aim of this study was to develop an Arabic version of the Pediatric Quality of Life (PedsQL) Multidimensional Fatigue Scale (child report) and to test its psychometric proprieties for the assessment of fatigue in Arabic children with cancer. The PedsQL Multidimensional Fatigue Scale (Arabic version) and the PedsQL TM 4.0 Generic Core scale (existing Arabic version) were completed by 70 Jordanian children with cancer. Cronbach's alpha coefficients were found to be 0.90 for the total PedsQL Multidimensional Fatigue Scale (Arabic version), 0.94 for the general fatigue subscale, 0.67 for the sleep/rest fatigue subscale, and 0.87 for the cognitive fatigue subscale. The PedsQL Multidimensional Fatigue Scale scores correlated significantly with the PedsQL TM 4.0 Generic Core scale and demonstrated good construct validity. The results demonstrate excellent reliability and good validity of the PedsQL Multidimensional Fatigue Scale (Arabic version) for children with cancer. This is the first validated scale that assesses fatigue in Arabic children with cancer. The English scale has been used with several pediatric clinical populations, so this Arabic version may be equally useful beyond the field of cancer.

DEVELOPMENT AND PSYCHOMETRIC TESTING OF A MULTIDIMENSIONAL INSTRUMENT OF PERCEIVED DISCRIMINATION AMONG AFRICAN AMERICANS IN THE JACKSON HEART STUDY

PubMed Central

Sims, Mario; Wyatt, Sharon B.; Gutierrez, Mary Lou; Taylor, Herman A.; Williams, David R.

2009-01-01

Objective Assessing the discrimination-health disparities hypothesis requires psychometrically sound, multidimensional measures of discrimination. Among the available discrimination measures, few are multidimensional and none have adequate psychometric testing in a large, African American sample. We report the development and psychometric testing of the multidimensional Jackson Heart Study Discrimination (JHSDIS) Instrument. Methods A multidimensional measure assessing the occurrence, frequency, attribution, and coping responses to perceived everyday and lifetime discrimination; lifetime burden of discrimination; and effect of skin color was developed and tested in the 5302-member cohort of the Jackson Heart Study. Internal consistency was calculated by using Cronbach α. coefficient. Confirmatory factor analysis established the dimensions, and intercorrelation coefficients assessed the discriminant validity of the instrument. Setting Tri-county area of the Jackson, MS metropolitan statistical area. Results The JHSDIS was psychometrically sound (overall α=.78, .84 and .77, respectively, for the everyday and lifetime subscales). Confirmatory factor analysis yielded 11 factors, which confirmed the a priori dimensions represented. Conclusions The JHSDIS combined three scales into a single multidimensional instrument with good psychometric properties in a large sample of African Americans. This analysis lays the foundation for using this instrument in research that will examine the association between perceived discrimination and CVD among African Americans. PMID:19341164

The multidimensional perturbation value: a single metric to measure similarity and activity of treatments in high-throughput multidimensional screens.

PubMed

Hutz, Janna E; Nelson, Thomas; Wu, Hua; McAllister, Gregory; Moutsatsos, Ioannis; Jaeger, Savina A; Bandyopadhyay, Somnath; Nigsch, Florian; Cornett, Ben; Jenkins, Jeremy L; Selinger, Douglas W

2013-04-01

Screens using high-throughput, information-rich technologies such as microarrays, high-content screening (HCS), and next-generation sequencing (NGS) have become increasingly widespread. Compared with single-readout assays, these methods produce a more comprehensive picture of the effects of screened treatments. However, interpreting such multidimensional readouts is challenging. Univariate statistics such as t-tests and Z-factors cannot easily be applied to multidimensional profiles, leaving no obvious way to answer common screening questions such as "Is treatment X active in this assay?" and "Is treatment X different from (or equivalent to) treatment Y?" We have developed a simple, straightforward metric, the multidimensional perturbation value (mp-value), which can be used to answer these questions. Here, we demonstrate application of the mp-value to three data sets: a multiplexed gene expression screen of compounds and genomic reagents, a microarray-based gene expression screen of compounds, and an HCS compound screen. In all data sets, active treatments were successfully identified using the mp-value, and simulations and follow-up analyses supported the mp-value's statistical and biological validity. We believe the mp-value represents a promising way to simplify the analysis of multidimensional data while taking full advantage of its richness.

The PedsQL Multidimensional Fatigue Scale in type 1 diabetes: feasibility, reliability, and validity.

PubMed

Varni, James W; Limbers, Christine A; Bryant, William P; Wilson, Don P

2009-08-01

The Pediatric Quality of Life Inventory (PedsQL, Mapi Research Trust, Lyon, France; www.pedsql.org) is a modular instrument designed to measure health-related quality of life and disease-specific symptoms in children and adolescents. The PedsQL Multidimensional Fatigue Scale was designed as a child self-report and parent proxy-report generic symptom-specific instrument to measure fatigue in pediatric patients. The objective of the present study was to determine the feasibility, reliability, and validity of the PedsQL Multidimensional Fatigue Scale in type 1 diabetes. The 18-item PedsQL Multidimensional Fatigue Scale (General Fatigue, Sleep/Rest Fatigue, and Cognitive Fatigue domains) and the PedsQL 4.0 Generic Core Scales were administered to 83 pediatric patients with type 1 diabetes and 84 parents. The PedsQL Multidimensional Fatigue Scale evidenced minimal missing responses (0.3% child report and 0.3% parent report), achieved excellent reliability for the Total Fatigue Scale score (alpha= 0.92 child report, 0.94 parent report), distinguished between pediatric patients with diabetes and healthy children, and was significantly correlated with the PedsQL 4.0 Generic Core Scales supporting construct validity. Pediatric patients with diabetes experienced fatigue that was comparable to pediatric patients with cancer on treatment, demonstrating the relative severity of their fatigue symptoms. The results demonstrate the measurement properties of the PedsQL Multidimensional Fatigue Scale in type 1 diabetes. The findings suggest that the PedsQL Multidimensional Fatigue Scale may be utilized in the standardized evaluation of fatigue in pediatric patients with type 1 diabetes.

The PedsQL Multidimensional Fatigue Scale in young adults: feasibility, reliability and validity in a University student population.

PubMed

Varni, James W; Limbers, Christine A

2008-02-01

The PedsQL (Pediatric Quality of Life Inventory) is a modular instrument designed to measure health-related quality of life (HRQOL) and disease-specific symptoms in children and adolescents ages 2-18. The PedsQL Multidimensional Fatigue Scale was designed as a generic symptom-specific instrument to measure fatigue in pediatric patients ages 2-18. Since a sizeable number of pediatric patients prefer to remain with their pediatric providers after age 18, the objective of the present study was to determine the feasibility, reliability, and validity of the PedsQL Multidimensional Fatigue Scale in young adults. The 18-item PedsQL Multidimensional Fatigue Scale (General Fatigue, Sleep/Rest Fatigue, and Cognitive Fatigue domains), the PedsQL 4.0 Generic Core Scales Young Adult Version, and the SF-8 Health Survey were completed by 423 university students ages 18-25. The PedsQL Multidimensional Fatigue Scale evidenced minimal missing responses, achieved excellent reliability for the Total Scale Score (alpha = 0.90), distinguished between healthy young adults and young adults with chronic health conditions, was significantly correlated with the relevant PedsQL 4.0 Generic Core Scales and the SF-8 standardized scores, and demonstrated a factor-derived structure largely consistent with the a priori conceptual model. The results demonstrate the measurement properties of the PedsQL Multidimensional Fatigue Scale in a convenience sample of young adult university students. The findings suggest that the PedsQL Multidimensional Fatigue Scale may be utilized in the evaluation of fatigue for a broad age range.

Fatigue and multidimensional disease severity in chronic obstructive pulmonary disease.

PubMed

Inal-Ince, Deniz; Savci, Sema; Saglam, Melda; Calik, Ebru; Arikan, Hulya; Bosnak-Guclu, Meral; Vardar-Yagli, Naciye; Coplu, Lutfi

2010-06-30

Fatigue is associated with longitudinal ratings of health in patients with chronic obstructive pulmonary disease (COPD). Although the degree of airflow obstruction is often used to grade disease severity in patients with COPD, multidimensional grading systems have recently been developed. The aim of this study was to investigate the relationship between perceived and actual fatigue level and multidimensional disease severity in patients with COPD. Twenty-two patients with COPD (aged 52-74 years) took part in the study. Multidimensional disease severity was measured using the SAFE and BODE indices. Perceived fatigue was assessed using the Fatigue Severity Scale (FSS) and the Fatigue Impact Scale (FIS). Peripheral muscle endurance was evaluated using the number of sit-ups, squats, and modified push-ups that each patient could do. Thirteen patients (59%) had severe fatigue, and their St George's Respiratory Questionnaire scores were significantly higher (p < 0.05). The SAFE index score was significantly correlated with the number of sit-ups, number of squats, FSS score and FIS score (p < 0.05). The BODE index was significantly associated with the numbers of sit-ups, squats and modified push-ups, and with the FSS and FIS scores (p < 0.05). Peripheral muscle endurance and fatigue perception in patients with COPD was related to multidimensional disease severity measured with both the SAFE and BODE indices. Improvements in perceived and actual fatigue levels may positively affect multidimensional disease severity and health status in COPD patients. Further research is needed to investigate the effects of fatigue perception and exercise training on patients with different stages of multidimensional COPD severity.

Central Schemes for Multi-Dimensional Hamilton-Jacobi Equations

NASA Technical Reports Server (NTRS)

Bryson, Steve; Levy, Doron; Biegel, Bryan (Technical Monitor)

2002-01-01

We present new, efficient central schemes for multi-dimensional Hamilton-Jacobi equations. These non-oscillatory, non-staggered schemes are first- and second-order accurate and are designed to scale well with an increasing dimension. Efficiency is obtained by carefully choosing the location of the evolution points and by using a one-dimensional projection step. First-and second-order accuracy is verified for a variety of multi-dimensional, convex and non-convex problems.

Assessment of Patient-Reported Outcome Instruments to Assess Chronic Low Back Pain.

PubMed

Ramasamy, Abhilasha; Martin, Mona L; Blum, Steven I; Liedgens, Hiltrud; Argoff, Charles; Freynhagen, Rainer; Wallace, Mark; McCarrier, Kelly P; Bushnell, Donald M; Hatley, Noël V; Patrick, Donald L

2017-06-01

 To identify patient-reported outcome (PRO) instruments that assess chronic low back pain (cLBP) symptoms (specifically pain qualities) and/or impacts for potential use in cLBP clinical trials to demonstrate treatment benefit and support labeling claims.  Literature review of existing PRO measures.  Publications detailing existing PRO measures for cLBP were identified, reviewed, and summarized. As recommended by the US Food & Drug Administration (FDA) PRO development guidance, standard measurement characteristics were reviewed, including development history, psychometric properties (validity and reliability), ability to detect change, and interpretation of observed changes.  Thirteen instruments were selected and reviewed: Low Back Pain Bothersomeness Scale, Neuropathic Pain Symptom Inventory, PainDETECT, Pain Quality Assessment Scale Revised, Revised Short Form McGill Pain Questionnaire, Low Back Pain Impact Questionnaire, Oswestry Disability Index, Pain Disability Index, Roland-Morris Disability Questionnaire, Brief Pain Inventory and Brief Pain Inventory Short Form, Musculoskeletal Outcomes Data Evaluation and Management System Spine Module, Orebro Musculoskeletal Pain Questionnaire, and the West Haven-Yale Multidimensional Pain Inventory Interference Scale. The instruments varied in the aspects of pain and/or impacts that they assessed, and none of the instruments fulfilled all criteria for use in clinical trials to support labeling claims based on recommendations outlined in the FDA PRO guidance.  There is an unmet need for a validated PRO instrument to evaluate cLBP-related symptoms and impacts for use in clinical trials. © 2017 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Ammonia Affects Astroglial Proliferation in Culture

PubMed Central

Bodega, Guillermo; Segura, Berta; Ciordia, Sergio; Mena, María del Carmen; López-Fernández, Luis Andrés; García, María Isabel; Trabado, Isabel; Suárez, Isabel

2015-01-01

Primary cultures of rat astroglial cells were exposed to 1, 3 and 5 mM NH4Cl for up to 10 days. Dose- and time-dependent reductions in cell numbers were seen, plus an increase in the proportion of cells in the S phase. The DNA content was reduced in the treated cells, and BrdU incorporation diminished. However, neither ammonia nor ammonia plus glutamine had any effect on DNA polymerase activity. iTRAQ analysis showed that exposure to ammonia induced a significant reduction in histone and heterochromatin protein 1 expression. A reduction in cell viability was also noted. The ammonia-induced reduction of proliferative activity in these cultured astroglial cells seems to be due to a delay in the completion of the S phase provoked by the inhibition of chromatin protein synthesis. PMID:26421615

The PedsQL in pediatric cancer: reliability and validity of the Pediatric Quality of Life Inventory Generic Core Scales, Multidimensional Fatigue Scale, and Cancer Module.

PubMed

Varni, James W; Burwinkle, Tasha M; Katz, Ernest R; Meeske, Kathy; Dickinson, Paige

2002-04-01

The Pediatric Quality of Life Inventory (PedsQL) is a modular instrument designed to measure health-related quality of life (HRQOL) in children and adolescents ages 2-18 years. The PedsQL 4.0 Generic Core Scales are multidimensional child self-report and parent proxy-report scales developed as the generic core measure to be integrated with the PedsQL disease specific modules. The PedsQL Multidimensional Fatigue Scale was designed to measure fatigue in pediatric patients. The PedsQL 3.0 Cancer Module was designed to measure pediatric cancer specific HRQOL. The PedsQL Generic Core Scales, Multidimensional Fatigue Scale, and Cancer Module were administered to 339 families (220 child self-reports; 337 parent proxy-reports). Internal consistency reliability for the PedsQL Generic Core Total Scale Score (alpha = 0.88 child, 0.93 parent report), Multidimensional Fatigue Total Scale Score (alpha = 0.89 child, 0.92 parent report) and most Cancer Module Scales (average alpha = 0.72 child, 0.87 parent report) demonstrated reliability acceptable for group comparisons. Validity was demonstrated using the known-groups method. The PedsQL distinguished between healthy children and children with cancer as a group, and among children on-treatment versus off-treatment. The validity of the PedsQL Multidimensional Fatigue Scale was further demonstrated through hypothesized intercorrelations with dimensions of generic and cancer specific HRQOL. The results demonstrate the reliability and validity of the PedsQL Generic Core Scales, Multidimensional Fatigue Scale, and Cancer Module in pediatric cancer. The PedsQL may be utilized as an outcome measure in clinical trials, research, and clinical practice. Copyright 2002 American Cancer Society.

The PedsQL Multidimensional Fatigue Scale in pediatric rheumatology: reliability and validity.

PubMed

Varni, James W; Burwinkle, Tasha M; Szer, Ilona S

2004-12-01

. The PedsQL (Pediatric Quality of Life Inventory) is a modular instrument designed to measure health related quality of life (HRQOL) in children and adolescents ages 2-18 years. The recently developed 18-item PedsQL Multidimensional Fatigue Scale was designed to measure fatigue in pediatric patients and comprises the General Fatigue Scale (6 items), Sleep/Rest Fatigue Scale (6 items), and Cognitive Fatigue Scale (6 items). The PedsQL 4.0 Generic Core Scales were developed as the generic core measure to be integrated with the PedsQL Disease-Specific Modules. The PedsQL 3.0 Rheumatology Module was designed to measure pediatric rheumatology-specific HRQOL. Methods. The PedsQL Multidimensional Fatigue Scale, Generic Core Scales, and Rheumatology Module were administered to 163 children and 154 parents (183 families accrued overall) recruited from a pediatric rheumatology clinic. Results. Internal consistency reliability for the PedsQL Multidimensional Fatigue Scale Total Score (a = 0.95 child, 0.95 parent report), General Fatigue Scale (a = 0.93 child, 0.92 parent), Sleep/Rest Fatigue Scale (a = 0.88 child, 0.90 parent), and Cognitive Fatigue Scale (a = 0.93 child, 0.96 parent) were excellent for group and individual comparisons. The validity of the PedsQL Multidimensional Fatigue Scale was confirmed through hypothesized intercorrelations with dimensions of generic and rheumatology-specific HRQOL. The PedsQL Multidimensional Fatigue Scale distinguished between healthy children and children with rheumatic diseases as a group, and was associated with greater disease severity. Children with fibromyalgia manifested greater fatigue than children with other rheumatic diseases. The results confirm the initial reliability and validity of the PedsQL Multidimensional Fatigue Scale in pediatric rheumatology.

