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Sample records for proteomics current state

  1. Proteomics of Staphylococcus aureus--current state and future challenges.

    PubMed

    Hecker, Michael; Engelmann, Susanne; Cordwell, Stuart J

    2003-04-01

    This paper presents a short review of the proteome of Staphylococcus aureus, a gram-positive human pathogen of increasing importance for human health as a result of the increasing antibiotic resistance. A proteome reference map is shown which can be used for future studies and is followed by a demonstration of how proteomics could be applied to obtain new information on S. aureus physiology. The proteomic approach can provide new data on the regulation of metabolism as well as of the stress or starvation responses. Proteomic signatures encompassing specific stress or starvation proteins are excellent tools to predict the physiological state of a cell population. Furthermore proteomics is very useful for analysing the size and function of known and unknown regulons and will open a new dimension in the comprehensive understanding of regulatory networks in pathogenicity. Finally, some fields of application of S. aureus proteomics are discussed, including proteomics and strain evaluation, the role of proteomics for analysis of antibiotic resistance or for discovering new targets and diagnostics tools. The review also shows that the post-genome era of S. aureus which began in 2001 with the publication of the genome sequence is still in a preliminary stage, however, the consequent application of proteomics in combination with DNA array techniques and supported by bioinformatics will provide a comprehensive picture on cell physiology and pathogenicity in the near future. PMID:12659740

  2. The Human Proteome Project: Current State and Future Direction

    PubMed Central

    Legrain, Pierre; Aebersold, Ruedi; Archakov, Alexander; Bairoch, Amos; Bala, Kumar; Beretta, Laura; Bergeron, John; Borchers, Christoph H.; Corthals, Garry L.; Costello, Catherine E.; Deutsch, Eric W.; Domon, Bruno; Hancock, William; He, Fuchu; Hochstrasser, Denis; Marko-Varga, György; Salekdeh, Ghasem Hosseini; Sechi, Salvatore; Snyder, Michael; Srivastava, Sudhir; Uhlén, Mathias; Wu, Cathy H.; Yamamoto, Tadashi; Paik, Young-Ki; Omenn, Gilbert S.

    2011-01-01

    After the successful completion of the Human Genome Project, the Human Proteome Organization has recently officially launched a global Human Proteome Project (HPP), which is designed to map the entire human protein set. Given the lack of protein-level evidence for about 30% of the estimated 20,300 protein-coding genes, a systematic global effort will be necessary to achieve this goal with respect to protein abundance, distribution, subcellular localization, interaction with other biomolecules, and functions at specific time points. As a general experimental strategy, HPP research groups will use the three working pillars for HPP: mass spectrometry, antibody capture, and bioinformatics tools and knowledge bases. The HPP participants will take advantage of the output and cross-analyses from the ongoing Human Proteome Organization initiatives and a chromosome-centric protein mapping strategy, termed C-HPP, with which many national teams are currently engaged. In addition, numerous biologically driven and disease-oriented projects will be stimulated and facilitated by the HPP. Timely planning with proper governance of HPP will deliver a protein parts list, reagents, and tools for protein studies and analyses, and a stronger basis for personalized medicine. The Human Proteome Organization urges each national research funding agency and the scientific community at large to identify their preferred pathways to participate in aspects of this highly promising project in a HPP consortium of funders and investigators. PMID:21742803

  3. The human proteome project: current state and future direction.

    PubMed

    Legrain, Pierre; Aebersold, Ruedi; Archakov, Alexander; Bairoch, Amos; Bala, Kumar; Beretta, Laura; Bergeron, John; Borchers, Christoph H; Corthals, Garry L; Costello, Catherine E; Deutsch, Eric W; Domon, Bruno; Hancock, William; He, Fuchu; Hochstrasser, Denis; Marko-Varga, György; Salekdeh, Ghasem Hosseini; Sechi, Salvatore; Snyder, Michael; Srivastava, Sudhir; Uhlén, Mathias; Wu, Cathy H; Yamamoto, Tadashi; Paik, Young-Ki; Omenn, Gilbert S

    2011-07-01

    After the successful completion of the Human Genome Project, the Human Proteome Organization has recently officially launched a global Human Proteome Project (HPP), which is designed to map the entire human protein set. Given the lack of protein-level evidence for about 30% of the estimated 20,300 protein-coding genes, a systematic global effort will be necessary to achieve this goal with respect to protein abundance, distribution, subcellular localization, interaction with other biomolecules, and functions at specific time points. As a general experimental strategy, HPP research groups will use the three working pillars for HPP: mass spectrometry, antibody capture, and bioinformatics tools and knowledge bases. The HPP participants will take advantage of the output and cross-analyses from the ongoing Human Proteome Organization initiatives and a chromosome-centric protein mapping strategy, termed C-HPP, with which many national teams are currently engaged. In addition, numerous biologically driven and disease-oriented projects will be stimulated and facilitated by the HPP. Timely planning with proper governance of HPP will deliver a protein parts list, reagents, and tools for protein studies and analyses, and a stronger basis for personalized medicine. The Human Proteome Organization urges each national research funding agency and the scientific community at large to identify their preferred pathways to participate in aspects of this highly promising project in a HPP consortium of funders and investigators. PMID:21742803

  4. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

    PubMed Central

    Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2015-01-01

    Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. PMID:25158685

  5. The human proteome project: Current state and future direction.

    PubMed

    Legrain, Pierre; Aebersold, Ruedi; Archakov, Alexander; Bairoch, Amos; Bala, Kumar; Beretta, Laura; Bergeron, John; Borchers, Christoph; Corthals, Garry L; Costello, Catherine E; Deutsch, Eric W; Domon, Bruno; Hancock, William; He, Fuchu; Hochstrasser, Denis; Marko-Varga, Gyorgy; Salekdeh, Ghasem Hosseini; Sechi, Salvatore; Snyder, Michael; Srivastava, Sudhir; Uhlen, Mathias; Hu, Cathy H; Yamamoto, Tadashi; Paik, Young-Ki; Omenn, Gilbert S

    2011-04-29

    After successful completion of the Human Genome Project (HGP), HUPO has recently officially launched a global Human Proteome Project (HPP) which is designed to map the entire human protein set. Given the presence of about 30% undisclosed proteins out of 20,300 protein gene products, a systematic global effort is necessary to achieve this goal with respect to protein abundance, distribution, subcellular localization, interaction with other biomolecules, and functions at specific time points. As a general experimental strategy, HPP groups employ the three working pillars for HPP: mass spectrometry, antibody capture, and bioinformatics tools and knowledge base. The HPP participants will take advantage of the output and cross-analyses from the ongoing HUPO initiatives and a chromosome-based protein mapping strategy, termed C-HPP with many national teams currently engaged. In addition, numerous biologically-driven projects will be stimulated and facilitated by the HPP. Timely planning with proper governance of HPP will deliver a protein parts list, reagents and tools for protein studies and analyses, and a stronger basis for personalized medicine. HUPO urges each national research funding agency and the scientific community at large to identify their preferred pathways to participate in aspects of this highly promising project in a HPP consortium of funders and investigators. PMID:21531903

  6. Current application of proteomics in biomarker discovery for inflammatory bowel disease.

    PubMed

    Chan, Patrick Py; Wasinger, Valerie C; Leong, Rupert W

    2016-02-15

    Recently, the field of proteomics has rapidly expanded in its application towards clinical research with objectives ranging from elucidating disease pathogenesis to discovering clinical biomarkers. As proteins govern and/or reflect underlying cellular processes, the study of proteomics provides an attractive avenue for research as it allows for the rapid identification of protein profiles in a biological sample. Inflammatory bowel disease (IBD) encompasses several heterogeneous and chronic conditions of the gastrointestinal tract. Proteomic technology provides a powerful means of addressing major challenges in IBD today, especially for identifying biomarkers to improve its diagnosis and management. This review will examine the current state of IBD proteomics research and its use in biomarker research. Furthermore, we also discuss the challenges of translating proteomic research into clinically relevant tools. The potential application of this growing field is enormous and is likely to provide significant insights towards improving our future understanding and management of IBD. PMID:26909226

  7. Current application of proteomics in biomarker discovery for inflammatory bowel disease

    PubMed Central

    Chan, Patrick PY; Wasinger, Valerie C; Leong, Rupert W

    2016-01-01

    Recently, the field of proteomics has rapidly expanded in its application towards clinical research with objectives ranging from elucidating disease pathogenesis to discovering clinical biomarkers. As proteins govern and/or reflect underlying cellular processes, the study of proteomics provides an attractive avenue for research as it allows for the rapid identification of protein profiles in a biological sample. Inflammatory bowel disease (IBD) encompasses several heterogeneous and chronic conditions of the gastrointestinal tract. Proteomic technology provides a powerful means of addressing major challenges in IBD today, especially for identifying biomarkers to improve its diagnosis and management. This review will examine the current state of IBD proteomics research and its use in biomarker research. Furthermore, we also discuss the challenges of translating proteomic research into clinically relevant tools. The potential application of this growing field is enormous and is likely to provide significant insights towards improving our future understanding and management of IBD. PMID:26909226

  8. Saliva proteome research: current status and future outlook.

    PubMed

    Schulz, Benjamin L; Cooper-White, Justin; Punyadeera, Chamindie K

    2013-09-01

    Human saliva harbours proteins of clinical relevance and about 30% of blood proteins are also present in saliva. This highlights that saliva can be used for clinical applications just as urine or blood. However, the translation of salivary biomarker discoveries into clinical settings is hampered by the dynamics and complexity of the salivary proteome. This review focuses on the current status of technological developments and achievements relating to approaches for unravelling the human salivary proteome. We discuss the dynamics of the salivary proteome, as well as the importance of sample preparation and processing techniques and their influence on downstream protein applications; post-translational modifications of salivary proteome and protein: protein interactions. In addition, we describe possible enrichment strategies for discerning post-translational modifications of salivary proteins, the potential utility of selected-reaction-monitoring techniques for biomarker discovery and validation, limitations to proteomics and the biomarker challenge and future perspectives. In summary, we provide recommendations for practical saliva sampling, processing and storage conditions to increase the quality of future studies in an emerging field of saliva clinical proteomics. We propose that the advent of technologies allowing sensitive and high throughput proteome-wide analyses, coupled to well-controlled study design, will allow saliva to enter clinical practice as an alternative to blood-based methods due to its simplistic nature of sampling, non-invasiveness, easy of collection and multiple collections by untrained professionals and cost-effective advantages. PMID:22612344

  9. Proteomic and other mass spectrometry based "omics" biomarker discovery and validation in pediatric venous thromboembolism and arterial ischemic stroke: current state, unmet needs, and future directions.

    PubMed

    Goldenberg, Neil A; Everett, Allen D; Graham, David; Bernard, Timothy J; Nowak-Göttl, Ulrike

    2014-12-01

    Venous thromboembolism (VTE) and arterial ischemic stroke (AIS) are increasingly-recognized health conditions in children, with both acute and chronic sequelae. Risk factors for, and pathogenesis of, VTE are readily related to three principal factors, consisting of venous stasis, endothelial damage, and the hypercoagulable state (i.e. thrombophilia), termed the triad of Virchow. In children, greater than 90% of VTE are provoked by an overt clinical risk factor, the most common of which is a central venous catheter. Risk factors for childhood-onset (beyond the neonatal period) AIS include sickle cell disease, infection, cerebral arteriopathy, and congenital cardiac disease. In perinatal AIS, risk factors are less well-defined, and have been hypothesized to include maternal-fetal conditions. While some acquired and inherited thrombophilias have been associated with increased risk of incident and/or recurrent VTE and AIS, knowledge of other diagnostic and prognostic biomarkers of VTE/AIS in children remains quite limited. To date, very few published studies have employed plasma mass spectrometry-based "omics" approaches (proteomics, lipidomics or metabolomics). Ongoing and future research efforts involving multicenter prospective study-derived plasma biobanks in pediatric VTE (such as the Kids-DOTT trial) and AIS (including VIPS) along with new multi-omics-compatible sample processing methods offer fertile opportunities for discovery and validation of both novel risk factors and prognostic markers, with great potential to achieve improved prognostic stratification in these diseases. PMID:25379629

  10. Current perspectives in proteomic analysis of abiotic stress in Grapevines

    PubMed Central

    George, Iniga S.; Haynes, Paul A.

    2014-01-01

    Grapes are an important crop plant which forms the basis of a globally important industry. Grape and wine production is particularly vulnerable to environmental and climatic fluctuations, which makes it essential for us to develop a greater understanding of the molecular level responses of grape plants to various abiotic stresses. The completion of the initial grape genome sequence in 2007 has led to a significant increase in research on grapes using proteomics approaches. In this article, we discuss some of the current research on abiotic stress in grapevines, in the context of abiotic stress research in other plant species. We also highlight some of the current limitations in grapevine proteomics and identify areas with promising scope for potential future research. PMID:25538720

  11. Proteome Analysis of Ground State Pluripotency

    PubMed Central

    Taleahmad, Sara; Mirzaei, Mehdi; Parker, Lindsay M.; Hassani, Seyedeh-Nafiseh; Mollamohammadi, Sepideh; Sharifi-Zarchi, Ali; Haynes, Paul A.; Baharvand, Hossein; Salekdeh, Ghasem Hosseini

    2015-01-01

    The differentiation potential of pluripotent embryonic stem cells (ESCs) can be manipulated via serum and medium conditions for direct cellular development or to maintain a naïve ground state. The self-renewal state of ESCs can thus be induced by adding inhibitors of mitogen activated protein kinase (MAPK) and glycogen synthase kinase-3 (Gsk3), known as 2 inhibitors (2i) treatment. We have used a shotgun proteomics approach to investigate differences in protein expressions between 2i- and serum-grown mESCs. The results indicated that 164 proteins were significantly upregulated and 107 proteins downregulated in 2i-grown cells compared to serum. Protein pathways in 2i-grown cells with the highest enrichment were associated with glycolysis and gluconeogenesis. Protein pathways related to organ development were downregulated in 2i-grown cells. In serum-grown ESCs, protein pathways involved in integrin and focal adhesion, and signaling proteins involved in the actin cytoskeleton regulation were enriched. We observed a number of nuclear proteins which were mostly involved in self-renewal maintenance and were expressed at higher levels in 2i compared to serum - Dnmt1, Map2k1, Parp1, Xpo4, Eif3g, Smarca4/Brg1 and Smarcc1/Baf155. Collectively, the results provided an insight into the key protein pathways used by ESCs in the ground state or metastable conditions through 2i or serum culture medium, respectively. PMID:26671762

  12. Asthma and COPD proteomics: current approaches and future directions.

    PubMed

    Terracciano, Rosa; Pelaia, Girolamo; Preianò, Mariaimmacolata; Savino, Rocco

    2015-02-01

    Although asthma and chronic obstructive pulmonary disease COPD represent the two most common chronic respiratory diseases worldwide, the mechanisms underlying their pathobiology need to be further elucidated. Presently, differentiation of asthma and COPD are largely based on clinical and lung function parameters. However, the complexity of these multifactorial diseases may lead to misclassification and to inappropriate management strategies. Recently, tremendous progress in MS has extended the sensitivity, accuracy, and speed of analysis, enabling the identification of thousands of proteins per experiment. Beyond identification, MS has also greatly implemented quantitation issues allowing to assess qualitative-quantitative differences in protein profiles of different samples, in particular diseased versus normal. Herein, we provide a summary of recent proteomics-based investigations in the field of asthma/COPD, highlighting major issues related to sampling and processing procedures for proteomic analyses of specific airway and parenchymal specimens (induced sputum, exhaled breath condensate, epithelial lining fluid, bronchoalveolar and nasal lavage fluid), as well as blood-derived specimen (plasma and serum). Within such a context, together with current difficulties and limitations mainly due to lack of general standardization in preanalytical sampling procedure, our discussion will focus on the challenges and possible benefits of proteomic studies in phenotypic stratification of asthma and COPD. PMID:25504544

  13. Proteomics, biomarkers, and HIV‐1: A current perspective

    PubMed Central

    Donnelly, Maire Rose

    2015-01-01

    Despite more than three decades of extensive research, HIV‐1 infection although well controlled with cART, remains incurable. Multifactorial complexity of the viral life‐cycle poses great challenges in understanding molecular mechanisms underlying this infection and the development of biomarkers, which we hope will lead us to its eradication. For a more in‐depth understanding of how the virus interacts with host target cells, T cells and macrophages, proteomic profiling techniques that offer strategies to investigate the proteome in its entirety were employed. Here, we review proteomic studies related to HIV‐1 infection and discuss perspectives and limitations of proteomic and systems biology approaches in future studies. PMID:26033875

  14. Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein-Profiling Technologies

    PubMed Central

    Bruce, Can; Stone, Kathryn; Gulcicek, Erol; Williams, Kenneth

    2013-01-01

    Mass spectrometry has become a major tool in the study of proteomes. The analysis of proteolytic peptides and their fragment ions by this technique enables the identification and quantitation of the precursor proteins in a mixture. However, deducing chemical structures and then protein sequences from mass-to-charge ratios is a challenging computational task. Software tools incorporating powerful algorithms and statistical methods improved our ability to process the large quantities of proteomics data. Repositories of spectral data make both data analysis and experimental design more efficient. New approaches in quantitative and statistical proteomics make possible a greater coverage of the proteome, the identification of more post-translational modifications and a greater sensitivity in the quantitation of targeted proteins. PMID:23504934

  15. Plant proteomics in India and Nepal: current status and challenges ahead.

    PubMed

    Deswal, Renu; Gupta, Ravi; Dogra, Vivek; Singh, Raksha; Abat, Jasmeet Kaur; Sarkar, Abhijit; Mishra, Yogesh; Rai, Vandana; Sreenivasulu, Yelam; Amalraj, Ramesh Sundar; Raorane, Manish; Chaudhary, Ram Prasad; Kohli, Ajay; Giri, Ashok Prabhakar; Chakraborty, Niranjan; Zargar, Sajad Majeed; Agrawal, Vishwanath Prasad; Agrawal, Ganesh Kumar; Job, Dominique; Renaut, Jenny; Rakwal, Randeep

    2013-10-01

    Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications. PMID:24431515

  16. Current strategies and findings in clinically relevant post-translational modification-specific proteomics

    PubMed Central

    Pagel, Oliver; Loroch, Stefan; Sickmann, Albert; Zahedi, René P

    2015-01-01

    Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical samples, often limited in sample amount. Thus, quantitative proteomics holds a great potential to discover, validate and accurately quantify biomarkers in body fluids and primary tissues. A major effort will be to improve the complete integration of robust but sensitive proteomics technology to clinical environments. Here, we discuss PTMs that are relevant for clinical research, with a focus on phosphorylation, glycosylation and proteolytic cleavage; furthermore, we give an overview on the current developments and novel findings in mass spectrometry-based PTM research. PMID:25955281

  17. Current Status of Proteomic Studies on Defense Responses in Rice.

    PubMed

    Chen, Xifeng; Bhadauria, Vijai; Ma, Bojun

    2016-01-01

    Biotic stresses are constraints to plant growth and development negatively impacting crop production. To counter such stresses, plants have developed stress-specific adaptations as well as simultaneous responses. The efficacy and magnitude of inducible adaptive responses are dependent on activation of signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification of proteins associated with defense mechanisms. Proteomics plays an important role in elucidating plant defense mechanisms by mining the differential regulation of proteins to various biotic stresses. Rice, one of the most widely cultivated food crops in world, is constantly challenged by a variety of biotic stresses, and high-throughput proteomics approaches have been employed to unravel the molecular mechanism of the biotic stresses-response in rice. In this review, we summarize the latest advances of proteomic studies on defense responses and discuss the potential relevance of the proteins identified by proteomic means in rice defense mechanism. Furthermore, we provide perspective for proteomics in unraveling the molecular mechanism of rice immunity. PMID:26364119

  18. Current Approaches on Viral Infection: Proteomics and Functional Validations

    PubMed Central

    Zheng, Jie; Tan, Boon Huan; Sugrue, Richard; Tang, Kai

    2012-01-01

    Viruses could manipulate cellular machinery to ensure their continuous survival and thus become parasites of living organisms. Delineation of sophisticated host responses upon virus infection is a challenging task. It lies in identifying the repertoire of host factors actively involved in the viral infectious cycle and characterizing host responses qualitatively and quantitatively during viral pathogenesis. Mass spectrometry based proteomics could be used to efficiently study pathogen-host interactions and virus-hijacked cellular signaling pathways. Moreover, direct host and viral responses upon infection could be further investigated by activity-based functional validation studies. These approaches involve drug inhibition of secretory pathway, immunofluorescence staining, dominant negative mutant of protein target, real-time PCR, small interfering siRNA-mediated knockdown, and molecular cloning studies. In this way, functional validation could gain novel insights into the high-content proteomic dataset in an unbiased and comprehensive way. PMID:23162545

  19. Proteomic evaluation of genetically modified crops: current status and challenges.

    PubMed

    Gong, Chun Yan; Wang, Tai

    2013-01-01

    Hectares of genetically modified (GM) crops have increased exponentially since 1996, when such crops began to be commercialized. GM biotechnology, together with conventional breeding, has become the main approach to improving agronomic traits of crops. However, people are concerned about the safety of GM crops, especially GM-derived food and feed. Many efforts have been made to evaluate the unintended effects caused by the introduction of exogenous genes. "Omics" techniques have advantages over targeted analysis in evaluating such crops because of their use of high-throughput screening. Proteins are key players in gene function and are directly involved in metabolism and cellular development or have roles as toxins, antinutrients, or allergens, which are essential for human health. Thus, proteomics can be expected to become one of the most useful tools in safety assessment. This review assesses the potential of proteomics in evaluating various GM crops. We further describe the challenges in ensuring homogeneity and sensitivity in detection techniques. PMID:23471542

  20. Proteomic indicators of oxidation and hydration state in colorectal cancer

    PubMed Central

    2016-01-01

    New integrative approaches are needed to harness the potential of rapidly growing datasets of protein expression and microbial community composition in colorectal cancer. Chemical and thermodynamic models offer theoretical tools to describe populations of biomacromolecules and their relative potential for formation in different microenvironmental conditions. The average oxidation state of carbon (ZC) can be calculated as an elemental ratio from the chemical formulas of proteins, and water demand per residue (\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${\\overline{n}}_{{\\mathrm{H}}_{2}\\mathrm{O}}$\\end{document}n¯H2O) is computed by writing the overall formation reactions of proteins from basis species. Using results reported in proteomic studies of clinical samples, many datasets exhibit higher mean ZC or \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${\\overline{n}}_{{\\mathrm{H}}_{2}\\mathrm{O}}$\\end{document}n¯H2O of proteins in carcinoma or adenoma compared to normal tissue. In contrast, average protein compositions in bacterial genomes often have lower ZC for bacteria enriched in fecal samples from cancer patients compared to healthy donors. In thermodynamic calculations, the potential for formation of the cancer-related proteins is energetically favored by changes in the chemical activity of H2O and fugacity of O2 that reflect the compositional differences. The compositional analysis suggests that a systematic change in chemical composition is an essential feature of cancer proteomes, and the thermodynamic descriptions show that the observed proteomic

  1. Proteomic evaluation of genetically modified crops: current status and challenges

    PubMed Central

    Gong, Chun Yan; Wang, Tai

    2013-01-01

    Hectares of genetically modified (GM) crops have increased exponentially since 1996, when such crops began to be commercialized. GM biotechnology, together with conventional breeding, has become the main approach to improving agronomic traits of crops. However, people are concerned about the safety of GM crops, especially GM-derived food and feed. Many efforts have been made to evaluate the unintended effects caused by the introduction of exogenous genes. “Omics” techniques have advantages over targeted analysis in evaluating such crops because of their use of high-throughput screening. Proteins are key players in gene function and are directly involved in metabolism and cellular development or have roles as toxins, antinutrients, or allergens, which are essential for human health. Thus, proteomics can be expected to become one of the most useful tools in safety assessment. This review assesses the potential of proteomics in evaluating various GM crops. We further describe the challenges in ensuring homogeneity and sensitivity in detection techniques. PMID:23471542

  2. Challenges, current status and future perspectives of proteomics in improving understanding, diagnosis and treatment of vascular disease

    PubMed Central

    Moxon, Joseph V.; Padula, Matthew P.; Herbert, Ben R.; Golledge, Jonathan

    2009-01-01

    Technical advances have seen the rapid adoption of genomics and multiplex genetic polymorphism identification to research on vascular diseases. The utilization of proteomics for the study of vascular diseases has been limited by comparison. In this review we outline currently available proteomics techniques, the challenges to using these approaches and modifications which may improve the utilization of proteomics in the study of vascular diseases. PMID:19541510

  3. Multiplexed immunofluorescence delineates proteomic cancer cell states associated with metabolism

    PubMed Central

    Sood, Anup; Miller, Alexandra M.; Brogi, Edi; Sui, Yunxia; Armenia, Joshua; McDonough, Elizabeth; Santamaria-Pang, Alberto; Carlin, Sean; Stamper, Aleksandra; Campos, Carl; Pang, Zhengyu; Li, Qing; Port, Elisa; Graeber, Thomas G.; Schultz, Nikolaus; Ginty, Fiona; Larson, Steven M.; Mellinghoff, Ingo K.

    2016-01-01

    The phenotypic diversity of cancer results from genetic and nongenetic factors. Most studies of cancer heterogeneity have focused on DNA alterations, as technologies for proteomic measurements in clinical specimen are currently less advanced. Here, we used a multiplexed immunofluorescence staining platform to measure the expression of 27 proteins at the single-cell level in formalin-fixed and paraffin-embedded samples from treatment-naive stage II/III human breast cancer. Unsupervised clustering of protein expression data from 638,577 tumor cells in 26 breast cancers identified 8 clusters of protein coexpression. In about one-third of breast cancers, over 95% of all neoplastic cells expressed a single protein coexpression cluster. The remaining tumors harbored tumor cells representing multiple protein coexpression clusters, either in a regional distribution or intermingled throughout the tumor. Tumor uptake of the radiotracer 18F-fluorodeoxyglucose was associated with protein expression clusters characterized by hormone receptor loss, PTEN alteration, and HER2 gene amplification. Our study demonstrates an approach to generate cellular heterogeneity metrics in routinely collected solid tumor specimens and integrate them with in vivo cancer phenotypes. PMID:27182557

  4. Designing biomedical proteomics experiments: state-of-the-art and future perspectives.

    PubMed

    Maes, Evelyne; Kelchtermans, Pieter; Bittremieux, Wout; De Grave, Kurt; Degroeve, Sven; Hooyberghs, Jef; Mertens, Inge; Baggerman, Geert; Ramon, Jan; Laukens, Kris; Martens, Lennart; Valkenborg, Dirk

    2016-05-01

    With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters. PMID:27031651

  5. Proteomics of boar seminal plasma - current studies and possibility of their application in biotechnology of animal reproduction.

    PubMed

    Strzeżek, Jerzy; Wysocki, Paweł; Kordan, Władysław; Kuklińska, Magdalena; Mogielnicka, Marzena; Soliwoda, Daniel; Fraser, Leyland

    2005-11-01

    Proteomics is critical to identify the properties and functions of proteins involved in the mechanism regulating the male reproductive tract function. This approach is important in male fertility assessment and clinical diagnosis of the physiological state of individual reproductive organs. Proteomics also provides a tool to understand the interactions of seminal plasma proteins with spermatozoa, which could provide a useful model for studying ligand-cell interaction occurring at the sperm cell surface. This review covers a selection of advances in the realm of functional proteomics of boar seminal plasma proteins and is focused on some fundamental proteomic technologies. Also, this review explores key themes in proteomics and their application in animal reproductive techniques. PMID:16372045

  6. Covering complete proteomes with X-ray structures: a current snapshot

    SciTech Connect

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-11-01

    The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  7. Cerebrospinal fluid proteomics and protein biomarkers in frontotemporal lobar degeneration: Current status and future perspectives.