Multidimensional scaling analysis of financial time series based on modified cross-sample entropy methods

NASA Astrophysics Data System (ADS)

He, Jiayi; Shang, Pengjian; Xiong, Hui

2018-06-01

Stocks, as the concrete manifestation of financial time series with plenty of potential information, are often used in the study of financial time series. In this paper, we utilize the stock data to recognize their patterns through out the dissimilarity matrix based on modified cross-sample entropy, then three-dimensional perceptual maps of the results are provided through multidimensional scaling method. Two modified multidimensional scaling methods are proposed in this paper, that is, multidimensional scaling based on Kronecker-delta cross-sample entropy (MDS-KCSE) and multidimensional scaling based on permutation cross-sample entropy (MDS-PCSE). These two methods use Kronecker-delta based cross-sample entropy and permutation based cross-sample entropy to replace the distance or dissimilarity measurement in classical multidimensional scaling (MDS). Multidimensional scaling based on Chebyshev distance (MDSC) is employed to provide a reference for comparisons. Our analysis reveals a clear clustering both in synthetic data and 18 indices from diverse stock markets. It implies that time series generated by the same model are easier to have similar irregularity than others, and the difference in the stock index, which is caused by the country or region and the different financial policies, can reflect the irregularity in the data. In the synthetic data experiments, not only the time series generated by different models can be distinguished, the one generated under different parameters of the same model can also be detected. In the financial data experiment, the stock indices are clearly divided into five groups. Through analysis, we find that they correspond to five regions, respectively, that is, Europe, North America, South America, Asian-Pacific (with the exception of mainland China), mainland China and Russia. The results also demonstrate that MDS-KCSE and MDS-PCSE provide more effective divisions in experiments than MDSC.

Multidimensional Risk Analysis: MRISK

NASA Technical Reports Server (NTRS)

McCollum, Raymond; Brown, Douglas; O'Shea, Sarah Beth; Reith, William; Rabulan, Jennifer; Melrose, Graeme

2015-01-01

Multidimensional Risk (MRISK) calculates the combined multidimensional score using Mahalanobis distance. MRISK accounts for covariance between consequence dimensions, which de-conflicts the interdependencies of consequence dimensions, providing a clearer depiction of risks. Additionally, in the event the dimensions are not correlated, Mahalanobis distance reduces to Euclidean distance normalized by the variance and, therefore, represents the most flexible and optimal method to combine dimensions. MRISK is currently being used in NASA's Environmentally Responsible Aviation (ERA) project o assess risk and prioritize scarce resources.

ComVisMD - compact visualization of multidimensional data: experimenting with cricket players data

NASA Astrophysics Data System (ADS)

Dandin, Shridhar B.; Ducassé, Mireille

2018-03-01

Database information is multidimensional and often displayed in tabular format (row/column display). Presented in aggregated form, multidimensional data can be used to analyze the records or objects. Online Analytical database Processing (OLAP) proposes mechanisms to display multidimensional data in aggregated forms. A choropleth map is a thematic map in which areas are colored in proportion to the measurement of a statistical variable being displayed, such as population density. They are used mostly for compact graphical representation of geographical information. We propose a system, ComVisMD inspired by choropleth map and the OLAP cube to visualize multidimensional data in a compact way. ComVisMD displays multidimensional data like OLAP Cube, where we are mapping an attribute a (first dimension, e.g. year started playing cricket) in vertical direction, object coloring based on b (second dimension, e.g. batting average), mapping varying-size circles based on attribute c (third dimension, e.g. highest score), mapping numbers based on attribute d (fourth dimension, e.g. matches played). We illustrate our approach on cricket players data, namely on two tables Country and Player. They have a large number of rows and columns: 246 rows and 17 columns for players of one country. ComVisMD’s visualization reduces the size of the tabular display by a factor of about 4, allowing users to grasp more information at a time than the bare table display.

Impact of multidimensional poverty on the self-efficacy of older people: Results from an Australian longitudinal study.

PubMed

Callander, Emily J; Schofield, Deborah J

2017-02-01

Self-efficacy has numerous benefits for active and healthy aging, including giving the people the ability to make positive changes to their living standards and lifestyles. The present study aims to determine whether falling into multidimensional poverty lowers self-efficacy. Longitudinal analysis of waves 7-11 (2007-2011) of the nationally representative Household, Income and Labor Dynamics in Australia survey using linear regression models. The analysis focused on the Australian population aged 65 years and older. The Freedom Poverty Measure was used to identify those in multidimensional poverty. Those who fell into multidimensional poverty for 3 or 4 years between 2007 and 2011 had their self-efficacy scores decline by an average of 27 points (SD 21.2). Those who fell into poverty had significantly lower self-efficacy scores in 2011 - up to 57% lower (-66.6%, -45.7% P < 0.0001) after being in multidimensional poverty for 3 or 4 years between 2007 and 2011 than those who were never in poverty. Falling into multidimensional poverty lowers the self-efficacy scores of older people. In order to improve the chances of older people making long-term changes to improve their living standards, feelings of self-efficacy should first be assessed and improved. Geriatr Gerontol Int 2017; 17: 308-314. © 2015 Japan Geriatrics Society.

Further Validation of the Multidimensional Fatigue Symptom Inventory-Short Form

PubMed Central

Stein, Kevin D.; Jacobsen, Paul B.; Blanchard, Chris M.; Thors, Christina

2008-01-01

A growing body of evidence is documenting the multidimensional nature of cancer-related fatigue. Although several multidimensional measures of fatigue have been developed, further validation of these scales is needed. To this end, the current study sought to evaluate the factorial and construct validity of the 30-item Multidimensional Fatigue Symptom Inventory-Short Form (MFSI-SF). A heterogeneous sample of 304 cancer patients (mean age 55 years) completed the MFSI-SF, along with several other measures of psychosocial functioning including the MOS-SF-36 and Fatigue Symptom Inventory, following the fourth cycle of chemotherapy treatment. The results of a confirmatory factor analysis indicated the 5-factor model provided a good fit to the data as evidenced by commonly used goodness of fit indices (CFI 0.90 and IFI 0.90). Additional evidence for the validity of the MFSI-SF was provided via correlations with other relevant instruments (range −0.21 to 0.82). In sum, the current study provides support for the MFSI-SF as a valuable tool for the multidimensional assessment of cancer-related fatigue. PMID:14711465

Large-scale Instability during Gravitational Collapse with Neutrino Transport and a Core-Collapse Supernova

NASA Astrophysics Data System (ADS)

Aksenov, A. G.; Chechetkin, V. M.

2018-04-01

Most of the energy released in the gravitational collapse of the cores of massive stars is carried away by neutrinos. Neutrinos play a pivotal role in explaining core-collape supernovae. Currently, mathematical models of the gravitational collapse are based on multi-dimensional gas dynamics and thermonuclear reactions, while neutrino transport is considered in a simplified way. Multidimensional gas dynamics is used with neutrino transport in the flux-limited diffusion approximation to study the role of multi-dimensional effects. The possibility of large-scale convection is discussed, which is interesting both for explaining SN II and for setting up observations to register possible high-energy (≳10MeV) neutrinos from the supernova. A new multi-dimensional, multi-temperature gas dynamics method with neutrino transport is presented.

Multidimensional Recurrence Quantification Analysis (MdRQA) for the Analysis of Multidimensional Time-Series: A Software Implementation in MATLAB and Its Application to Group-Level Data in Joint Action

PubMed Central

Wallot, Sebastian; Roepstorff, Andreas; Mønster, Dan

2016-01-01

We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels—from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size. The Appendix in Supplementary Material contains a software implementation in MATLAB to calculate MdRQA measures. PMID:27920748

GENERAL: Scattering Phase Correction for Semiclassical Quantization Rules in Multi-Dimensional Quantum Systems

NASA Astrophysics Data System (ADS)

Huang, Wen-Min; Mou, Chung-Yu; Chang, Cheng-Hung

2010-02-01

While the scattering phase for several one-dimensional potentials can be exactly derived, less is known in multi-dimensional quantum systems. This work provides a method to extend the one-dimensional phase knowledge to multi-dimensional quantization rules. The extension is illustrated in the example of Bogomolny's transfer operator method applied in two quantum wells bounded by step potentials of different heights. This generalized semiclassical method accurately determines the energy spectrum of the systems, which indicates the substantial role of the proposed phase correction. Theoretically, the result can be extended to other semiclassical methods, such as Gutzwiller trace formula, dynamical zeta functions, and semiclassical Landauer-Büttiker formula. In practice, this recipe enhances the applicability of semiclassical methods to multi-dimensional quantum systems bounded by general soft potentials.

Multidimensional Recurrence Quantification Analysis (MdRQA) for the Analysis of Multidimensional Time-Series: A Software Implementation in MATLAB and Its Application to Group-Level Data in Joint Action.

PubMed

Wallot, Sebastian; Roepstorff, Andreas; Mønster, Dan

2016-01-01

We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels-from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size. The Appendix in Supplementary Material contains a software implementation in MATLAB to calculate MdRQA measures.

Multi-dimensional simulations of core-collapse supernova explosions with CHIMERA

NASA Astrophysics Data System (ADS)

Messer, O. E. B.; Harris, J. A.; Hix, W. R.; Lentz, E. J.; Bruenn, S. W.; Mezzacappa, A.

2018-04-01

Unraveling the core-collapse supernova (CCSN) mechanism is a problem that remains essentially unsolved despite more than four decades of effort. Spherically symmetric models with otherwise high physical fidelity generally fail to produce explosions, and it is widely accepted that CCSNe are inherently multi-dimensional. Progress in realistic modeling has occurred recently through the availability of petascale platforms and the increasing sophistication of supernova codes. We will discuss our most recent work on understanding neutrino-driven CCSN explosions employing multi-dimensional neutrino-radiation hydrodynamics simulations with the Chimera code. We discuss the inputs and resulting outputs from these simulations, the role of neutrino radiation transport, and the importance of multi-dimensional fluid flows in shaping the explosions. We also highlight the production of 48Ca in long-running Chimera simulations.

Multidimensional Programming Methods for Energy Facility Siting: Alternative Approaches

NASA Technical Reports Server (NTRS)

Solomon, B. D.; Haynes, K. E.

1982-01-01

The use of multidimensional optimization methods in solving power plant siting problems, which are characterized by several conflicting, noncommensurable objectives is addressed. After a discussion of data requirements and exclusionary site screening methods for bounding the decision space, classes of multiobjective and goal programming models are discussed in the context of finite site selection. Advantages and limitations of these approaches are highlighted and the linkage of multidimensional methods with the subjective, behavioral components of the power plant siting process is emphasized.

Optimal multi-dimensional poverty lines: The state of poverty in Iraq

NASA Astrophysics Data System (ADS)

Ameen, Jamal R. M.

2017-09-01

Poverty estimation based on calories intake is unrealistic. The established concept of multidimensional poverty has methodological weaknesses in the treatment of different dimensions and there is disagreement in methods of combining them into a single poverty line. This paper introduces a methodology to estimate optimal multidimensional poverty lines and uses the Iraqi household socio-economic survey data of 2012 to demonstrate the idea. The optimal poverty line for Iraq is found to be 170.5 Thousand Iraqi Dinars (TID).

Comparative Transcriptome and iTRAQ Proteome Analyses of Citrus Root Responses to Candidatus Liberibacter asiaticus Infection

PubMed Central

Jiang, Nong-hui; Jiang, Bo; Zhang, Yong-yan; Wu, Bo; Hu, Min-lun; Zeng, Ji-wu; Yan, Hua-xue; Yi, Gan-jun; Zhong, Guang-yan

2015-01-01

Root samples of ‘Sanhu’ red tangerine trees infected with and without Candidatus Liberibacter asiaticus (CLas) were collected at 50 days post inoculation and subjected to RNA-sequencing and isobaric tags for relative and absolute quantification (iTRAQ) to profile the differentially expressed genes (DEGs) and proteins (DEPs), respectively. Quantitative real-time PCR was subsequently used to confirm the expression of 16 selected DEGs. Results showed that a total of 3956 genes and 78 proteins were differentially regulated by HLB-infection. Among the most highly up-regulated DEPs were sperm specific protein 411, copper ion binding protein, germin-like proteins, subtilisin-like proteins and serine carboxypeptidase-like 40 proteins whose transcript levels were concomitantly up-regulated as shown by RNA-seq data. Comparison between our results and those of the previously reported showed that known HLB-modulated biological pathways including cell-wall modification, protease-involved protein degradation, carbohydrate metabolism, hormone synthesis and signaling, transcription activities, and stress responses were similarly regulated by HLB infection but different or root-specific changes did exist. The root unique changes included the down-regulation in genes of ubiquitin-dependent protein degradation pathway, secondary metabolism, cytochrome P450s, UDP-glucosyl transferases and pentatricopeptide repeat containing proteins. Notably, nutrient absorption was impaired by HLB-infection as the expression of the genes involved in Fe, Zn, N and P adsorption and transportation were significantly changed. HLB-infection induced some cellular defense responses but simultaneously reduced the biosynthesis of the three major classes of secondary metabolites, many of which are known to have anti-pathogen activities. Genes involved in callose deposition were up-regulated whereas those involved in callose degradation were also up-regulated, indicating that the sieve tube elements in roots were hanging on the balance of life and death at this stage. In addition, signs of carbohydrate starvation were already eminent in roots at this stage. Other interesting genes and pathways that were changed by HLB-infection were also discussed based on our findings. PMID:26046530

Involvement of GABA Transporters in Atropine-Treated Myopic Retina As Revealed by iTRAQ Quantitative Proteomics

PubMed Central

2015-01-01

Atropine, a muscarinic antagonist, is known to inhibit myopia progression in several animal models and humans. However, the mode of action is not established yet. In this study, we compared quantitative iTRAQ proteomic analysis in the retinas collected from control and lens-induced myopic (LIM) mouse eyes treated with atropine. The myopic group received a (−15D) spectacle lens over the right eye on postnatal day 10 with or without atropine eye drops starting on postnatal day 24. Axial length was measured by optical low coherence interferometry (OLCI), AC-Master, and refraction was measured by automated infrared photorefractor at postnatal 24, 38, and 52 days. Retinal tissue samples were pooled from six eyes for each group. The experiments were repeated twice, and technical replicates were also performed for liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis. MetaCore was used to perform protein profiling for pathway analysis. We identified a total of 3882 unique proteins with <1% FDR by analyzing the samples in replicates for two independent experiments. This is the largest number of mouse retina proteome reported to date. Thirty proteins were found to be up-regulated (ratio for myopia/control > global mean ratio + 1 standard deviation), and 28 proteins were down-regulated (ratio for myopia/control < global mean ratio - 1 standard deviation) in myopic eyes as compared with control retinas. Pathway analysis using MetaCore revealed regulation of γ-aminobutyric acid (GABA) levels in the myopic eyes. Detailed analysis of the quantitative proteomics data showed that the levels of GABA transporter 1 (GAT-1) were elevated in myopic retina and significantly reduced after atropine treatment. These results were further validated with immunohistochemistry and Western blot analysis. In conclusion, this study provides a comprehensive quantitative proteomic analysis of atropine-treated mouse retina and suggests the involvement of GABAergic signaling in the antimyopic effects of atropine in mouse eyes. The GABAergic transmission in the neural retina plays a pivotal role in the maintenance of axial eye growth in mammals. PMID:25211393

Reduced expression of mitochondrial electron transport chain proteins from hibernating hearts relative to ischemic preconditioned hearts in the second window of protection.

PubMed

Cabrera, Jesús A; Butterick, Tammy A; Long, Eric K; Ziemba, Elizabeth A; Anderson, Lorraine B; Duffy, Cayla M; Sluiter, Willem; Duncker, Dirk J; Zhang, Jianyi; Chen, Yingjie; Ward, Herbert B; Kelly, Rosemary F; McFalls, Edward O

2013-07-01

Although protection against necrosis has been observed in both hibernating (HIB) and ischemic preconditioned hearts in the second window of protection (SWOP), a comparison of the mitochondrial proteome between the two entities has not been previously performed. Anesthetized swine underwent instrumentation with a fixed constrictor around the LAD artery and were followed for 12 weeks (HIB; N=7). A second group of anesthetized swine underwent ischemic preconditioning by inflating a balloon within the LAD artery 10 times for 2 min, each separated by 2 min reperfusion and were sacrificed 24h later (SWOP; N=7). Myocardial blood flow and high-energy nucleotides were obtained in the LAD region and normalized to remote regions. Post-sacrifice, protein content as measured with iTRAQ was compared in isolated mitochondria from the LAD area of a Sham heart. Basal regional blood flow in the LAD region when normalized to the remote region was 0.86±0.04 in HIB and 1.02±0.02 in SWOP tissue (P<0.05). Despite reduced regional blood flows in HIB hearts, ATP content in the LAD region, when normalized to the remote region was similar in HIB versus SWOP (1.06±0.06 and 1.02±0.05 respectively; NS) as was the transmural phosphocreatine (PCr) to ATP ratio (2.1±0.2 and 2.2±0.2 respectively; NS). Using iTRAQ, 64 common proteins were identified in HIB and SWOP hearts. Compared with SWOP, the relative abundance of mitochondrial proteins involved with electron transport chain (ETC) were reduced in HIB including NADH dehydrogenase, Cytochrome c reductase and oxidase, ATP synthase, and nicotinamide nucleotide transhydrogenase. Within chronically HIB heart tissue with reduced blood flow, the relative abundance of mitochondrial ETC proteins is decreased when compared with SWOP tissue. These data support the concept that HIB heart tissue subjected to chronically reduced blood flow is associated with a down-regulation in the expression of key mitochondrial proteins involved in electron transport. Published by Elsevier Ltd.

Quantitative proteomics and bioinformatic analysis provide new insight into the dynamic response of porcine intestine to Salmonella Typhimurium

PubMed Central

Collado-Romero, Melania; Aguilar, Carmen; Arce, Cristina; Lucena, Concepción; Codrea, Marius C.; Morera, Luis; Bendixen, Emoke; Moreno, Ángela; Garrido, Juan J.

2015-01-01

The enteropathogen Salmonella Typhimurium (S. Typhimurium) is the most commonly non-typhoideal serotype isolated in pig worldwide. Currently, one of the main sources of human infection is by consumption of pork meat. Therefore, prevention and control of salmonellosis in pigs is crucial for minimizing risks to public health. The aim of the present study was to use isobaric tags for relative and absolute quantification (iTRAQ) to explore differences in the response to Salmonella in two segment of the porcine gut (ileum and colon) along a time course of 1, 2, and 6 days post infection (dpi) with S. Typhimurium. A total of 298 proteins were identified in the infected ileum samples of which, 112 displayed significant expression differences due to Salmonella infection. In colon, 184 proteins were detected in the infected samples of which 46 resulted differentially expressed with respect to the controls. The higher number of changes in protein expression was quantified in ileum at 2 dpi. Further biological interpretation of proteomics data using bioinformatics tools demonstrated that the expression changes in colon were found in proteins involved in cell death and survival, tissue morphology or molecular transport at the early stages and tissue regeneration at 6 dpi. In ileum, however, changes in protein expression were mainly related to immunological and infection diseases, inflammatory response or connective tissue disorders at 1 and 2 dpi. iTRAQ has proved to be a proteomic robust approach allowing us to identify ileum as the earliest response focus upon S. Typhimurium in the porcine gut. In addition, new functions involved in the response to bacteria such as eIF2 signaling, free radical scavengers or antimicrobial peptides (AMP) expression have been identified. Finally, the impairment at of the enterohepatic circulation of bile acids and lipid metabolism by means the under regulation of FABP6 protein and FXR/RXR and LXR/RXR signaling pathway in ileum has been established for the first time in pigs. Taken together, our results provide a better understanding of the porcine response to Salmonella infection and the molecular mechanisms underlying Salmonella-host interactions. PMID:26389078

Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.).

PubMed

Wang, Shuzhen; Chen, Wenyue; Xiao, Wenfei; Yang, Changdeng; Xin, Ya; Qiu, Jieren; Hu, Weimin; Ying, Wu; Fu, Yaping; Tong, Jianxin; Hu, Guocheng; Chen, Zhongzhong; Fang, Xianping; Yu, Hong; Lai, Wenguo; Ruan, Songlin; Ma, Huasheng

2015-01-01

Rice hull, the outer cover of the rice grain, determines grain shape and size. Changes in the rice hull proteome in different growth stages may reflect the underlying mechanisms involved in grain development. To better understand these changes, isobaric tags for relative and absolute quantitative (iTRAQ) MS/MS was used to detect statistically significant changes in the rice hull proteome in the booting, flowering, and milk-ripe growth stages. Differentially expressed proteins were analyzed to predict their potential functions during development. Gene ontology (GO) terms and pathways were used to evaluate the biological mechanisms involved in rice hull at the three growth stages. In total, 5,268 proteins were detected and characterized, of which 563 were differentially expressed across the development stages. The results showed that the flowering and milk-ripe stage proteomes were more similar to each other (r=0.61) than either was to the booting stage proteome. A GO enrichment analysis of the differentially expressed proteins was used to predict their roles during rice hull development. The potential functions of 25 significantly differentially expressed proteins were used to evaluate their possible roles at various growth stages. Among these proteins, an unannotated protein (Q7X8A1) was found to be overexpressed especially in the flowering stage, while a putative uncharacterized protein (B8BF94) and an aldehyde dehydrogenase (Q9FPK6) were overexpressed only in the milk-ripe stage. Pathways regulated by differentially expressed proteins were also analyzed. Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), and two magnesium-chelatase subunits, ChlD (Q6ATS0), and ChlI (Q53RM0), were associated with chlorophyll biosynthesis at different developmental stages. The expression of Q9SDJ2 in the flowering and milk-ripe stages was validated by qRT-PCR. The 25 candidate proteins may be pivotal markers for controlling rice hull development at various growth stages and chlorophyll biosynthesis pathway related proteins, especially magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), may provide new insights into the molecular mechanisms of rice hull development and chlorophyll associated regulation.

Proteomic analysis of porcine mesenchymal stem cells derived from bone marrow and umbilical cord: implication of the proteins involved in the higher migration capability of bone marrow mesenchymal stem cells.

PubMed

Huang, Lei; Niu, Chenguang; Willard, Belinda; Zhao, Weimin; Liu, Lan; He, Wei; Wu, Tianwen; Yang, Shulin; Feng, Shutang; Mu, Yulian; Zheng, Lemin; Li, Kui

2015-04-15

Mesenchymal stem cells (MSCs) have the ability to proliferate in vivo with a large variety of differentiation potentials and therefore are widely used as an ideal material for cell therapy. MSCs derived from pig and human sources are similar in many aspects, such as cell immunophenotype and functional characteristics. However, differences in proteomics and the molecular mechanisms of cell functions between porcine bone marrow MSCs (BM-MSCs) and umbilical cord MSCs (UC-MSCs) are largely unknown. To the best of our knowledge, MSCs collected from different tissue have specific phenotype and differentiation ability in response to microenvironment, known as a niche. Porcine BM-MSCs and UC-MSCs were evaluated with flow cytometric and adipogenic and osteogenic differentiation analyses. We used isobaric tagging for relative and absolute quantitation (iTRAQ), combined with liquid chromatography-tandem mass spectrometry, to identify differentially expressed proteins (DEPs) between these two types of MSCs. Kyoto Encyclopedia of Genes and Genomes pathway and phenotype analyses were used to understand the links between cell migration ability and DEPs. Two separate iTRAQ experiments were conducted, identifying 95 DEPs (95% confidence interval). Five of these proteins were verified by Western blotting. These 95 DEPs were classified in terms of biological regulation, metabolic process, developmental process, immune system process, reproduction, death, growth, signaling, localization, response to stimulus, biological adhesion, and cellular component organization. Our study is the first to show results indicating that porcine BM-MSCs have a higher migration capability than UC-MSCs. Finally, one of the DEPs, Vimentin, was verified to have a positive role in MSC migration. These results represent the first attempt to use proteomics specifically targeted to porcine MSCs of different tissues. The identified components should help reveal a variety of tissue-specific functions in tissue-derived MSC populations and could serve as important tools for the regeneration of particular tissues in future stem cell-based tissue engineering studies using animal models.

Quantitative proteomics and bioinformatic analysis provide new insight into the dynamic response of porcine intestine to Salmonella Typhimurium.

PubMed

Collado-Romero, Melania; Aguilar, Carmen; Arce, Cristina; Lucena, Concepción; Codrea, Marius C; Morera, Luis; Bendixen, Emoke; Moreno, Ángela; Garrido, Juan J

2015-01-01

The enteropathogen Salmonella Typhimurium (S. Typhimurium) is the most commonly non-typhoideal serotype isolated in pig worldwide. Currently, one of the main sources of human infection is by consumption of pork meat. Therefore, prevention and control of salmonellosis in pigs is crucial for minimizing risks to public health. The aim of the present study was to use isobaric tags for relative and absolute quantification (iTRAQ) to explore differences in the response to Salmonella in two segment of the porcine gut (ileum and colon) along a time course of 1, 2, and 6 days post infection (dpi) with S. Typhimurium. A total of 298 proteins were identified in the infected ileum samples of which, 112 displayed significant expression differences due to Salmonella infection. In colon, 184 proteins were detected in the infected samples of which 46 resulted differentially expressed with respect to the controls. The higher number of changes in protein expression was quantified in ileum at 2 dpi. Further biological interpretation of proteomics data using bioinformatics tools demonstrated that the expression changes in colon were found in proteins involved in cell death and survival, tissue morphology or molecular transport at the early stages and tissue regeneration at 6 dpi. In ileum, however, changes in protein expression were mainly related to immunological and infection diseases, inflammatory response or connective tissue disorders at 1 and 2 dpi. iTRAQ has proved to be a proteomic robust approach allowing us to identify ileum as the earliest response focus upon S. Typhimurium in the porcine gut. In addition, new functions involved in the response to bacteria such as eIF2 signaling, free radical scavengers or antimicrobial peptides (AMP) expression have been identified. Finally, the impairment at of the enterohepatic circulation of bile acids and lipid metabolism by means the under regulation of FABP6 protein and FXR/RXR and LXR/RXR signaling pathway in ileum has been established for the first time in pigs. Taken together, our results provide a better understanding of the porcine response to Salmonella infection and the molecular mechanisms underlying Salmonella-host interactions.

Rapid, sensitive, and reusable detection of glucose by a robust radiofrequency integrated passive device biosensor chip.

PubMed

Kim, Nam-Young; Adhikari, Kishor Kumar; Dhakal, Rajendra; Chuluunbaatar, Zorigt; Wang, Cong; Kim, Eun-Soo

2015-01-15

Tremendous demands for sensitive and reliable label-free biosensors have stimulated intensive research into developing miniaturized radiofrequency resonators for a wide range of biomedical applications. Here, we report the development of a robust, reusable radiofrequency resonator based integrated passive device biosensor chip fabricated on a gallium arsenide substrate for the detection of glucose in water-glucose solutions and sera. As a result of the highly concentrated electromagnetic energy between the two divisions of an intertwined spiral inductor coupled with an interdigital capacitor, the proposed glucose biosensor chip exhibits linear detection ranges with high sensitivity at center frequency. This biosensor, which has a sensitivity of up to 199 MHz/mgmL(-1) and a short response time of less than 2 sec, exhibited an ultralow detection limit of 0.033 μM and a reproducibility of 0.61% relative standard deviation. In addition, the quantities derived from the measured S-parameters, such as the propagation constant (γ), impedance (Z), resistance (R), inductance (L), conductance (G) and capacitance (C), enabled the effective multi-dimensional detection of glucose.

Molecular understanding of Abeta peptide interaction with isoflurane, propofol, and thiopental: NMR spectroscopic study.

PubMed

Mandal, Pravat K; Williams, John P; Mandal, Ratna

2007-01-23

Abeta peptide is the major component of senile plaques (SP), which accumulate in the brain of a patient with Alzheimer's disease (AD). A recent report indicated that isoflurane enhanced Abeta oligomerization (micro-aggregation) and subsequent cytotoxicity of the Abeta peptide. A separate study showed that a clinically relevant concentration of isoflurane induces apoptosis and increases Abeta production in a human neuroglioma cell line. In vitro studies have indicated that halothane interacts specifically with Abeta peptide to induce oligomerization and that Abeta42 oligomerizes faster than Abeta40. The specific interactions of isoflurane, propofol, and thiopental with uniformly 15N labeled Abeta40 and Abeta42 peptide were investigated using multidimensional nuclear magnetic resonance (NMR) experiments. We found that isoflurane and propofol (at higher concentration) interact with Abeta40 peptides and induce Abeta oligomerization. Thiopental does not interact with specific residues (G29, A30, and I31) of Abeta40; hence, the peptide remains in the monomeric form. On the basis of our NMR study, thiopental does not oligomerize Abeta40 even at higher concentrations.

Profile and effects of consumer involvement in fresh meat.

PubMed

Verbeke, Wim; Vackier, Isabelle

2004-05-01

This study investigates the profile and effects of consumer involvement in fresh meat as a product category based on cross-sectional data collected in Belgium. Analyses confirm that involvement in meat is a multidimensional construct including four facets: pleasure value, symbolic value, risk importance and risk probability. Four involvement-based meat consumer segments are identified: straightforward, cautious, indifferent, and concerned. Socio-demographic differences between the segments relate to gender, age and presence of children. The segments differ in terms of extensiveness of the decision-making process, impact and trust in information sources, levels of concern, price consciousness, claimed meat consumption, consumption intention, and preferred place of purchase. The two segments with a strong perception of meat risks constitute two-thirds of the market. They can be typified as cautious meat lovers versus concerned meat consumers. Efforts aiming at consumer reassurance through quality improvement, traceability, labelling or communication may gain effectiveness when targeted specifically to these two segments. Whereas straightforward meat lovers focus mainly on taste as the decisive criterion, indifferent consumers are strongly price oriented.

Development of a measure of the motives underlying the selection of food: the food choice questionnaire.

PubMed

Steptoe, A; Pollard, T M; Wardle, J

1995-12-01

A number of factors are thought to influence people's dietary choices, including health, cost, convenience and taste, but there are no measures that address health-related and non-health-related factors in a systematic fashion. This paper describes the development of a multidimensional measure of motives related to food choice. The Food Choice Questionnaire (FCQ) was developed through factor analysis of responses from a sample of 358 adults ranging in age from 18 to 87 years. Nine factors emerged, and were labelled health, mood, convenience, sensory appeal, natural content, price, weight control, familiarity and ethical concern. The questionnaire structure was verified using confirmatory factor analysis in a second sample (n = 358), and test-retest reliability over a 2- to 3-week period was satisfactory. Convergent validity was investigated by testing associations between FCQ scales and measures of dietary restraint, eating style, the value of health, health locus of control and personality factors. Differences in motives for food choice associated with sex, age and income were found. The potential uses of this measure in health psychology and other areas are discussed.

Label-free nanoscale characterization of red blood cell structure and dynamics using single-shot transport of intensity equation

NASA Astrophysics Data System (ADS)

Poola, Praveen Kumar; John, Renu

2017-10-01

We report the results of characterization of red blood cell (RBC) structure and its dynamics with nanometric sensitivity using transport of intensity equation microscopy (TIEM). Conventional transport of intensity technique requires three intensity images and hence is not suitable for studying real-time dynamics of live biological samples. However, assuming the sample to be homogeneous, phase retrieval using transport of intensity equation has been demonstrated with single defocused measurement with x-rays. We adopt this technique for quantitative phase light microscopy of homogenous cells like RBCs. The main merits of this technique are its simplicity, cost-effectiveness, and ease of implementation on a conventional microscope. The phase information can be easily merged with regular bright-field and fluorescence images to provide multidimensional (three-dimensional spatial and temporal) information without any extra complexity in the setup. The phase measurement from the TIEM has been characterized using polymeric microbeads and the noise stability of the system has been analyzed. We explore the structure and real-time dynamics of RBCs and the subdomain membrane fluctuations using this technique.