    PubMed

    Oeckl, Patrick; Steinacker, Petra; Feneberg, Emily; Otto, Markus

    2015-07-01

    Frontotemporal lobar degeneration (FTLD) comprises a spectrum of rare neurodegenerative diseases with an estimated prevalence of 15-22 cases per 100,000 persons including the behavioral variant of frontotemporal dementia (bvFTD), progressive non-fluent aphasia (PNFA), semantic dementia (SD), FTD with motor neuron disease (FTD-MND), progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS). The pathogenesis of the diseases is still unclear and clinical diagnosis of FTLD is hampered by overlapping symptoms within the FTLD subtypes and with other neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Intracellular protein aggregates in the brain are a major hallmark of FTLD and implicate alterations in protein metabolism or function in the disease's pathogenesis. Cerebrospinal fluid (CSF) which surrounds the brain can be used to study changes in neurodegenerative diseases and to identify disease-related mechanisms or neurochemical biomarkers for diagnosis. In the present review, we will give an overview of the current literature on proteomic studies in CSF of FTLD patients. Reports of targeted and unbiased proteomic approaches are included and the results are discussed in regard of their informative value about disease pathology and the suitability to be used as diagnostic biomarkers. Finally, we will give some future perspectives on CSF proteomics and a list of candidate biomarkers which might be interesting for validation in further studies. This article is part of a Special Issue entitled: Neuroproteomics: Applications in neuroscience and neurology. PMID:25526887

  8. Covering complete proteomes with X-ray structures: A current snapshot

    SciTech Connect

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  9. Covering complete proteomes with X-ray structures: A current snapshot

    DOE PAGESBeta

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore » through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

  10. Steady State Tokamak Equilibria without Current Drive

    SciTech Connect

    Shaing, K.C.; Aydemir, A.Y.; Lin-Liu, Y.R.; Miller, R.L.

    1997-11-01

    Steady state tokamak equilibria without current drive are found. This is made possible by including the potato bootstrap current close to the magnetic axis. Tokamaks with this class of equilibria do not need seed current or current drive, and are intrinsically steady state. {copyright} {ital 1997} {ital The American Physical Society}

  11. GENOMIC AND PROTEOMIC ANALYSIS OF SURROGATE TISSUES FOR ASSESSING TOXIC EXPOSURES AND DISEASE STATES

    EPA Science Inventory

    Genomic and Proteomic Analysis of Surrogate Tissues for Assessing Toxic Exposures and Disease States
    David J. Dix and John C. Rockett
    Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, USEPA, ...

  12. Solid-state current transformer

    NASA Technical Reports Server (NTRS)

    Farnsworth, D. L. (Inventor)

    1976-01-01

    A signal transformation network which is uniquely characterized to exhibit a very low input impedance while maintaining a linear transfer characteristic when driven from a voltage source and when quiescently biased in the low microampere current range is described. In its simplest form, it consists of a tightly coupled two transistor network in which a common emitter input stage is interconnected directly with an emitter follower stage to provide virtually 100 percent negative feedback to the base input of the common emitter stage. Bias to the network is supplied via the common tie point of the common emitter stage collector terminal and the emitter follower base stage terminal by a regulated constant current source, and the output of the circuit is taken from the collector of the emitter follower stage.

  13. Solid state electrochemical current source

    DOEpatents

    Potanin, Alexander Arkadyevich; Vedeneev, Nikolai Ivanovich

    2002-04-30

    A cathode and a solid state electrochemical cell comprising said cathode, a solid anode and solid fluoride ion conducting electrolyte. The cathode comprises a metal oxide and a compound fluoride containing at least two metals with different valences. Representative compound fluorides include solid solutions of bismuth fluoride and potassium fluoride; and lead fluoride and potassium fluoride. Representative metal oxides include copper oxide, lead oxide, manganese oxide, vanadium oxide and silver oxide.

  14. Rosacea: current state of epidemiology.

    PubMed

    Tan, Jerry; Berg, Mats

    2013-12-01

    Case definitions are critical in epidemiologic research. However, modern disease indicators must now consider complex data from gene-based research along with traditional clinical parameters. Rosacea is a skin disorder with multiple signs and symptoms. In individuals, these features may be multiple or one may predominate. While studies on the epidemiology of rosacea have previously been sparse, there has been a recent increase in research activity. A broader body of epidemiological information that includes a greater variety of countries beyond Northern Europe and general population-based demographics is needed. As there are operational issues in current case definitions of rosacea subtypes--rationalization and standardization--universal consistent applications in future research is also imperative. Further improvement in disease definition combining new research information along with clinical pragmatism should increase the accuracy of rosacea case ascertainment and facilitate further epidemiological research. PMID:24229634

  15. Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state.

    PubMed

    Schokraie, Elham; Warnken, Uwe; Hotz-Wagenblatt, Agnes; Grohme, Markus A; Hengherr, Steffen; Förster, Frank; Schill, Ralph O; Frohme, Marcus; Dandekar, Thomas; Schnölzer, Martina

    2012-01-01

    Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state. PMID:23029181

  16. Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state

    PubMed Central

    Schokraie, Elham; Warnken, Uwe; Hotz-Wagenblatt, Agnes; Grohme, Markus A.; Hengherr, Steffen; Förster, Frank; Schill, Ralph O.; Frohme, Marcus; Dandekar, Thomas; Schnölzer, Martina

    2012-01-01

    Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state. PMID:23029181

  17. Large-Scale, Ion-Current-Based Proteomic Investigation of the Rat Striatal Proteome in a Model of Short- and Long-Term Cocaine Withdrawal.

    PubMed

    Shen, Shichen; Jiang, Xiaosheng; Li, Jun; Straubinger, Robert M; Suarez, Mauricio; Tu, Chengjian; Duan, Xiaotao; Thompson, Alexis C; Qu, Jun

    2016-05-01

    Given the tremendous detriments of cocaine dependence, effective diagnosis and patient stratification are critical for successful intervention yet difficult to achieve due to the largely unknown molecular mechanisms involved. To obtain new insights into cocaine dependence and withdrawal, we employed a reproducible, reliable, and large-scale proteomics approach to investigate the striatal proteomes of rats (n = 40, 10 per group) subjected to chronic cocaine exposure, followed by either short- (WD1) or long- (WD22) term withdrawal. By implementing a surfactant-aided precipitation/on-pellet digestion procedure, a reproducible and sensitive nanoLC-Orbitrap MS analysis, and an optimized ion-current-based MS1 quantification pipeline, >2000 nonredundant proteins were quantified confidently without missing data in any replicate. Although cocaine was cleared from the body, 129/37 altered proteins were observed in WD1/WD22 that are implicated in several biological processes related closely to drug-induced neuroplasticity. Although many of these changes recapitulate the findings from independent studies reported over the last two decades, some novel insights were obtained and further validated by immunoassays. For example, significantly elevated striatal protein kinase C activity persisted over the 22 day cocaine withdrawal. Cofilin-1 activity was up-regulated in WD1 and down-regulated in WD22. These discoveries suggest potentially distinct structural plasticity after short- and long-term cocaine withdrawal. In addition, this study provides compelling evidence that blood vessel narrowing, a long-known effect of cocaine use, occurred after long-term but not short-term withdrawal. In summary, this work developed a well-optimized paradigm for ion-current-based quantitative proteomics in brain tissues and obtained novel insights into molecular alterations in the striatum following cocaine exposure and withdrawal. PMID:27018876

  18. Nanoscaled Proteomic Analysis

    NASA Astrophysics Data System (ADS)

    Xu, Yan; Jia, Lee

    2013-09-01

    Global proteomics research is currently hampered by the extremely complexity of the proteome and the absence of techniques like the polymerase chain reaction in genomics which enables multiplication of a single protein molecule. Since all the existing analytical technologies cannot overcome the detection limit and the dynamic concentration barrier, development of improved analytical technologies at nanoscale, ideally those that could recognize single protein molecule in the presence of high abundant of others, is a high priority for proteomics. In this chapter, we will show the state-of-the-art of nanoproteomics, i.e., the application of nanotechnologies to proteomics. Various nanomaterials including carbon nanomaterials, magnetic nanoparticles, silica nanoparticles, polymer and copolymer nanoparticles, metal and metal oxide nanoparticles have been used to improve sensitivity, specificity, and repeatability of proteomic analysis especially when the multidimensional separation system coupled with MALDI-TOF-MS is used. Among them, gold nanoparticles (GNPs) and carbon nanotubes (CNTs) are the two most important nanomaterials: while GNPs are frequently utilized for enzyme immobilization, high throughput bioassay, selection of target-peptides and target-protein, CNTs including single-walled carbon nanotubes (SWCNTs) and mutiple-walled carbon nanotubes (MWCNTs) have wide applications to electronic sensor, sensitive immunodetection, nanobiocatalysis, affinity probes, MALDI matrices, protein digestion, peptides enrichment and analysis. In perspectives, a deep understanding of the structures and property of nanomaterials and interdisciplinary applications of nanotechnology to proteomics will certainly be revolutionary and intellectually rewarding.

  19. Protein lysine acetylation in bacteria: Current state of the art.

    PubMed

    Ouidir, Tassadit; Kentache, Takfarinas; Hardouin, Julie

    2016-01-01

    Post-translational modifications of proteins are key events in cellular metabolism and physiology regulation. Lysine acetylation is one of the best studied protein modifications in eukaryotes, but, until recently, ignored in bacteria. However, proteomic advances have highlighted the diversity of bacterial lysine-acetylated proteins. The current data support the implication of lysine acetylation in various metabolic pathways, adaptation and virulence. In this review, we present a broad overview of the current knowledge of lysine acetylation in bacteria. We emphasize particularly the significant contribution of proteomics in this field. PMID:26390373

  20. The Discovery of Novel Genomic, Transcriptomic, and Proteomic Biomarkers in Cardiovascular and Peripheral Vascular Disease: The State of the Art

    PubMed Central

    de Franciscis, Stefano; Metzinger, Laurent; Serra, Raffaele

    2016-01-01

    Cardiovascular disease (CD) and peripheral vascular disease (PVD) are leading causes of mortality and morbidity in western countries and also responsible of a huge burden in terms of disability, functional decline, and healthcare costs. Biomarkers are measurable biological elements that reflect particular physiological or pathological states or predisposition towards diseases and they are currently widely studied in medicine and especially in CD. In this context, biomarkers can also be used to assess the severity or the evolution of several diseases, as well as the effectiveness of particular therapies. Genomics, transcriptomics, and proteomics have opened new windows on disease phenomena and may permit in the next future an effective development of novel diagnostic and prognostic medicine in order to better prevent or treat CD. This review will consider the current evidence of novel biomarkers with clear implications in the improvement of risk assessment, prevention strategies, and medical decision making in the field of CD. PMID:27298828

  1. Proteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling

    PubMed Central

    Maiguel, Dony; Faridi, Mohd Hafeez; Barth, Constantinos J.; Salem, Saeed M.; Singhal, Mudita; Stoub, Darren; Krastins, Bryan; Ogihara, Mitsunori; Zaki, Mohammed J.; Gupta, Vineet

    2009-01-01

    During atherogenesis and vascular inflammation quiescent platelets are activated to increase the surface expression and ligand affinity of the integrin αIIbβ3 via inside-out signaling. Diverse signals such as thrombin, ADP and epinephrine transduce signals through their respective GPCRs to activate protein kinases that ultimately lead to the phosphorylation of the cytoplasmic tail of the integrin αIIbβ3 and augment its function. The signaling pathways that transmit signals from the GPCR to the cytosolic domain of the integrin are not well defined. In an effort to better understand these pathways, we employed a combination of proteomic profiling and computational analyses of isolated human platelets. We analyzed ten independent human samples and identified a total of 1507 unique proteins in platelets. This is the most comprehensive platelet proteome assembled to date and includes 190 membrane-associated and 262 phosphorylated proteins, which were identified via independent proteomic and phospho-proteomic profiling. We used this proteomic dataset to create a platelet protein-protein interaction (PPI) network and applied novel contextual information about the phosphorylation step to introduce limited directionality in the PPI graph. This newly developed contextual PPI network computationally recapitulated an integrin signaling pathway. Most importantly, our approach not only provided insights into the mechanism of integrin αIIbβ3 activation in resting platelets but also provides an improved model for analysis and discovery of PPI dynamics and signaling pathways in the future. PMID:19859549

  2. Current Progress in Tonoplast Proteomics Reveals Insights into the Function of the Large Central Vacuole

    PubMed Central

    Trentmann, Oliver; Haferkamp, Ilka

    2013-01-01

    Vacuoles of plants fulfill various biologically important functions, like turgor generation and maintenance, detoxification, solute sequestration, or protein storage. Different types of plant vacuoles (lytic versus protein storage) are characterized by different functional properties apparently caused by a different composition/abundance and regulation of transport proteins in the surrounding membrane, the tonoplast. Proteome analyses allow the identification of vacuolar proteins and provide an informative basis for assigning observed transport processes to specific carriers or channels. This review summarizes techniques required for vacuolar proteome analyses, like e.g., isolation of the large central vacuole or tonoplast membrane purification. Moreover, an overview about diverse published vacuolar proteome studies is provided. It becomes evident that qualitative proteomes from different plant species represent just the tip of the iceberg. During the past few years, mass spectrometry achieved immense improvement concerning its accuracy, sensitivity, and application. As a consequence, modern tonoplast proteome approaches are suited for detecting alterations in membrane protein abundance in response to changing environmental/physiological conditions and help to clarify the regulation of tonoplast transport processes. PMID:23459586

  3. Solid state recording current meter conversion

    USGS Publications Warehouse

    Cheng, Ralph T.; Wang, Lichen

    1985-01-01

    The authors describe the conversion of an Endeco-174 current meter to a solid-state recording current meter. A removable solid-state module was designed to fit in the space originally occupied by an 8-track tape cartridge. The module contains a CPU and 128 kilobytes of nonvolatile CMOS memory. The solid-state module communicates with any terminal or computer using an RS-232C interface at 4800 baud rate. A primary consideration for conversion was to keep modifications of the current meter to a minimum. The communication protocol was designed to emulate the Endeco tape translation unit, thus the need for a translation unit was eliminated and the original data reduction programs can be used without any modification. After conversion, the data recording section of the current meter contains no moving parts; the storage capacity of the module is equivalent to that of the original tape cartridge.

  4. The audacity of proteomics: a chance to overcome current challenges in schizophrenia research.

    PubMed

    Baloyianni, Nicoletta; Tsangaris, George Th

    2009-12-01

    The evidence on the mechanisms underlying schizophrenia seems to support a series of divergent possibilities that may play a contributory role in the disease pathogenesis. Hypotheses regarding disease mechanisms range from structural and neurodevelopmental abnormalities to neurotransmitter deficits and genetic predisposition. Nevertheless, little progress has been made in the field of schizophrenia with respect to the key pathophysiological processes, and this is a fundamental barrier to identifying or predicting the therapeutic value of novel drug targets. All multi-omics approaches, including proteomics, would be perfectly suited to such a complex disease as a means of tackling the widening chasm between the aforementioned hypotheses. Proteomic studies have been performed in a variety of tissues and biological fluids, from post-mortem CNS tissue to cerebrospinal fluid and blood, and in recently generated mutant animal models with schizophrenia-like phenotypes. In this review, we present an overview of several proteomic studies in the field of schizophrenia research and discuss how proteomics could assist with identifying schizophrenia markers more efficiently, covering both clinical and basic research. PMID:19929611

  5. Deep Imaging: How Much of the Proteome Does Current Top-Down Technology Already Resolve?

    PubMed Central

    Wright, Elise P.; Prasad, Kali A. G.; Padula, Matthew P.; Coorssen, Jens R.

    2014-01-01

    Effective proteome analyses are based on interplay between resolution and detection. It had been claimed that resolution was the main factor limiting the use of two-dimensional gel electrophoresis. Improved protein detection now indicates that this is unlikely to be the case. Using a highly refined protocol, the rat brain proteome was extracted, resolved, and detected. In order to overcome the stain saturation threshold, high abundance protein species were excised from the gel following standard imaging. Gels were then imaged again using longer exposure times, enabling detection of lower abundance, less intensely stained protein species. This resulted in a significant enhancement in the detection of resolved proteins, and a slightly modified digestion protocol enabled effective identification by standard mass spectrometric methods. The data indicate that the resolution required for comprehensive proteome analyses is already available, can assess multiple samples in parallel, and preserve critical information concerning post-translational modifications. Further optimization of staining and detection methods promises additional improvements to this economical, widely accessible and effective top-down approach to proteome analysis. PMID:24489691

  6. Progress in Mining the Human Proteome for Disease Applications

    PubMed Central

    2011-01-01

    Abstract Currently available technologies allow in-depth analysis of multiple facets of the proteome that have clinical relevance and that complement current genomics-based approaches. Although some progress has been made in our knowledge of the human proteome in health and in disease, there is an urgent need to chart a coherent road map with clearly defined milestones to guide proteomics efforts. Areas of emphasis include: (1) building resources, (2) filling gaps in our understanding of biological variation, and (3) systematically characterizing proteome alterations that occur in well-defined disease states, all of which require an organized and collaborative effort. PMID:21375461

  7. Proteome turnover in bacteria: current status for Corynebacterium glutamicum and related bacteria

    PubMed Central

    Trötschel, Christian; Albaum, Stefan P; Poetsch, Ansgar

    2013-01-01

    With the advent of high-resolution mass spectrometry together with sophisticated data analysis and interpretation algorithms, determination of protein synthesis and degradation rates (i.e. protein turnover) on a proteome-wide scale by employing stable isotope-labelled amino acids has become feasible. These dynamic data provide a deeper understanding of protein homeostasis and stress response mechanisms in microorganisms than well-established ‘steady state’ proteomics approaches. In this article, we summarize the technological challenges and solutions both on the biochemistry/mass spectrometry and bioinformatics level for turnover proteomics with a focus on chromatographic techniques. Although the number of available case studies for Corynebacterium glutamicum and related actinobacteria is still very limited, our review illustrates the potential of protein turnover studies for an improved understanding of questions in the area of biotechnology and biomedicine. Here, new insights from investigations of growth phase transition and different stress dynamics including iron, acid and heat stress for pathogenic but also for industrial actinobacteria are presented. Finally, we will comment on the advantages of integrated software solutions for biologists and briefly discuss the remaining technical challenges and upcoming possibilities for protein turnover analysis. PMID:23425033

  8. Colonization State Influences the Hemocyte Proteome in a Beneficial Squid–Vibrio Symbiosis*

    PubMed Central

    Schleicher, Tyler R.; VerBerkmoes, Nathan C.; Shah, Manesh; Nyholm, Spencer V.

    2014-01-01

    The squid Euprymna scolopes and the luminescent bacterium Vibrio fischeri form a highly specific beneficial light organ symbiosis. Not only does the host have to select V. fischeri from the environment, but it must also prevent subsequent colonization by non-symbiotic microorganisms. Host macrophage-like hemocytes are believed to play a role in mediating the symbiosis with V. fischeri. Previous studies have shown that the colonization state of the light organ influences the host's hemocyte response to the symbiont. To further understand the molecular mechanisms behind this process, we used two quantitative mass-spectrometry-based proteomic techniques, isobaric tags for relative and absolute quantification (iTRAQ) and label-free spectral counting, to compare and quantify the adult hemocyte proteomes from colonized (sym) and uncolonized (antibiotic-treated/cured) squid. Overall, iTRAQ allowed for the quantification of 1,024 proteins with two or more peptides. Thirty-seven unique proteins were determined to be significantly different between sym and cured hemocytes (p value < 0.05), with 20 more abundant proteins and 17 less abundant in sym hemocytes. The label-free approach resulted in 1,241 proteins that were identified in all replicates. Of 185 unique proteins present at significantly different amounts in sym hemocytes (as determined by spectral counting), 92 were more abundant and 93 were less abundant. Comparisons between iTRAQ and spectral counting revealed that 30 of the 37 proteins quantified via iTRAQ exhibited trends similar to those identified by the label-free method. Both proteomic techniques mutually identified 16 proteins that were significantly different between the two groups of hemocytes (p value < 0.05). The presence of V. fischeri in the host light organ influenced the abundance of proteins associated with the cytoskeleton, adhesion, lysosomes, proteolysis, and the innate immune response. These data provide evidence that colonization by V. fischeri

  9. Molecular chaperones: guardians of the proteome in normal and disease states

    PubMed Central

    Jeng, Wilson; Lee, Sukyeong; Sung, Nuri; Lee, Jungsoon; Tsai, Francis T.F.

    2015-01-01

    Proteins must adopt a defined three-dimensional structure in order to gain functional activity, or must they? An ever-increasing number of intrinsically disordered proteins and amyloid-forming polypeptides challenge this dogma. While molecular chaperones and proteases are traditionally associated with protein quality control inside the cell, it is now apparent that molecular chaperones not only promote protein folding in the “forward” direction by facilitating folding and preventing misfolding and aggregation, but also facilitate protein unfolding and even disaggregation resulting in the recovery of functional protein from aggregates. Here, we review our current understanding of ATP-dependent molecular chaperones that harness the energy of ATP binding and hydrolysis to fuel their chaperone functions. An emerging theme is that most of these chaperones do not work alone, but instead function together with other chaperone systems to maintain the proteome. Hence, molecular chaperones are the major component of the proteostasis network that guards and protects the proteome from damage. Furthermore, while a decline of this network is detrimental to cell and organismal health, a controlled perturbation of the proteostasis network may offer new therapeutic avenues against human diseases. PMID:26918154

  10. Proteome Analysis of Rat Hippocampus Following Morphine-induced Amnesia and State-dependent Learning

    PubMed Central

    Jafarinejad-Farsangi, Saeideh; Farazmand, Ali; Rezayof, Ameneh; Darbandi, Niloufar

    2015-01-01

    Morphine’s effects on learning and memory processes are well known to depend on synaptic plasticity in the hippocampus. Whereas the role of the hippocampus in morphine-induced amnesia and state-dependent learning is established, the biochemical and molecular mechanisms underlying these processes are poorly understood. The present study intended to investigate whether administration of morphine can change the expression level of rat hippocampal proteins during learning of a passive avoidance task. A step-through type passive avoidance task was used for the assessment of memory retention. To identify the complex pattern of protein expression induced by morphine, we compared rat hippocampal proteome either in morphine-induced amnesia or in state-dependent learning by two-dimensional gel electerophoresis and combined mass spectrometry (MS and MS/MS). Post-training administration of morphine decreased step-through latency. Pre-test administration of morphine induced state-dependent retrieval of the memory acquired under post-training morphine influence. In the hippocampus, a total of 18 proteins were identified whose MASCOT (Modular Approach to Software Construction Operation and Test) scores were inside 95% confidence level. Of these, five hippocampal proteins altered in morphine-induced amnesia and ten proteins were found to change in the hippocampus of animals that had received post-training and pre-test morphine. These proteins show known functions in cytoskeletal architecture, cell metabolism, neurotransmitter secretion and neuroprotection. The findings indicate that the effect of morphine on memory formation in passive avoidance learning has a morphological correlate on the hippocampal proteome level. In addition, our proteomicscreensuggests that morphine induces memory impairment and state-dependent learning through modulating neuronal plasticity. PMID:25901168

  11. [Current state of competence assessment in nursing].

    PubMed

    Darmann-Finck, Ingrid; Reuschenbach, Bernd

    2013-01-01

    Competency measurement is central to the optimisation of outcome oriented educational processes in nursing, similar to the concept of evidence based practice. The classification of measurement tools provides the basis for describing the current state of research and development in relation to competence measurement in nursing science, and any gaps are identified. The article concludes with questioning the importance of outcome oriented quality orientation in order to achieve an increase in quality during training. Further methodological developments and qualitative studies are needed to examine the context specific processes of interaction and learning, beyond competence diagnostics. PMID:23415340

  12. Affinity Proteomics in the mountains: Alpbach 2015.

    PubMed

    Taussig, Michael J

    2016-09-25

    The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167

  13. The Role of Proteomics in the Diagnosis and Treatment of Women's Cancers: Current Trends in Technology and Future Opportunities

    PubMed Central

    Breuer, Eun-Kyoung Yim; Murph, Mandi M.

    2011-01-01

    Technological and scientific innovations over the last decade have greatly contributed to improved diagnostics, predictive models, and prognosis among cancers affecting women. In fact, an explosion of information in these areas has almost assured future generations that outcomes in cancer will continue to improve. Herein we discuss the current status of breast, cervical, and ovarian cancers as it relates to screening, disease diagnosis, and treatment options. Among the differences in these cancers, it is striking that breast cancer has multiple predictive tests based upon tumor biomarkers and sophisticated, individualized options for prescription therapeutics while ovarian cancer lacks these tools. In addition, cervical cancer leads the way in innovative, cancer-preventative vaccines and multiple screening options to prevent disease progression. For each of these malignancies, emerging proteomic technologies based upon mass spectrometry, stable isotope labeling with amino acids, high-throughput ELISA, tissue or protein microarray techniques, and click chemistry in the pursuit of activity-based profiling can pioneer the next generation of discovery. We will discuss six of the latest techniques to understand proteomics in cancer and highlight research utilizing these techniques with the goal of improvement in the management of women's cancers. PMID:21886869

  14. [Male contraception - the current state of knowledge].

    PubMed

    Zdrojewicz, Zygmynt; Kasperska, Karolina; Lewandowska, Marta

    2016-08-01

    Contraception is important from a health, psychological and socioeconomic point of view. Due to the fact that male-based contraceptive methods are mostly represented by condoms and vasectomy, researchers are working on the new solutions, which could let the men be more involved in a conscious family planning. In this review we will present the current state of knowledge on this subject. There is a lot going on in the field of hormonal contraception. Studies including testosterone, progestins, synthetic androgens and other derivatives are on a different stages of clinical trials and mostly demonstrate high efficacy rates. Recent discovers of Izumo and Juno proteins, essential for the fertilization process, give hope for an easily reversible, non-hormonal method. Researchers are also trying to interfere with the process of spermatogenesis using BRDT inhibitor - JQ1, or neutralize the sperm by injecting styrene maleic anhydride (SMA) into the lumen of the vas deferens. The other studies explore processes involved in proper sperm motility. A vaccine which induces an immune response to the reproductive system is also an interesting method. The latest research use ultrasound waves and mechanical device which blocks the patency of vas deferens. The aim of the study current state of knowledge male contraception. PMID:27591451

  15. [Male contraception - the current state of knowledge].

    PubMed

    Zdrojewicz, Zygmynt; Kasperska, Karolina; Lewandowska, Marta

    2016-07-01

    Contraception is important from a health, psychological and socioeconomic point of view. Due to the fact that male-based contraceptive methods are mostly represented by condoms and vasectomy, researchers are working on the new solutions, which could let the men be more involved in a conscious family planning. In this review we will present the current state of knowledge on this subject. There is a lot going on in the field of hormonal contraception. Studies including testosterone, progestins, synthetic androgens and other derivatives are on a different stages of clinical trials and mostly demonstrate high efficacy rates. Recent discovers of Izumo and Juno proteins, essential for the fertilization process, give hope for an easily reversible, non-hormonal method. Researchers are also trying to interfere with the process of spermatogenesis using BRDT inhibitor - JQ1, or neutralize the sperm by injecting styrene maleic anhydride (SMA) into the lumen of the vas deferens. The other studies explore processes involved in proper sperm motility. A vaccine which induces an immune response to the reproductive system is also an interesting method. The latest research use ultrasound waves and mechanical device which blocks the patency of vas deferens. The aim of the study current state of knowledge male contraception. PMID:27590656

  16. Current Proteomic Methods to Investigate the Dynamics of Histone Turnover in the Central Nervous System.

    PubMed

    Farrelly, L A; Dill, B D; Molina, H; Birtwistle, M R; Maze, I

    2016-01-01

    Characterizing the dynamic behavior of nucleosomes in the central nervous system is vital to our understanding of brain-specific chromatin-templated processes and their roles in transcriptional plasticity. Histone turnover-the complete loss of old, and replacement by new, nucleosomal histones-is one such phenomenon that has recently been shown to be critical for cell-type-specific transcription in brain, synaptic plasticity, and cognition. Such revelations that histones, long believed to static proteins in postmitotic cells, are highly dynamic in neurons were only possible owing to significant advances in analytical chemistry-based techniques, which now provide a platform for investigations of histone dynamics in both healthy and diseased tissues. Here, we discuss both past and present proteomic methods (eg, mass spectrometry, human "bomb pulse labeling") for investigating histone turnover in brain with the hope that such information may stimulate future investigations of both adaptive and aberrant forms of "neuroepigenetic" plasticity. PMID:27423867

  17. Current Proteomic Methods to Investigate the Dynamics of Histone Turnover in the Central Nervous System

    PubMed Central

    Farrelly, L.A.; Dill, B.D.; Molina, H.; Birtwistle, M.R.; Maze, I.