Rapid, Sensitive, and Reusable Detection of Glucose by a Robust Radiofrequency Integrated Passive Device Biosensor Chip

PubMed Central

Kim, Nam-Young; Adhikari, Kishor Kumar; Dhakal, Rajendra; Chuluunbaatar, Zorigt; Wang, Cong; Kim, Eun-Soo

2015-01-01

Tremendous demands for sensitive and reliable label-free biosensors have stimulated intensive research into developing miniaturized radiofrequency resonators for a wide range of biomedical applications. Here, we report the development of a robust, reusable radiofrequency resonator based integrated passive device biosensor chip fabricated on a gallium arsenide substrate for the detection of glucose in water-glucose solutions and sera. As a result of the highly concentrated electromagnetic energy between the two divisions of an intertwined spiral inductor coupled with an interdigital capacitor, the proposed glucose biosensor chip exhibits linear detection ranges with high sensitivity at center frequency. This biosensor, which has a sensitivity of up to 199 MHz/mgmL−1 and a short response time of less than 2 sec, exhibited an ultralow detection limit of 0.033 μM and a reproducibility of 0.61% relative standard deviation. In addition, the quantities derived from the measured S-parameters, such as the propagation constant (γ), impedance (Z), resistance (R), inductance (L), conductance (G) and capacitance (C), enabled the effective multi-dimensional detection of glucose. PMID:25588958

A model of the complex between human {beta}-microseminoprotein and CRISP-3 based on NMR data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghasriani, Houman; Fernlund, Per; Udby, Lene

2009-01-09

{beta}-Microseminoprotein (MSP), a 10 kDa seminal plasma protein, forms a tight complex with cysteine-rich secretory protein 3 (CRISP-3) from granulocytes. The 3D structure of human MSP has been determined but there is as yet no 3D structure for CRISP-3. We have now studied the complex between human MSP and CRISP-3 with multidimensional NMR. {sup 15}N-HSQC spectra show substantial differences between free and complexed hMSP. Using several 3D-NMR spectra of triply labeled hMSP in complex with a recombinant N-terminal domain of CRISP-3, most of the backbone of hMSP could be assigned. The data show that only one side of hMSP, comprisingmore » {beta}-strands 1, 4, 5, and 8 are affected by the complex formation, indicating that {beta}-strands 1 and 8 form the main binding surface. Based on this we present a tentative structure for the hMSP-CRISP-3 complex using the known crystal structure of triflin as a model of CRISP-3.« less

Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex.

PubMed

Jiang, F; Kumar, R A; Jones, R A; Patel, D J

1996-07-11

The catalytic properties of RNA and its well known role in gene expression and regulation are the consequence of its unique solution structures. Identification of the structural determinants of ligand recognition by RNA molecules is of fundamental importance for understanding the biological functions of RNA, as well as for the rational design of RNA Sequences with specific catalytic activities. Towards this latter end, Szostak et al. used in vitro selection techniques to isolate RNA sequences ('aptamers') containing a high-affinity binding site for ATP, the universal currency of cellular energy, and then used this motif to engineer ribozymes with polynucleotide kinase activity. Here we present the solution structure, as determined by multidimensional NMR spectroscopy and molecular dynamics calculations, of both uniformly and specifically 13C-, 15N-labelled 40-mer RNA containing the ATP-binding motif complexed with AMP. The aptamer adopts an L-shaped structure with two nearly orthogonal stems, each capped proximally by a G x G mismatch pair, binding the AMP ligand at their junction in a GNRA-like motif.

Psychometric Properties of Creative Self-Efficacy Inventory Among Distinguished Students in Saudi Arabian Universities.

PubMed

Alotaibi, Khaled N

2016-06-01

This study examined the psychometric properties of the Arabic version of Abbott's Creative Self-Efficacy inventory. Saudi honors students (157 men vs. 163 women) participated. These students are undergraduates (M age = 19.5 year, SD = 1.9) who complete 30 credit hours with a grade point average of no less than 4.5 out of 5. The results showed that the internal consistency (α = .87) and the test-retest reliabilities (r = .73) were satisfactory. The study sample was separated into two subsamples. The data from the first subsample (n = 60) were used to conduct an exploratory factor analysis, whereas the data from the second subsample (n = 260) were used to perform a confirmatory factor analysis. The results of exploratory factor analysis and confirmatory factor analysis indicated that creative self-efficacy was not a unidimensional construct but consisted of two factors labeled "creative thinking self-efficacy" and "creative performance self-efficacy." As expected, this two-factor model fit the data adequately, supporting prior research that treated creative self-efficacy as multidimensional construct. © The Author(s) 2016.

Autofluorescence lifetime metrology for label-free detection of cartilage matrix degradation

NASA Astrophysics Data System (ADS)

Nickdel, Mohammad B.; Lagarto, João. L.; Kelly, Douglas J.; Manning, Hugh B.; Yamamoto, Kazuhiro; Talbot, Clifford B.; Dunsby, Christopher; French, Paul; Itoh, Yoshifumi

2014-03-01

Degradation of articular cartilage extracellular matrix (ECM) by proteolytic enzyme is the hallmark of arthritis that leads to joint destruction. Detection of early biochemical changes in cartilage before irreversible structural damages become apparent is highly desirable. Here we report that the autofluorescence decay profile of cartilage is significantly affected by proteolytic degradation of cartilage ECM and can be characterised by measurements of the autofluorescence lifetime (AFL). A multidimensional fluorometer utilizing ultraviolet excitation at 355 nm or 375 nm coupled to a fibreoptic probe was developed for single point time-resolved AFL measurements of porcine articular cartilage explants treated with different proteinases. Degradation of cartilage matrix components by treating with bacterial collagenase, matrix metalloproteinase 1, or trypsin resulted in significant reduction of AFL of the cartilage in both a dose and time dependent manner. Differences in cartilage AFL were also confirmed by fluorescence lifetime imaging microscopy (FLIM). Our data suggest that AFL of cartilage tissue is a potential non-invasive readout to monitor cartilage matrix integrity that may be utilized for diagnosis of arthritis as well as monitoring the efficacy of anti-arthritic therapeutic agents.

Multi-dimensional simulations of core-collapse supernova explosions with CHIMERA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Messer, Bronson; Harris, James Austin; Hix, William Raphael

Unraveling the core-collapse supernova (CCSN) mechanism is a problem that remains essentially unsolved despite more than four decades of effort. Spherically symmetric models with otherwise high physical fidelity generally fail to produce explosions, and it is widely accepted that CCSNe are inherently multi-dimensional. Progress in realistic modeling has occurred recently through the availability of petascale platforms and the increasing sophistication of supernova codes. We will discuss our most recent work on understanding neutrino-driven CCSN explosions employing multi-dimensional neutrino-radiation hydrodynamics simulations with the Chimera code. We discuss the inputs and resulting outputs from these simulations, the role of neutrino radiation transport,more » and the importance of multi-dimensional fluid flows in shaping the explosions. We also highlight the production of 48Ca in long-running Chimera simulations.« less

Improving Multidimensional Wireless Sensor Network Lifetime Using Pearson Correlation and Fractal Clustering

PubMed Central

Almeida, Fernando R.; Brayner, Angelo; Rodrigues, Joel J. P. C.; Maia, Jose E. Bessa

2017-01-01

An efficient strategy for reducing message transmission in a wireless sensor network (WSN) is to group sensors by means of an abstraction denoted cluster. The key idea behind the cluster formation process is to identify a set of sensors whose sensed values present some data correlation. Nowadays, sensors are able to simultaneously sense multiple different physical phenomena, yielding in this way multidimensional data. This paper presents three methods for clustering sensors in WSNs whose sensors collect multidimensional data. The proposed approaches implement the concept of multidimensional behavioral clustering. To show the benefits introduced by the proposed methods, a prototype has been implemented and experiments have been carried out on real data. The results prove that the proposed methods decrease the amount of data flowing in the network and present low root-mean-square error (RMSE). PMID:28590450

The Role of a Multidimensional Concept of Trust in the Performance of Global Virtual Teams

NASA Technical Reports Server (NTRS)

Bodensteiner, Nan Muir; Stecklein, Jonette M.

2002-01-01

This paper focuses on the concept of trust as an important ingredient of effective global virtual team performance. Definitions of trust and virtual teams are presented. The concept of trust is developed from its unilateral application (trust, absence of trust) to a multidimensional concept including cognitive and affective components. The special challenges of a virtual team are then discussed with particular emphasis on how a multidimensional concept of trust impacts these challenges. Propositions suggesting the multidimensional concept of trust moderates the negative impacts of distance, cross cultural and organizational differences, the effects of electronically mediated communication, reluctance to share information and a lack of hi story/future on the performance of virtual teams are stated. The paper concludes with recommendations and a set of techniques to build both cognitive and affective trust in virtual teams.

Improving Multidimensional Wireless Sensor Network Lifetime Using Pearson Correlation and Fractal Clustering.

PubMed

Almeida, Fernando R; Brayner, Angelo; Rodrigues, Joel J P C; Maia, Jose E Bessa

2017-06-07

An efficient strategy for reducing message transmission in a wireless sensor network (WSN) is to group sensors by means of an abstraction denoted cluster. The key idea behind the cluster formation process is to identify a set of sensors whose sensed values present some data correlation. Nowadays, sensors are able to simultaneously sense multiple different physical phenomena, yielding in this way multidimensional data. This paper presents three methods for clustering sensors in WSNs whose sensors collect multidimensional data. The proposed approaches implement the concept of multidimensional behavioral clustering . To show the benefits introduced by the proposed methods, a prototype has been implemented and experiments have been carried out on real data. The results prove that the proposed methods decrease the amount of data flowing in the network and present low root-mean-square error (RMSE).

Multidimensional Profiling of Task Stress States for Human Factors: A Brief Review.

PubMed

Matthews, Gerald

2016-09-01

This article advocates multidimensional assessment of task stress in human factors and reviews the use of the Dundee Stress State Questionnaire (DSSQ) for evaluation of systems and operators. Contemporary stress research has progressed from an exclusive focus on environmental stressors to transactional perspectives on the stress process. Performance impacts of stress reflect the operator's dynamic attempts to understand and cope with task demands. Multidimensional stress assessments are necessary to gauge the different forms of system-operator interaction. This review discusses the theoretical and practical use of the DSSQ in evaluating multidimensional patterns of stress response. It presents psychometric evidence for the multidimensional perspective and illustrative profiles of subjective state response to task stressors and environments. Evidence is also presented on stress state correlations with related variables, including personality, stress process measures, psychophysiological response, and objective task performance. Evidence supports the validity of the DSSQ as a task stress measure. Studies of various simulated environments show that different tasks elicit different profiles of stress state response. Operator characteristics such as resilience predict individual differences in state response to stressors. Structural equation modeling may be used to understand performance impacts of stress states. Multidimensional assessment affords insight into the stress process in a variety of human factors contexts. Integrating subjective and psychophysiological assessment is a priority for future research. Stress state measurement contributes to evaluating system design, countermeasures to stress and fatigue, and performance vulnerabilities. It may also support personnel selection and diagnostic monitoring of operators. © 2016, Human Factors and Ergonomics Society.

Efficient implementation of multidimensional fast fourier transform on a distributed-memory parallel multi-node computer

DOEpatents

Bhanot, Gyan V [Princeton, NJ; Chen, Dong [Croton-On-Hudson, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Steinmacher-Burow, Burkhard D [Mount Kisco, NY; Vranas, Pavlos M [Bedford Hills, NY

2012-01-10

The present in invention is directed to a method, system and program storage device for efficiently implementing a multidimensional Fast Fourier Transform (FFT) of a multidimensional array comprising a plurality of elements initially distributed in a multi-node computer system comprising a plurality of nodes in communication over a network, comprising: distributing the plurality of elements of the array in a first dimension across the plurality of nodes of the computer system over the network to facilitate a first one-dimensional FFT; performing the first one-dimensional FFT on the elements of the array distributed at each node in the first dimension; re-distributing the one-dimensional FFT-transformed elements at each node in a second dimension via "all-to-all" distribution in random order across other nodes of the computer system over the network; and performing a second one-dimensional FFT on elements of the array re-distributed at each node in the second dimension, wherein the random order facilitates efficient utilization of the network thereby efficiently implementing the multidimensional FFT. The "all-to-all" re-distribution of array elements is further efficiently implemented in applications other than the multidimensional FFT on the distributed-memory parallel supercomputer.

Efficient implementation of a multidimensional fast fourier transform on a distributed-memory parallel multi-node computer

DOEpatents

Bhanot, Gyan V [Princeton, NJ; Chen, Dong [Croton-On-Hudson, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Steinmacher-Burow, Burkhard D [Mount Kisco, NY; Vranas, Pavlos M [Bedford Hills, NY

2008-01-01

The present in invention is directed to a method, system and program storage device for efficiently implementing a multidimensional Fast Fourier Transform (FFT) of a multidimensional array comprising a plurality of elements initially distributed in a multi-node computer system comprising a plurality of nodes in communication over a network, comprising: distributing the plurality of elements of the array in a first dimension across the plurality of nodes of the computer system over the network to facilitate a first one-dimensional FFT; performing the first one-dimensional FFT on the elements of the array distributed at each node in the first dimension; re-distributing the one-dimensional FFT-transformed elements at each node in a second dimension via "all-to-all" distribution in random order across other nodes of the computer system over the network; and performing a second one-dimensional FFT on elements of the array re-distributed at each node in the second dimension, wherein the random order facilitates efficient utilization of the network thereby efficiently implementing the multidimensional FFT. The "all-to-all" re-distribution of array elements is further efficiently implemented in applications other than the multidimensional FFT on the distributed-memory parallel supercomputer.

Image matrix processor for fast multi-dimensional computations

DOEpatents

Roberson, George P.; Skeate, Michael F.

1996-01-01

An apparatus for multi-dimensional computation which comprises a computation engine, including a plurality of processing modules. The processing modules are configured in parallel and compute respective contributions to a computed multi-dimensional image of respective two dimensional data sets. A high-speed, parallel access storage system is provided which stores the multi-dimensional data sets, and a switching circuit routes the data among the processing modules in the computation engine and the storage system. A data acquisition port receives the two dimensional data sets representing projections through an image, for reconstruction algorithms such as encountered in computerized tomography. The processing modules include a programmable local host, by which they may be configured to execute a plurality of different types of multi-dimensional algorithms. The processing modules thus include an image manipulation processor, which includes a source cache, a target cache, a coefficient table, and control software for executing image transformation routines using data in the source cache and the coefficient table and loading resulting data in the target cache. The local host processor operates to load the source cache with a two dimensional data set, loads the coefficient table, and transfers resulting data out of the target cache to the storage system, or to another destination.

Multidimensional Mixing Behavior of Steam-Water Flow in a Downcomer Annulus During LBLOCA Reflood Phase with a Direct Vessel Injection Mode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Tae-Soon; Yun, Byong-Jo; Euh, Dong-Jin

Multidimensional thermal-hydraulic behavior in the downcomer annulus of a pressurized water reactor (PWR) vessel with a direct vessel injection mode is presented based on the experimental observation in the MIDAS (multidimensional investigation in downcomer annulus simulation) steam-water test facility. From the steady-state test results to simulate the late reflood phase of a large-break loss-of-coolant accident (LBLOCA), isothermal lines show the multidimensional phenomena of a phasic interaction between steam and water in the downcomer annulus very well. MIDAS is a steam-water separate effect test facility, which is 1/4.93 linearly scaled down to a 1400-MW(electric) PWR type of a nuclear reactor, focusedmore » on understanding multidimensional thermal-hydraulic phenomena in a downcomer annulus with various types of safety injection during the refill or reflood phase of an LBLOCA. The initial and the boundary conditions are scaled from the pretest analysis based on the preliminary calculation using the TRAC code. The superheated steam with a superheating degree of 80 K at a given downcomer pressure of 180 kPa is injected equally through three intact cold legs into the downcomer.« less

A multidimensional evaluation of a nursing information-literacy program.

PubMed Central

Fox, L M; Richter, J M; White, N E

1996-01-01

The goal of an information-literacy program is to develop student skills in locating, evaluating, and applying information for use in critical thinking and problem solving. This paper describes a multidimensional evaluation process for determining nursing students' growth in cognitive and affective domains. Results indicate improvement in student skills as a result of a nursing information-literacy program. Multidimensional evaluation produces a well-rounded picture of student progress based on formal measurement as well as informal feedback. Developing new educational programs can be a time-consuming challenge. It is important, when expending so much effort, to ensure that the goals of the new program are achieved and benefits to students demonstrated. A multidimensional approach to evaluation can help to accomplish those ends. In 1988, The University of Northern Colorado School of Nursing began working with a librarian to integrate an information-literacy component, entitled Pathways to Information Literacy, into the curriculum. This article describes the program and discusses how a multidimensional evaluation process was used to assess program effectiveness. The evaluation process not only helped to measure the effectiveness of the program but also allowed the instructors to use several different approaches to evaluation. PMID:8826621

A Scalar Product Model for the Multidimensional Scaling of Choice

ERIC Educational Resources Information Center

Bechtel, Gordon G.; And Others

1971-01-01

Contains a solution for the multidimensional scaling of pairwise choice when individuals are represented as dimensional weights. The analysis supplies an exact least squares solution and estimates of group unscalability parameters. (DG)

Modeling Individual Cyclic Variation in Human Behavior.

PubMed

Pierson, Emma; Althoff, Tim; Leskovec, Jure

2018-04-01

Cycles are fundamental to human health and behavior. Examples include mood cycles, circadian rhythms, and the menstrual cycle. However, modeling cycles in time series data is challenging because in most cases the cycles are not labeled or directly observed and need to be inferred from multidimensional measurements taken over time. Here, we present Cyclic Hidden Markov Models (CyH-MMs) for detecting and modeling cycles in a collection of multidimensional heterogeneous time series data. In contrast to previous cycle modeling methods, CyHMMs deal with a number of challenges encountered in modeling real-world cycles: they can model multivariate data with both discrete and continuous dimensions; they explicitly model and are robust to missing data; and they can share information across individuals to accommodate variation both within and between individual time series. Experiments on synthetic and real-world health-tracking data demonstrate that CyHMMs infer cycle lengths more accurately than existing methods, with 58% lower error on simulated data and 63% lower error on real-world data compared to the best-performing baseline. CyHMMs can also perform functions which baselines cannot: they can model the progression of individual features/symptoms over the course of the cycle, identify the most variable features, and cluster individual time series into groups with distinct characteristics. Applying CyHMMs to two real-world health-tracking datasets-of human menstrual cycle symptoms and physical activity tracking data-yields important insights including which symptoms to expect at each point during the cycle. We also find that people fall into several groups with distinct cycle patterns, and that these groups differ along dimensions not provided to the model. For example, by modeling missing data in the menstrual cycles dataset, we are able to discover a medically relevant group of birth control users even though information on birth control is not given to the model.

Modeling Individual Cyclic Variation in Human Behavior

PubMed Central

Pierson, Emma; Althoff, Tim; Leskovec, Jure

2018-01-01

Cycles are fundamental to human health and behavior. Examples include mood cycles, circadian rhythms, and the menstrual cycle. However, modeling cycles in time series data is challenging because in most cases the cycles are not labeled or directly observed and need to be inferred from multidimensional measurements taken over time. Here, we present Cyclic Hidden Markov Models (CyH-MMs) for detecting and modeling cycles in a collection of multidimensional heterogeneous time series data. In contrast to previous cycle modeling methods, CyHMMs deal with a number of challenges encountered in modeling real-world cycles: they can model multivariate data with both discrete and continuous dimensions; they explicitly model and are robust to missing data; and they can share information across individuals to accommodate variation both within and between individual time series. Experiments on synthetic and real-world health-tracking data demonstrate that CyHMMs infer cycle lengths more accurately than existing methods, with 58% lower error on simulated data and 63% lower error on real-world data compared to the best-performing baseline. CyHMMs can also perform functions which baselines cannot: they can model the progression of individual features/symptoms over the course of the cycle, identify the most variable features, and cluster individual time series into groups with distinct characteristics. Applying CyHMMs to two real-world health-tracking datasets—of human menstrual cycle symptoms and physical activity tracking data—yields important insights including which symptoms to expect at each point during the cycle. We also find that people fall into several groups with distinct cycle patterns, and that these groups differ along dimensions not provided to the model. For example, by modeling missing data in the menstrual cycles dataset, we are able to discover a medically relevant group of birth control users even though information on birth control is not given to the model. PMID:29780976

Portable laser synthesizer for high-speed multi-dimensional spectroscopy

DOEpatents

Demos, Stavros G [Livermore, CA; Shverdin, Miroslav Y [Sunnyvale, CA; Shirk, Michael D [Brentwood, CA

2012-05-29

Portable, field-deployable laser synthesizer devices designed for multi-dimensional spectrometry and time-resolved and/or hyperspectral imaging include a coherent light source which simultaneously produces a very broad, energetic, discrete spectrum spanning through or within the ultraviolet, visible, and near infrared wavelengths. The light output is spectrally resolved and each wavelength is delayed with respect to each other. A probe enables light delivery to a target. For multidimensional spectroscopy applications, the probe can collect the resulting emission and deliver this radiation to a time gated spectrometer for temporal and spectral analysis.

An asymptotic preserving multidimensional ALE method for a system of two compressible flows coupled with friction

NASA Astrophysics Data System (ADS)

Del Pino, S.; Labourasse, E.; Morel, G.

2018-06-01

We present a multidimensional asymptotic preserving scheme for the approximation of a mixture of compressible flows. Fluids are modelled by two Euler systems of equations coupled with a friction term. The asymptotic preserving property is mandatory for this kind of model, to derive a scheme that behaves well in all regimes (i.e. whatever the friction parameter value is). The method we propose is defined in ALE coordinates, using a Lagrange plus remap approach. This imposes a multidimensional definition and analysis of the scheme.

Patent data mining method and apparatus

DOEpatents

Boyack, Kevin W.; Grafe, V. Gerald; Johnson, David K.; Wylie, Brian N.

2002-01-01

A method of data mining represents related patents in a multidimensional space. Distance between patents in the multidimensional space corresponds to the extent of relationship between the patents. The relationship between pairings of patents can be expressed based on weighted combinations of several predicates. The user can select portions of the space to perceive. The user also can interact with and control the communication of the space, focusing attention on aspects of the space of most interest. The multidimensional spatial representation allows more ready comprehension of the structure of the relationships among the patents.

Pathways into chronic multidimensional poverty amongst older people: a longitudinal study.

PubMed

Callander, Emily J; Schofield, Deborah J

2016-03-07

The use of multidimensional poverty measures is becoming more common for measuring the living standards of older people. However, the pathways into poverty are relatively unknown, nor is it known how this affects the length of time people are in poverty for. Using Waves 1 to 12 of the nationally representative Household, Income and Labour Dynamics in Australia (HILDA) survey, longitudinal analysis was undertaken to identify the order that key forms of disadvantage develop - poor health, low income and insufficient education attainment - amongst Australians aged 65 years and over in multidimensional poverty, and the relationship this has with chronic poverty. Path analysis and linear regression models were used. For all older people with at least a Year 10 level of education attainment earlier mental health was significantly related to later household income (p = 0.001) and wealth (p = 0.017). For all older people with at less than a Year 10 level of education attainment earlier household income was significantly related to later mental health (p = 0.021). When limited to those in multidimensional poverty who were in income poverty and also had poor health, older people generally fell into income poverty first and then developed poor health. The order in which income poverty and poor health were developed had a significant influence on the length of time older people with less than a Year 10 level of education attainment were in multidimensional poverty for. Those who developed poor health first then fell into income poverty spend significantly less time in multidimensional poverty (-4.90, p < .0001) than those who fell into income poverty then developed poor health. Knowing the order that different forms of disadvantage develop, and the influence this has on poverty entrenchment, is of use to policy makers wishing to provide interventions to prevent older people being in long-term multidimensional poverty.

Identification of novel biomarker candidates for hypertrophic cardiomyopathy and other cardiovascular diseases leading to heart failure.

PubMed

Rehulkova, H; Rehulka, P; Myslivcova Fucikova, A; Stulik, J; Pudil, R

2016-11-23

In-depth proteome discovery analysis represents new strategy in an effort to identify novel reliable specific protein markers for hypertrophic cardiomyopathy and other life threatening cardiovascular diseases. To systematically identify novel protein biomarkers of cardiovascular diseases with high mortality we employed an isobaric tag for relative and absolute quantitation (iTRAQ) proteome technology to make comparative analysis of plasma samples obtained from patients suffering from non-obstructive hypertrophic cardiomyopathy, stable dilated cardiomyopathy, aortic valve stenosis, chronic stable coronary artery disease and stable arterial hypertension. We found 128 plasma proteins whose abundances were uniquely regulated among the analyzed cardiovascular pathologies. 49 of them have not been described yet. Additionally, application of statistical exploratory analyses of the measured protein profiles indicated the relationship in pathophysiology of the examined cardiovascular pathologies.

Potential proteins targeted by let-7f-5p in HeLa cells.

PubMed

Wang, Yu; Chen, Xiujuan; Zhang, Yi; Song, Jiandong

2017-07-24

MicroRNAs are a class of small, endogenous, non-coding RNAs mediating posttranscriptional gene silencing. The current authors hypothesized that let-7f-5p is likely involved in cell invasion and proliferation by regulating the expression of target genes. The current study combined let-7f-5p with iTRAQ to assess its effect on gene expression in HeLa cells. Results indicated that 164 proteins were expressed at different levels in HeLa cells overexpressing let-7f-5p and negative controls and that 172 proteins were expressed at different levels in let-7f-5p-silenced HeLa cells and negative controls. Results indicated that let-7f-5p may suppress insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) in HeLa cells.

A Multidimensional Scaling Analysis of Schizophrenics' and Normals' Perceptions of Verbal Similarity

ERIC Educational Resources Information Center

Neufeld, Richard W. J.

1975-01-01

Twenty-eight schizophrenics (14 paranoid and 14 nonparanoid) were compared with 14 normals on their judgments of similarity among words. The judgments were analyzed using an individual-differences multidimensional scaling procedure. (Editor)

[Development and application of a multidimensional suicide prevention program for Korean elders by utilizing a community network].

PubMed

Jo, Kae Hwa; Kim, Yeong Kyeong

2008-06-01

The purpose of this study was to develop a multidimensional suicide prevention program for Korean elders by utilizing a community network and to evaluate its effect. A non-equivalent control group pretest-posttest design was used. The subjects were recruited from two different elderly institutions located in D city and K province, Korea. Nineteen subjects in the control group received no intervention and 20 subjects in the experimental group received a multidimensional suicide prevention program. There were more significant decreases in depression, suicide ideation, and increases in life satisfaction in the experimental group compared to the control group. According to the above results, the multidimensional suicide prevention program for Korean elders decreased stressful events like depression, and suicide ideation and increased life satisfaction through the community network. These findings suggest that this program can be used as an efficient intervention for elders in a critical situation.

Visual modeling in an analysis of multidimensional data

NASA Astrophysics Data System (ADS)

Zakharova, A. A.; Vekhter, E. V.; Shklyar, A. V.; Pak, A. J.

2018-01-01

The article proposes an approach to solve visualization problems and the subsequent analysis of multidimensional data. Requirements to the properties of visual models, which were created to solve analysis problems, are described. As a perspective direction for the development of visual analysis tools for multidimensional and voluminous data, there was suggested an active use of factors of subjective perception and dynamic visualization. Practical results of solving the problem of multidimensional data analysis are shown using the example of a visual model of empirical data on the current state of studying processes of obtaining silicon carbide by an electric arc method. There are several results of solving this problem. At first, an idea of possibilities of determining the strategy for the development of the domain, secondly, the reliability of the published data on this subject, and changes in the areas of attention of researchers over time.

Quantum and Multidimensional Explanations in a Neurobiological Context of Mind.

PubMed

Korf, Jakob

2015-08-01

This article examines the possible relevance of physical-mathematical multidimensional or quantum concepts aiming at understanding the (human) mind in a neurobiological context. Some typical features of the quantum and multidimensional concepts are briefly introduced, including entanglement, superposition, holonomic, and quantum field theories. Next, we consider neurobiological principles, such as the brain and its emerging (physical) mind, evolutionary and ontological origins, entropy, syntropy/neg-entropy, causation, and brain energy metabolism. In many biological processes, including biochemical conversions, protein folding, and sensory perception, the ubiquitous involvement of quantum mechanisms is well recognized. Quantum and multidimensional approaches might be expected to help describe and model both brain and mental processes, but an understanding of their direct involvement in mental activity, that is, without mediation by molecular processes, remains elusive. More work has to be done to bridge the gap between current neurobiological and physical-mathematical concepts with their associated quantum-mind theories. © The Author(s) 2014.

Hypothalamus proteomics from mouse models with obesity and anorexia reveals therapeutic targets of appetite regulation

PubMed Central

Manousopoulou, A; Koutmani, Y; Karaliota, S; Woelk, C H; Manolakos, E S; Karalis, K; Garbis, S D

2016-01-01

Objective: This study examined the proteomic profile of the hypothalamus in mice exposed to a high-fat diet (HFD) or with the anorexia of acute illness. This comparison could provide insight on the effects of these two opposite states of energy balance on appetite regulation. Methods: Four to six-week-old male C56BL/6J mice were fed a normal (control 1 group; n=7) or a HFD (HFD group; n=10) for 8 weeks. The control 2 (n=7) and lipopolysaccharide (LPS) groups (n=10) were fed a normal diet for 8 weeks before receiving an injection of saline and LPS, respectively. Hypothalamic regions were analysed using a quantitative proteomics method based on a combination of techniques including iTRAQ stable isotope labeling, orthogonal two-dimensional liquid chromatography hyphenated with nanospray ionization and high-resolution mass spectrometry. Key proteins were validated with quantitative PCR. Results: Quantitative proteomics of the hypothalamous regions profiled a total of 9249 protein groups (q<0.05). Of these, 7718 protein groups were profiled with a minimum of two unique peptides for each. Hierachical clustering of the differentiated proteome revealed distinct proteomic signatures for the hypothalamus under the HFD and LPS nutritional conditions. Literature research with in silico bioinformatics interpretation of the differentiated proteome identified key biological relevant proteins and implicated pathways. Furthermore, the study identified potential pharmacologic targets. In the LPS groups, the anorexigen pro-opiomelanocortin was downregulated. In mice with obesity, nuclear factor-κB, glycine receptor subunit alpha-4 (GlyR) and neuropeptide Y levels were elevated, whereas serotonin receptor 1B levels decreased. Conclusions: High-precision quantitative proteomics revealed that under acute systemic inflammation in the hypothalamus as a response to LPS, homeostatic mechanisms mediating loss of appetite take effect. Conversely, under chronic inflammation in the hypothalamus as a response to HFD, mechanisms mediating a sustained ‘perpetual cycle' of appetite enhancement were observed. The GlyR protein may constitute a novel treatment target for the reduction of central orexigenic signals in obesity. PMID:27110685

Hypothalamus proteomics from mouse models with obesity and anorexia reveals therapeutic targets of appetite regulation.

PubMed

Manousopoulou, A; Koutmani, Y; Karaliota, S; Woelk, C H; Manolakos, E S; Karalis, K; Garbis, S D

2016-04-25

This study examined the proteomic profile of the hypothalamus in mice exposed to a high-fat diet (HFD) or with the anorexia of acute illness. This comparison could provide insight on the effects of these two opposite states of energy balance on appetite regulation. Four to six-week-old male C56BL/6J mice were fed a normal (control 1 group; n=7) or a HFD (HFD group; n=10) for 8 weeks. The control 2 (n=7) and lipopolysaccharide (LPS) groups (n=10) were fed a normal diet for 8 weeks before receiving an injection of saline and LPS, respectively. Hypothalamic regions were analysed using a quantitative proteomics method based on a combination of techniques including iTRAQ stable isotope labeling, orthogonal two-dimensional liquid chromatography hyphenated with nanospray ionization and high-resolution mass spectrometry. Key proteins were validated with quantitative PCR. Quantitative proteomics of the hypothalamous regions profiled a total of 9249 protein groups (q<0.05). Of these, 7718 protein groups were profiled with a minimum of two unique peptides for each. Hierachical clustering of the differentiated proteome revealed distinct proteomic signatures for the hypothalamus under the HFD and LPS nutritional conditions. Literature research with in silico bioinformatics interpretation of the differentiated proteome identified key biological relevant proteins and implicated pathways. Furthermore, the study identified potential pharmacologic targets. In the LPS groups, the anorexigen pro-opiomelanocortin was downregulated. In mice with obesity, nuclear factor-κB, glycine receptor subunit alpha-4 (GlyR) and neuropeptide Y levels were elevated, whereas serotonin receptor 1B levels decreased. High-precision quantitative proteomics revealed that under acute systemic inflammation in the hypothalamus as a response to LPS, homeostatic mechanisms mediating loss of appetite take effect. Conversely, under chronic inflammation in the hypothalamus as a response to HFD, mechanisms mediating a sustained 'perpetual cycle' of appetite enhancement were observed. The GlyR protein may constitute a novel treatment target for the reduction of central orexigenic signals in obesity.

Plasma-based proteomics reveals immune response, complement and coagulation cascades pathway shifts in heat-stressed lactating dairy cows.