    2016-01-01

    Characterizing the dynamic behavior of nucleosomes in the central nervous system is vital to our understanding of brain-specific chromatin-templated processes and their roles in transcriptional plasticity. Histone turnover—the complete loss of old, and replacement by new, nucleosomal histones—is one such phenomenon that has recently been shown to be critical for cell-type-specific transcription in brain, synaptic plasticity, and cognition. Such revelations that histones, long believed to static proteins in postmitotic cells, are highly dynamic in neurons were only possible owing to significant advances in analytical chemistry-based techniques, which now provide a platform for investigations of histone dynamics in both healthy and diseased tissues. Here, we discuss both past and present proteomic methods (eg, mass spectrometry, human “bomb pulse labeling”) for investigating histone turnover in brain with the hope that such information may stimulate future investigations of both adaptive and aberrant forms of “neuroepigenetic” plasticity. PMID:27423867

  18. Proteome analysis of the Escherichia coli heat shock response under steady-state conditions

    PubMed Central

    Lüders, Svenja; Fallet, Claas; Franco-Lara, Ezequiel

    2009-01-01

    In this study a proteomic approach was used to investigate the steady-state response of Escherichia coli to temperature up-shifts in a cascade of two continuously operated bioreactors. The first reactor served as cell source with optimal settings for microbial growth, while in the second chemostat the cells were exposed to elevated temperatures. By using this reactor configuration, which has not been reported to be used for the study of bacterial stress responses so far, it is possible to study temperature stress under well-defined, steady-state conditions. Specifically the effect on the cellular adaption to temperature stress using two-dimensional gel electrophoresis was examined and compared at the cultivation temperatures of 37°C and 47.5°C. As expected, the steady-state study with the double bioreactor configuration delivered a different protein spectrum compared to that obtained with standard batch experiments in shaking flasks and bioreactors. Setting a high cut-out spot-to-spot size ratio of 5, proteins involved in defence against oxygen stress, functional cell envelope proteins, chaperones and proteins involved in protein biosynthesis, the energy metabolism and the amino acid biosynthesis were found to be differently expressed at high cultivation temperatures. The results demonstrate the complexity of the stress response in a steady-state culture not reported elsewhere to date. PMID:19772559

  19. On the Current Thermal State of Mars.

    NASA Astrophysics Data System (ADS)

    Grott, M.; Breuer, D.

    2008-09-01

    Introduction: The current thermal state of Mars is a fundamental unknown in Mars science. Although is has a huge influence on the planet's current geodynamic activity and controls the possibility for basal melting at the polar caps [1], constraints on this quantities are very scarce. This situation has lately been improved by the study of lithospheric deformation at the north polar cap [2] which constrained the current Martian elastic lithosphere thickness Te, an indirect measure of the temperatures in the planetary interior. Using radar sounding data obtained bySHARAD, the shallow radar onboard the Mars Reconnaissance Orbiter, [2] found that the current Martian lithosphere is extremely stiff and Te is larger than 300 km today. This is surprising as this value is almost twice as large as previously estimated from theoretical considerations and flexure studies [3][1]. In order to be consistent with the planets thermal evolution, [2] argue that the amount of radioactive elements in the Martian interior needs to be subchondritic. This appears to be problematic as geochemical analysis of the SNC meteorites implies higher concentrations of radioactive elements [4]. Furthermore, if the concentration of heat producing elements is indeed reduced, the resulting low interior temperatures will inhibit partial mantle melting and magmatism. However, geological evidence suggests that Mars has been volcanically active in the recent past [5]. In order to address these inconsistencies, we reinvestigate the thermal evolution of Mars and examine its current thermal state for a wide range of initial condition using the current elastic thickness Te and the potential for partial mantle melting to constrain our models. Modeling: We investigate the thermal evolution of Mars by solving the energy balance equations for the core and mantle, treating the mantle energy transport by parametrized convection models. This is done using scaling laws for stagnant lid convection and our model is

  20. Proteomics technology in systems biology.

    PubMed

    Smith, Jeffrey C; Figeys, Daniel

    2006-08-01

    It has now become apparent that a full understanding of a biological process (e.g. a disease state) is only possible if all biomolecular interactions are taken into account. Systems biology works towards understanding the intricacies of cellular life through the collaborative efforts of biologists, chemists, mathematicians and computer scientists and recently, a number of laboratories around the world have embarked upon such research agendas. The fields of genomics and proteomics are foundational in systems biology studies and a great deal of research is currently being conducted in each worldwide. Moreover, many technological advances (particularly in mass spectrometry) have led to a dramatic rise in the number of proteomic studies over the past two decades. This short review summarizes a selection of technological innovations in proteomics that contribute to systems biology studies. PMID:16880956

  1. Quantitative proteomics analyses of activation states of human THP-1 macrophages.

    PubMed

    Meijer, Kees; Weening, Desiree; de Vries, Marcel P; Priebe, Marion G; Vonk, Roel J; Roelofsen, Han

    2015-10-14

    Macrophages display large functional and phenotypical plasticity. They can adopt a broad range of activation states depending on their microenvironment. Various surface markers are used to characterize these differentially polarized macrophages. However, this is not informative for the functions of the macrophage. In order to have a better understanding of the functional changes of macrophages upon differential polarization, we studied differences in LPS- and IL4-stimulated macrophages. The THP-1 human monocytic cell line, was used as a model system. Cells were labeled, differentiated and stimulated with either LPS or IL-4 in a quantitative SILAC proteomics set-up. The resulting sets of proteins were functionally clustered. LPS-stimulated macrophages show increased secretion of proinflammatory peptides, leading to increased pressure on protein biosynthesis and processing. IL4-stimulated macrophages show upregulation of cell adhesion and extracellular matrix remodeling. Our approach provides an integrated view of polarization-induced functional changes and proves useful for studying functional differences between subsets of macrophages. Moreover, the identified polarization specific proteins may contribute to a better characterization of different activation states in situ and their role in various inflammatory processes. PMID:26200757

  2. Biogas production: current state and perspectives.

    PubMed

    Weiland, Peter

    2010-01-01

    Anaerobic digestion of energy crops, residues, and wastes is of increasing interest in order to reduce the greenhouse gas emissions and to facilitate a sustainable development of energy supply. Production of biogas provides a versatile carrier of renewable energy, as methane can be used for replacement of fossil fuels in both heat and power generation and as a vehicle fuel. For biogas production, various process types are applied which can be classified in wet and dry fermentation systems. Most often applied are wet digester systems using vertical stirred tank digester with different stirrer types dependent on the origin of the feedstock. Biogas is mainly utilized in engine-based combined heat and power plants, whereas microgas turbines and fuel cells are expensive alternatives which need further development work for reducing the costs and increasing their reliability. Gas upgrading and utilization as renewable vehicle fuel or injection into the natural gas grid is of increasing interest because the gas can be used in a more efficient way. The digestate from anaerobic fermentation is a valuable fertilizer due to the increased availability of nitrogen and the better short-term fertilization effect. Anaerobic treatment minimizes the survival of pathogens which is important for using the digested residue as fertilizer. This paper reviews the current state and perspectives of biogas production, including the biochemical parameters and feedstocks which influence the efficiency and reliability of the microbial conversion and gas yield. PMID:19777226

  3. Mass spectrometry-based plasma proteomics: state of the art and future outlook.

    PubMed

    Pernemalm, Maria; Lehtiö, Janne

    2014-08-01

    Mass spectrometry-based plasma proteomics is a field where intense research has been performed during the last decade. Being closely linked to biomarker discovery, the field has received a fair amount of criticism, mostly due to the low number of novel biomarkers reaching the clinic. However, plasma proteomics is under gradual development with improvements on fractionation methods, mass spectrometry instrumentation and analytical approaches. These recent developments have contributed to the revival of plasma proteomics. The goal of this review is to summarize these advances, focusing in particular on fractionation methods, both for targeted and global mass spectrometry-based plasma analysis. PMID:24661227

  4. Current state of sewage treatment in China.

    PubMed

    Jin, Lingyun; Zhang, Guangming; Tian, Huifang

    2014-12-01

    The study reported and analyzed the current state of wastewater treatment plants (WWTPs) in urban China from the aspects of scale, treatment processes, sludge handling, geographical distribution, and discharge standards. By 2012, there were 3340 WWTPs in operation in China with a capacity of 1.42 × 10(8) m(3)/d. The number of medium-scale WWTPs (1-10 × 10(4) m(3)/d) counted for 75% of total WWTPs. On average, the chemical oxygen demand (COD) removal efficiencies of small-scale, medium-scale, large-scale and super-large-scale WWTPs were 81, 85.5, 87.5 and 86.5%, respectively. Generally speaking, the nutrients removal instead of COD removal was of concern. As to the different processes, oxidation ditch, anaerobic-anoxic-oxic (A(2)/O) and sequencing batch reactor (SBR) were the mainstream technologies in China. These technologies had minor difference in terms of overall COD removal efficiency. The sludge treatment in WWTPs was basically "thickening-coagulation-mechanical dehydration" and the major disposal method was sanitary landfill in China. The distributions of WWTPs and their utilization showed significant regional characteristics. The sewage treatment capacity of China concentrated on the coastal areas and middle reaches of Yangtze River, which were the economically developed zones. Besides, most WWTPs enforced the Class 1 or Class 2 discharge standards, but few realized wastewater reuse. Finally, existing problems were discussed, including low removal efficiency of nitrogen and phosphorus, emerging contaminants, low reuse of reclaimed water, poor sludge treatment and disposal, low execution standard of effluent, and emissions of greenhouse gas from WWTPs. Suggestions regarding potential technical and administrative measures were given. PMID:25189479

  5. Current state of diagnostic technologies in the autoimmunology laboratory.

    PubMed

    Tozzoli, Renato; Bonaguri, Chiara; Melegari, Alessandra; Antico, Antonio; Bassetti, Danila; Bizzaro, Nicola

    2013-01-01

    The methods for detecting and measuring autoantibodies have evolved markedly in recent years, encompassing three generations of analytical technologies. Many different immunoassay methods have been developed and used for research and laboratory practice purposes, from the early conventional (or monoplex) analytical methods able to detect single autoantibodies to the more recent multiplex platforms that can quantify tens of molecules. Although it has been in use for over 50 years, indirect immunofluorescence remains the standard method for research on many types of autoantibodies, due to its characteristics of diagnostic sensitivity and also to recent technological innovations which permit it a greater level of automation and standardization. The recent multiplex immunometric methods, with varying levels of automation, present characteristics of higher diagnostic accuracy, but are not yet widely diffused in autoimmunology laboratories due to the limited number of autoantibodies that are detectable, and due to the high cost of reagents and systems. Technological advancement in autoimmunology continues to evolve rapidly, and in the coming years new proteomic techniques will be able to radically change the approach to diagnostics and possibly also clinical treatment of autoimmune diseases. The scope of this review is to update the state of the art of technologies and methods for the measurement of autoantibodies, with special reference to innovations in indirect immunofluorescence and in multiple proteomic methods. PMID:23092800

  6. Proteomics of Foodborne Bacterial Pathogens

    NASA Astrophysics Data System (ADS)

    Fagerquist, Clifton K.

    This chapter is intended to be a relatively brief overview of proteomic techniques currently in use for the identification and analysis of microorganisms with a special emphasis on foodborne pathogens. The chapter is organized as follows. First, proteomic techniques are introduced and discussed. Second, proteomic applications are presented specifically as they relate to the identification and qualitative/quantitative analysis of foodborne pathogens.

  7. Embryology in the era of proteomics.

    PubMed

    Katz-Jaffe, M G; Gardner, D K

    2007-09-01

    Currently, relatively little is known regarding the protein production of mammalian embryos. Unlike the genome, the proteome itself is dynamic reflecting both internal and external environmental stimuli. Until now the lack of sensitivity has remained a stumbling block for the global introduction of proteomics into the field of mammalian embryology. However, new developments in mass spectrometry have been revolutionary, utilizing protein profiling and peptide sequencing to elucidate underlying biological processes. The sensitivity of these platforms have allowed for the development of new protocols that are capable of profiling the proteome of individual mammalian oocytes and embryos. This information is fundamental to unravelling the complexity of embryo physiology including the dialogue between the developing embryo and its maternal environment. Such proteomic approaches are also assisting in the optimization of ART techniques, including oocyte cryopreservation and in vitro maturation. Embryo selection for transfer is another area of ART that should benefit in this era of proteomics. Currently, mammalian embryos are selected for transfer based on morphological grading systems. Although of great value, analysis of morphology alone cannot determine the embryo's physiological state or chromosomal complement. Subsequently, there is a need to identify in culture those embryos with the highest implantation potential. Proteomic analysis of the embryonic secretome (proteins produced by the embryo and secreted into the surrounding medium) followed by the identification of specific proteins critical for implantation, may lead to the development of a non-invasive viability assay to assist in the selection of embryos for transfer. PMID:17477967

  8. Proteomics: a subcellular look at spermatozoa

    PubMed Central

    2011-01-01

    Background Male-factor infertility presents a vexing problem for many reproductively active couples. Many studies have focused on abnormal sperm parameters. Recent advances in proteomic techniques, especially in mass spectrometry, have aided in the study of sperm and more specifically, sperm proteins. The aim of this study was to review the current literature on the various proteomic techniques, and their usefulness in diagnosing sperm dysfunction and potential applications in the clinical setting. Methods Review of PubMed database. Key words: spermatozoa, proteomics, protein, proteome, 2D-PAGE, mass spectrometry. Results Recently employed proteomic methods, such as two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in gel electrophoresis, have identified numerous sperm-specific proteins. They also have provided a further understanding of protein function involved in sperm processes and for the differentiation between normal and abnormal states. In addition, studies on the sperm proteome have demonstrated the importance of post-translational modifications, and their ability to bring about physiological changes in sperm function. No longer do researchers believe that in order for them to elucidate the biochemical functions of genes, mere knowledge of the human genome sequence is sufficient. Moreover, a greater understanding of the physiological function of every protein in the tissue-specific proteome is essential in order to unravel the biological display of the human genome. Conclusion Recent advances in proteomic techniques have provided insight into sperm function and dysfunction. Several multidimensional separation techniques can be utilized to identify and characterize spermatozoa. Future developments in bioinformatics can further assist researchers in understanding the vast amount of data collected in proteomic studies. Moreover, such advances in proteomics may help to decipher metabolites which can act as biomarkers in

  9. Fish Vaccines: Current State and Future Advances

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In aquaculture, the development and use of vaccines is now making rapid progress to achieve its full potential as an effective disease prevention tool. Currently, USDA, APHIS, CVB licenses 17 fish vaccines of which 2 are modified live and 14 are killed vaccines. The objective of vaccination is to pr...

  10. Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications

    SciTech Connect

    Baker, Erin Shammel; Liu, Tao; Petyuk, Vladislav A.; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.; Anderson, Gordon A.; Smith, Richard D.

    2012-08-31

    Mass spectrometry (MS)-based proteomics measurements have become increasingly utilized in a wide range of biological and biomedical applications, and have significantly enhanced the understanding of the complex and dynamic nature of the proteome and its connections to biology and diseases. While some MS techniques such as those for targeted analysis are increasingly applied with great success, others such as global quantitative analysis (for e.g. biomarker discovery) are more challenging and continue to be developed and refined to provide the desired throughput, sensitivity and/ or specificity. New MS capabilities and proteomics-based pipelines/strategies also keep enhancing for the advancement of clinical proteomics applications such as protein biomarker discovery and validation. Herein, we provide a brief review to summarize the current state of MS-based proteomics with respect to its advantages and present limitations, while highlighting its potential in future clinical applications.

  11. Current State of Clostridium difficile Treatment Options

    PubMed Central

    Venugopal, Anilrudh A.; Johnson, Stuart

    2012-01-01

    Recent reports of reduced response to standard therapies for Clostridium difficile infection (CDI) and the risk for recurrent CDI that is common with all currently available treatment agents have posed a significant challenge to clinicians. Current recommendations include metronidazole for treatment of mild to moderate CDI and vancomycin for severe CDI. Results from small clinical trials suggest that nitazoxanide and teicoplanin may be alternative options to standard therapies, whereas rifaximin has demonstrated success in uncontrolled trials for the management of multiple recurrences. Anecdotal reports have also suggested that tigecycline might be useful as an adjunctive agent for the treatment of severe complicated CDI. Reports of resistance will likely limit the clinical use of fusidic acid and bacitracin and, possibly, rifaximin if resistance to this agent becomes widespread. Treatment of patients with multiple CDI recurrences and those with severe complicated CDI is based on limited clinical evidence, and new treatments or strategies are needed. PMID:22752868

  12. Digital mammography: current state and future aspects.

    PubMed

    Fischer, U; Hermann, K P; Baum, F

    2006-01-01

    The introduction of digital technique in mammography has been the last step in completing the process of digitalization in diagnostic imaging. Meanwhile, some different digital techniques as well as a couple of different digital mammography systems were developed and have already been available for some years. In this review article, the relevant data of key studies are reported, the current status is defined, and perspectives of digital mammography are described. PMID:16132935

  13. State Profiles: Current Status of Public Sector Labor Relations.

    ERIC Educational Resources Information Center

    Labor Management Services Administration (DOL), Washington, DC. Div. of Public Employee Labor Relations.

    This guide summarizes the coverage of public employees by state labor relations laws. For each state, the guide describes legal provisions, current situation, and current legislative activity. The report also includes data on population, public employment, work stoppages, and state revenues and expenditures. Agencies useful in gathering and…

  14. Bi-layer steady state current cloak

    NASA Astrophysics Data System (ADS)

    Zeng, Lunwu

    2014-02-01

    We report that bi-layer copper and polystyrene cylinders can cloak steady current. We fabricated two hollow cylinders, the one made of copper, and the other made of polystyrene. Two hollow copper and polystyrene cylinders nested concentric bi-layer hollow copper and polystyrene cylinders. The background media are made of aluminum. Theory and experiment demonstrated that the electric potential gradients are parallel and equal outside the outer circle, the iso-potential lines are parallel outside the outer circle, and the electric potential is zero in the inner circle.

  15. Application of meta-transcriptomics and -proteomics to analysis of in situ physiological state

    SciTech Connect

    Konopka, Allan; Wilkins, Michael J.

    2012-05-18

    Analysis of the growth-limiting factor or environmental stressors affecting microbes in situ is of fundamental importance but analytically difficult. Microbes can reduce in situ limiting nutrient concentrations to sub-micromolar levels, and contaminated ecosystems may contain multiple stressors. The patterns of gene or protein expression by microbes in nature can be used to infer growth limitations, because they are regulated in response to environmental conditions. Experimental studies under controlled conditions in the laboratory provide the physiological underpinnings for developing these physiological indicators. Although regulatory networks may differ among specific microbes, there are some broad principles that can be applied, related to limiting nutrient acquisition, resource allocation, and stress responses. As technologies for transcriptomics and proteomics mature, the capacity to apply these approaches to complex microbial communities will accelerate. Global proteomics has the particular advantage that it reflects expressed catalytic activities. Furthermore, the high mass accuracy of some proteomic approaches allows mapping back to specific microbial strains. For example, at the Rifle IFRC field site in Western Colorado, the physiological status of Fe(III)-reducing populations has been tracked over time. Members of a 'subsurface clade' within the Geobacter predominated during carbon amendment to the subsurface environment. At the functional level, proteomic identifications produced inferences regarding (i) temporal changes in anabolism and catabolism of acetate, (ii) the onset of N2 fixation when N became limiting, and (iii) expression of phosphate transporters during periods of intense growth. The application of these approaches in situ can lead to discovery of novel physiological adaptations.

  16. Spaceflight osteoporosis: current state and future perspective.

    PubMed

    Cappellesso, R; Nicole, L; Guido, A; Pizzol, D

    2015-10-01

    Osteoporosis is one of the established major consequences of long-duration spaceflights in astronauts seriously undermining their health after their returning on Earth. Indeed, astronauts typically lose more bone mass during one month than postmenopausal women on Earth lose in one year. To date, countermeasures mainly consist in exercise and supplementation while pharmacological treatment as those used in postmenopausal women are not routine. However, it is evident that exercise and supplementation alone are not enough to maintain bone homeostasis. In this paper we describe the current countermeasures for bone loss during long-term spaceflight, review the modern treatment which are successfully employed to prevent osteoporosis on Earth and that could be quickly used also for astronauts and finally focus on the recent cellular and molecular understanding of bone homeostasis which might provide the basis for the development of future targeted therapies. PMID:26494042

  17. Current State of Opioid Therapy and Abuse.

    PubMed

    Manchikanti, Laxmaiah; Kaye, Adam M; Kaye, Alan D

    2016-05-01

    Currently, there is growing tension between the twin challenges of opioid therapy for chronic pain and adverse consequences of abuse, leading to multiple complications including respiratory failure and death. The recent data from Centers for Disease Control and Prevention (CDC) have shown continued escalation of prescription opioid use with opioid overdose deaths topping all previous estimations. Numerous policy initiatives, advisories, and guidelines have been advanced through the years to control the opioid epidemic. The strategies to prevent opioid abuse and to maintain opioid therapy when medically necessary fall into primary and secondary prevention categories. The primary prevention category is extremely crucial, since it involves education of primary care providers and patients at the starting point of opioid therapy. The education of surgeons and other prescribers is as crucial as the education of primary care physicians. PMID:27048483

  18. Current state of imaging in dermatology.

    PubMed

    Hibler, Brian P; Qi, Qiaochu; Rossi, Anthony M

    2016-03-01

    Medical imaging has dramatically transformed the practice of medicine, especially the field of dermatology. Imaging is used to facilitate the transfer of information between providers, document cutaneous disease, assess response to therapy, and plays a crucial role in monitoring and diagnosing skin cancer. Advancements in imaging technology and overall improved quality of imaging have augmented the utility of photography. We provide an overview of current imaging technologies used in dermatology with a focus on their role in skin cancer diagnosis. Future technologies include three-dimensional, total-body photography, mobile smartphone applications, and computerassisted diagnostic devices. With these advancements, we are better equipped to capture and monitor skin conditions longitudinally and achieve improved diagnostic accuracy of skin cancer. PMID:26963110

  19. Current state of cardiac rehabilitation in Japan.

    PubMed

    Goto, Yoichi

    2014-01-01

    In Japan, metabolic risk factors have been increasing due to the westernization and urbanization of lifestyle. This justifiably raises a concern that the incidence of coronary heart disease (CHD) in Japan will increase over time, and indeed, recent epidemiological studies in Japan suggest the incidence of acute myocardial infarction (AMI) is increasing. Cardiac rehabilitation (CR) in Japan has been traditionally performed in the inpatient setting. To obtain reimbursement, a CR facility must fulfill certain criteria including being a medical institution with a cardiology/cardiac surgery section which has at least a cardiologist/cardiac surgeon and an experienced CR physician as full-time employees. These criteria create challenges to the availability of outpatient CR after hospital discharge. A recent analysis found outpatient CR participation rate was estimated to be between 3.8 and 7.6% in Japan. This review describes recent trends in the incidence of AMI and the current status of the use of CR in Japan. PMID:24607022

  20. The current state of Socio-hydrology

    NASA Astrophysics Data System (ADS)

    Sivapalan, Murugesu; Viglione, Alberto; Di Baldassarre, Giuliano; Pande, Saket

    2016-04-01

    Socio-hydrology was introduced 4 years ago into the scientific lexicon, and elicited several reactions about the meaning and originality of the concept. However, there has also been much activity triggered by the original paper, including further commentaries that clarified the definitions, and several papers that acted on the definitions, and through them further clarified and illustrated the meaning and usefulness of socio-hydrology for understanding coupled human-water systems and underpinning sustainable water management. This presentation discusses how useful these recent studies have been towards the need for socio-hydrology to explain phenomena, such as rise and decline of human population or food production in water scarce basins ('pendulum swing'), the levee effect, small scale farmer suicides, anthropogenic droughts, etc… We also discuss its foundation as a Science, its similarities and dissimilarities with other fields that study human-water interactions, such as hydro-sociology and hydro-economics, its foundation as a Science, current gaps and the challenges that lie ahead.

  1. ECLAIRs detection plane: current state of development

    NASA Astrophysics Data System (ADS)

    Lacombe, K.; Pons, R.; Amoros, C.; Atteia, J.-L.; Barret, D.; Billot, M.; Bordon, S.; Cordier, B.; Gevin, O.; Godet, O.; Gonzalez, F.; Houret, B.; Mercier, K.; Mandrou, P.; Marty, W.; Nasser, G.; Rambaud, D.; Ramon, P.; Rouaix, G.; Waegebaert, V.

    2014-07-01

    ECLAIRs, a 2-D coded-mask imaging camera on-board the Sino-French SVOM space mission, will detect and locate Gamma-ray bursts (GRBs) in near real time in the 4-150 keV energy band. The design of ECLAIRs has been mainly driven by the objective of achieving a low-energy threshold of 4 keV, unprecedented for this type of instrument. The detection plane is an assembly of 6400 Schottky CdTe semiconductor detectors of size 4x4x1 mm3 organized on elementary hybrid matrices of 4x8 detectors. The detectors will be polarized from -300V to -500V and operated at -20°C to reduce both the leakage current and the polarization effect induced by the Schottky contact. The remarkable low-energy threshold homogeneity required for the detection plane has been achieved thanks to: i) an extensive characterization and selection of the detectors, ii) the development of a specific low-noise 32-channel ASIC, iii) the realization of an innovative hybrid module composed of a thick film ceramic (holding 32 CdTe detectors with their high voltage grid), associated to an HTCC ceramic (housing the ASIC chip within an hermetic enclosure). In this paper, we start describing a complete hybrid matrix, and then the manufacturing of a first set of 50 matrices (representing 1600 detectors, i.e. a quarter of ECLAIRs detector's array). We show how this manufacturing allowed to validate the different technologies used for this hybridization, as well as the industrialization processes. During this phase, we systematically measured the leakage current on Detector Ceramics after an outgassing, and the Equivalent Noise Charge (ENC) for each of the 32 channels on ASIC Ceramics, in order to optimize the coupling of the two ceramics. Finally, we performed on each hybrid module, spectral measurements at -20°C in our vacuum chamber, using several calibrated radioactive sources (241Am and 55Fe), to check the performance homogeneity of the 50 modules. The results demonstrated that the 32-detector hybrid matrices

  2. Ion Current-Based Proteomic Profiling for Understanding the Inhibitory Effect of Tumor Necrosis Factor Alpha on Myogenic Differentiation.

    PubMed

    Tu, Chengjian; Bu, Yahao; Vujcic, Marija; Shen, Shichen; Li, Jun; Qu, Miao; Hangauer, David; Clements, James L; Qu, Jun

    2016-09-01

    Despite a demonstrated role for TNF-α in promoting muscle wasting and cachexia, the associated molecular mechanisms and signaling pathways of myoblast differentiation dysregulated by TNF-α remain poorly understood. This study presents well-controlled proteomic profiling as a means to investigate the mechanisms of TNF-α-regulated myogenic differentiation. Primary human muscle precursor cells (MPCs) cultured in growth medium (GM), differentiation medium (DM) to induce myogenic differentiation, and DM with 20 ng/mL of TNF-α (n = 5/group) were comparatively analyzed by an ion current-based quantitative platform consisting of reproducible sample preparation/on-pellet digestion, a long-column nano-LC separation, and ion current-based differential analysis. The inhibition of myogenic differentiation by TNF-α was confirmed by reduced formation of multinucleated myotubes and the recovered expression of altered myogenic proteins such as MYOD and myogenin during myogenic differentiation. Functional analysis and validation by immunoassay analysis suggested that the cooperation of NF-κB and STAT proteins is responsible for dysregulated differentiation in MPCs by TNF-α treatment. Increased MHC class I components such as HLA-A, HLA-B, HLA-C, and beta-2-microglobulin were also observed in cultures in DM treated with TNF-α. Interestingly, inhibition of the cholesterol biosynthesis pathway during myogenic differentiation induced by serum starvation was not recovered by TNF-α treatment, which combined with previous reports, implies that this process may be an early event of myogenesis. This finding could lay the foundation for the potential use of statins in modulating myogenesis through cholesterol, for example, in stem cell-based myocardial infarction treatment, where differentiation of myoblasts and stem cells into force-generating mature muscle cells is a key step to the therapeutic capacity. In conclusion, the landscapes of altered transcription regulators, metabolic

  3. Application of meta-transcriptomics and -proteomics to analysis of in situ physiological state

    PubMed Central

    Konopka, Allan; Wilkins, Michael J.