PubMed

Min, Li; Cheng, Jianbo; Zhao, Shengguo; Tian, He; Zhang, Yangdong; Li, Songli; Yang, Hongjian; Zheng, Nan; Wang, Jiaqi

2016-09-02

Heat stress (HS) has an enormous economic impact on the dairy industry. In recent years, many researchers have investigated changes in the gene expression and metabolomics profiles in dairy cows caused by HS. However, the proteomics profiles of heat-stressed dairy cows have not yet been completely elucidated. We compared plasma proteomics from HS-free and heat-stressed dairy cows using an iTRAQ labeling approach. After the depletion of high abundant proteins in the plasma, 1472 proteins were identified. Of these, 85 proteins were differentially abundant in cows exposed to HS relative to HS-free. Database searches combined with GO and KEGG pathway enrichment analyses revealed that many components of the complement and coagulation cascades were altered in heat-stressed cows compared with HS-free cows. Of these, many factors in the complement system (including complement components C1, C3, C5, C6, C7, C8, and C9, complement factor B, and factor H) were down-regulated by HS, while components of the coagulation system (including coagulation factors, vitamin K-dependent proteins, and fibrinogens) were up-regulated by HS. In conclusion, our results indicate that HS decreases plasma levels of complement system proteins, suggesting that immune function is impaired in dairy cows exposed to HS. Though many aspects of heat stress (HS) have been extensively researched, relatively little is known about the proteomics profile changes that occur during heat exposure. In this work, we employed a proteomics approach to investigate differential abundance of plasma proteins in HS-free and heat-stressed dairy cows. Database searches combined with GO and KEGG pathway enrichment analyses revealed that HS resulted in a decrease in complement components, suggesting that heat-stressed dairy cows have impaired immune function. In addition, through integrative analyses of proteomics and previous metabolomics, we showed enhanced glycolysis, lipid metabolic pathway shifts, and nitrogen repartitioning in dairy cows exposed to HS. Our findings expand our current knowledge on the effects of HS on plasma proteomics in dairy cows and offer a new perspective for future research. Copyright © 2016 Elsevier B.V. All rights reserved.

Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells.

PubMed

Majeran, Wojciech; Zybailov, Boris; Ytterberg, A Jimmy; Dunsmore, Jason; Sun, Qi; van Wijk, Klaas J

2008-09-01

Chloroplasts of maize leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C(4) photosynthesis. Chloroplasts contain thylakoid and envelope membranes that contain the photosynthetic machineries and transporters but also proteins involved in e.g. protein homeostasis. These chloroplast membranes must be specialized within each cell type to accommodate C(4) photosynthesis and regulate metabolic fluxes and activities. This quantitative study determined the differentiated state of BS and M chloroplast thylakoid and envelope membrane proteomes and their oligomeric states using innovative gel-based and mass spectrometry-based protein quantifications. This included native gels, iTRAQ, and label-free quantification using an LTQ-Orbitrap. Subunits of Photosystems I and II, the cytochrome b(6)f, and ATP synthase complexes showed average BS/M accumulation ratios of 1.6, 0.45, 1.0, and 1.33, respectively, whereas ratios for the light-harvesting complex I and II families were 1.72 and 0.68, respectively. A 1000-kDa BS-specific NAD(P)H dehydrogenase complex with associated proteins of unknown function containing more than 15 proteins was observed; we speculate that this novel complex possibly functions in inorganic carbon concentration when carboxylation rates by ribulose-bisphosphate carboxylase/oxygenase are lower than decarboxylation rates by malic enzyme. Differential accumulation of thylakoid proteases (Egy and DegP), state transition kinases (STN7,8), and Photosystem I and II assembly factors was observed, suggesting that cell-specific photosynthetic electron transport depends on post-translational regulatory mechanisms. BS/M ratios for inner envelope transporters phosphoenolpyruvate/P(i) translocator, Dit1, Dit2, and Mex1 were determined and reflect metabolic fluxes in carbon metabolism. A wide variety of hundreds of other proteins showed differential BS/M accumulation. Mass spectral information and functional annotations are available through the Plant Proteome Database. These data are integrated with previous data, resulting in a model for C(4) photosynthesis, thereby providing new rationales for metabolic engineering of C(4) pathways and targeted analysis of genetic networks that coordinate C(4) differentiation.

Trajectories of Multidimensional Caregiver Burden in Chinese Informal Caregivers for Dementia: Evidence from Exploratory and Confirmatory Factor Analysis of the Zarit Burden Interview.

PubMed

Li, Dan; Hu, Nan; Yu, Yueyi; Zhou, Aihong; Li, Fangyu; Jia, Jianping

2017-01-01

Despite its popularity, the latent structure of 22-item Zarit Burden Interview (ZBI) remains unclear. There has been no study exploring how caregiver multidimensional burden changed. The aim of the work was to validate the latent structure of ZBI and to investigate how multidimensional burden evolves with increasing global burden. We studied 1,132 dyads of dementia patients and their informal caregivers. The caregivers completed the ZBI and a questionnaire regarding caregiving. The total sample was randomly split into two equal subsamples. Exploratory factor analysis (EFA) was performed in the first subsample. In the second subsample, confirmatory factor analysis (CFA) was conducted to validate models generated from EFA. The mean of weighted factor score was calculated to assess the change of dimension burden against the increasing ZBI total score. The result of EFA and CFA supported that a five-factor structure, including role strain, personal strain, incompetency, dependency, and guilt, had the best goodness-of-fit. The trajectories of multidimensional burden suggested that three different dimensions (guilt, role strain and personal strain) became the main subtype of burden in sequence as the ZBI total score increased from mild to moderate. Factor dependency contributed prominently to the total burden in severe stage. The five-factor ZBI is a psychometrically robust measure for assessing multidimensional burden in Chinese caregivers. The changes of multidimensional burden have deepened our understanding of the psychological characteristics of caregiving beyond a single total score and may be useful for developing interventions to reduce caregiver burden.

Simulation of range imaging-based estimation of respiratory lung motion. Influence of noise, signal dimensionality and sampling patterns.

PubMed

Wilms, M; Werner, R; Blendowski, M; Ortmüller, J; Handels, H

2014-01-01

A major problem associated with the irradiation of thoracic and abdominal tumors is respiratory motion. In clinical practice, motion compensation approaches are frequently steered by low-dimensional breathing signals (e.g., spirometry) and patient-specific correspondence models, which are used to estimate the sought internal motion given a signal measurement. Recently, the use of multidimensional signals derived from range images of the moving skin surface has been proposed to better account for complex motion patterns. In this work, a simulation study is carried out to investigate the motion estimation accuracy of such multidimensional signals and the influence of noise, the signal dimensionality, and different sampling patterns (points, lines, regions). A diffeomorphic correspondence modeling framework is employed to relate multidimensional breathing signals derived from simulated range images to internal motion patterns represented by diffeomorphic non-linear transformations. Furthermore, an automatic approach for the selection of optimal signal combinations/patterns within this framework is presented. This simulation study focuses on lung motion estimation and is based on 28 4D CT data sets. The results show that the use of multidimensional signals instead of one-dimensional signals significantly improves the motion estimation accuracy, which is, however, highly affected by noise. Only small differences exist between different multidimensional sampling patterns (lines and regions). Automatically determined optimal combinations of points and lines do not lead to accuracy improvements compared to results obtained by using all points or lines. Our results show the potential of multidimensional breathing signals derived from range images for the model-based estimation of respiratory motion in radiation therapy.

The Use of the Visualisation of Multidimensional Data Using PCA to Evaluate Possibilities of the Division of Coal Samples Space Due to their Suitability for Fluidised Gasification

NASA Astrophysics Data System (ADS)

Jamróz, Dariusz; Niedoba, Tomasz; Surowiak, Agnieszka; Tumidajski, Tadeusz

2016-09-01

Methods serving to visualise multidimensional data through the transformation of multidimensional space into two-dimensional space, enable to present the multidimensional data on the computer screen. Thanks to this, qualitative analysis of this data can be performed in the most natural way for humans, through the sense of sight. An example of such a method of multidimensional data visualisation is PCA (principal component analysis) method. This method was used in this work to present and analyse a set of seven-dimensional data (selected seven properties) describing coal samples obtained from Janina and Wieczorek coal mines. Coal from these mines was previously subjected to separation by means of a laboratory ring jig, consisting of ten rings. With 5 layers of both types of coal (with 2 rings each) were obtained in this way. It was decided to check if the method of multidimensional data visualisation enables to divide the space of such divided samples into areas with different suitability for the fluidised gasification process. To that end, the card of technological suitability of coal was used (Sobolewski et al., 2012; 2013), in which key, relevant and additional parameters, having effect on the gasification process, were described. As a result of analyses, it was stated that effective determination of coal samples suitability for the on-surface gasification process in a fluidised reactor is possible. The PCA method enables the visualisation of the optimal subspace containing the set requirements concerning the properties of coals intended for this process.

Prose Representation: A Multidimensional Scaling Approach.

ERIC Educational Resources Information Center

LaPorte, Ronald E.; Voss, James F.

1979-01-01

Multidimensional scaling was used to study the comprehension of prose. Undergraduates rated the similarity of twenty nouns before and after reading passages containing those nouns. Results indicated that the scaling analysis provided an effective valid indicator of prose representation. (Author/JKS)

Femtosecond Multidimensional Imaging - Watching Chemistry from the Molecule's Point of View

NASA Astrophysics Data System (ADS)

Geßner, O.; Lee, A. M. D.; Chrysostom, E. t.-H.; Hayden, C. C.; Stolow, Albert

Using Femtosecond Multidimensional Imaging we disentangle the complex neutral dissociation mechanism of the NO dimer. We characterize all electronic configurations from start to finish and directly observe the evolution of intramolecular vibrational energy redistribution (IVR).

IMPROVING WOMEN'S PRECONCEPTIONAL HEALTH

PubMed Central

Hillemeier, Marianne M.; Downs, Danielle Symons; Feinberg, Mark E.; Weisman, Carol S.; Chuang, Cynthia H.; Parrott, Roxanne; Velott, Diana; Francis, Lori A.; Baker, Sara A.; Dyer, Anne-Marie; Chinchilli, Vernon M.

2009-01-01

Purpose Improving the health of women before pregnancy is an important strategy for reducing adverse pregnancy outcomes for mother and child. This paper reports the first pretest–posttest results from a randomized trial of a unique, multidimensional, small group format intervention, Strong Healthy Women, designed to improve the health behaviors and health status of preconceptional and interconceptional women. Methods Nonpregnant pre- and interconceptional women ages 18−35 were recruited in 15 low-income rural communities in Central Pennsylvania (n = 692). Women were randomized in a ratio of 2-to-1 to intervention and control groups; participants received a baseline and follow-up health risk assessment at 14 weeks and completed questionnaires to assess behavioral variables. The analytic sample for this report consists of 362 women who completed both risk assessments. Outcomes include measures of attitudinal and health-related behavior change. Main Findings Women in the intervention group were significantly more likely than controls to report higher self-efficacy for eating healthy food and to perceive higher preconceptional control of birth outcomes; greater intent to eat healthy foods and be more physically active; and greater frequency of reading food labels, physical activity consistent with recommended levels, and daily use of a multivitamin with folic acid. Significant dose effects were found: Each additional intervention session attended was associated with higher perceived internal preconceptional control of birth outcomes, reading food labels, engaging in relaxation exercise or meditation for stress management, and daily use of a multivitamin with folic acid. Conclusions The attitudinal and behavior changes attributable to the intervention were related primarily to nutrition and physical activity. These results show that these topics can be successfully addressed with pre- and interconceptional women outside the clinical setting in community-based interventions. PMID:19059553

Improving women's preconceptional health: findings from a randomized trial of the Strong Healthy Women intervention in the Central Pennsylvania women's health study.

PubMed

Hillemeier, Marianne M; Downs, Danielle Symons; Feinberg, Mark E; Weisman, Carol S; Chuang, Cynthia H; Parrott, Roxanne; Velott, Diana; Francis, Lori A; Baker, Sara A; Dyer, Anne-Marie; Chinchilli, Vernon M

2008-01-01

Improving the health of women before pregnancy is an important strategy for reducing adverse pregnancy outcomes for mother and child. This paper reports the first pretest-posttest results from a randomized trial of a unique, multidimensional, small group format intervention, Strong Healthy Women, designed to improve the health behaviors and health status of preconceptional and interconceptional women. Nonpregnant pre- and interconceptional women ages 18-35 were recruited in 15 low-income rural communities in Central Pennsylvania (n = 692). Women were randomized in a ratio of 2-to-1 to intervention and control groups; participants received a baseline and follow-up health risk assessment at 14 weeks and completed questionnaires to assess behavioral variables. The analytic sample for this report consists of 362 women who completed both risk assessments. Outcomes include measures of attitudinal and health-related behavior change. Women in the intervention group were significantly more likely than controls to report higher self-efficacy for eating healthy food and to perceive higher preconceptional control of birth outcomes; greater intent to eat healthy foods and be more physically active; and greater frequency of reading food labels, physical activity consistent with recommended levels, and daily use of a multivitamin with folic acid. Significant dose effects were found: Each additional intervention session attended was associated with higher perceived internal preconceptional control of birth outcomes, reading food labels, engaging in relaxation exercise or meditation for stress management, and daily use of a multivitamin with folic acid. The attitudinal and behavior changes attributable to the intervention were related primarily to nutrition and physical activity. These results show that these topics can be successfully addressed with pre- and interconceptional women outside the clinical setting in community-based interventions.

Label-free assay based on immobilized capillary enzyme reactor of Leishmania infantum nucleoside triphosphate diphosphohydrolase (LicNTPDase-2-ICER-LC/UV).

PubMed

Magalhães, Luana; de Oliveira, Arthur Henrique Cavalcante; de Souza Vasconcellos, Raphael; Mariotini-Moura, Christiane; de Cássia Firmino, Rafaela; Fietto, Juliana Lopes Rangel; Cardoso, Carmen Lúcia

2016-01-01

Nucleoside triphosphate diphosphohydrolase (NTPDase) is an enzyme belonging to the apyrase family that participates in the hydrolysis of the nucleosides di- and triphosphate to the corresponding nucleoside monophosphate. This enzyme underlies the virulence of parasites such as Leishmania. Recently, an NTPDase from Leishmania infantum (LicNTPDase-2) was cloned and expressed and has been considered as a new drug target for the treatment of leishmaniasis. With the intent of developing label-free online screening methodologies, LicNTPDase-2 was covalently immobilized onto a fused silica capillary tube in the present study to create an immobilized capillary enzyme reactor (ICER) based on LicNTPDase-2 (LicNTPDase-2-ICER). To perform the activity assays, a multidimensional chromatographic method was developed employing the LicNTPDase-2-ICER in the first dimension, and an analytical Ascentis C8 column was used in the second dimension to provide analytical separation of the substrates and products. The validated LicNTPDase-2-ICER method provided the following kinetic parameters of the immobilized enzyme: KM of 2.2 and 1.8mmolL(-1) for the ADP and ATP substrates, respectively. Suramin (1mmolL(-1)) was also shown to inhibit 32.9% of the enzymatic activity. The developed method is applicable to kinetic studies and enables the recognition of the ligands. Furthermore, a comparison of the values of LicNTPDase-2-ICER with those obtained with an LC method using free enzyme in solution showed that LicNTPDase-2-ICER-LC/UV was an accurate and reproducible method that enabled automated measurements for the rapid screening of ligands. Copyright © 2015 Elsevier B.V. All rights reserved.

A randomized, multicenter, open-label study of poly-L-lactic acid for HIV-1 facial lipoatrophy.

PubMed

Carey, Dianne L; Baker, David; Rogers, Gary D; Petoumenos, Kathy; Chuah, John; Easey, Nicole; Machon, Kirsty; Cooper, David A; Emery, Sean; Carr, Andrew

2007-12-15

Facial lipoatrophy can stigmatize and can reduce quality of life, self esteem, and antiretroviral adherence. Poly-L-lactic acid (PLA) injections seem safe and effective, but no randomized study has included objective endpoints. HIV-positive adults with moderate/severe facial lipoatrophy were randomized to 4 open-label PLA treatments administered every 2 weeks from week 0 (immediate group, n = 51) or after week 24 (deferred group, n = 50). The primary endpoint was mean change in facial soft tissue volume (FSTV), as assessed by spiral computed tomography. Analyses were by intention to treat. At week 24, mean changes in FSTV were 0 cm3 in the intermediate group and -10 cm3 in the deferred group (between-group difference of 10 [95% confidence interval (CI): -7 to 28] cm3; P = 0.24). The immediate group had a greater mean change in soft tissue depth at the maxilla (2.2 mm [95% CI: 1.6 to 2.9]; P < 0.0001) and base of the nasal septum (1.0 mm [95% CI: 0.3 to 1.6]; P = 0.003) levels. PLA did not have an impact on peripheral fat mass, viral load, or antiretroviral adherence. Patient and physician subjectively assessed facial lipoatrophy severity (P < 0.0001), 2 of 8 Short Form-36 Health Survey and 2 of 5 Multidimensional Body-Self Relations Questionnaire-Appearance Scales, scores improved significantly. The median duration of treatment-related adverse events was 2 (interquartile range: 1 to 3) days. PLA did not increase FSTV, although tissue thickness in injection planes increased modestly, an improvement observed by patients. PLA was safe and well tolerated. Facial lipoatrophy severity and some quality-of-life domains improved.