    2012-01-01

    Analysis of the growth-limiting factor or environmental stressors affecting microbes in situ is of fundamental importance but analytically difficult. Microbes can reduce in situ limiting nutrient concentrations to sub-micromolar levels, and contaminated ecosystems may contain multiple stressors. The patterns of gene or protein expression by microbes in nature can be used to infer growth limitations, because they are regulated in response to environmental conditions. Experimental studies under controlled conditions in the laboratory provide the physiological underpinnings for developing these physiological indicators. Although regulatory networks may differ among specific microbes, there are some broad principles that can be applied, related to limiting nutrient acquisition, resource allocation, and stress responses. As technologies for transcriptomics and proteomics mature, the capacity to apply these approaches to complex microbial communities will accelerate. Global proteomics has the particular advantage that it reflects expressed catalytic activities. Furthermore, the high mass accuracy of some proteomic approaches allows mapping back to specific microbial strains. For example, at the Rifle IFRC field site in Western Colorado, the physiological status of Fe(III)-reducing populations has been tracked over time. Members of a “subsurface clade” within the Geobacter predominated during carbon amendment to the subsurface environment. At the functional level, proteomic identifications produced inferences regarding (i) temporal changes in anabolism and catabolism of acetate, (ii) the onset of N2 fixation when N became limiting, and (iii) expression of phosphate transporters during periods of intense growth. The application of these approaches in situ can lead to discovery of novel physiological adaptations. PMID:22783237

  4. Quantum backflow states from eigenstates of the regularized current operator

    NASA Astrophysics Data System (ADS)

    Halliwell, J. J.; Gillman, E.; Lennon, O.; Patel, M.; Ramirez, I.

    2013-11-01

    We present an exhaustive class of states with quantum backflow—the phenomenon in which a state consisting entirely of positive momenta has negative current and the probability flows in the opposite direction to the momentum. They are characterized by a general function of momenta subject to very weak conditions. Such a family of states is of interest in the light of a recent experimental proposal to measure backflow. We find one particularly simple state which has surprisingly large backflow—about 41% of the lower bound on flux derived by Bracken and Melloy. We study the eigenstates of a regularized current operator and we show how some of these states, in a certain limit, lead to our class of backflow states. This limit also clarifies the correspondence between the spectrum of the regularized current operator, which has just two non-zero eigenvalues in our chosen regularization, and the usual current operator.

  5. Reproducible ion-current-based approach for 24-plex comparison of the tissue proteomes of hibernating versus normal myocardium in swine models.

    PubMed

    Qu, Jun; Young, Rebeccah; Page, Brian J; Shen, Xiaomeng; Tata, Nazneen; Li, Jun; Duan, Xiaotao; Fallavollita, James A; Canty, John M

    2014-05-01

    Hibernating myocardium is an adaptive response to repetitive myocardial ischemia that is clinically common, but the mechanism of adaptation is poorly understood. Here we compared the proteomes of hibernating versus normal myocardium in a porcine model with 24 biological replicates. Using the ion-current-based proteomic strategy optimized in this study to expand upon previous proteomic work, we identified differentially expressed proteins in new molecular pathways of cardiovascular interest. The methodological strategy includes efficient extraction with detergent cocktail; precipitation/digestion procedure with high, quantitative peptide recovery; reproducible nano-LC/MS analysis on a long, heated column packed with small particles; and quantification based on ion-current peak areas. Under the optimized conditions, high efficiency and reproducibility were achieved for each step, which enabled a reliable comparison of 24 the myocardial samples. To achieve confident discovery of differentially regulated proteins in hibernating myocardium, we used highly stringent criteria to define "quantifiable proteins". These included the filtering criteria of low peptide FDR and S/N > 10 for peptide ion currents, and each protein was quantified independently from ≥2 distinct peptides. For a broad methodological validation, the quantitative results were compared with a parallel, well-validated 2D-DIGE analysis of the same model. Excellent agreement between the two orthogonal methods was observed (R = 0.74), and the ion-current-based method quantified almost one order of magnitude more proteins. In hibernating myocardium, 225 significantly altered proteins were discovered with a low false-discovery rate (∼3%). These proteins are involved in biological processes including metabolism, apoptosis, stress response, contraction, cytoskeleton, transcription, and translation. This provides compelling evidence that hibernating myocardium adapts to chronic ischemia. The major metabolic

  6. Proteomics research in India: an update.

    PubMed

    Reddy, Panga Jaipal; Atak, Apurva; Ghantasala, Saicharan; Kumar, Saurabh; Gupta, Shabarni; Prasad, T S Keshava; Zingde, Surekha M; Srivastava, Sanjeeva

    2015-09-01

    After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India. PMID:25868663

  7. The State of the Human Proteome in 2013 as viewed through PeptideAtlas: Comparing the Kidney, Urine, and Plasma Proteomes for the Biology and Disease-driven Human Proteome Project

    PubMed Central

    Farrah, Terry; Deutsch, Eric W.; Omenn, Gilbert S.; Sun, Zhi; Watts, Julian D.; Yamamoto, Tadashi; Shteynberg, David; Harris, Micheleen M.; Moritz, Robert L.

    2014-01-01

    The kidney, urine, and plasma proteomes are intimately related: proteins and metabolic waste products are filtered from the plasma by the kidney and excreted via the urine, while kidney proteins may be secreted into the circulation or released into the urine. Shotgun proteomics datasets derived from human kidney, urine, and plasma samples were collated and processed using a uniform software pipeline, and relative protein abundances were estimated by spectral counting. The resulting PeptideAtlas builds yielded 4005, 2491, and 3553 nonredundant proteins at 1% FDR for the kidney, urine, and plasma proteomes, respectively—for kidney and plasma, the largest high-confidence protein sets to date. The same pipeline applied to all available human data yielded a 2013 Human PeptideAtlas build containing 12,644 nonredundant proteins and at least one peptide for each of ~14,000 Swiss-Prot entries, an increase over 2012 of ~7.5% of the predicted human proteome. We demonstrate that abundances are correlated between plasma and urine, examine the most abundant urine proteins not derived from either plasma or kidney, and consider the biomarker potential of proteins associated with renal decline. This analysis forms part of the Biology and Disease-driven Human Proteome Project (B/D-HPP) and a contribution to the Chromosome-centric Human Proteome Project (C-HPP) special issue. PMID:24261998

  8. Low T3 State Is Correlated with Cardiac Mitochondrial Impairments after Ischemia Reperfusion Injury: Evidence from a Proteomic Approach

    PubMed Central

    Forini, Francesca; Ucciferri, Nadia; Kusmic, Claudia; Nicolini, Giuseppina; Cecchettini, Antonella; Rocchiccioli, Silvia; Citti, Lorenzo; Iervasi, Giorgio

    2015-01-01

    Mitochondria are major determinants of cell fate in ischemia/reperfusion injury (IR) and common effectors of cardio-protective strategies in cardiac ischemic disease. Thyroid hormone homeostasis critically affects mitochondrial function and energy production. Since a low T3 state (LT3S) is frequently observed in the post infarction setting, the study was aimed to investigate the relationship between 72 h post IR T3 levels and both the cardiac function and the mitochondrial proteome in a rat model of IR. The low T3 group exhibits the most compromised cardiac performance along with the worst mitochondrial activity. Accordingly, our results show a different remodeling of the mitochondrial proteome in the presence or absence of a LT3S, with alterations in groups of proteins that play a key role in energy metabolism, quality control and regulation of cell death pathways. Overall, our findings highlight a relationship between LT3S in the early post IR and poor cardiac and mitochondrial outcomes, and suggest a potential implication of thyroid hormone in the cardio-protection and tissue remodeling in ischemic disease. PMID:26561807

  9. Proteins interacting with monoamine transporters: current state and future challenges.

    PubMed

    Sager, Jonathan J; Torres, Gonzalo E

    2011-08-30

    Plasma membrane and vesicular transporters for the biogenic amines, dopamine, norepinephrine, and serotonin, represent a group of proteins that play a crucial role in the regulation of neurotransmission. Clinically, mono amine transporters are the primary targets for the actions of many therapeutic agents used to treat mood disorders, as well as the site of action for highly addictive psychostimulants such as cocaine, amphetamine, methamphetamine, and 3,4-methylenedioxymethamphetamine. Over the past decade, the use of approaches such as yeast two-hybrid and proteomics has identified a multitude of transporter interacting proteins, suggesting that the function and regulation of these transporters are more complex than previously anticipated. With the increasing number of interacting proteins, the rules dictating transporter synthesis, assembly, targeting, trafficking, and function are beginning to be deciphered. Although many of these protein interactions have yet to be fully characterized, current knowledge is beginning to shed light on novel transporter mechanisms involved in monoamine homeostasis, the molecular actions of psychostimulants, and potential disease mechanisms. While future studies resolving the spatial and temporal resolution of these, and yet unknown, interactions will be needed, the realization that monoamine transporters do not work alone opens the path to a plethora of possible pharmacological interventions. PMID:21797260

  10. Theory of current states in narrow superconducting channels

    SciTech Connect

    Ivlev, B.I.; Kopnin, N.B.

    1984-03-01

    The properties of narrow superconducting channels carrying a direct current are reviewed. Among the topics covered are the stability of the normal state of the current-carrying channel and the mechanism for a transition from this normal state to the superconducting state. In a homogeneous channel, the transition occurs through the formation of a critical nucleus and is a first-order phase transition. In a channel with inhomogeneities, the transition is quite different. In this case the normal state can exist only down to a certain value of the current, below which the normal state is absolutely unstable. The review is devoted primarily to the theory of the resistive state of narrow channels, which exists at currents above the critical Ginzburg-Landau current. The description is based on the concept of phase-slippage centers. Phenomenological models are discussed, as is a model of a fluctuational excitation of phase-slippage centers. The results obtained from the microscopic dynamic theory of superconductivity are discussed at length. Among these results are the voltage-current characteristic of the resistive state, the abrupt change in the voltage on this characteristic, and the structure of the phase-slippage centers.

  11. Proteomic Technologies for the Study of Osteosarcoma

    PubMed Central

    Byrum, Stephanie D.; Washam, Charity L.; Montgomery, Corey O.; Tackett, Alan J.; Suva, Larry J.

    2012-01-01

    Osteosarcoma is the most common primary bone cancer of children and is established during stages of rapid bone growth. The disease is a consequence of immature osteoblast differentiation, which gives way to a rapidly synthesized incompletely mineralized and disorganized bone matrix. The mechanism of osteosarcoma tumorogenesis is poorly understood, and few proteomic studies have been used to interrogate the disease thus far. Accordingly, these studies have identified proteins that have been known to be associated with other malignancies, rather than being osteosarcoma specific. In this paper, we focus on the growing list of available state-of-the-art proteomic technologies and their specific application to the discovery of novel osteosarcoma diagnostic and therapeutic targets. The current signaling markers/pathways associated with primary and metastatic osteosarcoma that have been identified by early-stage proteomic technologies thus far are also described. PMID:22550414

  12. Postgenomics: Proteomics and Bioinformatics in Cancer Research

    PubMed Central

    2003-01-01

    Now that the human genome is completed, the characterization of the proteins encoded by the sequence remains a challenging task. The study of the complete protein complement of the genome, the “proteome,” referred to as proteomics, will be essential if new therapeutic drugs and new disease biomarkers for early diagnosis are to be developed. Research efforts are already underway to develop the technology necessary to compare the specific protein profiles of diseased versus nondiseased states. These technologies provide a wealth of information and rapidly generate large quantities of data. Processing the large amounts of data will lead to useful predictive mathematical descriptions of biological systems which will permit rapid identification of novel therapeutic targets and identification of metabolic disorders. Here, we present an overview of the current status and future research approaches in defining the cancer cell's proteome in combination with different bioinformatics and computational biology tools toward a better understanding of health and disease. PMID:14615629

  13. Proteomics for systems toxicology

    PubMed Central

    Titz, Bjoern; Elamin, Ashraf; Martin, Florian; Schneider, Thomas; Dijon, Sophie; Ivanov, Nikolai V.; Hoeng, Julia; Peitsch, Manuel C.

    2014-01-01

    Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology. Proteomic measurements are an integral component of this integrative strategy because protein alterations closely mirror biological effects, such as biological stress responses or global tissue alterations. Here, we provide an overview of the technical foundations and highlight select applications of proteomics for systems toxicology studies. With a focus on mass spectrometry-based proteomics, we summarize the experimental methods for quantitative proteomics and describe the computational approaches used to derive biological/mechanistic insights from these datasets. To illustrate how proteomics has been successfully employed to address mechanistic questions in toxicology, we summarized several case studies. Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework. We conclude that, owing to the critical importance of protein-level measurements and recent technological advances, proteomics will be an integral part of integrative systems toxicology approaches in the future. PMID:25379146

  14. Visualization and data analysis-current state and exascale challenges

    SciTech Connect

    Ahrens, James P; Rodgers, David; Springmeyer, Becky

    2010-12-21

    Talk about Visualization and Data Analysis Current State and Exascale challenges. The goal is to update with colleagues our current status in our research. What challenges we need to face, and what future possibilities. Our goal is to propose to approach the problems with the visualization approach operating on the supercomputing platform. This presentation is about the L2 Milestone, we intend to discuss further possibilities of enhancing our results and optimizing our solutions.

  15. The Current State of Biomarkers in Systemic Sclerosis

    PubMed Central

    2010-01-01

    Scleroderma is a complex, multisystem autoimmune rheumatic disease with wide heterogeneity in phenotype and outcome. There are often coexisting ongoing pathologic processes including immune system activation, progressive fibrosis, and vascular disease in subsets of patients. Currently, it is challenging to identify patients at risk for developing adverse outcomes and to determine which patients are responding to current therapies. For these reasons, it is highly valuable to find easily measurable biomarkers that may represent ongoing disease activity or treatment response. This review examines the current state of biomarker development in systemic sclerosis and identifies areas in which further work should be directed. PMID:20425531

  16. Coupling enrichment methods with proteomics for understanding and treating disease.

    PubMed

    Kumar, Amit; Baycin-Hizal, Deniz; Shiloach, Joseph; Bowen, Michael A; Betenbaugh, Michael J

    2015-02-01

    Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of drugs to treat human disease, including target and drug evaluation, understanding mechanisms of drug action, and biomarker discovery. Currently, the genetic sequences of many major organisms are available, which have helped greatly in characterizing proteomes in model animal systems and humans. Through proteomics, global profiles of different disease states can be characterized (e.g. changes in types and relative levels as well as changes in PTMs such as glycosylation or phosphorylation). Although intracellular proteomics can provide a broad overview of physiology of cells and tissues, it has been difficult to quantify the low abundance proteins which can be important for understanding the diseased states and treatment progression. For this reason, there is increasing interest in coupling comparative proteomics methods with subcellular fractionation and enrichment techniques for membranes, nucleus, phosphoproteome, glycoproteome as well as low abundance serum proteins. In this review, we will provide examples of where the utilization of different proteomics-coupled enrichment techniques has aided target and biomarker discovery, understanding the drug targeting mechanism, and mAb discovery. Taken together, these improvements will help to provide a better understanding of the pathophysiology of various diseases including cancer, autoimmunity, inflammation, cardiovascular disease, and neurological conditions, and in the design and development of better medicines for treating these afflictions. PMID:25523641

  17. Current state of care for diabetic retinopathy in India.

    PubMed

    Ramasamy, Kim; Raman, Rajiv; Tandon, Manish

    2013-08-01

    In this article we review the current state of care of diabetic retinopathy in India. We discuss the magnitude of the problem; diabetes, and diabetic retinopathy in India. We highlight the causes of vision loss in diabetic retinopathy. The current level of awareness among general population and physicians is a concern. Current screening strategies practiced in India and the situational analysis of ophthalmologists in India are also reviewed. We review the current management of diabetic macular edema and proliferative diabetic retinopathy. To know the current practice pattern among retinal surgeons in India, a survey was done and the results of the survey are presented. There are few studies in the Indian population which have found some genetic risk and protective factors and a summary of these studies are also presented in this article. PMID:23657764

  18. The Current State of Marketing Activity among Higher Education Institutions.

    ERIC Educational Resources Information Center

    Newman, Cynthia M.

    2002-01-01

    Investigated the current state of marketing, marketing research, and planning practices at four-year higher education institutions. Builds upon previous studies by Blackburn (1979) and Goldgehn (1982 and 1989). Determined whether the use and apparent understanding of marketing and its attendant activities by admissions and enrollment management…

  19. Current density and state density in diluted magnetic semiconductor nanostructures

    NASA Astrophysics Data System (ADS)

    Pérez Merchancano, S. T.; Paredes Gutiérrez, H.; Zuñiga, J. A.

    2016-02-01

    We study in this paper the spin-polarized current density components in diluted magnetic semiconductor tunnelling diodes with different sample geometries. We calculate the resonant JxV and the density of states. The differential conductance curves are analyzed as functions of the applied voltage and the magnetic potential strength induced by the magnetic ions.

  20. Trends in State Coordination and Governance: Historical and Current Perspectives.

    ERIC Educational Resources Information Center

    Epper, Rhonda Martin; Russell, Alene Bycer

    This report examines the roles and functions of state coordinating and governing boards of higher education. Data are from a study reviewing 20 years' worth of data and a current survey. After an introductory section, the first section analyzes historical trends which suggest modest growth in appropriations over the period. Section 2, based on the…

  1. The Current State of Predicting Furrow Irrigation Erosion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There continues to be a need to predict furrow irrigation erosion to estimate on- and off-site impacts of irrigation management. The objective of this paper is to review the current state of furrow erosion prediction technology considering four models: SISL, WEPP, WinSRFR and APEX. SISL is an empiri...

  2. Current Sensor Based Home Appliance and State of Appliance Recognition

    NASA Astrophysics Data System (ADS)

    Saitoh, Takeshi; Osaki, Tomoyuki; Konishi, Ryosuke; Sugahara, Kazunori

    This paper presents a current sensor-based home appliance and its state recognition method for intelligent outlets. Our system has three main functions: remote control, monitoring, and power supply schedule management. This research focuses particular on the monitoring function. To recognize the appliance and the state of the appliance, we extract ten features based on a measured current signal. In the experiment, we gather a number of signals with various appliances, and find that three features Irms, Iavg, and Ipeak yield valid recognition results of 84.3%, 86.4%, and 90.3% for classifying the state of the appliance into three categories. Moreover, sufficient recognition rates of 97.4%, 97.7%, and 99.0% are obtained by consideration of three candidates.

  3. Current Major Depression Among Smokers Using a State Quitline

    PubMed Central

    Hebert, Kiandra K.; Cummins, Sharon E.; Hernandez, Sandra; Tedeschi, Gary J.; Zhu, Shu-Hong

    2010-01-01

    Background Smokers seeking treatment to quit smoking are generally not assessed for current depression, yet depression among smokers may influence quitting outcome. Purpose This study aims to formally assess current major depression among smokers calling a state tobacco quitline. Methods A total of 844 smokers calling the California Smokers’ Helpline in 2007 were screened for depression by the mood module of the Patient Health Questionnaire (PHQ-9). The Social Functioning Questionnaire (SFQ) was also administered to these callers. Two months after the screening, follow-up evaluations were conducted to assess cessation outcome. Results In all, 24.2% of smokers met criteria for current major depression and 16.5% reported symptoms indicating mild depression. Callers with current major depression were more likely to be heavy smokers and on Medicaid. Moreover, 74.0% of smokers with current major depression had substantial social and occupational functioning deficits. Two months later, those with major depression at baseline were significantly less likely to have quit smoking (18.5% vs 28.4%). Conclusions Almost one in four smokers to the California Smokers’ Helpline met criteria for current major depression. Over 400,000 smokers call state quitlines in the U.S. for help with quitting each year, which means that as many as 100,000 smokers with serious depressive symptoms are using these services annually. The large number of depressed smokers who seek help suggests a need to develop appropriate interventions to help them quit successfully. PMID:21146767

  4. Proteomic analysis of temperature dependent extracellular proteins from Aspergillus fumigatus grown under solid-state culture condition.

    PubMed

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

    2013-06-01

    Fungal species of the genus Aspergillus are filamentous ubiquitous saprophytes that play a major role in lignocellulosic biomass recycling and also are considered as cell factories for the production of organic acids, pharmaceuticals, and industrially important enzymes. Analysis of extracellular secreted biomass degrading enzymes using complex lignocellulosic biomass as a substrate by solid-state fermentation could be a more practical approach to evaluate application of the enzymes for lignocellulosic biorefinery. This study isolated a fungal strain from compost, identified as Aspergillus fumigatus, and further analyzed it for lignocellulolytic enzymes at different temperatures using label free quantitative proteomics. The profile of secretome composition discovered cellulases, hemicellulases, lignin degrading proteins, peptidases and proteases, and transport and hypothetical proteins; while protein abundances and further their hierarchical clustering analysis revealed temperature dependent expression of these enzymes during solid-state fermentation of sawdust. The enzyme activities and protein abundances as determined by exponentially modified protein abundance index (emPAI) indicated the maximum activities at the range of 40-50 °C, demonstrating the thermophilic nature of the isolate A. fumigatus LF9. Characterization of the thermostability of secretome suggested the potential of the isolated fungal strain in the production of thermophilic biomass degrading enzymes for industrial application. PMID:23647126

  5. Highly Multiplexed and Reproducible Ion-Current-Based Strategy for Large-Scale Quantitative Proteomics and the Application to Protein Expression Dynamics Induced by Methylprednisolone in 60 Rats

    PubMed Central

    2015-01-01

    A proteome-level time-series study of drug effects (i.e., pharmacodynamics) is critical for understanding mechanisms of action and systems pharmacology, but is challenging, because of the requirement of a proteomics method for reliable quantification of many biological samples. Here, we describe a highly reproducible strategy, enabling a global, large-scale investigation of the expression dynamics of corticosteroid-regulated proteins in livers from adrenalectomized rats over 11 time points after drug dosing (0.5–66 h, N = 5/point). The analytical advances include (i) exhaustive tissue extraction with a Polytron/sonication procedure in a detergent cocktail buffer, and a cleanup/digestion procedure providing very consistent protein yields (relative standard deviation (RSD%) of 2.7%–6.4%) and peptide recoveries (4.1–9.0%) across the 60 animals; (ii) an ultrahigh-pressure nano-LC setup with substantially improved temperature stabilization, pump-noise suppression, and programmed interface cleaning, enabling excellent reproducibility for continuous analyses of numerous samples; (iii) separation on a 100-cm-long column (2-μm particles) with high reproducibility for days to enable both in-depth profiling and accurate peptide ion-current match; and (iv) well-controlled ion-current-based quantification. To obtain high-quality quantitative data necessary to describe the 11 time-points protein expression temporal profiles, strict criteria were used to define “quantifiable proteins”. A total of 323 drug-responsive proteins were revealed with confidence, and the time profiles of these proteins provided new insights into the diverse temporal changes of biological cascades associated with hepatic metabolism, response to hormone stimuli, gluconeogenesis, inflammatory responses, and protein translation processes. Most profile changes persisted well after the drug was eliminated. The developed strategy can also be broadly applied in preclinical and clinical research, where

  6. Effect of transverse current on Andreev bound state

    SciTech Connect

    Takahashi, Y.; Hashimoto, Y.; Yun, D. H.; Kim, S. W.; Nakamura, T.; Iye, Y.; Katsumoto, S.

    2013-12-04

    In a superconductor-normal-superconductor (SNS) structure, the effect of transverse current across the normal part on the transport through Andreev bound states (ABSs) has been examined. Here a ballistic InAs two-dimensional electron system (2DES) is used as the N-layer to form ABSs. At the same time the 2DES has strong spin-orbit interaction, hence there should emerge the spin-Hall effect associated with the transverse current. We have observed strong reduction of characteristic oscillation in the conductance versus bias voltage, which may be attributed to spin polarization due to the spin-Hall effect.

  7. Understanding the Current Dynamical States of Globular Clusters

    NASA Astrophysics Data System (ADS)

    Pooley, David

    2008-09-01

    We appear to be on the verge of a major paradigm shift in our understanding of the current dynamical states of Galactic globular clusters. Fregeau (2008) brought together two recent theoretical breakthroughs as well as an observational breakthrough made possible by Chandra -- that a globular cluster's X-ray source population scales with its dynamical encounter frequency -- to persuasively argue that we have misunderstood the dynamical states of Galactic globular clusters. The observational evidence hinges on Chandra results from clusters which are classified as "core collapsed," of which there are only a handful of observations. I propose a nearly complete census with Chandra of the rest of the "core collapsed" globular clusters.

  8. Steady-state current transfer and scattering theory.

    PubMed

    Ben-Moshe, Vered; Rai, Dhurba; Skourtis, Spiros S; Nitzan, Abraham

    2010-08-01

    The correspondence between the steady-state theory of current transfer and scattering theory in a system of coupled tight-binding models of one-dimensional wires is explored. For weak interwire coupling both calculations give nearly identical results, except at singular points associated with band edges. The effect of decoherence in each of these models is studied using a generalization of the Liouville-von Neuman equation suitable for steady-state situations. An example of a single impurity model is studied in detail, leading to a lattice model of scattering off target that affects both potential scattering and decoherence. For an impurity level lying inside the energy band, the transmission coefficient diminishes with increasing dephasing rate, while the opposite holds for impurity energy outside the band. The efficiency of current transfer in the coupled wire system decreases with increasing dephasing. PMID:20707524

  9. Proteomic Profiling of the Retinas in a Neonatal Rat Model of Oxygen-Induced Retinopathy with a Reproducible Ion-Current-Based MS1 Approach

    PubMed Central

    Shen, Xiaomeng; Li, Jun; Wang, Lianshui; Aranda, Jacob V.; Qu, Jun

    2015-01-01

    Investigation of the retina proteome during hypoxia-induced retinal neovascularization is valuable for understanding pathogenesis of retinopathy of prematurity (ROP). Here we employed a reproducible ion-current-based MS1 quantification approach (ICB) to explore the retinal proteomic changes in early stage of ROP in a rat model of oxygen-induced retinopathy (OIR). Retina proteins, which are rich in membrane proteins, were efficiently extracted by a detergent-cocktail and subjected to precipitation/on-pellet-digestion, followed by nano-LC-MS analysis on a 75-cm column with a 7-h gradient. The high reproducibility of sample preparation and chromatography separation enabled excellent peak alignment and contributed to the superior performance of ICB over parallel label-free approaches. In this study, sum-of-intensity with rejection was incorporated to determine the protein ratios. In total, 1325 unique protein groups were quantified from rat retinas (n = 4/group) with at least two distinct peptides at a protein FDR of 1%. Thirty-two significantly altered proteins were observed with confidence, and the elevated glial fibrillary acidic protein and decreased crystalline proteins in OIR retinas agree well with previous studies. Selected key alterations were further validated by Western blot analysis. Interestingly, Rab21/RhoA/ROCK2/moesin signaling pathway was found to be involved in retinal neovascularization of OIR. Moreover, highly elevated annexin A3, a potential angiogenic mediator, was observed in OIR retinas and may serve as a potential therapeutic target. In conclusion, reproducible ICB profiling enabled reliable discovery of many altered mediators and pathways in OIR retinas, thereby providing new insights into molecular mechanisms involved in pathogenesis of ROP. PMID:25780855

  10. Proteomic profiling of the retinas in a neonatal rat model of oxygen-induced retinopathy with a reproducible ion-current-based MS1 approach.

    PubMed

    Tu, Chengjian; Beharry, Kay D; Shen, Xiaomeng; Li, Jun; Wang, Lianshui; Aranda, Jacob V; Qu, Jun

    2015-05-01

    Investigation of the retina proteome during hypoxia-induced retinal neovascularization is valuable for understanding pathogenesis of retinopathy of prematurity (ROP). Here we employed a reproducible ion-current-based MS1 quantification approach (ICB) to explore the retinal proteomic changes in early stage of ROP in a rat model of oxygen-induced retinopathy (OIR). Retina proteins, which are rich in membrane proteins, were efficiently extracted by a detergent-cocktail and subjected to precipitation/on-pellet-digestion, followed by nano-LC-MS analysis on a 75-cm column with a 7-h gradient. The high reproducibility of sample preparation and chromatography separation enabled excellent peak alignment and contributed to the superior performance of ICB over parallel label-free approaches. In this study, sum-of-intensity with rejection was incorporated to determine the protein ratios. In total, 1325 unique protein groups were quantified from rat retinas (n = 4/group) with at least two distinct peptides at a protein FDR of 1%. Thirty-two significantly altered proteins were observed with confidence, and the elevated glial fibrillary acidic protein and decreased crystalline proteins in OIR retinas agree well with previous studies. Selected key alterations were further validated by Western blot analysis. Interestingly, Rab21/RhoA/ROCK2/moesin signaling pathway was found to be involved in retinal neovascularization of OIR. Moreover, highly elevated annexin A3, a potential angiogenic mediator, was observed in OIR retinas and may serve as a potential therapeutic target. In conclusion, reproducible ICB profiling enabled reliable discovery of many altered mediators and pathways in OIR retinas, thereby providing new insights into molecular mechanisms involved in pathogenesis of ROP. PMID:25780855

  11. Proteome Studies of Filamentous Fungi

    SciTech Connect

    Baker, Scott E.; Panisko, Ellen A.

    2011-04-20

    The continued fast pace of fungal genome sequence generation has enabled proteomic analysis of a wide breadth of organisms that span the breadth of the Kingdom Fungi. There is some phylogenetic bias to the current catalog of fungi with reasonable DNA sequence databases (genomic or EST) that could be analyzed at a global proteomic level. However, the rapid development of next generation sequencing platforms has lowered the cost of genome sequencing such that in the near future, having a genome sequence will no longer be a time or cost bottleneck for downstream proteomic (and transcriptomic) analyses. High throughput, non-gel based proteomics offers a snapshot of proteins present in a given sample at a single point in time. There are a number of different variations on the general method and technologies for identifying peptides in a given sample. We present a method that can serve as a “baseline” for proteomic studies of fungi.

  12. The Cysteine Proteome

    PubMed Central

    Go, Young-Mi; Chandler, Joshua D.; Jones, Dean P.

    2015-01-01

    The cysteine (Cys) proteome is a major component of the adaptive interface between the genome and the exposome. The thiol moiety of Cys undergoes a range of biologic modifications enabling biological switching of structure and reactivity. These biological modifications include sulfenylation and disulfide formation, formation of higher oxidation states, S-nitrosylation, persulfidation, metallation, and other modifications. Extensive knowledge about these systems and their compartmentalization now provides a foundation to develop advanced integrative models of Cys proteome regulation. In particular, detailed understanding of redox signaling pathways and sensing networks is becoming available to discriminate network structures. This research focuses attention on the need for atlases of Cys modifications to develop systems biology models. Such atlases will be especially useful for integrative studies linking the Cys proteome to imaging and other omics platforms, providing a basis for improved redox-based therapeutics. Thus, a framework is emerging to place the Cys proteome as a complement to the quantitative proteome in the omics continuum connecting the genome to the exposome. PMID:25843657

  13. Molecular Biologist's Guide to Proteomics

    PubMed Central

    Graves, Paul R.; Haystead, Timothy A. J.

    2002-01-01

    The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems. PMID:11875127

  14. The Current Status of Medical Marijuana in the United States

    PubMed Central

    2014-01-01

    Medical marijuana is currently a controversial issue in medicine. There are strong pro and con opinions but relatively little scientific data on which to base medical decisions. The unfortunate scheduling of marijuana in class I has limited research and only serves to fuel the controversy. This article will review the history of laws to regulate drugs in the United States in the 20th century to provide context for the current status of medical marijuana. It will include the rationale for opposing medical marijuana laws and the problem of the Schedule I inclusion of marijuana as well as other drugs. It will examine the problems associated with smoking raw marijuana and review other routes of administration. Finally, it examines the inadvisability of medicine's promotion of smoked marijuana. PMID:24765557

  15. Fueling Requirements for Steady State high butane current fraction discharges

    SciTech Connect

    R.Raman

    2003-10-08

    The CT injector originally used for injecting CTs into 1T toroidal field discharges in the TdeV tokamak was shipped PPPL from the Affiliated Customs Brokers storage facility in Montreal during November 2002. All components were transported safely, without damage, and are currently in storage at PPPL, waiting for further funding in order to begin advanced fueling experiments on NSTX. The components are currently insured through the University of Washington. Several technical presentations were made to investigate the feasibility of the CT injector installation on NSTX. These technical presentations, attached to this document, were: (1) Motivation for Compact Toroida Injection in NSTX; (2) Assessment of the Engineering Feasibility of Installing CTF-II on NSTX; (3) Assessment of the Cost for CT Installation on NSTX--A Peer Review; and (4) CT Fueling for NSTX FY 04-08 steady-state operation needs.

  16. Persistent Probability Currents in Non-equilibrium Steady States

    NASA Astrophysics Data System (ADS)

    Zia, Royce; Mellor, Andrew; Mobilia, Mauro; Fox-Kemper, Baylor; Weiss, Jeffrey

    For many interesting phenomena in nature, from all life forms to the global climate, the fundamental hypothesis of equilibrium statistical mechanics does not apply. Instead, they are perhaps better characterized by non-equilibrium steady states, evolving with dynamical rules which violate detailed balance. In particular, such dynamics leads to the existence of non-trivial, persistent probability currents - a principal characteristic of non-equilibrium steady states. In turn, they give rise to the notion of 'probability angular momentum'. Observable manifestations of such abstract concepts will be illustrated in two distinct contexts: a heterogeneous nonlinear voter model and our ocean heat content. Supported in part by grants from the Bloom Agency (Leeds, UK) and the US National Science Foundation: OCE-1245944. AM acknowledges the support of EPSRC Industrial CASE Studentship, Grant No. EP/L50550X/1.

  17. Animal Models of Psychosis: Current State and Future Directions

    PubMed Central

    Forrest, Alexandra D.; Coto, Carlos A.; Siegel, Steven J.

    2014-01-01

    Psychosis is an abnormal mental state characterized by disorganization, delusions and hallucinations. Animal models have become an increasingly important research tool in the effort to understand both the underlying pathophysiology and treatment of psychosis. There are multiple animal models for psychosis, with each formed by the coupling of a manipulation and a measurement. In this manuscript we do not address the diseases of which psychosis is a prominent comorbidity. Instead, we summarize the current state of affairs and future directions for animal models of psychosis. To accomplish this, our manuscript will first discuss relevant behavioral and electrophysiological measurements. We then provide an overview of the different manipulations that are combined with these measurements to produce animal models. The strengths and limitations of each model will be addressed in order to evaluate its cross-species comparability. PMID:25215267

  18. Skewness of steady-state current fluctuations in nonequilibrium systems

    NASA Astrophysics Data System (ADS)

    Belousov, Roman; Cohen, E. G. D.; Wong, Chun-Shang; Goree, John A.; Feng, Yan

    2016-04-01

    A skewness of the probability for instantaneous current fluctuations, in a nonequilibrium steady state, is observed experimentally in a dusty plasma. This skewness is attributed to the spatial asymmetry, which is imminent to the nonequilibrium systems due to the external hydrodynamic gradient. Using the modern framework of the large deviation theory, we extend the Onsager-Machlup ansatz for equilibrium fluctuations to systems with a preferred spatial direction, and provide a modulated Gaussian probability distribution, which is tested by simulations. This probability distribution is also of potential interest for other statistical disciplines. Connections with the principles of statistical mechanics, due to Boltzmann and Gibbs, are discussed as well.

  19. Geographical Information Systems and Health: Current State and Future Directions

    PubMed Central

    2012-01-01

    This paper provides an introduction to Geographical Information Systems (GIS) and how they can be used. It reviews the current state of GIS use in health care before identifying the barriers to more pervasive use of GIS in health. Finally, it makes recommendations for the direction of health GIS research over the next decade and concludes with a call to action to health informatics researchers to stop ignoring a tool and methodology that has such immense potential for improving the health of our communities. PMID:22844644

  20. Assessment of voice quality: Current state-of-the-art.

    PubMed

    Barsties, Ben; De Bodt, Marc

    2015-06-01

    Voice quality is not clearly defined but it can be concluded that it is a multidimensional perceived construct. Therefore, there are broadly two approaches to measure voice quality: (1) subjective measurements to score a client's voice that reflects his or her judgment of the voice and (2) objective measurements by applying specific algorithm to quantify certain aspects of a correlate of vocal production. This paper proposes a collection and discusses a number of critical issues of the current state-of-the-art in voice quality assessments of auditory-perceptual judgment, objective-acoustic analysis and aerodynamic measurements in clinical practice and research that maybe helpful for clinicians and researchers. PMID:25440411

  1. A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting.

    PubMed

    Byron, Adam; Askari, Janet A; Humphries, Jonathan D; Jacquemet, Guillaume; Koper, Ewa J; Warwood, Stacey; Choi, Colin K; Stroud, Matthew J; Chen, Christopher S; Knight, David; Humphries, Martin J

    2015-01-01

    Integrin activation, which is regulated by allosteric changes in receptor conformation, enables cellular responses to the chemical, mechanical and topological features of the extracellular microenvironment. A global view of how activation state converts the molecular composition of the region proximal to integrins into functional readouts is, however, lacking. Here, using conformation-specific monoclonal antibodies, we report the isolation of integrin activation state-dependent complexes and their characterization by mass spectrometry. Quantitative comparisons, integrating network, clustering, pathway and image analyses, define multiple functional protein modules enriched in a conformation-specific manner. Notably, active integrin complexes are specifically enriched for proteins associated with microtubule-based functions. Visualization of microtubules on micropatterned surfaces and live cell imaging demonstrate that active integrins establish an environment that stabilizes microtubules at the cell periphery. These data provide a resource for the interrogation of the global molecular connections that link integrin activation to adhesion signalling. PMID:25609142

  2. A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting

    PubMed Central

    Byron, Adam; Askari, Janet A.; Humphries, Jonathan D.; Jacquemet, Guillaume; Koper, Ewa J.; Warwood, Stacey; Choi, Colin K.; Stroud, Matthew J.; Chen, Christopher S.; Knight, David; Humphries, Martin J.

    2015-01-01

    Integrin activation, which is regulated by allosteric changes in receptor conformation, enables cellular responses to the chemical, mechanical and topological features of the extracellular microenvironment. A global view of how activation state converts the molecular composition of the region proximal to integrins into functional readouts is, however, lacking. Here, using conformation-specific monoclonal antibodies, we report the isolation of integrin activation state-dependent complexes and their characterization by mass spectrometry. Quantitative comparisons, integrating network, clustering, pathway and image analyses, define multiple functional protein modules enriched in a conformation-specific manner. Notably, active integrin complexes are specifically enriched for proteins associated with microtubule-based functions. Visualization of microtubules on micropatterned surfaces and live cell imaging demonstrate that active integrins establish an environment that stabilizes microtubules at the cell periphery. These data provide a resource for the interrogation of the global molecular connections that link integrin activation to adhesion signalling. PMID:25609142

  3. Ultra-Fast Sample Preparation for High-Throughput Proteomics

    SciTech Connect

    Lopez-Ferrer, Daniel; Hixson, Kim K.; Belov, Mikhail E.; Smith, Richard D.

    2011-06-21

    Sample preparation oftentimes can be the Achilles Heel of any analytical process and in the field of proteomics, preparing samples for mass spectrometric analysis is no exception. Current goals, concerning proteomic sample preparation on a large scale, include efforts toward improving reproducibility, reducing the time of processing and ultimately the automation of the entire workflow. This chapter reviews an array of recent approaches applied to bottom-up proteomics sample preparation to reduce the processing time down from hours to minutes. The current state-of-the-art in the field uses different energy inputs like microwave, ultrasound or pressure to perform the four basic steps in sample preparation: protein extraction, denaturation, reduction and alkylation, and digestion. No single energy input for enhancement of proteome sample preparation has become the universal gold standard. Instead, a combination of different energy inputs tend to produce the best results. This chapter further describes the future trends in the field such as the hyphenation of sample preparation with downstream detection and analysis systems. Finally, a detailed protocol describing the combined use of both pressure cycling technology and ultrasonic energy inputs to hasten proteomic sample preparation is presented.

  4. Proteomics links the redox state to calcium signaling during bleaching of the scleractinian coral Acropora microphthalma on exposure to high solar irradiance and thermal stress.

    PubMed

    Weston, Andrew J; Dunlap, Walter C; Beltran, Victor H; Starcevic, Antonio; Hranueli, Daslav; Ward, Malcolm; Long, Paul F

    2015-03-01

    Shipboard experiments were each performed over a 2 day period to examine the proteomic response of the symbiotic coral Acropora microphthalma exposed to acute conditions of high temperature/low light or high light/low temperature stress. During these treatments, corals had noticeably bleached. The photosynthetic performance of residual algal endosymbionts was severely impaired but showed signs of recovery in both treatments by the end of the second day. Changes in the coral proteome were determined daily and, using recently available annotated genome sequences, the individual contributions of the coral host and algal endosymbionts could be extracted from these data. Quantitative changes in proteins relevant to redox state and calcium metabolism are presented. Notably, expression of common antioxidant proteins was not detected from the coral host but present in the algal endosymbiont proteome. Possible roles for elevated carbonic anhydrase in the coral host are considered: to restore intracellular pH diminished by loss of photosynthetic activity, to indirectly limit intracellular calcium influx linked with enhanced calmodulin expression to impede late-stage symbiont exocytosis, or to enhance inorganic carbon transport to improve the photosynthetic performance of algal symbionts that remain in hospite. Protein effectors of calcium-dependent exocytosis were present in both symbiotic partners. No caspase-family proteins associated with host cell apoptosis, with exception of the autophagy chaperone HSP70, were detected, suggesting that algal loss and photosynthetic dysfunction under these experimental conditions were not due to host-mediated phytosymbiont destruction. Instead, bleaching occurred by symbiont exocytosis and loss of light-harvesting pigments of algae that remain in hospite. These proteomic data are, therefore, consistent with our premise that coral endosymbionts can mediate their own retention or departure from the coral host, which may manifest as

  5. Proteomics Links the Redox State to Calcium Signaling During Bleaching of the Scleractinian Coral Acropora microphthalma on Exposure to High Solar Irradiance and Thermal Stress

    PubMed Central

    Weston, Andrew J.; Dunlap, Walter C.; Beltran, Victor H.; Starcevic, Antonio; Hranueli, Daslav; Ward, Malcolm; Long, Paul F.

    2015-01-01

    Shipboard experiments were each performed over a 2 day period to examine the proteomic response of the symbiotic coral Acropora microphthalma exposed to acute conditions of high temperature/low light or high light/low temperature stress. During these treatments, corals had noticeably bleached. The photosynthetic performance of residual algal endosymbionts was severely impaired but showed signs of recovery in both treatments by the end of the second day. Changes in the coral proteome were determined daily and, using recently available annotated genome sequences, the individual contributions of the coral host and algal endosymbionts could be extracted from these data. Quantitative changes in proteins relevant to redox state and calcium metabolism are presented. Notably, expression of common antioxidant proteins was not detected from the coral host but present in the algal endosymbiont proteome. Possible roles for elevated carbonic anhydrase in the coral host are considered: to restore intracellular pH diminished by loss of photosynthetic activity, to indirectly limit intracellular calcium influx linked with enhanced calmodulin expression to impede late-stage symbiont exocytosis, or to enhance inorganic carbon transport to improve the photosynthetic performance of algal symbionts that remain in hospite. Protein effectors of calcium-dependent exocytosis were present in both symbiotic partners. No caspase-family proteins associated with host cell apoptosis, with exception of the autophagy chaperone HSP70, were detected, suggesting that algal loss and photosynthetic dysfunction under these experimental conditions were not due to host-mediated phytosymbiont destruction. Instead, bleaching occurred by symbiont exocytosis and loss of light-harvesting pigments of algae that remain in hospite. These proteomic data are, therefore, consistent with our premise that coral endosymbionts can mediate their own retention or departure from the coral host, which may manifest as

  6. Compact solid-state neutral particle analyzer in current mode.

    PubMed

    Zhu, Y B; Bortolon, A; Heidbrink, W W; Celle, S L; Roquemore, A L

    2012-10-01

    Solid state neutral particle analyzer (ssNPA) arrays are operated in current mode on the DIII-D tokamak and the National Spherical Torus Experiment (NSTX). Compared with conventional pulse-counting NPAs, current-mode operation sacrifices energy resolution to obtain economical, high-bandwidth, pitch-angle resolved measurements. With the success from a new three-channel near-vertical-view current mode ssNPA on DIII-D, the apertures on an existing array on NSTX were expanded to increase the particle influx. The sightlines of both arrays intersect heating beams, enabling both active and passive charge exchange measurements. The spatial resolution at beam intersection is typically 5 cm on both devices. Directly deposited ultra-thin foils on the detector surface block stray photons below the energy of 1 keV and also set low energy threshold about 25 keV for deuterium particle detection. Oscillations in neutral flux produced by high frequency magnetohydrodynamics (MHD) instabilities are readily detected. PMID:23126831

  7. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state

    PubMed Central

    2012-01-01

    Background Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. Results The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from

  8. Immunocapture strategies in translational proteomics

    PubMed Central

    Fredolini, Claudia; Byström, Sanna; Pin, Elisa; Edfors, Fredrik; Tamburro, Davide; Iglesias, Maria Jesus; Häggmark, Anna; Hong, Mun-Gwan; Uhlen, Mathias; Nilsson, Peter; Schwenk, Jochen M

    2016-01-01

    Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field’s current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics. PMID:26558424

  9. Nanoscale Proteomics

    SciTech Connect

    Shen, Yufeng; Tolic, Nikola; Masselon, Christophe D.; Pasa-Tolic, Liljiana; Camp, David G.; Anderson, Gordon A.; Smith, Richard D.; Lipton, Mary S.

    2004-02-01

    This paper describes efforts to develop a liquid chromatography (LC)/mass spectrometry (MS) technology for ultra-sensitive proteomics studies, i.e. nanoscale proteomics. The approach combines high-efficiency nano-scale LC with advanced MS, including high sensitivity and high resolution Fourier transform ion cyclotron resonance (FTICR) MS, to perform both single-stage MS and tandem MS (MS/MS) proteomic analyses. The technology developed enables large-scale protein identification from nanogram size proteomic samples and characterization of more abundant proteins from sub-picogram size complex samples. Protein identification in such studies using MS is feasible from <75 zeptomole of a protein, and the average proteome measurement throughput is >200 proteins/h and ~3 h/sample. Higher throughput (>1000 proteins/h) and more sensitive detection limits can be obtained using a “accurate mass and time” tag approach developed at our laboratory. These capabilities lay the foundation for studies from single or limited numbers of cells.

  10. Sweetened beverages and health: current state of scientific understandings.

    PubMed

    Rippe, James M; Saltzman, Edward

    2013-01-01

    This article summarizes the presentations from the "Sweetened Beverages and Health: Current State of Scientific Understandings" symposium held at the ASN Annual Meeting in Boston, MA on April 23, 2013. The metabolic and health effects of sugar-sweetened beverages were discussed from a variety of points of view by 5 different presenters. Dr. David Allison drew a distinction between conjecture and proof related to sweetened beverages and obesity. Dr. Richard Mattes discussed differences between solid and liquid calories. Dr. Miguel Alonso-Alonso reviewed potential contributions of functional neuroimaging, particularly as they relate to whether sugar is potentially "addictive." Dr. Kimber Stanhope discussed work related to experiments comparing fructose to glucose. Dr. James Rippe presented evidence from randomized controlled trials from his research organization showing no differences among high-fructose corn syrup, sucrose, glucose, or fructose at normal human consumption amounts. PMID:24038246

  11. Single-cell genome sequencing: current state of the science.

    PubMed

    Gawad, Charles; Koh, Winston; Quake, Stephen R

    2016-03-01

    The field of single-cell genomics is advancing rapidly and is generating many new insights into complex biological systems, ranging from the diversity of microbial ecosystems to the genomics of human cancer. In this Review, we provide an overview of the current state of the field of single-cell genome sequencing. First, we focus on the technical challenges of making measurements that start from a single molecule of DNA, and then explore how some of these recent methodological advancements have enabled the discovery of unexpected new biology. Areas highlighted include the application of single-cell genomics to interrogate microbial dark matter and to evaluate the pathogenic roles of genetic mosaicism in multicellular organisms, with a focus on cancer. We then attempt to predict advances we expect to see in the next few years. PMID:26806412

  12. The potential versus current state of water splitting with hematite.

    PubMed

    Zandi, Omid; Hamann, Thomas W

    2015-09-21

    This review describes the potential of hematite as a photoanode material for photoelectrochemical (PEC) water splitting. The current understanding of key loss-mechanisms of hematite are introduced and correlated to performance enhancement strategies. The significant voltage loss associated with overcoming the competitive water oxidation and surface state recombination has recently been surmounted through a combination of high temperature annealing and surface modification with water oxidation catalysts. Substantial efforts have been made at nanostructuring electrodes to increase the charge separation efficiency without sacrificing light absorption. Even in optimized nanostructured electrodes, however, charge separation continues to be the primary barrier to achieving efficient water splitting with hematite. Specifically, significant depletion region recombination results in voltage dependant photocurrent which constrains the fill factor. Thus, future directions to enhance the efficiency of hematite electrodes are discussed with an emphasis on circumventing depletion region recombination. PMID:26267040

  13. The Current State of Silicone-Based Dielectric Elastomer Transducers.

    PubMed

    Madsen, Frederikke B; Daugaard, Anders E; Hvilsted, Søren; Skov, Anne L

    2016-03-01

    Silicone elastomers are promising materials for dielectric elastomer transducers (DETs) due to their superior properties such as high efficiency, reliability and fast response times. DETs consist of thin elastomer films sandwiched between compliant electrodes, and they constitute an interesting class of transducer due to their inherent lightweight and potentially large strains. For the field to progress towards industrial implementation, a leap in material development is required, specifically targeting longer lifetime and higher energy densities to provide more efficient transduction at lower driving voltages. In this review, the current state of silicone elastomers for DETs is summarised and critically discussed, including commercial elastomers, composites, polymer blends, grafted elastomers and complex network structures. For future developments in the field it is essential that all aspects of the elastomer are taken into account, namely dielectric losses, lifetime and the very often ignored polymer network integrity and stability. PMID:26773231

  14. Recommendations for biomarker identification and qualification in clinical proteomics.

    PubMed

    Mischak, Harald; Allmaier, Günter; Apweiler, Rolf; Attwood, Teresa; Baumann, Marc; Benigni, Ariela; Bennett, Samuel E; Bischoff, Rainer; Bongcam-Rudloff, Erik; Capasso, Giovambattista; Coon, Joshua J; D'Haese, Patrick; Dominiczak, Anna F; Dakna, Mohammed; Dihazi, Hassan; Ehrich, Jochen H; Fernandez-Llama, Patricia; Fliser, Danilo; Frokiaer, Jorgen; Garin, Jerome; Girolami, Mark; Hancock, William S; Haubitz, Marion; Hochstrasser, Denis; Holman, Rury R; Ioannidis, John P A; Jankowski, Joachim; Julian, Bruce A; Klein, Jon B; Kolch, Walter; Luider, Theo; Massy, Ziad; Mattes, William B; Molina, Franck; Monsarrat, Bernard; Novak, Jan; Peter, Karlheinz; Rossing, Peter; Sánchez-Carbayo, Marta; Schanstra, Joost P; Semmes, O John; Spasovski, Goce; Theodorescu, Dan; Thongboonkerd, Visith; Vanholder, Raymond; Veenstra, Timothy D; Weissinger, Eva; Yamamoto, Tadashi; Vlahou, Antonia

    2010-08-25

    Clinical proteomics has yielded some early positive results-the identification of potential disease biomarkers-indicating the promise for this analytical approach to improve the current state of the art in clinical practice. However, the inability to verify some candidate molecules in subsequent studies has led to skepticism among many clinicians and regulatory bodies, and it has become evident that commonly encountered shortcomings in fundamental aspects of experimental design mainly during biomarker discovery must be addressed in order to provide robust data. In this Perspective, we assert that successful studies generally use suitable statistical approaches for biomarker definition and confirm results in independent test sets; in addition, we describe a brief set of practical and feasible recommendations that we have developed for investigators to properly identify and qualify proteomic biomarkers, which could also be used as reporting requirements. Such recommendations should help put proteomic biomarker discovery on the solid ground needed for turning the old promise into a new reality. PMID:20739680

  15. ["Good dying"--definition and current state of research].

    PubMed

    Hutter, Nico; Stößel, Ulrich; Meffert, Cornelia; Körner, Mirjam; Bozzaro, Claudia; Becker, Gerhild; Baumeister, Harald

    2015-08-01

    The advances of modern medicine did not only result in prolongation of life expectancy, but also led to a shift from dying at home to dying in public institutions. In western countries most people die at advanced age in medical facilities. Hence, the question regarding the conditions, which should be provided by society and especially medicine, to allow terminally ill people to experience "good dying" is substantial. For this purpose, an examination of patients', family members' and health care providers' understanding of the term " good dying" is required. The present paper aims at shedding light on the term "good dying" and to summarize the current state of research. Therefore, the attributes of "good dying" will be described from the perspectives of patients, family members and health care providers, which are discussed and examined in current medical-sociological research. These attributes can be illustrated on three dimensions: Quality of life at the end of life (e. g. pain relief, mental well-being), quality of dying (e. g. avoiding prolonged dying, autonomy, presence of relatives) and quality of health care at the end of life (e. g. patient-oriented health care, positive communication between health care providers and patients, availability of guidelines). Although the attributes of "good dying" are described in detail in the existing literature, further studies have to clarify the relevance and impact of these attributes as predictors of "good dying". PMID:26306020

  16. Proton Therapy Expansion Under Current United States Reimbursement Models

    SciTech Connect

    Kerstiens, John; Johnstone, Peter A.S.

    2014-06-01

    Purpose: To determine whether all the existing and planned proton beam therapy (PBT) centers in the United States can survive on a local patient mix that is dictated by insurers, not by number of patients. Methods and Materials: We determined current and projected cancer rates for 10 major US metropolitan areas. Using published utilization rates, we calculated patient percentages who are candidates for PBT. Then, on the basis of current published insurer coverage policies, we applied our experience of what would be covered to determine the net number of patients for whom reimbursement is expected. Having determined the net number of covered patients, we applied our average beam delivery times to determine the total number of minutes needed to treat that patient over the course of their treatment. We then calculated our expected annual patient capacity per treatment room to determine the appropriate number of treatment rooms for the area. Results: The population of patients who will be both PBT candidates and will have treatments reimbursed by insurance is significantly smaller than the population who should receive PBT. Coverage decisions made by insurers reduce the number of PBT rooms that are economically viable. Conclusions: The expansion of PBT centers in the US is not sustainable under the current reimbursement model. Viability of new centers will be limited to those operating in larger regional metropolitan areas, and few metropolitan areas in the US can support multiple centers. In general, 1-room centers require captive (non–PBT-served) populations of approximately 1,000,000 lives to be economically viable, and a large center will require a population of >4,000,000 lives. In areas with smaller populations or where or a PBT center already exists, new centers require subsidy.