The Multidimensional Aggression Scale for the Structured Doll Play Interview

ERIC Educational Resources Information Center

Abramson, Paul R.; And Others

1974-01-01

A multidimensional aggression scoring system for preschool children's responses to the structured doll play interview is described. The system, which incorporates previous investigator's findings, scales doll play responses along three dimensions of aggression: intensity, agent, and directionality. (Author)

The space transformation in the simulation of multidimensional random fields

USGS Publications Warehouse

Christakos, G.

1987-01-01

Space transformations are proposed as a mathematically meaningful and practically comprehensive approach to simulate multidimensional random fields. Within this context the turning bands method of simulation is reconsidered and improved in both the space and frequency domains. ?? 1987.

A Comprehensive Approach to the Patient at End of Life: Assessment of Multidimensional Suffering

PubMed Central

Wachholtz, Amy B.; Fitch, Christina E.; Makowski, Suzana; Tjia, Jennifer

2016-01-01

Pain is a multidimensional, complex experience. There are many challenges in identifying and meeting the needs of patients experiencing pain. Evaluation of pain from a bio-psycho-social-spiritual framework is particularly germane for patients approaching the end of life. This review explores the relation between the psychospiritual dimensions of suffering and the experience of physical pain, and how to assess and treat pain in a multidimensional framework. A review of empirical data on the relation between pain and suffering as well as interdisciplinary evidence-based approaches to alleviate suffering are provided. PMID:27043799

Multidimensional display controller for displaying to a user an aspect of a multidimensional space visible from a base viewing location along a desired viewing orientation

DOEpatents

Davidson, George S.; Anderson, Thomas G.

2001-01-01

A display controller allows a user to control a base viewing location, a base viewing orientation, and a relative viewing orientation. The base viewing orientation and relative viewing orientation are combined to determine a desired viewing orientation. An aspect of a multidimensional space visible from the base viewing location along the desired viewing orientation is displayed to the user. The user can change the base viewing location, base viewing orientation, and relative viewing orientation by changing the location or other properties of input objects.

Recent advances in multidimensional ultrafast spectroscopy

NASA Astrophysics Data System (ADS)

Oliver, Thomas A. A.

2018-01-01

Multidimensional ultrafast spectroscopies are one of the premier tools to investigate condensed phase dynamics of biological, chemical and functional nanomaterial systems. As they reach maturity, the variety of frequency domains that can be explored has vastly increased, with experimental techniques capable of correlating excitation and emission frequencies from the terahertz through to the ultraviolet. Some of the most recent innovations also include extreme cross-peak spectroscopies that directly correlate the dynamics of electronic and vibrational states. This review article summarizes the key technological advances that have permitted these recent advances, and the insights gained from new multidimensional spectroscopic probes.

Exploration of multidimensional interactive classroom teaching for CCD principle and application course

NASA Astrophysics Data System (ADS)

Fu, Xinghu; Tan, Ailing; Zhang, Baojun; Fu, Guangwei; Bi, Weihong

2017-08-01

The CCD principle and application course is professional and comprehensive. It involves many subject contents. The course content includes eight aspects. In order to complete the teaching tasks within a limited time, improve the classroom teaching quality and prompt students master the course content faster and better, so the multidimensional interactive classroom teaching is proposed. In the teaching practice, the interactive relationship between the frontier science, scientific research project, living example and classroom content is researched detailedly. Finally, it has been proved practically that the proposed multidimensional interactive classroom teaching can achieved good teaching effect.

Recent advances in multidimensional ultrafast spectroscopy

PubMed Central

2018-01-01

Multidimensional ultrafast spectroscopies are one of the premier tools to investigate condensed phase dynamics of biological, chemical and functional nanomaterial systems. As they reach maturity, the variety of frequency domains that can be explored has vastly increased, with experimental techniques capable of correlating excitation and emission frequencies from the terahertz through to the ultraviolet. Some of the most recent innovations also include extreme cross-peak spectroscopies that directly correlate the dynamics of electronic and vibrational states. This review article summarizes the key technological advances that have permitted these recent advances, and the insights gained from new multidimensional spectroscopic probes. PMID:29410844

Invited Article: Single-shot THz detection techniques optimized for multidimensional THz spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teo, Stephanie M.; Ofori-Okai, Benjamin K.; Werley, Christopher A.

Multidimensional spectroscopy at visible and infrared frequencies has opened a window into the transfer of energy and quantum coherences at ultrafast time scales. For these measurements to be performed in a manageable amount of time, one spectral axis is typically recorded in a single laser shot. An analogous rapid-scanning capability for THz measurements will unlock the multidimensional toolkit in this frequency range. Here, we first review the merits of existing single-shot THz schemes and discuss their potential in multidimensional THz spectroscopy. We then introduce improved experimental designs and noise suppression techniques for the two most promising methods: frequency-to-time encoding withmore » linear spectral interferometry and angle-to-time encoding with dual echelons. Both methods, each using electro-optic detection in the linear regime, were able to reproduce the THz temporal waveform acquired with a traditional scanning delay line. Although spectral interferometry had mediocre performance in terms of signal-to-noise, the dual echelon method was easily implemented and achieved the same level of signal-to-noise as the scanning delay line in only 4.5% of the laser pulses otherwise required (or 22 times faster). This reduction in acquisition time will compress day-long scans to hours and hence provides a practical technique for multidimensional THz measurements.« less

Image matrix processor for fast multi-dimensional computations

DOEpatents

Roberson, G.P.; Skeate, M.F.

1996-10-15

An apparatus for multi-dimensional computation is disclosed which comprises a computation engine, including a plurality of processing modules. The processing modules are configured in parallel and compute respective contributions to a computed multi-dimensional image of respective two dimensional data sets. A high-speed, parallel access storage system is provided which stores the multi-dimensional data sets, and a switching circuit routes the data among the processing modules in the computation engine and the storage system. A data acquisition port receives the two dimensional data sets representing projections through an image, for reconstruction algorithms such as encountered in computerized tomography. The processing modules include a programmable local host, by which they may be configured to execute a plurality of different types of multi-dimensional algorithms. The processing modules thus include an image manipulation processor, which includes a source cache, a target cache, a coefficient table, and control software for executing image transformation routines using data in the source cache and the coefficient table and loading resulting data in the target cache. The local host processor operates to load the source cache with a two dimensional data set, loads the coefficient table, and transfers resulting data out of the target cache to the storage system, or to another destination. 10 figs.

Multi-dimensional Fokker-Planck equation analysis using the modified finite element method

NASA Astrophysics Data System (ADS)

Náprstek, J.; Král, R.

2016-09-01

The Fokker-Planck equation (FPE) is a frequently used tool for the solution of cross probability density function (PDF) of a dynamic system response excited by a vector of random processes. FEM represents a very effective solution possibility, particularly when transition processes are investigated or a more detailed solution is needed. Actual papers deal with single degree of freedom (SDOF) systems only. So the respective FPE includes two independent space variables only. Stepping over this limit into MDOF systems a number of specific problems related to a true multi-dimensionality must be overcome. Unlike earlier studies, multi-dimensional simplex elements in any arbitrary dimension should be deployed and rectangular (multi-brick) elements abandoned. Simple closed formulae of integration in multi-dimension domain have been derived. Another specific problem represents the generation of multi-dimensional finite element mesh. Assembling of system global matrices should be subjected to newly composed algorithms due to multi-dimensionality. The system matrices are quite full and no advantages following from their sparse character can be profited from, as is commonly used in conventional FEM applications in 2D/3D problems. After verification of partial algorithms, an illustrative example dealing with a 2DOF non-linear aeroelastic system in combination with random and deterministic excitations is discussed.

Fatigue in children: reliability and validity of the Dutch PedsQL™ Multidimensional Fatigue Scale.

PubMed

Gordijn, M Suzanne; Suzanne Gordijn, M; Cremers, Eline M P; Kaspers, Gertjan J L; Gemke, Reinoud J B J

2011-09-01

The aim of the study is to report on the feasibility, reliability, validity, and the norm-references of the Dutch version of the PedsQL™ Multidimensional Fatigue Scale. The study participants are four hundred and ninety-seven parents of children aged 2-18 years and 366 children aged 5-18 years from various day care facilities, elementary schools, and a high school who completed the Dutch version of the PedsQL™ Multidimensional Fatigue Scale. The number of missing items was minimal. All scales showed satisfactory internal consistency reliability, with Cronbach's coefficient alpha exceeding 0.70. Test-retest reliability was good to excellent (ICCs 0.68-0.84) and inter-observer reliability varied from moderate to excellent (ICCs 0.56-0.93) for total scores. Parent/child concordance for total scores was poor to good (ICCs 0.25-0.68). The PedsQL™ Multidimensional Fatigue Scale was able to distinguish between healthy children and children with an impaired health condition. The Dutch version of the PedsQL™ Multidimensional Fatigue Scale demonstrates an adequate feasibility, reliability, and validity in another sociocultural context. With the obtained norm-references, it can be utilized as a tool in the evaluation of fatigue in healthy and chronically ill children aged 2-18 years.

Assessment of health surveys: fitting a multidimensional graded response model.

PubMed

Depaoli, Sarah; Tiemensma, Jitske; Felt, John M

The multidimensional graded response model, an item response theory (IRT) model, can be used to improve the assessment of surveys, even when sample sizes are restricted. Typically, health-based survey development utilizes classical statistical techniques (e.g. reliability and factor analysis). In a review of four prominent journals within the field of Health Psychology, we found that IRT-based models were used in less than 10% of the studies examining scale development or assessment. However, implementing IRT-based methods can provide more details about individual survey items, which is useful when determining the final item content of surveys. An example using a quality of life survey for Cushing's syndrome (CushingQoL) highlights the main components for implementing the multidimensional graded response model. Patients with Cushing's syndrome (n = 397) completed the CushingQoL. Results from the multidimensional graded response model supported a 2-subscale scoring process for the survey. All items were deemed as worthy contributors to the survey. The graded response model can accommodate unidimensional or multidimensional scales, be used with relatively lower sample sizes, and is implemented in free software (example code provided in online Appendix). Use of this model can help to improve the quality of health-based scales being developed within the Health Sciences.

Nonlinear Conservation Laws and Finite Volume Methods

NASA Astrophysics Data System (ADS)

Leveque, Randall J.

Introduction Software Notation Classification of Differential Equations Derivation of Conservation Laws The Euler Equations of Gas Dynamics Dissipative Fluxes Source Terms Radiative Transfer and Isothermal Equations Multi-dimensional Conservation Laws The Shock Tube Problem Mathematical Theory of Hyperbolic Systems Scalar Equations Linear Hyperbolic Systems Nonlinear Systems The Riemann Problem for the Euler Equations Numerical Methods in One Dimension Finite Difference Theory Finite Volume Methods Importance of Conservation Form - Incorrect Shock Speeds Numerical Flux Functions Godunov's Method Approximate Riemann Solvers High-Resolution Methods Other Approaches Boundary Conditions Source Terms and Fractional Steps Unsplit Methods Fractional Step Methods General Formulation of Fractional Step Methods Stiff Source Terms Quasi-stationary Flow and Gravity Multi-dimensional Problems Dimensional Splitting Multi-dimensional Finite Volume Methods Grids and Adaptive Refinement Computational Difficulties Low-Density Flows Discrete Shocks and Viscous Profiles Start-Up Errors Wall Heating Slow-Moving Shocks Grid Orientation Effects Grid-Aligned Shocks Magnetohydrodynamics The MHD Equations One-Dimensional MHD Solving the Riemann Problem Nonstrict Hyperbolicity Stiffness The Divergence of B Riemann Problems in Multi-dimensional MHD Staggered Grids The 8-Wave Riemann Solver Relativistic Hydrodynamics Conservation Laws in Spacetime The Continuity Equation The 4-Momentum of a Particle The Stress-Energy Tensor Finite Volume Methods Multi-dimensional Relativistic Flow Gravitation and General Relativity References

Invited Article: Single-shot THz detection techniques optimized for multidimensional THz spectroscopy.

PubMed

Teo, Stephanie M; Ofori-Okai, Benjamin K; Werley, Christopher A; Nelson, Keith A

2015-05-01

Multidimensional spectroscopy at visible and infrared frequencies has opened a window into the transfer of energy and quantum coherences at ultrafast time scales. For these measurements to be performed in a manageable amount of time, one spectral axis is typically recorded in a single laser shot. An analogous rapid-scanning capability for THz measurements will unlock the multidimensional toolkit in this frequency range. Here, we first review the merits of existing single-shot THz schemes and discuss their potential in multidimensional THz spectroscopy. We then introduce improved experimental designs and noise suppression techniques for the two most promising methods: frequency-to-time encoding with linear spectral interferometry and angle-to-time encoding with dual echelons. Both methods, each using electro-optic detection in the linear regime, were able to reproduce the THz temporal waveform acquired with a traditional scanning delay line. Although spectral interferometry had mediocre performance in terms of signal-to-noise, the dual echelon method was easily implemented and achieved the same level of signal-to-noise as the scanning delay line in only 4.5% of the laser pulses otherwise required (or 22 times faster). This reduction in acquisition time will compress day-long scans to hours and hence provides a practical technique for multidimensional THz measurements.

DICON: interactive visual analysis of multidimensional clusters.

PubMed

Cao, Nan; Gotz, David; Sun, Jimeng; Qu, Huamin

2011-12-01

Clustering as a fundamental data analysis technique has been widely used in many analytic applications. However, it is often difficult for users to understand and evaluate multidimensional clustering results, especially the quality of clusters and their semantics. For large and complex data, high-level statistical information about the clusters is often needed for users to evaluate cluster quality while a detailed display of multidimensional attributes of the data is necessary to understand the meaning of clusters. In this paper, we introduce DICON, an icon-based cluster visualization that embeds statistical information into a multi-attribute display to facilitate cluster interpretation, evaluation, and comparison. We design a treemap-like icon to represent a multidimensional cluster, and the quality of the cluster can be conveniently evaluated with the embedded statistical information. We further develop a novel layout algorithm which can generate similar icons for similar clusters, making comparisons of clusters easier. User interaction and clutter reduction are integrated into the system to help users more effectively analyze and refine clustering results for large datasets. We demonstrate the power of DICON through a user study and a case study in the healthcare domain. Our evaluation shows the benefits of the technique, especially in support of complex multidimensional cluster analysis. © 2011 IEEE

Multidimensional Identity Model Revisited: Implications for Student Affairs

ERIC Educational Resources Information Center

Pope, Raechele L.; Reynolds, Amy L.

2017-01-01

This chapter explores the connection between the authors' foundational Multidimensional Identity Model and intersectionality. The authors discuss the challenges and promises of capturing a holistic, intersectional perspective in identity theory, as well as how to engage the concept of identity as practitioners.

A Framework for Dimensionality Assessment for Multidimensional Item Response Models

ERIC Educational Resources Information Center

Svetina, Dubravka; Levy, Roy

2014-01-01

A framework is introduced for considering dimensionality assessment procedures for multidimensional item response models. The framework characterizes procedures in terms of their confirmatory or exploratory approach, parametric or nonparametric assumptions, and applicability to dichotomous, polytomous, and missing data. Popular and emerging…

Uncertainty of Comparative Judgments and Multidimensional Structure

ERIC Educational Resources Information Center

Sjoberg, Lennart

1975-01-01

An analysis of preferences with respect to silhouette drawings of nude females is presented. Systematic intransitivities were discovered. The dispersions of differences (comparatal dispersons) were shown to reflect the multidimensional structure of the stimuli, a finding expected on the basis of prior work. (Author)

Multidimensional Perspectives on Principal Leadership Effectiveness

ERIC Educational Resources Information Center

Beycioglu, Kadir, Ed.; Pashiardis, Petros, Ed.

2015-01-01

Exceptional management skills are crucial to success in educational environments. As school leaders, principals are expected to effectively supervise the school system while facing a multitude of issues and demands. "Multidimensional Perspectives on Principal Leadership Effectiveness" combines best practices and the latest approaches in…

The Multidimensional Structure of Verbal Comprehension Test Items.