  17. Beyond astronaut's capabilities: The current state of the art.

    PubMed

    Gemignani, Jessica; Gheysens, Tom; Summerer, Leopold

    2015-08-01

    Space agencies have developed extensive expertise with sustaining human presence in low earth orbits and microgravity. Prolonged human presence in space beyond EarthâĂŹs orbit presents additional, some still unsolved issues. These are linked to the distance to Earth (impossibility of effective tele-operation, psychological effects linked to remoteness from Earth, required autonomy, the handling of emergencies, long mission durations), and to the environments beyond the Earth magnetosphere (radiation levels, local environments including atmospheres, dust, gravity, day-night cycles). These issues have impacts on the spacecraft design, the mission operations, astronaut selection and preparation and required supporting/ enabling technologies. This paper builds upon previous work by Rossini et al. , in critically reviewing and updating the current state of scientific research on enhancing astronaut's capabilities to face some of these challenges. In particular, it discusses the pertinence and feasibility of two approaches aiming at enhancing the chances of success of human missions: induced hibernation state and brain-machine interfaces. PMID:26737075

  18. A Sydney proteome story.

    PubMed

    Williams, Keith L; Gooley, Andrew A; Wilkins, Marc R; Packer, Nicolle H

    2014-07-31

    This is the story of the experience of a multidisciplinary group at Macquarie University in Sydney as we participated in, and impacted upon, major currents that washed through protein science as the field of Proteomics emerged. The large scale analysis of proteins became possible. This is not a history of the field. Instead we have tried to encapsulate the stimulating personal ride we had transiting from conventional academe, to a Major National Research Facility, to the formation of Proteomics company Proteome Systems Ltd. There were lots of blind alleys, wrong directions, but we also got some things right and our efforts, along with those of many other groups around the world, did change the face of protein science. While the transformation is by no means yet complete, protein science is very different from the field in the 1990s. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez. PMID:24735915

  19. Plant proteomics methods and protocols.

    PubMed

    Jorrin-Novo, Jesus V

    2014-01-01

    In this first, introductory chapter, it is intended to summarize from a methodological point of view the state of the art in plant proteomics, focusing on mass spectrometry-based strategies. Thus, this chapter is mainly directed at beginners or at those trying to get into the field, rather than at those with real experience or a long trajectory in plant proteomics research. The different alternative workflows, methods, techniques, and protocols from the experimental design to the data analysis will be briefly commented, with cross references to previous monographs and reviews, as well as to the rest of the book chapters. The difficulty of working with proteins, together with the power, limitations, and challenges of the approach will also be briefly discussed.Proteins, as molecular entities, and the cell proteome, as a whole, are much more complex than what we thought in the past and can be studied in a single experiment. Because of that, fractionation and complementary strategies are required for its study. The MS analysis of complex samples may result in up to 100,000-peptide spectra that cannot be easily analyzed with standard procedures. Therefore, proteomics, more than other -omics, needs a dry lab, time, and an effort in data mining.As main conclusion, it can be stated that proteomics is in its beginnings. It is starting to make important contributions to a proper gene annotation, identification, and characterization of gene products or protein species and to the knowledge of living organisms, having also an enormous application potential to translational research. However, and despite its great potential, and as in any other experimental approach, it is far from being a Pandora's Box. In the case of plant research, the full potential of proteomics is quite far from being totally exploited, and second-, third-, and fourth-generation proteomics techniques are still of very limited use. Most of the plant proteomics papers so far published belong to the

  20. Current state of hereditary angioedema management: A patient survey

    PubMed Central

    Busse, Paula; Christiansen, Sandra C.; Li, Henry; Lumry, William; Davis-Lorton, Mark; Bernstein, Jonathan A.; Frank, Michael; Castaldo, Anthony; Long, Janet F.; Zuraw, Bruce L.; Riedl, Marc

    2015-01-01

    Hereditary angioedema (HAE) is a chronic disease with a high burden of disease that is poorly understood and often misdiagnosed. Availability of treatments, including C1 esterase inhibitor (C1INH) replacement, ecallantide, and icatibant, marks a significant advance for HAE patients. We aimed to better understand the current state of HAE care, from a patient perspective, after the introduction of several novel therapies. One session of the United States Hereditary Angioedema Association 2013 patient summit was devoted to data collection for this study. Patients attending the summit were self-selected, and HAE diagnosis was self-reported. Survey questions assessed patient characteristics, burden of disease, and treatment. Participant responses were captured using an audience response system. We surveyed 149 (80%) type I and II HAE (HAE-C1INH) and 37 (20%) HAE with normal C1INH (HAE-nlC1INH) patients. HAE-C1INH (72%) and HAE-nlCINH patients (76%) equally reported that HAE had a significant impact on quality of life (QOL). A third of HAE-C1INH patients were diagnosed within one year of their first HAE attack, but another third reported a delay of more than 10 years. Most HAE-C1INH (88%) and HAE-nlC1INH (76%) patients had on-demand treatment available. HAE-C1INH patients frequently had an individual treatment plan (76%) compared with 50% of HAE-nlC1INH patients. Most HAE-C1INH patients went to the emergency department (ED) or were hospitalized less than once every six months (80%). Our findings show that HAE management is improving with good access to on-demand and prophylactic treatment options. However, HAE patients still have a significant burden of disease and continued research and educational efforts are needed. PMID:25976438

  1. Novel Molecular Insights into Classical and Alternative Activation States of Microglia as Revealed by Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Proteomics.

    PubMed

    Bell-Temin, Harris; Culver-Cochran, Ashley E; Chaput, Dale; Carlson, Christina M; Kuehl, Melanie; Burkhardt, Brant R; Bickford, Paula C; Liu, Bin; Stevens, Stanley M

    2015-12-01

    Microglia, the resident immune cells of the brain, have been shown to display a complex spectrum of roles that span from neurotrophic to neurotoxic depending on their activation status. Microglia can be classified into four stages of activation, M1, which most closely matches the classical (pro-inflammatory) activation stage, and the alternative activation stages M2a, M2b, and M2c. The alternative activation stages have not yet been comprehensively analyzed through unbiased, global-scale protein expression profiling. In this study, BV2 mouse immortalized microglial cells were stimulated with agonists specific for each of the four stages and total protein expression for 4644 protein groups was quantified using SILAC-based proteomic analysis. After validating induction of the various stages through a targeted cytokine assay and Western blotting of activation states, the data revealed novel insights into the similarities and differences between the various states. The data identify several protein groups whose expression in the anti-inflammatory, pro-healing activation states are altered presumably to curtail inflammatory activation through differential protein expression, in the M2a state including CD74, LYN, SQST1, TLR2, and CD14. The differential expression of these proteins promotes healing, limits phagocytosis, and limits activation of reactive nitrogen species through toll-like receptor cascades. The M2c state appears to center around the down-regulation of a key member in the formation of actin-rich phagosomes, SLP-76. In addition, the proteomic data identified a novel activation marker, DAB2, which is involved in clathrin-mediated endocytosis and is significantly different between M2a and either M1 or M2b states. Western blot analysis of mouse primary microglia stimulated with the various agonists of the classical and alternative activation states revealed a similar trend of DAB2 expression compared with BV2 cells. PMID:26424600

  2. Novel Molecular Insights into Classical and Alternative Activation States of Microglia as Revealed by Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Proteomics*

    PubMed Central

    Bell-Temin, Harris; Culver-Cochran, Ashley E.; Chaput, Dale; Carlson, Christina M.; Kuehl, Melanie; Burkhardt, Brant R.; Bickford, Paula C.; Liu, Bin; Stevens, Stanley M.

    2015-01-01

    Microglia, the resident immune cells of the brain, have been shown to display a complex spectrum of roles that span from neurotrophic to neurotoxic depending on their activation status. Microglia can be classified into four stages of activation, M1, which most closely matches the classical (pro-inflammatory) activation stage, and the alternative activation stages M2a, M2b, and M2c. The alternative activation stages have not yet been comprehensively analyzed through unbiased, global-scale protein expression profiling. In this study, BV2 mouse immortalized microglial cells were stimulated with agonists specific for each of the four stages and total protein expression for 4644 protein groups was quantified using SILAC-based proteomic analysis. After validating induction of the various stages through a targeted cytokine assay and Western blotting of activation states, the data revealed novel insights into the similarities and differences between the various states. The data identify several protein groups whose expression in the anti-inflammatory, pro-healing activation states are altered presumably to curtail inflammatory activation through differential protein expression, in the M2a state including CD74, LYN, SQST1, TLR2, and CD14. The differential expression of these proteins promotes healing, limits phagocytosis, and limits activation of reactive nitrogen species through toll-like receptor cascades. The M2c state appears to center around the down-regulation of a key member in the formation of actin-rich phagosomes, SLP-76. In addition, the proteomic data identified a novel activation marker, DAB2, which is involved in clathrin-mediated endocytosis and is significantly different between M2a and either M1 or M2b states. Western blot analysis of mouse primary microglia stimulated with the various agonists of the classical and alternative activation states revealed a similar trend of DAB2 expression compared with BV2 cells. PMID:26424600

  3. Functional proteomics of barley and barley chloroplasts – strategies, methods and perspectives

    PubMed Central

    Petersen, Jørgen; Rogowska-Wrzesinska, Adelina; Jensen, Ole N.

    2013-01-01

    Barley (Hordeum vulgare) is an important cereal grain that is used in a range of products for animal and human consumption. Crop yield and seed quality has been optimized during decades by plant breeding programs supported by biotechnology and molecular biology techniques. The recently completed whole-genome sequencing of barley revealed approximately 26,100 open reading frames, which provides a foundation for detailed molecular studies of barley by functional genomics and proteomics approaches. Such studies will provide further insights into the mechanisms of, for example, drought and stress tolerance, micronutrient utilization, and photosynthesis in barley. In the present review we present the current state of proteomics research for investigations of barley chloroplasts, i.e., the organelle that contain the photosynthetic apparatus in the plant. We describe several different proteomics strategies and discuss their applications in characterization of the barley chloroplast as well as future perspectives for functional proteomics in barley research. PMID:23515231

  4. Centipede venom: recent discoveries and current state of knowledge.

    PubMed

    Undheim, Eivind A B; Fry, Bryan G; King, Glenn F

    2015-03-01

    Centipedes are among the oldest extant venomous predators on the planet. Armed with a pair of modified, venom-bearing limbs, they are an important group of predatory arthropods and are infamous for their ability to deliver painful stings. Despite this, very little is known about centipede venom and its composition. Advances in analytical tools, however, have recently provided the first detailed insights into the composition and evolution of centipede venoms. This has revealed that centipede venom proteins are highly diverse, with 61 phylogenetically distinct venom protein and peptide families. A number of these have been convergently recruited into the venoms of other animals, providing valuable information on potential underlying causes of the occasionally serious complications arising from human centipede envenomations. However, the majority of venom protein and peptide families bear no resemblance to any characterised protein or peptide family, highlighting the novelty of centipede venoms. This review highlights recent discoveries and summarises the current state of knowledge on the fascinating venom system of centipedes. PMID:25723324

  5. Current state and perspectives of truffle genetics and sustainable biotechnology.

    PubMed

    Poma, Anna; Limongi, Tania; Pacioni, Giovanni

    2006-09-01

    Mycorrhizal fungi belonging to the genus Tuber produce, after the establishment of a productive interaction with a plant host, hypogeous fruitbodies of great economic value known as ''truffles''. This review summarizes the state of art on life cycle, genetic, and biotechnological investigations of Tuber spp. The ascocarp formation in truffles is a consequence of the activation of the sexual phase of the biological cycle. The formation of a dikaryotic secondary mycelium and the karyogamy in the ascal cell (followed by meiosis with ascospores formation) have been hypothesized by several authors but some doubts yet arise from the Tuber cycle by considering that a series of abnormalities have been pointed out in respect to other Ascomycetes. It is unclear if binucleated hyphal cells are derived from the fusion of mononucleated cells belonging to mycelia from different mating types or from one only. According to the karyotypes of Tuber melanosporum, Tuber magnatum, and Tuber borchii, the numbers of hyphal chromosomes suggest a chromosome number of eight (2n); these values are in the range of those of several Ascomycetes and observed for Tuber aestivum (2n=10). The importance and growth in interest during the last years in the fungi protoplasts isolation and transformation techniques can be related to current developments in Tuber genetics and biotechnology. T. borchii could be transformed through liposome-mediated delivery of genetic material as mycelial protoplasts isolation and fusion with liposomes has already been established. On the other hand, Agrobacterium-mediated transformation has been successfully established for T. borchii. PMID:16802150

  6. Current state of genome-scale modeling in filamentous fungi.

    PubMed

    Brandl, Julian; Andersen, Mikael R

    2015-06-01

    The group of filamentous fungi contains important species used in industrial biotechnology for acid, antibiotics and enzyme production. Their unique lifestyle turns these organisms into a valuable genetic reservoir of new natural products and biomass degrading enzymes that has not been used to full capacity. One of the major bottlenecks in the development of new strains into viable industrial hosts is the alteration of the metabolism towards optimal production. Genome-scale models promise a reduction in the time needed for metabolic engineering by predicting the most potent targets in silico before testing them in vivo. The increasing availability of high quality models and molecular biological tools for manipulating filamentous fungi renders the model-guided engineering of these fungal factories possible with comprehensive metabolic networks. A typical fungal model contains on average 1138 unique metabolic reactions and 1050 ORFs, making them a vast knowledge-base of fungal metabolism. In the present review we focus on the current state as well as potential future applications of genome-scale models in filamentous fungi. PMID:25700817

  7. Current State of Value-Based Purchasing Programs.

    PubMed

    Chee, Tingyin T; Ryan, Andrew M; Wasfy, Jason H; Borden, William B

    2016-05-31

    The US healthcare system is rapidly moving toward rewarding value. Recent legislation, such as the Affordable Care Act and the Medicare Access and CHIP Reauthorization Act, solidified the role of value-based payment in Medicare. Many private insurers are following Medicare's lead. Much of the policy attention has been on programs such as accountable care organizations and bundled payments; yet, value-based purchasing (VBP) or pay-for-performance, defined as providers being paid fee-for-service with payment adjustments up or down based on value metrics, remains a core element of value payment in Medicare Access and CHIP Reauthorization Act and will likely remain so for the foreseeable future. This review article summarizes the current state of VBP programs and provides analysis of the strengths, weaknesses, and opportunities for the future. Multiple inpatient and outpatient VBP programs have been implemented and evaluated; the impact of those programs has been marginal. Opportunities to enhance the performance of VBP programs include improving the quality measurement science, strengthening both the size and design of incentives, reducing health disparities, establishing broad outcome measurement, choosing appropriate comparison targets, and determining the optimal role of VBP relative to alternative payment models. VBP programs will play a significant role in healthcare delivery for years to come, and they serve as an opportunity for providers to build the infrastructure needed for value-oriented care. PMID:27245648

  8. Sunscreens in the United States: current status and future outlook.

    PubMed

    Jou, Paul C; Tomecki, Kenneth J

    2014-01-01

    Incidence rates of nonmelanoma skin cancer and melanoma has been on the rise in the United States for the past 20 years. UV radiation (UVR) exposure remains the most preventable environmental risk factor for these cancers. Aside from sun avoidance, sunscreens remain our best protection. UVR directly damages DNA and cause indirect cellular damage through the creation of reactive oxygen species, the sum of which leads to cutaneous immunosuppression and a tumorigenic milieu. The current generation of sunscreens protect from UVR through two main mechanisms: absorption and deflection. In the US, new Food and Drug Association rules require sunscreen manufacturers to evaluate their products not only on sun protection factor but also on broad spectrum UVA protection by the end of 2013. New labeling requirements will also be instituted. The American Academy of Dermatology and the American Academy of Pediatrics have provided specific recommendations for proper sun protection and sunscreen usage. Plant polyphenols such as those isolated from green tea, pomegranate, and grape seed remain an interesting avenue of research as additives to sunscreens or stand-alone products that appear to modulate the immunosuppressive effects of UVR on the skin. Additionally, although UVR induces endogenous cutaneous production of vitamin D, its damaging effects overshadow this positive benefit, especially in light of the ease of achieving recommended amounts of vitamin D through diet and supplementation. PMID:25207382

  9. Current State of Agile User-Centered Design: A Survey

    NASA Astrophysics Data System (ADS)

    Hussain, Zahid; Slany, Wolfgang; Holzinger, Andreas

    Agile software development methods are quite popular nowadays and are being adopted at an increasing rate in the industry every year. However, these methods are still lacking usability awareness in their development lifecycle, and the integration of usability/User-Centered Design (UCD) into agile methods is not adequately addressed. This paper presents the preliminary results of a recently conducted online survey regarding the current state of the integration of agile methods and usability/UCD. A world wide response of 92 practitioners was received. The results show that the majority of practitioners perceive that the integration of agile methods with usability/UCD has added value to their adopted processes and to their teams; has resulted in the improvement of usability and quality of the product developed; and has increased the satisfaction of the end-users of the product developed. The top most used HCI techniques are low-fidelity prototyping, conceptual designs, observational studies of users, usability expert evaluations, field studies, personas, rapid iterative testing, and laboratory usability testing.

  10. Ecopharmacovigilance: Current state, challenges, and opportunities in China.

    PubMed

    Wang, Jun; Hu, Xiamin

    2014-01-01

    In a context of severe pharmaceutical pollution, "ecopharmacovigilance" (EPV) has been an area of novel interest. It aims to ensure that significant environmental issues associated with pharmaceuticals in the environment are identified in a timely way, and managed appropriately. EPV has become a research hotspot as a comprehensive and boundary science in Europe and North America, and regulatory requirements governing the comprehensive environmental risk assessment (ERA) of pharmaceuticals exist in these regions. A speedy Chinese pharmaceutical industry development and drug consumption, China should shoulder more international responsibility and contribute to the worldwide EPV. Compared to the west, EPV in China is in its infancy. We analyzed the current state of EPV-related practice in China and found that many efforts have been made by the Chinese government and specialists to control the ever-worsening environmental pharmaceutical pollution problems, including consummating related policies and regulations, revealing the occurrence and behavior of pharmaceutical residues in environment and developing new technologies to improve their removal performance. Besides, we posed some recommendations on appropriate EPV implementation that can be taken with China in future. These include, building perfect laws and regulation system on EPV, defining the evaluation index for EPV, continuing the clinical rational medication and the pharmaceutical take-back programs in China, popularizing the concept of EPV in China, and strengthening the policy-guided and scientific researches of EPV in pharmaceutical firms and academia. PMID:24550578

  11. Ebola Hemorrhagic Fever and the Current State of Vaccine Development

    PubMed Central

    Hong, Joo Eun; Hong, Kee-Jong; Choi, Woo Young; Lee, Won-Ja; Choi, Yeon Hwa; Jeong, Chung-Hyeon; Cho, Kwang-il

    2014-01-01

    Current Ebola virus outbreak in West Africa already reached the total number of 1,323 including 729 deaths by July 31st. the fatality is around 55% in the southeastern area of Guinea, Sierra Leone, Liberia, and Nigeria. The number of patients with Ebola Hemorrhagic Fever (EHF) was continuously increasing even though the any effective therapeutics or vaccines has not been developed yet. The Ebola virus in Guinea showed 98% homology with Zaire Ebola Virus. Study of the pathogenesis of Ebola virus infection and assess of the various candidates of vaccine have been tried for a long time, especially in United States and some European countries. Even though the attenuated live vaccine and DNA vaccine containing Ebola viral genes were tested and showed efficacy in chimpanzees, those candidates still need clinical tests requiring much longer time than the preclinical development to be approved for the practical treatment. It can be expected to eradicate Ebola virus by a safe and efficient vaccine development similar to the case of smallpox virus which was extinguished from the world by the variola vaccine. PMID:25562048

  12. Biodiesel production--current state of the art and challenges.

    PubMed

    Vasudevan, Palligarnai T; Briggs, Michael

    2008-05-01

    Biodiesel is a clean-burning fuel produced from grease, vegetable oils, or animal fats. Biodiesel is produced by transesterification of oils with short-chain alcohols or by the esterification of fatty acids. The transesterification reaction consists of transforming triglycerides into fatty acid alkyl esters, in the presence of an alcohol, such as methanol or ethanol, and a catalyst, such as an alkali or acid, with glycerol as a byproduct. Because of diminishing petroleum reserves and the deleterious environmental consequences of exhaust gases from petroleum diesel, biodiesel has attracted attention during the past few years as a renewable and environmentally friendly fuel. Since biodiesel is made entirely from vegetable oil or animal fats, it is renewable and biodegradable. The majority of biodiesel today is produced by alkali-catalyzed transesterification with methanol, which results in a relatively short reaction time. However, the vegetable oil and alcohol must be substantially anhydrous and have a low free fatty acid content, because the presence of water or free fatty acid or both promotes soap formation. In this article, we examine different biodiesel sources (edible and nonedible), virgin oil versus waste oil, algae-based biodiesel that is gaining increasing importance, role of different catalysts including enzyme catalysts, and the current state-of-the-art in biodiesel production. PMID:18205018

  13. Ecopharmacovigilance: Current state, challenges, and opportunities in China

    PubMed Central

    Wang, Jun; Hu, Xiamin

    2014-01-01

    In a context of severe pharmaceutical pollution, “ecopharmacovigilance” (EPV) has been an area of novel interest. It aims to ensure that significant environmental issues associated with pharmaceuticals in the environment are identified in a timely way, and managed appropriately. EPV has become a research hotspot as a comprehensive and boundary science in Europe and North America, and regulatory requirements governing the comprehensive environmental risk assessment (ERA) of pharmaceuticals exist in these regions. A speedy Chinese pharmaceutical industry development and drug consumption, China should shoulder more international responsibility and contribute to the worldwide EPV. Compared to the west, EPV in China is in its infancy. We analyzed the current state of EPV-related practice in China and found that many efforts have been made by the Chinese government and specialists to control the ever-worsening environmental pharmaceutical pollution problems, including consummating related policies and regulations, revealing the occurrence and behavior of pharmaceutical residues in environment and developing new technologies to improve their removal performance. Besides, we posed some recommendations on appropriate EPV implementation that can be taken with China in future. These include, building perfect laws and regulation system on EPV, defining the evaluation index for EPV, continuing the clinical rational medication and the pharmaceutical take-back programs in China, popularizing the concept of EPV in China, and strengthening the policy-guided and scientific researches of EPV in pharmaceutical firms and academia. PMID:24550578

  14. Ebola hemorrhagic Fever and the current state of vaccine development.

    PubMed

    Hong, Joo Eun; Hong, Kee-Jong; Choi, Woo Young; Lee, Won-Ja; Choi, Yeon Hwa; Jeong, Chung-Hyeon; Cho, Kwang-Il

    2014-12-01

    Current Ebola virus outbreak in West Africa already reached the total number of 1,323 including 729 deaths by July 31st. the fatality is around 55% in the southeastern area of Guinea, Sierra Leone, Liberia, and Nigeria. The number of patients with Ebola Hemorrhagic Fever (EHF) was continuously increasing even though the any effective therapeutics or vaccines has not been developed yet. The Ebola virus in Guinea showed 98% homology with Zaire Ebola Virus. Study of the pathogenesis of Ebola virus infection and assess of the various candidates of vaccine have been tried for a long time, especially in United States and some European countries. Even though the attenuated live vaccine and DNA vaccine containing Ebola viral genes were tested and showed efficacy in chimpanzees, those candidates still need clinical tests requiring much longer time than the preclinical development to be approved for the practical treatment. It can be expected to eradicate Ebola virus by a safe and efficient vaccine development similar to the case of smallpox virus which was extinguished from the world by the variola vaccine. PMID:25562048

  15. Current Status of Liver Allocation in the United States.

    PubMed

    Elwir, Saleh; Lake, John

    2016-03-01

    The liver transplant allocation system is currently based upon the Model for End-Stage Liver Disease (MELD) score and allocates organs preferentially to patients with the highest scores (ie, the sickest patients) within a defined geographic unit. In addition, certain patient populations, such as patients with hepatocellular carcinoma and portopulmonary hypertension, receive MELD exception points to account for their increased waitlist mortality, which is not reflected by their MELD score. Significant geographic variation in the access to liver transplantation exists throughout the United States. Both the Organ Procurement and Transplant Network Board of Directors and the Health Resources and Services Administration have determined these geographic disparities to be unacceptable. The liver transplant community has worked to develop methods to reduce these geographic disparities and to reexamine how MELD exception points are granted to certain patient populations. As a result, numerous policy changes have been adopted throughout the years that have broadened the sharing of organs through wider geographic sharing. Despite all of these changes, variation in access to liver transplantation continues to exist, and, thus, the liver transplant community continues to examine new ways to address geographic disparities. This paper reviews several of the key changes to the liver allocation system that have occurred since the implementation of MELD allocation in 2002 and provides an overview of potential changes to the system. PMID:27231445

  16. Centipede Venom: Recent Discoveries and Current State of Knowledge

    PubMed Central

    Undheim, Eivind A. B.; Fry, Bryan G.; King, Glenn F.

    2015-01-01

    Centipedes are among the oldest extant venomous predators on the planet. Armed with a pair of modified, venom-bearing limbs, they are an important group of predatory arthropods and are infamous for their ability to deliver painful stings. Despite this, very little is known about centipede venom and its composition. Advances in analytical tools, however, have recently provided the first detailed insights into the composition and evolution of centipede venoms. This has revealed that centipede venom proteins are highly diverse, with 61 phylogenetically distinct venom protein and peptide families. A number of these have been convergently recruited into the venoms of other animals, providing valuable information on potential underlying causes of the occasionally serious complications arising from human centipede envenomations. However, the majority of venom protein and peptide families bear no resemblance to any characterised protein or peptide family, highlighting the novelty of centipede venoms. This review highlights recent discoveries and summarises the current state of knowledge on the fascinating venom system of centipedes. PMID:25723324

  17. Current state of the hydrothermal geochemistry studies at Cerro Prieto

    SciTech Connect

    Fausto L, J.J.; Jimenez S, M.E.; Esquer P, I.

    1981-01-01

    The current state of hydrothermal geochemistry studies being carried out at the field are reported. These studies are based on the results of chemical analysis of water samples collected during 1979 and 1980 at the geothermal wells of the area known as Cerro Prieto I, as well as from those located in the Cerro Prieto II and Cerro Prieto III areas, some of which have only recently started flowing. Data are presented on the chemical variations of the main chemical constituents dissolved in the waters, as well as on the Na/K and Na-K-Ca chemical relations and the temperatures calculated from them and from SiO/sub 2/. Fluid recharge into the reservoir and its direction of flow are interpreted from isotherm contour maps of the field prepared from Na/K and Na-K-Ca geothermometry and from concentration contour maps of some of the main chemical constituents. Well M-43 is discussed as an example of a well affected by well completion problems in its production casing. Its behavior is explained on the basis of the chemical characteristics of the produced water. The chemical changes that have taken place in some of the wells during production are explained by correlating the chemistry with the production mechanisms of the well (steam-water production rates).

  18. Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling Networks Away from a Pro-growth State.

    PubMed

    Sacco, Francesca; Silvestri, Alessandra; Posca, Daniela; Pirrò, Stefano; Gherardini, Pier Federico; Castagnoli, Luisa; Mann, Matthias; Cesareni, Gianni

    2016-03-23

    Metformin is the most frequently prescribed drug for type 2 diabetes. In addition to its hypoglycemic effects, metformin also lowers cancer incidence. This anti-cancer activity is incompletely understood. Here, we profiled the metformin-dependent changes in the proteome and phosphoproteome of breast cancer cells using high-resolution mass spectrometry. In total, we quantified changes of 7,875 proteins and 15,813 phosphosites after metformin changes. To interpret these datasets, we developed a generally applicable strategy that overlays metformin-dependent changes in the proteome and phosphoproteome onto a literature-derived network. This approach suggested that metformin treatment makes cancer cells more sensitive to apoptotic stimuli and less sensitive to pro-growth stimuli. These hypotheses were tested in vivo; as a proof-of-principle, we demonstrated that metformin inhibits the p70S6K-rpS6 axis in a PP2A-phosphatase dependent manner. In conclusion, analysis of deep proteomics reveals both detailed and global mechanisms that contribute to the anti-cancer activity of metformin. PMID:27135362

  19. Genomes to Proteomes

    SciTech Connect

    Panisko, Ellen A.; Grigoriev, Igor; Daly, Don S.; Webb-Robertson, Bobbie-Jo; Baker, Scott E.

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  20. The Origins and Current State of Plastic Surgery Residency in the United States.

    PubMed

    Mackay, Donald Roy; Johnson, Shane

    2015-11-01

    The history of plastic surgery residency training in the United States dates back to the establishment of plastic surgery as a specialty. The pivotal role played by the American Board of Plastic Surgery is outlined. The history of the early regulatory bodies leading to the formation of the Accreditation Council for Graduate Medical Education and the Residency Review Committees and the establishment of the American Council of Academic Plastic Surgeons gives context to our current training models. PMID:26594962

  1. Proteomics of Leaf Tissues from Populus

    SciTech Connect

    Hurst, Gregory {Greg} B; Yang, Xiaohan; Tschaplinski, Timothy J; Tuskan, Gerald A; Lankford, Patricia K; Shah, Manesh B; Jawdy, Sara; Gunter, Lee E; Engle, Nancy L

    2010-01-01

    Trees of the genus Populus are farmed commercially for wood and fiber, and are a potential bioenergy crop. As a scientific model organism, P. trichocarpa was the first forest tree for which the genome sequence has been determined. Knowledge of the Populus proteome will provide a deeper understanding of gene expression patterns in various tissues of the plant. To build on our previous profile of the proteome of xylem tissue in Populus (Kalluri et al., Proteomics 2009, 9, 4871), we are currently developing methods for studying the proteome of Populus leaves.

  2. Cardiovascular pharmacogenomics; state of current knowledge and implementation in practice.

    PubMed

    Shahabi, Payman; Dubé, Marie-Pierre

    2015-04-01

    Pharmacogenomics (PGx) is the science that examines how an individual's genetic make-up affects the safety and efficacy of therapeutic drugs. PGx of response to cardiovascular (CV) medications is of the most successfully translated branches of PGx into the clinical workout. However, the clinical implementation of PGx of CV drugs is yet far beyond the growth of our understanding of the role of genetics in drug therapy. A considerable amount of efforts have been devoted by the regulatory agents like the food and drug administration (FDA) as well as the expert-based networks such as the Clinical Pharmacogenetics Implementation Consortium (CPIC) to overcome the existing barriers. This has been done, at least in part, for some of the most widely prescribed CV drugs, including clopidogrel, warfarin and simvastatin for which the PGx knowledge have been satisfactorily robust to provoke the CPIC to issue the guidelines for these drugs and the FDA to update the drugs' labeling, both strongly recommended the use of genotype-guided dosing for these medications, provided that the genetic data are available. For other drugs, however, studies have produced contradictory results and further large and well-designed clinical trials are required to expand and confirm the clinical utility of their PGx data. This review paper presents the current state of knowledge in the field of PGx of CV medications and describes the facilities assisting to the translation of PGx data into the clinical practice. Afterward, the existing body of PGx literature of the most-commonly used CV medications is comprehensively discussed. PMID:25838112

  3. Current state of forest mapping with Landsat data in Siberia

    NASA Astrophysics Data System (ADS)

    Maksyutov, Shamil; Sedykh, Vladimir; Kuzmenko, Ekaterina; Farber, Sergey; Kalinicheva, Svetlana; Fedorov, Alexander; Schepaschenko, Dmitry

    2016-04-01

    We review a current state of a forest type mapping with Landsat data in Siberia. Target algorithm should be based on dynamic vegetation approach to be applicable to the analysis of the forest type distribution for Siberia, aiming at capability of mapping Siberian forest landscapes for applications such as predicting response of forest composition to climate change. We present data for several areas in West Siberian middle taiga, Central Siberia and East Siberia near Yakutsk. Analysis of the field survey, forest inventory data was made to produce forest type classification accounting for several stages for forest succession and variations in habitats and landforms. Supervised classification was applied to the areas were the ground truth and inventory data are available, including several limited area maps and vegetation survey transects. In Laryegan basin in West Siberia the upland forest areas are dominated by mix of Scots pine on sandy soils and Siberian pine with presence of fir and spruce on the others. Abundance of Scots pine decreases to the west due to change in soils. Those types are separable using Landsat spectral data. In the permafrost area around Yakutsk the most widespread succession type is birch to larch. Three stages of the birch to larch succession are detectable from Landsat image. When Landsat data is used in both West and East Siberia, distinction between deciduous broad-leaved species (birch, aspen, and willow) is generally difficult. Similar problem exist for distinguishing between dark coniferous species (Siberian pine, fir and spruce). Image classification can be improved by applying landform type analysis, such as separation into floodplain, terrace, sloping hills. Additional layers of information can be a promising way to complement Landsat data.

  4. Salivary biomarkers for detection of oral squamous cell carcinoma – current state and recent advances

    PubMed Central

    Yakob, Maha; Fuentes, Laurel; Wang, Marilene B.; Abemayor, Elliot; Wong, David T.W.

    2014-01-01

    Oral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral cavity. Detection of OSCC is currently based on thorough clinical oral examination combined with biopsy for histological analysis. Most cases of OSCC are not detected until the cancer has developed into advanced stages; thus, a reliable early stage diagnostic marker is needed. This literature review presents an overview of the status of current advances in salivary diagnostics for OSCC. Though many protein and mRNA salivary biomarkers have been identified that can detect OSCC with high sensitivity and specificity, the most discernable findings occur with the use of multiple markers. Studies that incorporate proteomic, transcriptomic, and potentially additional “omics”, including methylomics, need to be initiated to bring technology to clinical applications and allow the best use of saliva in diagnosing OSCC. PMID:24883261

  5. Evaluation of the Current State of Integrated Water Quality Modelling

    NASA Astrophysics Data System (ADS)

    Arhonditsis, G. B.; Wellen, C. C.; Ecological Modelling Laboratory

    2010-12-01

    Environmental policy and management implementation require robust methods for assessing the contribution of various point and non-point pollution sources to water quality problems as well as methods for estimating the expected and achieved compliance with the water quality goals. Water quality models have been widely used for creating the scientific basis for management decisions by providing a predictive link between restoration actions and ecosystem response. Modelling water quality and nutrient transport is challenging due a number of constraints associated with the input data and existing knowledge gaps related to the mathematical description of landscape and in-stream biogeochemical processes. While enormous effort has been invested to make watershed models process-based and spatially-distributed, there has not been a comprehensive meta-analysis of model credibility in watershed modelling literature. In this study, we evaluate the current state of integrated water quality modeling across the range of temporal and spatial scales typically utilized. We address several common modeling questions by providing a quantitative assessment of model performance and by assessing how model performance depends on model development. The data compiled represent a heterogeneous group of modeling studies, especially with respect to complexity, spatial and temporal scales and model development objectives. Beginning from 1992, the year when Beven and Binley published their seminal paper on uncertainty analysis in hydrological modelling, and ending in 2009, we selected over 150 papers fitting a number of criteria. These criteria involved publications that: (i) employed distributed or semi-distributed modelling approaches; (ii) provided predictions on flow and nutrient concentration state variables; and (iii) reported fit to measured data. Model performance was quantified with the Nash-Sutcliffe Efficiency, the relative error, and the coefficient of determination. Further, our

  6. The proteome of human saliva

    NASA Astrophysics Data System (ADS)

    Griffin, Timothy J.

    2013-05-01

    Human saliva holds tremendous potential for transforming disease and health diagnostics given its richness of molecular information and non-invasive collection. Enumerating its molecular constituents is an important first step towards reaching this potential. Among the molecules in saliva, proteins and peptides arguably have the most value: they can directly indicate biochemical functions linked to a health condition/disease state, and they are attractive targets for biomarker assay development. However, cataloging and defining the human salivary proteome is challenging given the dynamic, chemically heterogeneous and complex nature of the system. In addition, the overall human saliva proteome is composed of several "sub-proteomes" which include: intact full length proteins, proteins carrying post-translational modifications (PTMs), low molecular weight peptides, and the metaproteome, derived from protein products from nonhuman organisms (e.g. microbes) present in the oral cavity. Presented here will be a summary of communal efforts to meet the challenge of characterizing the multifaceted saliva proteome, focusing on the use of mass spectrometry as the proteomic technology of choice. Implications of these efforts to characterize the salivary proteome in the context of disease diagnostics will also be discussed.

  7. The Current State of Naïve Human Pluripotency

    PubMed Central

    Dodsworth, Benjamin T.; Flynn, Rowan

    2015-01-01

    Abstract Naïve or ground state pluripotency is a cellular state in vitro which resembles cells of the preimplantation epiblast in vivo. This state was first observed in mouse embryonic stem cells and is characterized by high rates of proliferation, the ability to differentiate widely, and global hypomethylation. Human pluripotent stem cells (hPSCs) correspond to a later or “primed” stage of embryonic development. The conversion of hPSCs to a naïve state is desirable as their features should facilitate techniques such as gene editing and more efficient differentiation. Here we review protocols which now allow derivation of naïve human pluripotent stem cells by transgene expression or the use of media formulations containing inhibitors and growth factors and correlate this with pathways involved. Maintenance of these ground state cells is possible using a combination of basic fibroblast growth factor and human leukemia inhibitory factor together with dual inhibition of glycogen synthase kinase 3 beta, and mitogen‐activated protein kinase kinase (MEK). Close similarity between the ground state hPSC and the in vivo preimplantation epiblast have been shown both by demonstrating similar upregulation of endogenous retroviruses and correlation of global RNA‐seq data. This suggests that the human naïve state is not an in vitro artifact. Stem Cells 2015;33:3181–3186 PMID:26119873

  8. Protein translation machinery holds a key for transition of planktonic cells to biofilm state in Enterococcus faecalis: A proteomic approach.

    PubMed

    Qayyum, Shariq; Sharma, Divakar; Bisht, Deepa; Khan, Asad U

    2016-06-10

    Enterococcus faecalis is a member of human gut microflora causing nosocomial infection involving biofilm formation. Ethyl methyl sulfonate induced mutants were analysed using crystal violet assay, SEM and CLSM microscopy which confirmed AK-E12 as biofilm efficient and AK-F6 as biofilm deficient mutants. Growth curve pattern revealed AK-E12 was fast growing whereas, AK-F6 was found slow growing mutant. 2D-Electrophorosis and MALDI-TOF analysis revealed over and underexpression of many translation-elongation associated proteins in mutants compared to wild type. Protein translation elongation factor G, translation elongation factor Tu and ribosomal subunit interface proteins were underexpressed and UTP-glucose-1-phosphate uridylyl transferase and cell division protein divIVA were overexpressed in AK-E12 as compared to wild type. In AK-F6, except 10 kDa chaperonin which was over-expressed other selected proteins were found to be suppressed. RT-PCR confirmed proteomic data except for the translation elongation factor G which showed contradictory data of proteome expression in AK-E12. Protein-protein interaction networks were constructed using STRING 10.0 which demonstrated strong connection of translation-elongation proteins with other proteins. Hence, it concludes from the data that translation elongation factors are important in transition of planktonic cells to biofilm cells in Enterococcus faecalis. PMID:27144316

  9. Fault current limiter with solid-state circuit breakers

    NASA Astrophysics Data System (ADS)

    Bălan, H.; Neamț, L.; Buzdugan, M. I.; Varodi, T.; Pop, E.

    2016-08-01

    Switching of power circuit breakers is an important technical issue, especially at short circuit, since the fault current cause thermal and dynamic stresses, and the power quality worsens. Recently, the development of distributed renewable electricity induces the short circuit protection problematic because the distributed production of electric energy cause the transport networks to lose their radial character and disturbs the protective relays coordination. The modern technologies for power switching uses static fault current limiters, which offers a viable solution to remove the problems caused by large fault currents in the system. An appropriate design of the current limiting device reduces the thermal and dynamic stress and limits the fault current to a low value. The static switches are based on high power semiconductor devices that offer advantages compared to mechanical switches. Using a fault current limiter that minimizes the effect of distributed generation of electricity in a radial network on the co-ordination of protective relays is a solution to this problem in terms of switching speed and lifespan of power switches.

  10. ProCon - PROteomics CONversion tool.

    PubMed

    Mayer, Gerhard; Stephan, Christian; Meyer, Helmut E; Kohl, Michael; Marcus, Katrin; Eisenacher, Martin

    2015-11-01

    With the growing amount of experimental data produced in proteomics experiments and the requirements/recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics data in public repositories arises. For such an upload one needs proteomics data in a standardized format. Therefore, it is desirable, that the proprietary vendor's software will integrate in the future such an export functionality using the standard formats for proteomics results defined by the HUPO-PSI group. Currently not all search engines and analysis tools support these standard formats. In the meantime there is a need to provide user-friendly free-to-use conversion tools that can convert the data into such standard formats in order to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. ProCon is such a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML. It allows the conversion of Sequest™/Comet .out files, of search results from the popular and often used ProteomeDiscoverer® 1.x (x=versions 1.1 to1.4) software and search results stored in the LIMS systems ProteinScape® 1.3 and 2.1 into mzIdentML and PRIDE XML. This article is part of a Special Issue entitled: Computational Proteomics. PMID:26182917

  11. Current Developments in Communications Law in the United States

    ERIC Educational Resources Information Center

    Hadl, Robert D.

    1973-01-01

    Article reviews some of the major developments in communications law in the United States in the past year (1972). Significant events are covered in the areas of cable television, television programming and domestic satelites. (Author)

  12. Current State of the U.S. Ethanol Industry

    SciTech Connect

    Urbanchuk, John

    2010-11-30

    The objective of this study is to provide a comprehensive overview of the state of the U.S. ethanol industry and to outline the major forces that will affect the development of the industry over the next decade.

  13. Current challenges in detecting food allergens by shotgun and targeted proteomic approaches: a case study on traces of peanut allergens in baked cookies.

    PubMed

    Pedreschi, Romina; Nørgaard, Jørgen; Maquet, Alain

    2012-02-01

    There is a need for selective and sensitive methods to detect the presence of food allergens at trace levels in highly processed food products. In this work, a combination of non-targeted and targeted proteomics approaches are used to illustrate the difficulties encountered in the detection of the major peanut allergens Ara h 1, Ara h 2 and Ara h 3 from a representative processed food matrix. Shotgun proteomics was employed for selection of the proteotypic peptides for targeted approaches via selective reaction monitoring. Peanut presence through detection of the proteotypic Ara h 3/4 peptides AHVQVVDSNGNR (m/z 432.5, 3+) and SPDIYNPQAGSLK (m/z 695.4, 2+) was confirmed and the developed method was able to detect peanut presence at trace levels (≥10 μg peanut g(-1) matrix) in baked cookies. PMID:22413066

  14. Current Challenges in Detecting Food Allergens by Shotgun and Targeted Proteomic Approaches: A Case Study on Traces of Peanut Allergens in Baked Cookies

    PubMed Central

    Pedreschi, Romina; Nørgaard, Jørgen; Maquet, Alain

    2012-01-01

    There is a need for selective and sensitive methods to detect the presence of food allergens at trace levels in highly processed food products. In this work, a combination of non-targeted and targeted proteomics approaches are used to illustrate the difficulties encountered in the detection of the major peanut allergens Ara h 1, Ara h 2 and Ara h 3 from a representative processed food matrix. Shotgun proteomics was employed for selection of the proteotypic peptides for targeted approaches via selective reaction monitoring. Peanut presence through detection of the proteotypic Ara h 3/4 peptides AHVQVVDSNGNR (m/z 432.5, 3+) and SPDIYNPQAGSLK (m/z 695.4, 2+) was confirmed and the developed method was able to detect peanut presence at trace levels (≥10 μg peanut g−1 matrix) in baked cookies. PMID:22413066

  15. Parasites, proteomes and systems: has Descartes’ clock run out of time?

    PubMed Central

    WASTLING, J. M.; ARMSTRONG, S. D.; KRISHNA, R.; XIA, D.

    2012-01-01

    SUMMARY Systems biology aims to integrate multiple biological data types such as genomics, transcriptomics and proteomics across different levels of structure and scale; it represents an emerging paradigm in the scientific process which challenges the reductionism that has dominated biomedical research for hundreds of years. Systems biology will nevertheless only be successful if the technologies on which it is based are able to deliver the required type and quality of data. In this review we discuss how well positioned is proteomics to deliver the data necessary to support meaningful systems modelling in parasite biology. We summarise the current state of identification proteomics in parasites, but argue that a new generation of quantitative proteomics data is now needed to underpin effective systems modelling. We discuss the challenges faced to acquire more complete knowledge of protein post-translational modifications, protein turnover and protein-protein interactions in parasites. Finally we highlight the central role of proteome-informatics in ensuring that proteomics data is readily accessible to the user-community and can be translated and integrated with other relevant data types. PMID:22828391

  16. High School Feedback: An Analysis of States' Current Efforts

    ERIC Educational Resources Information Center

    Data Quality Campaign, 2011

    2011-01-01

    There is increased demand from multiple stakeholders for information about K-12 students' success after high school. When this information is provided back to high schools, it is often referred to as "high school feedback" information. This working document captures knowledge about states' capacity to and progress in providing high school feedback…

  17. Current Status of Teacher Shortage in the United States.

    ERIC Educational Resources Information Center

    Capa, Yesim; Loadman, William E.; Bryant, B. J.

    Every year the American Association of Employment in Education (AAEE) conducts a survey of the status of teacher supply and demand in the United States. In 2001, the 25th annual survey sent a survey instrument to 1,265 teacher preparation institutions to study the supply side of teacher availability, and responses were received from 494…

  18. Current status of the state-and-transition framework

    Technology Transfer Automated Retrieval System (TEKTRAN)

    State-and-transition models (STM) have been widely adopted as a tool for explaining plant community dynamics and response to disturbance within rangeland ecosystems. Our understanding of the STM concepts has advanced substantially since they were introduced by Westoby et al. (1989) and modified by ...

  19. Adult Cigarette Smoking in the United States: Current Estimates

    MedlinePlus

    ... Report 2015;64(44):1233–40 [accessed 2016 Mar 14]. U.S. Department of Health and Human Services. ... Office on Smoking and Health, 2014 [accessed 2016 Mar 14]. Centers for Disease Control and Prevention . State ...

  20. Social validity assessments: is current practice state of the art?

    PubMed Central

    Schwartz, I S; Baer, D M

    1991-01-01

    The use of evaluative feedback from consumers to guide program planning and evaluation is often referred to as the assessment of social validity. Differing views of its role and value in applied behavior analysis have emerged, and increasingly stereotyped assessments of social validity are becoming commonplace. This paper argues that current applications of social validity assessments are straying from the point originally proposed for them. Thus, several suggestions for improving current social validity assessment are proposed, including (a) expanding the definition of consumers to acknowledge the variety of community members able and likely to affect a program's survival, (b) increasing the psychometric rigor of social validity assessments, (c) extending assessment to heretofore underrepresented populations, (d) implementing widespread application of well-designed social validity assessments, (e) increasing meaningful consumer involvement in the planning and evaluation of behavioral programs, and (f) educating consumers to make better informed programming decisions. PMID:1890040

  1. State-of-the-art housekeeping proteins for quantitative western blotting: Revisiting the first draft of the human proteome.

    PubMed

    Lee, Hyun-Gwan; Jo, Jihoon; Hong, Hyun-Hee; Kim, Kee K; Park, Joong-Ki; Cho, Sung-Jin; Park, Chungoo

    2016-07-01

    Western blotting (WB) analysis is the most popular and widely used methodology for protein detection and characterization over recent decades. In accordance with the advancement of the technologies for the acquisition of WB signals, a quantitative value is used to present the abundance of target proteins in a complex sample, thereby requiring the use of specific proteins as internal references that represent total proteins. Heretofore, proteins encoded by housekeeping genes such as GAPDH, β-tubulin and β-actin have been commonly used as loading controls without any hesitation because their mRNA expression levels tend to be high and constant in many different cells and tissues. Experimentally, however, some of the housekeeping reference proteins are often displayed with inconsistent expression levels in both homogeneous and heterogeneous tissues, and, in terms of mRNA levels, they have a weak correlation to the abundance of proteins. To estimate accurate, reliable, and reproducible protein quantifications, it is crucial to define appropriate reference controls. For this paper, we explored the recently released large-scale, human proteomic database ProteomicsDB including 16 857 liquid chromatography tandem-mass-spectrometry data from 27 human tissues, and suggest 20 ubiquitously- and constitutively-expressed, putative internal-reference controls for the quantification of differential protein expressions. Intriguingly, the most commonly used, known housekeeping genes were entirely excluded in our newly defined candidates. Although the applications of the candidates under many different biological conditions and in other organisms are yet to be empirically verified, we propose reliable, potential loading controls for a WB analysis in this paper. PMID:27125885

  2. Left ventricular assist devices-current state and perspectives.

    PubMed

    Prinzing, Anatol; Herold, Ulf; Berkefeld, Anna; Krane, Markus; Lange, Rüdiger; Voss, Bernhard

    2016-08-01

    Mechanical circulatory support devices have become an important treatment tool for severe acute and chronic heart failure, since heart transplantation cannot meet the demands because of a lack of available donor organs. Since implantation of the first ventricular assist device a constant development of the suitability of these devices has been made. This review will introduce different generations of left ventricular assist devices (LVAD) and elaborate on clinical indications, risk stratification and current literature. PMID:27621895

  3. [Physiotherapeutic care marketing research: current state-of-the art].

    PubMed

    Babaskin, D V

    2011-01-01

    Successful introduction of modern technologies into the national health care systems strongly depends on the current pharmaceutical market situation. The present article is focused on the peculiarities of marketing research with special reference to physiotherapeutic services and commodities. Analysis of the structure and sequence of marketing research processes is described along with the methods applied for the purpose including their support by the use of Internet resources and technologies. PMID:21574299

  4. Minimally invasive veneers: current state of the art

    PubMed Central

    Vanlıoğlu, Burçin Akoğlu; Kulak-Özkan, Yasemin

    2014-01-01

    Ceramic veneers are considered a conservative solution for patients requiring improvement of the shape, color, or position of their anterior teeth. Ceramic veneers have been extensively and successfully used to mask intrinsic staining, to give the appearance of straightening, and to correct minor malformations of anterior teeth without the removal of substantial amounts of sound tooth substance. The current literature was reviewed to search for the most important parameters determining the long-term success and correct application of ceramic veneers. PMID:25506248

  5. Left ventricular assist devices—current state and perspectives

    PubMed Central

    Herold, Ulf; Berkefeld, Anna; Krane, Markus; Lange, Rüdiger; Voss, Bernhard

    2016-01-01

    Mechanical circulatory support devices have become an important treatment tool for severe acute and chronic heart failure, since heart transplantation cannot meet the demands because of a lack of available donor organs. Since implantation of the first ventricular assist device a constant development of the suitability of these devices has been made. This review will introduce different generations of left ventricular assist devices (LVAD) and elaborate on clinical indications, risk stratification and current literature. PMID:27621895

  6. Minimally invasive veneers: current state of the art.

    PubMed

    Vanlıoğlu, Burçin Akoğlu; Kulak-Özkan, Yasemin

    2014-01-01

    Ceramic veneers are considered a conservative solution for patients requiring improvement of the shape, color, or position of their anterior teeth. Ceramic veneers have been extensively and successfully used to mask intrinsic staining, to give the appearance of straightening, and to correct minor malformations of anterior teeth without the removal of substantial amounts of sound tooth substance. The current literature was reviewed to search for the most important parameters determining the long-term success and correct application of ceramic veneers. PMID:25506248

  7. Melanoma control in the United States: current status.

    PubMed

    Koh, H K; Geller, A C

    1995-01-01

    Screening and education for melanoma/skin cancer are receiving increasing worldwide attention. In an attempt to improve melanoma control in the United States, where incidence and mortality rates continue to increase, the American Academy of Dermatology (AAD) has provided free skin cancer screenings to more than 600,000 Americans and prevention messages to millions more. This chapter reviews and summarizes ongoing melanoma control activities in the United States, including prevention, education, and early detection/screening. We also address outcome measures in melanoma control and suggest that the unique external and visible nature of skin cancer blurs the distinction between screening and education. Measuring and evaluating the benefits of international melanoma control activities presents many challenging tasks. Future collaborative work must include complementary strategies in melanoma/skin cancer prevention, education, and screening to combat the worldwide increase in melanoma incidence and mortality. PMID:7597293

  8. Current trends in suicidal behavior in the United States.

    PubMed

    Frederick, C J

    1978-04-01

    Suicidal behavior in the United States from 1900 to 1975 is reviewed. The data presented cover demographic variables such as: age, sex, color, and geographic area. While the overall suicide rate continues to increase, the most striking upturn can be seen in both sexes between the ages of 15 to 25 years. The need for a wide range of innovative approaches and increased research is manifest. PMID:677350

  9. State Poverty-Based Education Funding: A Survey of Current Programs and Options for Improvement.

    ERIC Educational Resources Information Center

    Carey, Kevin

    This paper describes the current status of state poverty-based education funding programs, discussing how to implement or improve them. Researchers surveyed education finance officials in the 49 states with multiple school districts. Results indicate that 38 states currently distribute some education funds on the basis of poverty. A total of 75…

  10. Proteomic profiling of lymphocytes in autoimmunity, inflammation and cancer

    PubMed Central

    2014-01-01

    Lymphocytes play important roles in the balance between body defense and noxious agents involved in a number of diseases, e.g. autoimmune diseases, allergic inflammation and cancer. The proteomic analyses have been applied to identify and validate disease-associated and disease-specific biomarkers for therapeutic strategies of diseases. The proteomic profiles of lymphocytes may provide more information to understand their functions and roles in the development of diseases, although proteomic approaches in lymphocytes are still limited. The present review overviewed the proteomics-based studies on lymphocytes to headlight the proteomic profiles of lymphocytes in diseases, such as autoimmune diseases, allergic inflammation and cancer, with a special focus on lung diseases. We will explore the potential significance of diagnostic biomarkers and therapeutic targets from the current status in proteomic studies of lymphocytes and discuss the value of the currently available proteomic methodologies in the lymphocytes research. PMID:24397796

  11. Cell death proteomics database: consolidating proteomics data on cell death.

    PubMed

    Arntzen, Magnus Ø; Bull, Vibeke H; Thiede, Bernd

    2013-05-01

    Programmed cell death is a ubiquitous process of utmost importance for the development and maintenance of multicellular organisms. More than 10 different types of programmed cell death forms have been discovered. Several proteomics analyses have been performed to gain insight in proteins involved in the different forms of programmed cell death. To consolidate these studies, we have developed the cell death proteomics (CDP) database, which comprehends data from apoptosis, autophagy, cytotoxic granule-mediated cell death, excitotoxicity, mitotic catastrophe, paraptosis, pyroptosis, and Wallerian degeneration. The CDP database is available as a web-based database to compare protein identifications and quantitative information across different experimental setups. The proteomics data of 73 publications were integrated and unified with protein annotations from UniProt-KB and gene ontology (GO). Currently, more than 6,500 records of more than 3,700 proteins are included in the CDP. Comparing apoptosis and autophagy using overrepresentation analysis of GO terms, the majority of enriched processes were found in both, but also some clear differences were perceived. Furthermore, the analysis revealed differences and similarities of the proteome between autophagosomal and overall autophagy. The CDP database represents a useful tool to consolidate data from proteome analyses of programmed cell death and is available at http://celldeathproteomics.uio.no. PMID:23537399

  12. Miniature x-ray tubes: current state and future prospects

    NASA Astrophysics Data System (ADS)

    Filip, V.; Filip, L. D.; Okuyama, F.

    2013-03-01

    Over the last decade, field emission miniature x-ray tubes emerged as cutting-edge applications of nanotechnology, possessing massive potential for use in various important fields, including that of precision medical therapy. The article essentially presents a review of such new devices reported in the literature. Additional discussions on the necessity of stabilizing the electron beam that generates x-rays are also included, and a simple technique for minimizing the current fluctuations is described. It is also pointed out that further miniaturization of field emission x-ray sources may need new concepts in designing the tube in shapes acting as ``self focusing'' structures for the electron beams.