ERIC Educational Resources Information Center

Peled, Zimra

1984-01-01

The multidimensional structure of verbal comprehension test items was investigated. Empirical evidence was provided to support the theory that item tasks are multivariate-multiordered composites of faceted components: language, contextual knowledge, and cognitive operation. Linear and circular properties of cylindrical manifestation were…

Psychological distress increases the risk of falling into poverty amongst older Australians: the overlooked costs-of-illness.

PubMed

Callander, Emily J; Schofield, Deborah J

2018-04-17

This paper aimed to identify whether high psychological distress is associated with an increased risk of income and multidimensional poverty amongst older adults in Australia. We undertook longitudinal analysis of the nationally representative Household Income and Labour Dynamics in Australian (HILDA) survey using modified Poisson regression models to estimate the relative risk of falling into income poverty and multidimensional poverty between 2010 and 2012 for males and females, adjusting for age, employment status, place of residence, marital status and housing tenure; and Population Attributable Risk methodology to estimate the proportion of poverty directly attributable to psychological distress, measured by the Kessler 10 scale. For males, having high psychological distress increased the risk of falling into income poverty by 1.68 (95% CI: 1.02 to 2.75) and the risk of falling into multidimensional poverty by 3.40 (95% CI: 1.91 to 6.04). For females, there was no significant difference in the risk of falling into income poverty between those with high and low psychological distress (p = 0.1008), however having high psychological distress increased the risk of falling into multidimensional poverty by 2.15 (95% CI: 1.30 to 3.55). Between 2009 and 2012, 8.0% of income poverty cases for people aged 65 and over (95% CI: 7.8% to 8.4%), and 19.5% of multidimensional poverty cases for people aged 65 and over (95% CI: 19.2% to 19.9%) can be attributed to high psychological distress. The elevated risk of falling into income and multidimensional poverty has been an overlooked cost of poor mental health.

Effect of asthma on falling into poverty: the overlooked costs of illness.

PubMed

Callander, Emily J; Schofield, Deborah J

2015-05-01

Studies on the indirect costs of asthma have taken a narrow view of how the condition affects the living standards of patients by examining only the association with employment and income. To build on the current cost-of-illness literature and identify whether having asthma is associated with an increased risk of poverty, thus giving a more complete picture of the costs of asthma to individuals and society. Longitudinal analysis of the nationally representative Household Income and Labour Dynamics in Australian survey to estimate the relative risk of income poverty, multidimensional poverty, and long-term multidimensional poverty between 2007 and 2012 and population attributable risk method to estimate the proportion of poverty between 2007 and 2012 directly attributable to asthma. No significant difference was found in the risk of falling into income poverty between those with and without asthma (P = .07). Having asthma increased the risk of falling into multidimensional poverty by 1.35 (95% confidence interval [CI], 1.01-1.83) and the risk of falling into chronic multidimensional poverty by 2.22 (95% CI, 1.20-4.10). Between 2007 and 2012, a total of 5.2% of income poverty cases (95% CI, 5.1%-5.4%), 7.8% of multidimensional poverty cases (95% CI, 7.7%-8.0%), and 19.6% of chronic multidimensional poverty cases (95% CI, 19.2%-20.0%) can be attributed to asthma. Asthma is associated with an increased risk of falling into poverty. This should be taken into consideration when considering the suitability of different treatment options for patients with asthma. Copyright © 2015 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Multidimensional Scaling Applied to Linguistic Relationships.

ERIC Educational Resources Information Center

Black, Paul

1973-01-01

As the several specific applications in this paper demonstrate, multidimensional scaling provides a long-needed means for investigating and describing spatial relationships among speech varieties. It is especially applicable to the relationships among varieties of a single language (or more properly, linguistic "cline"), which, as is…

A Multidimensional Software Engineering Course

ERIC Educational Resources Information Center

Barzilay, O.; Hazzan, O.; Yehudai, A.

2009-01-01

Software engineering (SE) is a multidimensional field that involves activities in various areas and disciplines, such as computer science, project management, and system engineering. Though modern SE curricula include designated courses that address these various subjects, an advanced summary course that synthesizes them is still missing. Such a…

Some Small Sample Results for Maximum Likelihood Estimation in Multidimensional Scaling.

ERIC Educational Resources Information Center

Ramsay, J. O.

1980-01-01

Some aspects of the small sample behavior of maximum likelihood estimates in multidimensional scaling are investigated with Monte Carlo techniques. In particular, the chi square test for dimensionality is examined and a correction for bias is proposed and evaluated. (Author/JKS)

Multidimensional Screening as a Pharmacology Laboratory Experience.

ERIC Educational Resources Information Center

Malone, Marvin H.; And Others

1979-01-01

A multidimensional pharmacodynamic screening experiment that addresses drug interaction is included in the pharmacology-toxicology laboratory experience of pharmacy students at the University of the Pacific. The student handout with directions for the procedure is reproduced, drug compounds tested are listed, and laboratory evaluation results are…

A multidimensional generalization of Heilbronn's theorem on the average length of a finite continued fraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Illarionov, A A

2014-03-31

Heilbronn's theorem on the average length of a finite continued fraction is generalized to the multidimensional case in terms of relative minima of the lattices which were introduced by Voronoy and Minkowski. Bibliography: 21 titles.

High Order Finite Difference Methods, Multidimensional Linear Problems and Curvilinear Coordinates

NASA Technical Reports Server (NTRS)

Nordstrom, Jan; Carpenter, Mark H.

1999-01-01

Boundary and interface conditions are derived for high order finite difference methods applied to multidimensional linear problems in curvilinear coordinates. The boundary and interface conditions lead to conservative schemes and strict and strong stability provided that certain metric conditions are met.

Assisting College Students with Athletic Disengagement

ERIC Educational Resources Information Center

Van Lone, Jeffrey S.; Siembor, Michael; Mistler, Brian J.; Mapstone, David J.

2017-01-01

This article examines college student disengagement from sports, presents a multidimensional concept of athletic identity, and introduces a new measure intended to assist college counselors in their work with disengaged athletes. The Multidimensional Athletic Identity and Engagement Scale (MAIES) is introduced (Cronbach alpha 0.98, with subscale…

Application of the Allan Variance to Time Series Analysis in Astrometry and Geodesy: A Review.

PubMed

Malkin, Zinovy

2016-04-01

The Allan variance (AVAR) was introduced 50 years ago as a statistical tool for assessing the frequency standards deviations. For the past decades, AVAR has increasingly been used in geodesy and astrometry to assess the noise characteristics in geodetic and astrometric time series. A specific feature of astrometric and geodetic measurements, as compared with clock measurements, is that they are generally associated with uncertainties; thus, an appropriate weighting should be applied during data analysis. In addition, some physically connected scalar time series naturally form series of multidimensional vectors. For example, three station coordinates time series X, Y, and Z can be combined to analyze 3-D station position variations. The classical AVAR is not intended for processing unevenly weighted and/or multidimensional data. Therefore, AVAR modifications, namely weighted AVAR (WAVAR), multidimensional AVAR (MAVAR), and weighted multidimensional AVAR (WMAVAR), were introduced to overcome these deficiencies. In this paper, a brief review is given of the experience of using AVAR and its modifications in processing astrogeodetic time series.

A Multidimensional Ideal Point Item Response Theory Model for Binary Data.

PubMed

Maydeu-Olivares, Albert; Hernández, Adolfo; McDonald, Roderick P

2006-12-01

We introduce a multidimensional item response theory (IRT) model for binary data based on a proximity response mechanism. Under the model, a respondent at the mode of the item response function (IRF) endorses the item with probability one. The mode of the IRF is the ideal point, or in the multidimensional case, an ideal hyperplane. The model yields closed form expressions for the cell probabilities. We estimate and test the goodness of fit of the model using only information contained in the univariate and bivariate moments of the data. Also, we pit the new model against the multidimensional normal ogive model estimated using NOHARM in four applications involving (a) attitudes toward censorship, (b) satisfaction with life, (c) attitudes of morality and equality, and (d) political efficacy. The normal PDF model is not invariant to simple operations such as reverse scoring. Thus, when there is no natural category to be modeled, as in many personality applications, it should be fit separately with and without reverse scoring for comparisons.

Igloo-Plot: a tool for visualization of multidimensional datasets.

PubMed

Kuntal, Bhusan K; Ghosh, Tarini Shankar; Mande, Sharmila S

2014-01-01

Advances in science and technology have resulted in an exponential growth of multivariate (or multi-dimensional) datasets which are being generated from various research areas especially in the domain of biological sciences. Visualization and analysis of such data (with the objective of uncovering the hidden patterns therein) is an important and challenging task. We present a tool, called Igloo-Plot, for efficient visualization of multidimensional datasets. The tool addresses some of the key limitations of contemporary multivariate visualization and analysis tools. The visualization layout, not only facilitates an easy identification of clusters of data-points having similar feature compositions, but also the 'marker features' specific to each of these clusters. The applicability of the various functionalities implemented herein is demonstrated using several well studied multi-dimensional datasets. Igloo-Plot is expected to be a valuable resource for researchers working in multivariate data mining studies. Igloo-Plot is available for download from: http://metagenomics.atc.tcs.com/IglooPlot/. Copyright © 2014 Elsevier Inc. All rights reserved.

Trellis coding with multidimensional QAM signal sets

NASA Technical Reports Server (NTRS)

Pietrobon, Steven S.; Costello, Daniel J.

1993-01-01

Trellis coding using multidimensional QAM signal sets is investigated. Finite-size 2D signal sets are presented that have minimum average energy, are 90-deg rotationally symmetric, and have from 16 to 1024 points. The best trellis codes using the finite 16-QAM signal set with two, four, six, and eight dimensions are found by computer search (the multidimensional signal set is constructed from the 2D signal set). The best moderate complexity trellis codes for infinite lattices with two, four, six, and eight dimensions are also found. The minimum free squared Euclidean distance and number of nearest neighbors for these codes were used as the selection criteria. Many of the multidimensional codes are fully rotationally invariant and give asymptotic coding gains up to 6.0 dB. From the infinite lattice codes, the best codes for transmitting J, J + 1/4, J + 1/3, J + 1/2, J + 2/3, and J + 3/4 bit/sym (J an integer) are presented.

Transforming community services through the use of a multidimensional model of clinical leadership.

PubMed

Leigh, Jacqueline Anne; Wild, Jill; Hynes, Celia; Wells, Stuart; Kurien, Anish; Rutherford, June; Rosen, Lyn; Ashcroft, Tim; Hartley, Victoria

2015-03-01

To evaluate the application of a Multidimensional Model of Clinical Leadership on the community healthcare leader and on transforming community services. Healthcare policy advocates clinical leadership as the vehicle to transform community and healthcare services. Few studies have identified the key components of an effective clinical leadership development model. The first two stages of Kirkpatrick's (Personnel Administrator 28, 1983, 62) Four/Five Levels of Evaluation were used to evaluate the application of the multidimensional model of clinical leadership. Eighty community healthcare leaders were exposed to this multidimensional clinical leadership development model through attendance of a community clinical leadership development programme. Twenty five leaders participated in focus group interviews. Data from the interviews were analysed utilising thematic content analysis. Three key themes emerged that influenced the development of best practice principles for clinical leadership development: 1. Personal leadership development 2. Organisational leadership 3. The importance of multiprofessional action learning/reflective groups Emergent best practice principles for clinical leadership development include adopting a multidimensional development approach. This approach encompasses: preparing the individual leader in the role and seeking organisational leadership development that promotes the vision and corporate values of the organisation and delivers on service improvement and innovation. Moreover, application of the Multidimensional Model of Clinical Leadership could offer the best platform for embedding the Six C's of Nursing (Compassion in Practice - Our Culture of Compassionate Care, Department of Health, Crown Copyright, 2012) within the culture of the healthcare organisation: care, compassion, courage, commitment, communication, and competency. This is achieved in part through the application of emotional intelligence to understand self and to develop the personal integrity of the healthcare leader and through supporting a culture of lifelong leadership learning. Embedding the best practice principles of clinical leadership development within a multidimensional model of clinical leadership provides a promising approach to: equipping the healthcare leader with those transferable leadership skills required to help them embark on a journey of lifelong leadership learning; and producing the healthcare leader who is caring, compassionate and can confidently and effectively transform community services. © 2014 John Wiley & Sons Ltd.

Approximate series solution of multi-dimensional, time fractional-order (heat-like) diffusion equations using FRDTM.

PubMed

Singh, Brajesh K; Srivastava, Vineet K

2015-04-01

The main goal of this paper is to present a new approximate series solution of the multi-dimensional (heat-like) diffusion equation with time-fractional derivative in Caputo form using a semi-analytical approach: fractional-order reduced differential transform method (FRDTM). The efficiency of FRDTM is confirmed by considering four test problems of the multi-dimensional time fractional-order diffusion equation. FRDTM is a very efficient, effective and powerful mathematical tool which provides exact or very close approximate solutions for a wide range of real-world problems arising in engineering and natural sciences, modelled in terms of differential equations.

Approximate series solution of multi-dimensional, time fractional-order (heat-like) diffusion equations using FRDTM

PubMed Central

Singh, Brajesh K.; Srivastava, Vineet K.

2015-01-01

The main goal of this paper is to present a new approximate series solution of the multi-dimensional (heat-like) diffusion equation with time-fractional derivative in Caputo form using a semi-analytical approach: fractional-order reduced differential transform method (FRDTM). The efficiency of FRDTM is confirmed by considering four test problems of the multi-dimensional time fractional-order diffusion equation. FRDTM is a very efficient, effective and powerful mathematical tool which provides exact or very close approximate solutions for a wide range of real-world problems arising in engineering and natural sciences, modelled in terms of differential equations. PMID:26064639

Addendum to foundations of multidimensional wave field signal theory: Gaussian source function

NASA Astrophysics Data System (ADS)

Baddour, Natalie

2018-02-01

Many important physical phenomena are described by wave or diffusion-wave type equations. Recent work has shown that a transform domain signal description from linear system theory can give meaningful insight to multi-dimensional wave fields. In N. Baddour [AIP Adv. 1, 022120 (2011)], certain results were derived that are mathematically useful for the inversion of multi-dimensional Fourier transforms, but more importantly provide useful insight into how source functions are related to the resulting wave field. In this short addendum to that work, it is shown that these results can be applied with a Gaussian source function, which is often useful for modelling various physical phenomena.

Prologue: Reading Comprehension Is Not a Single Ability.

PubMed

Catts, Hugh W; Kamhi, Alan G

2017-04-20

In this initial article of the clinical forum on reading comprehension, we argue that reading comprehension is not a single ability that can be assessed by one or more general reading measures or taught by a small set of strategies or approaches. We present evidence for a multidimensional view of reading comprehension that demonstrates how it varies as a function of reader ability, text, and task. The implications of this view for instruction of reading comprehension are considered. Reading comprehension is best conceptualized with a multidimensional model. The multidimensionality of reading comprehension means that instruction will be more effective when tailored to student performance with specific texts and tasks.

Assessment of Daily and Weekly Fatigue among African American Cancer Survivors

PubMed Central

Sobel, Rina M.; McSorley, Anna-Michelle M.; Roesch, Scott C.; Malcarne, Vanessa L.; Hawes, Starlyn M.; Sadler, Georgia Robins

2013-01-01

This investigation evaluates two common measures of cancer-related fatigue, one multidimensional/retrospective and one unidimensional/same-day. Fifty-two African American survivors of diverse cancers completed fatigue visual analogue scales once daily, and the Multidimensional Fatigue Symptom Inventory (MFSI) once weekly, for four weeks. Zero-order correlations showed retrospectivefatigue was significantly related to average, peak, and most recent same-dayfatigue. Multilevel random coefficient modeling showed unidimensional fatigue shared the most variance with the MFSI’s General subscale for three weeks, and with the Vigor subscale for one week. Researchers and clinicians may wish to prioritize multidimensional measures when assessing cancer-related fatigue, if appropriate. PMID:23844922

Simulation of a Multidimensional Input Quantum Perceptron

NASA Astrophysics Data System (ADS)

Yamamoto, Alexandre Y.; Sundqvist, Kyle M.; Li, Peng; Harris, H. Rusty

2018-06-01

In this work, we demonstrate the improved data separation capabilities of the Multidimensional Input Quantum Perceptron (MDIQP), a fundamental cell for the construction of more complex Quantum Artificial Neural Networks (QANNs). This is done by using input controlled alterations of ancillary qubits in combination with phase estimation and learning algorithms. The MDIQP is capable of processing quantum information and classifying multidimensional data that may not be linearly separable, extending the capabilities of the classical perceptron. With this powerful component, we get much closer to the achievement of a feedforward multilayer QANN, which would be able to represent and classify arbitrary sets of data (both quantum and classical).