  13. Mining the plasma proteome for disease applications across seven logs of protein abundance.

    PubMed

    Zhang, Q; Faca, V; Hanash, S

    2011-01-01

    The current state of proteomics technologies has sufficiently advanced to allow in-depth quantitative analysis of the plasma proteome and development of a related knowledge base. Here we review approaches that have been applied to increase depth of analysis by mass spectrometry given the substantial complexity of plasma and the vast dynamic range of protein abundance. Fractionation strategies resulting in reduced complexity of individual fractions followed by mass spectrometry analysis of digests from individual fractions has allowed well in excess of 1000 proteins to be identified and quantified with high confidence that span more than seven logs of protein abundance. Such depth of analysis has contributed to elucidation of plasma proteome variation in health and of protein changes associated with disease states. PMID:21062094

  14. Imaging of HCC—Current State of the Art

    PubMed Central

    Schraml, Christina; Kaufmann, Sascha; Rempp, Hansjoerg; Syha, Roland; Ketelsen, Dominik; Notohamiprodjo, Mike; Nikolaou, Konstantin

    2015-01-01

    Early diagnosis of hepatocellular carcinoma (HCC) is crucial for optimizing treatment outcome. Ongoing advances are being made in imaging of HCC regarding detection, grading, staging, and also treatment monitoring. This review gives an overview of the current international guidelines for diagnosing HCC and their discrepancies as well as critically summarizes the role of magnetic resonance imaging (MRI) and computed tomography (CT) techniques for imaging in HCC. The diagnostic performance of MRI with nonspecific and hepatobililiary contrast agents and the role of functional imaging with diffusion-weighted imaging will be discussed. On the other hand, CT as a fast, cheap and easily accessible imaging modality plays a major role in the clinical routine work-up of HCC. Technical advances in CT, such as dual energy CT and volume perfusion CT, are currently being explored for improving detection, characterization and staging of HCC with promising results. Cone beam CT can provide a three-dimensional analysis of the liver with tumor and vessel characterization comparable to cross-sectional imaging so that this technique is gaining an increasing role in the peri-procedural imaging of HCC treated with interventional techniques. PMID:26854169

  15. Imaging of HCC-Current State of the Art.

    PubMed

    Schraml, Christina; Kaufmann, Sascha; Rempp, Hansjoerg; Syha, Roland; Ketelsen, Dominik; Notohamiprodjo, Mike; Nikolaou, Konstantin

    2015-01-01

    Early diagnosis of hepatocellular carcinoma (HCC) is crucial for optimizing treatment outcome. Ongoing advances are being made in imaging of HCC regarding detection, grading, staging, and also treatment monitoring. This review gives an overview of the current international guidelines for diagnosing HCC and their discrepancies as well as critically summarizes the role of magnetic resonance imaging (MRI) and computed tomography (CT) techniques for imaging in HCC. The diagnostic performance of MRI with nonspecific and hepatobililiary contrast agents and the role of functional imaging with diffusion-weighted imaging will be discussed. On the other hand, CT as a fast, cheap and easily accessible imaging modality plays a major role in the clinical routine work-up of HCC. Technical advances in CT, such as dual energy CT and volume perfusion CT, are currently being explored for improving detection, characterization and staging of HCC with promising results. Cone beam CT can provide a three-dimensional analysis of the liver with tumor and vessel characterization comparable to cross-sectional imaging so that this technique is gaining an increasing role in the peri-procedural imaging of HCC treated with interventional techniques. PMID:26854169

  16. Bassoonists' medical problems-current state of knowledge.

    PubMed

    Dawson, William J

    2012-06-01

    Specific musical instruments can be a source of physical problems to their players. Based on reviews of the literature and personal experience, this paper summarizes current knowledge of problems affecting musicians who play instruments in the bassoon family (including the bassoon, contrabassoon, and several other instruments). Prevalence rates are higher in reports of surveys (ranging up to 86%), compared to clinical reports of patients seen and treated. Significant risk factors include young age, small body size, female gender, and use of large instruments. Problems unique to bassoonists are rare; most physical difficulties also are seen in general musculoskeletal clinical practices and in musicians playing all types of instruments. The left upper extremity is more commonly affected by overuse-related conditions in bassoonists. Non-playing-related problems are equally important for consideration (such as degenerative disorders and acute trauma), since they also affect practice and performance. Little experimental data exist to validate current and widely-held principles of treatment, rehabilitation, and prevention. PMID:22739824

  17. Current state of herbicides in herbicide-resistant crops.

    PubMed

    Green, Jerry M

    2014-09-01

    Current herbicide and herbicide trait practices are changing in response to the rapid spread of glyphosate-resistant weeds. Growers urgently needed glyphosate when glyphosate-resistant crops became available because weeds were becoming widely resistant to most commonly used selective herbicides, making weed management too complex and time consuming for large farm operations. Glyphosate made weed management easy and efficient by controlling all emerged weeds at a wide range of application timings. However, the intensive use of glyphosate over wide areas and concomitant decline in the use of other herbicides led eventually to the widespread evolution of weeds resistant to glyphosate. Today, weeds that are resistant to glyphosate and other herbicide types are threatening current crop production practices. Unfortunately, all commercial herbicide modes of action are over 20 years old and have resistant weed problems. The severity of the problem has prompted the renewal of efforts to discover new weed management technologies. One technology will be a new generation of crops with resistance to glyphosate, glufosinate and other existing herbicide modes of action. Other technologies will include new chemical, biological, cultural and mechanical methods for weed management. From the onset of commercialization, growers must now preserve the utility of new technologies by integrating their use with other weed management technologies in diverse and sustainable systems. PMID:24446395

  18. Pediatric Heart Failure: Current State and Future Possibilities

    PubMed Central

    Jang, Gi Young

    2015-01-01

    Heart failure is a complex pathophysiological syndrome that can occur in children from a variety of diseases, including cardiomyopathies, myocarditis, and congenital heart disease. The condition is associated with a high rate of morbidity and mortality and places a significant burden on families of affected children and to society as a whole. Current medical therapy is taken largely from the management of heart failure in adults, though clear survival benefit of these medications are lacking. Ventricular assist devices (VADs) have taken an increasingly important role in the management of advanced heart failure in children. The predominant role of these devices has been as a bridge to heart transplantation, and excellent results are currently achieved for most children with cardiomyopathies. There is an ongoing investigation to improve outcomes in high-risk populations, such as small infants and those with complex congenital heart disease, including patients with functionally univentricular hearts. Additionally, there is an active investigation and interest in expansion of VADs beyond the predominant utilization as a bridge to a heart transplant into ventricular recovery, device explant without a heart transplantation (bridge to recovery), and placement of devices without the expectation of recovery or transplantation (destination therapy). PMID:25653697

  19. Advanced Imaging in Femoroacetabular Impingement: Current State and Future Prospects.

    PubMed

    Bittersohl, Bernd; Hosalkar, Harish S; Hesper, Tobias; Tiderius, Carl Johan; Zilkens, Christoph; Krauspe, Rüdiger

    2015-01-01

    Symptomatic femoroacetabular impingement (FAI) is now a known precursor of early osteoarthritis (OA) of the hip. In terms of clinical intervention, the decision between joint preservation and joint replacement hinges on the severity of articular cartilage degeneration. The exact threshold during the course of disease progression when the cartilage damage is irreparable remains elusive. The intention behind radiographic imaging is to accurately identify the morphology of osseous structural abnormalities and to accurately characterize the chondrolabral damage as much as possible. However, both plain radiographs and computed tomography (CT) are insensitive for articular cartilage anatomy and pathology. Advanced magnetic resonance imaging (MRI) techniques include magnetic resonance arthrography and biochemically sensitive techniques of delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), T1rho (T1ρ), T2/T2* mapping, and several others. The diagnostic performance of these techniques to evaluate cartilage degeneration could improve the ability to predict an individual patient-specific outcome with non-surgical and surgical care. This review discusses the facts and current applications of biochemical MRI for hip joint cartilage assessment covering the roles of dGEMRIC, T2/T2*, and T1ρ mapping. The basics of each technique and their specific role in FAI assessment are outlined. Current limitations and potential pitfalls as well as future directions of biochemical imaging are also outlined. PMID:26258129

  20. Advanced Imaging in Femoroacetabular Impingement: Current State and Future Prospects

    PubMed Central

    Bittersohl, Bernd; Hosalkar, Harish S.; Hesper, Tobias; Tiderius, Carl Johan; Zilkens, Christoph; Krauspe, Rüdiger

    2015-01-01

    Symptomatic femoroacetabular impingement (FAI) is now a known precursor of early osteoarthritis (OA) of the hip. In terms of clinical intervention, the decision between joint preservation and joint replacement hinges on the severity of articular cartilage degeneration. The exact threshold during the course of disease progression when the cartilage damage is irreparable remains elusive. The intention behind radiographic imaging is to accurately identify the morphology of osseous structural abnormalities and to accurately characterize the chondrolabral damage as much as possible. However, both plain radiographs and computed tomography (CT) are insensitive for articular cartilage anatomy and pathology. Advanced magnetic resonance imaging (MRI) techniques include magnetic resonance arthrography and biochemically sensitive techniques of delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), T1rho (T1ρ), T2/T2* mapping, and several others. The diagnostic performance of these techniques to evaluate cartilage degeneration could improve the ability to predict an individual patient-specific outcome with non-surgical and surgical care. This review discusses the facts and current applications of biochemical MRI for hip joint cartilage assessment covering the roles of dGEMRIC, T2/T2*, and T1ρ mapping. The basics of each technique and their specific role in FAI assessment are outlined. Current limitations and potential pitfalls as well as future directions of biochemical imaging are also outlined. PMID:26258129

  1. Current state of the art of vision based SLAM

    NASA Astrophysics Data System (ADS)

    Muhammad, Naveed; Fofi, David; Ainouz, Samia

    2009-02-01

    The ability of a robot to localise itself and simultaneously build a map of its environment (Simultaneous Localisation and Mapping or SLAM) is a fundamental characteristic required for autonomous operation of the robot. Vision Sensors are very attractive for application in SLAM because of their rich sensory output and cost effectiveness. Different issues are involved in the problem of vision based SLAM and many different approaches exist in order to solve these issues. This paper gives a classification of state-of-the-art vision based SLAM techniques in terms of (i) imaging systems used for performing SLAM which include single cameras, stereo pairs, multiple camera rigs and catadioptric sensors, (ii) features extracted from the environment in order to perform SLAM which include point features and line/edge features, (iii) initialisation of landmarks which can either be delayed or undelayed, (iv) SLAM techniques used which include Extended Kalman Filtering, Particle Filtering, biologically inspired techniques like RatSLAM, and other techniques like Local Bundle Adjustment, and (v) use of wheel odometry information. The paper also presents the implementation and analysis of stereo pair based EKF SLAM for synthetic data. Results prove the technique to work successfully in the presence of considerable amounts of sensor noise. We believe that state of the art presented in the paper can serve as a basis for future research in the area of vision based SLAM. It will permit further research in the area to be carried out in an efficient and application specific way.

  2. Mobile-health: A review of current state in 2015.

    PubMed

    Silva, Bruno M C; Rodrigues, Joel J P C; de la Torre Díez, Isabel; López-Coronado, Miguel; Saleem, Kashif

    2015-08-01

    Health telematics is a growing up issue that is becoming a major improvement on patient lives, especially in elderly, disabled, and chronically ill. In recent years, information and communication technologies improvements, along with mobile Internet, offering anywhere and anytime connectivity, play a key role on modern healthcare solutions. In this context, mobile health (m-Health) delivers healthcare services, overcoming geographical, temporal, and even organizational barriers. M-Health solutions address emerging problems on health services, including, the increasing number of chronic diseases related to lifestyle, high costs of existing national health services, the need to empower patients and families to self-care and handle their own healthcare, and the need to provide direct access to health services, regardless of time and place. Then, this paper presents a comprehensive review of the state of the art on m-Health services and applications. It surveys the most significant research work and presents a deep analysis of the top and novel m-Health services and applications proposed by industry. A discussion considering the European Union and United States approaches addressing the m-Health paradigm and directives already published is also considered. Open and challenging issues on emerging m-Health solutions are proposed for further works. PMID:26071682

  3. Scientific Workflow Management in Proteomics

    PubMed Central

    de Bruin, Jeroen S.; Deelder, André M.; Palmblad, Magnus

    2012-01-01

    Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond. PMID:22411703

  4. Invited review: Current state of genetic improvement in dairy sheep.

    PubMed

    Carta, A; Casu, Sara; Salaris, S

    2009-12-01

    Dairy sheep have been farmed traditionally in the Mediterranean basin in southern Europe, central Europe, eastern Europe, and in Near East countries. Currently, dairy sheep farming systems vary from extensive to intensive according to the economic relevance of the production chain and the specific environment and breed. Modern breeding programs were conceived in the 1960s. The most efficient selection scheme for local dairy sheep breeds is based on pyramidal management of the population with the breeders of nucleus flocks at the top, where pedigree and official milk recording, artificial insemination, controlled natural mating, and breeding value estimation are carried out to generate genetic progress. The genetic progress is then transferred to the commercial flocks through artificial insemination or natural-mating rams. Increasing milk yield is still the most profitable breeding objective for several breeds. Almost all milk is used for cheese production and, consequently, milk content traits are very important. Moreover, other traits are gaining interest for selection: machine milking ability and udder morphology, resistance to diseases (mastitis, internal parasites, scrapie), and traits related to the nutritional value of milk (fatty acid composition). Current breeding programs based on the traditional quantitative approach have achieved appreciable genetic gains for milk yield. In many cases, further selection goals such as milk composition, udder morphology, somatic cell count, and scrapie resistance have been implemented. However, the possibility of including other traits of selective interest is limited by high recording costs. Also, the organizational effort needed to apply the traditional quantitative approach limits the diffusion of current selection programs outside the European Mediterranean area. In this context, the application of selection schemes assisted by molecular information, to improve either traditional dairy traits or traits costly to record

  5. Quantum coherence of the molecular states and their corresponding currents in nanoscale Aharonov-Bohm interferometers

    NASA Astrophysics Data System (ADS)

    Liu, Jian-Heng; Tu, Matisse Wei-Yuan; Zhang, Wei-Min

    2016-07-01

    By considering a nanoscale Aharonov-Bohm (AB) interferometer consisting of a laterally coupled double dot coupled to the source and drain electrodes, we investigate the AB phase dependence of the bonding and antibonding states and the transport currents via the bonding and antibonding state channels. The relations of the AB phase dependence between the quantum states and the associated transport current components are analyzed, which provides useful information for the reconstruction of quantum states through the measurement of the transport current in such systems. We also obtain the validity of the experimental analysis [given in T. Hatano et al., Phys. Rev. Lett. 106, 076801 (2011), 10.1103/PhysRevLett.106.076801] that bonding state currents in different energy configurations are almost the same. With the coherent properties in the quantum dot states as well as in the transport currents, we also provide a way to manipulate the bonding and antibonding states through the AB magnetic flux.

  6. Living donor liver transplantation in Brazil—current state

    PubMed Central

    Andraus, Wellington; D’Alburquerque, Luiz A. C.

    2016-01-01

    Currently in Brazil, living donor liver transplantation (LDLT) represents 8.5% of liver transplantation (LT), being the majority pediatric one. Up to now, according to Brazilian Organ Transplantation Association (ABTO) annual report, 2,086 procedures have been done nationwide, most of them in southeast and south regions. Based on national centers reports, biliary complication is the most common recipient postoperative complication (14.5–20.6%), followed by hepatic artery thrombosis (3.1–10.7%) and portal vein thrombosis (2.3–9.1%). Patient and graft overall 5-y survival correspond to 76% and 74%, respectively. Regarding the donor, morbidity rate ranges from 12.4% to 28.3%, with a national mortality rate of 0.14%. In conclusion, Brazilian LDLT programs enhance international experience that this is a feasible and safe procedure, as well as an excellent alternative strategy to overcome organs shortage. PMID:27115012

  7. Renewable energy sources in Bulgaria: Current state and trends

    NASA Astrophysics Data System (ADS)

    Kolev, K.

    The over-dependency of Bulgaria on imported fuel stressed the importance of developing a new energy strategy based on energy saving which includes also using renewable energy sources (RES). The target is the substitution of at least 2 percent of the real primary energy consumption with RES by 2010. The author gives a generalized analysis of the available RES in Bulgaria -solar, wind, geothermal, biomass and mini-hydraulic. The potentialities of each source for its usage as a suitable energy supply are pointed out, as well as the current status of research and implementation work, problems connected with legislation, financing and production of particular facilities. The governmental policy concerning RES is considered briefly. A description is given to the project 'Technical and Economical Assessment of Possibilities for Expansion of the RES-part in the Energy Balance of the Country' developed and started in 1994 in the framework of the PHARE program.

  8. Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge

    PubMed Central

    Martins, Joana; Vasconcelos, Vitor

    2015-01-01

    Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential. PMID:26580631

  9. Living donor liver transplantation in Brazil-current state.

    PubMed

    Andraus, Wellington; Canedo, Bernardo F; D'Alburquerque, Luiz A C

    2016-04-01

    Currently in Brazil, living donor liver transplantation (LDLT) represents 8.5% of liver transplantation (LT), being the majority pediatric one. Up to now, according to Brazilian Organ Transplantation Association (ABTO) annual report, 2,086 procedures have been done nationwide, most of them in southeast and south regions. Based on national centers reports, biliary complication is the most common recipient postoperative complication (14.5-20.6%), followed by hepatic artery thrombosis (3.1-10.7%) and portal vein thrombosis (2.3-9.1%). Patient and graft overall 5-y survival correspond to 76% and 74%, respectively. Regarding the donor, morbidity rate ranges from 12.4% to 28.3%, with a national mortality rate of 0.14%. In conclusion, Brazilian LDLT programs enhance international experience that this is a feasible and safe procedure, as well as an excellent alternative strategy to overcome organs shortage. PMID:27115012

  10. The current state of prostate-specific antigen testing.

    PubMed

    Lewis, Ryan; Hornberger, Brad

    2016-09-01

    Since prostate-specific antigen (PSA) testing was approved in 1994, the incidence of metastasis and mortality from prostate cancer have significantly decreased. However, PSA screening for prostate cancer has limitations and few large randomized controlled trials have been conducted to determine the mortality benefit of PSA screening. Two studies that have been conducted are the Prostate, Lung, Colorectal, and Ovarian (PLCO) screening trial and the European Randomized Study of Screening for Prostate Cancer (ERSPC). These were the two main studies the US Preventive Services Task Force (USPSTF) used in its recommendation against prostate cancer screening in 2012. However, new evidence has demonstrated that the PLCO trial had significant limitations and the results of the ERSPC trial were more significant than previously thought. This article describes the strengths and weaknesses of the USPSTF's recommendation, along with current guidelines for prostate cancer screening. PMID:27575906

  11. Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge.

    PubMed

    Martins, Joana; Vasconcelos, Vitor

    2015-11-01

    Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential. PMID:26580631

  12. Current State of Vascular Resections in Pancreatic Cancer Surgery

    PubMed Central

    Hackert, Thilo; Schneider, Lutz; Büchler, Markus W.

    2015-01-01

    Pancreatic cancer (PDAC) is the fourth leading cause of cancer-related mortality in the Western world and, even in 2014, a therapeutic challenge. The only chance for long-term survival is radical surgical resection followed by adjuvant chemotherapy which can be performed in about 20% of all PDAC patients by the time of diagnosis. As pancreatic surgery has significantly changed during the past years, extended operations, including vascular resections, have become more frequently performed in specialized centres and the border of resectability has been pushed forward to achieve a potentially curative approach in the respective patients in combination with neoadjuvant and adjuvant treatment strategies. In contrast to adjuvant treatment which has to be regarded as a cornerstone to achieve long-term survival after resection, neoadjuvant treatment strategies for locally advanced findings are currently under debate. This overview summarizes the possibilities and evidence of vascular, namely, venous and arterial, resections in PDAC surgery. PMID:26609306

  13. Sediments Contamination with Organic Micropollutants: Current State and Perspectives

    NASA Astrophysics Data System (ADS)

    Popenda, Agnieszka; Włodarczyk-Makuła, Maria

    2016-06-01

    This study focused on the sediment contamination with some organic micropollutants based on the monitoring data together with available literature in Poland. The following persistent organic pollutants (POPs): polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and chlorinated pesticides (CP) were characterized in sediments with respect to current legislations in force. Based on accessible data, higher PAHs, PCBs and CP concentrations were found in river sediments than in lake sediments. Especially, sediments of the Oder River and its tributary in the southern part of Poland, were highly polluted. In order to minimize the risk of the secondary pollution of surface waters, it is necessary to introduce consolidated management system with sediments proceeding. Furthermore, it is also of great importance to elaborate specific regulations concerning conditions of sediments management.

  14. Poliomyelitis in the United States: A Historical Perspective and Current Vaccination Policy.

    ERIC Educational Resources Information Center

    Farizo, Karen M.; And Others

    1990-01-01

    Examines poliomyelitis in the United States by reviewing clinical manifestations and outcomes, history, recent epidemiologic characteristics, characteristics of currently available vaccines, controversies surrounding vaccination policy, current poliovirus vaccination recommendations, and prospects for worldwide eradication. Poliomyelitis remains…

  15. Computer-Assisted Orthopedic Surgery: Current State and Future Perspective

    PubMed Central

    Zheng, Guoyan; Nolte, Lutz P.

    2015-01-01

    Introduced about two decades ago, computer-assisted orthopedic surgery (CAOS) has emerged as a new and independent area, due to the importance of treatment of musculoskeletal diseases in orthopedics and traumatology, increasing availability of different imaging modalities, and advances in analytics and navigation tools. The aim of this paper is to present the basic elements of CAOS devices and to review state-of-the-art examples of different imaging modalities used to create the virtual representations, of different position tracking devices for navigation systems, of different surgical robots, of different methods for registration and referencing, and of CAOS modules that have been realized for different surgical procedures. Future perspectives will also be outlined. PMID:26779486

  16. Computer-Assisted Orthopedic Surgery: Current State and Future Perspective.

    PubMed

    Zheng, Guoyan; Nolte, Lutz P

    2015-01-01

    Introduced about two decades ago, computer-assisted orthopedic surgery (CAOS) has emerged as a new and independent area, due to the importance of treatment of musculoskeletal diseases in orthopedics and traumatology, increasing availability of different imaging modalities, and advances in analytics and navigation tools. The aim of this paper is to present the basic elements of CAOS devices and to review state-of-the-art examples of different imaging modalities used to create the virtual representations, of different position tracking devices for navigation systems, of different surgical robots, of different methods for registration and referencing, and of CAOS modules that have been realized for different surgical procedures. Future perspectives will also be outlined. PMID:26779486

  17. Setting the Standard in Proteomics - Office of Cancer Clinical Proteomics Research

    Cancer.gov

    In a recently published article in the journal of Molecular and Cellular Proteomics, researchers outlined “best practices” for developing and publishing proteomic studies involving one of the field's signature state-of-the-art tools - targeted mass spectrometry (MS).

  18. Phenotypic Variability in Resting-State Functional Connectivity: Current Status

    PubMed Central

    Gordon, Evan M.

    2013-01-01

    Abstract We reviewed the extant literature with the goal of assessing the extent to which resting-state functional connectivity is associated with phenotypic variability in healthy and disordered populations. A large corpus of work has accumulated to date (125 studies), supporting the association between intrinsic functional connectivity and individual differences in a wide range of domains—not only in cognitive, perceptual, motoric, and linguistic performance, but also in behavioral traits (e.g., impulsiveness, risky decision making, personality, and empathy) and states (e.g., anxiety and psychiatric symptoms) that are distinguished by cognitive and affective functioning, and in neurological conditions with cognitive and motor sequelae. Further, intrinsic functional connectivity is sensitive to remote (e.g., early-life stress) and enduring (e.g., duration of symptoms) life experience, and it exhibits plasticity in response to recent experience (e.g., learning and adaptation) and pharmacological treatment. The most pervasive associations were observed with the default network; associations were also widespread between the cingulo-opercular network and both cognitive and affective behaviors, while the frontoparietal network was associated primarily with cognitive functions. Associations of somatomotor, frontotemporal, auditory, and amygdala networks were relatively restricted to the behaviors linked to their respective putative functions. Surprisingly, visual network associations went beyond visual function to include a variety of behavioral traits distinguished by affective function. Together, the reviewed evidence sets the stage for testing causal hypothesis about the functional role of intrinsic connectivity and augments its potential as a biomarker for healthy and disordered brain function. PMID:23294010

  19. Cancer Treatment-Related Cardiotoxicity: Understanding the Current State of Knowledge and Developing Future Research Priorities

    Cancer.gov

    Cancer Treatment-Related Cardiotoxicity: Understanding the Current State of Knowledge and Developing Future Research Priorities, a 2013 workshop sponsored by the Epidemiology and Genomics Research Program.

  20. Current state in the development of candidate therapeutic HPV vaccines.

    PubMed

    Yang, Andrew; Jeang, Jessica; Cheng, Kevin; Cheng, Ting; Yang, Benjamin; Wu, T-C; Hung, Chien-Fu

    2016-08-01

    The identification of human papillomavirus (HPV) as an etiological factor for HPV-associated malignancies creates the opportunity to control these cancers through vaccination. Currently, available preventive HPV vaccines have not yet demonstrated strong evidences for therapeutic effects against established HPV infections and lesions. Furthermore, HPV infections remain extremely common. Thus, there is urgent need for therapeutic vaccines to treat existing HPV infections and HPV-associated diseases. Therapeutic vaccines differ from preventive vaccines in that they are aimed at generating cell-mediated immunity rather than neutralizing antibodies. The HPV-encoded early proteins, especially oncoproteins E6 and E7, form ideal targets for therapeutic HPV vaccines since they are consistently expressed in HPV-associated malignancies and precancerous lesions, playing crucial roles in the generation and maintenance of HPV-associated disease. Our review will cover various therapeutic vaccines in development for the treatment of HPV-associated lesions and cancers. Furthermore, we review strategies to enhance vaccine efficacy and the latest clinical trials on therapeutic HPV vaccines. PMID:26901118

  1. Current state and novel approaches of antiplatelet therapy.

    PubMed

    Metharom, Pat; Berndt, Michael C; Baker, Ross I; Andrews, Robert K

    2015-06-01

    An unresolved problem with clinical use of antiplatelet therapy is that a significant number of individuals either still get thrombosis or run the risk of life-threatening bleeding. Antiplatelet drugs are widely used clinically, either chronically for people at risk of athero/thrombotic disease or to prevent thrombus formation during surgery. However, a subpopulation may be resistant to standard doses, while the platelet targets of these drugs are also critical for the normal hemostatic function of platelets. In this review, we will briefly examine current antiplatelet therapy and existing targets while focusing on new potential approaches for antiplatelet therapy and improved monitoring of effects on platelet reactivity in individuals, ultimately to improve antithrombosis with minimal bleeding. Primary platelet adhesion-signaling receptors, glycoprotein (GP)Ib-IX-V and GPVI, that bind von Willebrand factor/collagen and other prothrombotic factors are not targeted by drugs in clinical use, but they are of particular interest because of their key role in thrombus formation at pathological shear. PMID:25838432

  2. Small-molecule PSMA ligands. Current state, SAR and perspectives.

    PubMed

    Machulkin, Alexey E; Ivanenkov, Yan A; Aladinskaya, Anastasia V; Veselov, Mark S; Aladinskiy, Vladimir A; Beloglazkina, Elena K; Koteliansky, Victor E; Shakhbazyan, Artem G; Sandulenko, Yuri B; Majouga, Alexander G

    2016-09-01

    Prostate cancer (PC) is the prevalent malignancy widespread among men in the Western World. Prostate specific membrane antigen (PSMA) is an established PC marker and has been considered as a promising biological target for anti-PC drug delivery and diagnostics. The protein was found to be overexpressed in PC cells, including metastatic, and the neovasculature of solid tumors. These properties make PSMA-based approach quite appropriate for effective PC imaging and specific drug therapy. Through the past decade, a variety of PSMA-targeted agents has been systematically evaluated. Small-molecule compounds have several advantages over other classes, such as improved pharmacokinetics and rapid blood clearance. These low-weight ligands have similar structure and can be divided into three basic categories in accordance with the type of their zinc-binding core-head. Several PSMA binders are currently undergoing clinical trials generally for PC imaging. The main goal of the present review is to describe the recent progress achieved within the title field and structure activity relationships (SAR) disclosed for different PSMA ligands. Recent in vitro and in vivo studies for each type of the compounds described have also been briefly summarized. PMID:26887438

  3. The current state of scaffolds for musculoskeletal regenerative applications.

    PubMed

    Smith, Benjamin D; Grande, Daniel A

    2015-04-01

    Musculoskeletal disease and injury are highly prevalent conditions that lead to many surgical procedures. Autologous tissue transfer, allograft transplantation and nontissue prosthetics are currently used for the surgical treatment of critical-sized defects. However, the field of tissue engineering is actively investigating tissue-replacement solutions, many of which involve 3D scaffolds. Scaffolds must provide a balance of shape, biomechanical function and biocompatibility in order to achieve tissue replacement success. Different tissues can have different requirements for success, which has led to the development of various materials with unique characteristics. Articular cartilage scaffolds have the most robust clinical experience, with many scaffolds, mostly constructed of natural materials, showing promise, but levels of success vary. Tendon scaffolds also have proven clinical applications, with human-dermis-derived scaffolds showing the most potential. Synthetic and naturally derived meniscus scaffolds have been investigated in few clinical studies, but the results are encouraging. Bone scaffolds are limited to amorphous pastes and putties, owing to difficulties achieving adequate vascularization and biomechanical optimization. The complex physiological function and vascular demands of skeletal muscle have limited the widespread clinical use of scaffolds for engineering this tissue. Continued progress in preclinical study, not only of scaffolds, but also of other facets of tissue engineering, should enable the successful translation of musculoskeletal tissue engineering solutions to the clinic. PMID:25776947

  4. Current HDTV overview in the United States, Japan, and Europe

    NASA Astrophysics Data System (ADS)

    Cripps, Dale E.

    1991-08-01

    Vast resources are being spent on three continents, preparing for the commercialization of HDTV. The forces that together will launch this new industry are moving at dizzying speeds. This paper covers the highlights of events past and present and offers some predictions for the future. Difficult standards problems that keep brakes on the industry, and that will continue for some time to come. Standards committees have been set up around the world and are hard at work. It is a job with considerable technical and political challenges. By the time major plans and resources come together for commercialization of HDTV, one can trust that there will be adequately stable standards. But to observe the current status is to see a mess. High definition is not only consumer television. Because of its versatility, it is much more likely to find its way first into areas offering high returns such as medicine, education, printing, corporate communications, military and space, and even criminal control. HDTV is very likely to deliver movies and cultural events to theaters, and may also become the platform for a new generation of computers.

  5. A prospective look at the current state of open abdomens.

    PubMed

    Teixeira, Pedro G R; Salim, Ali; Inaba, Kenji; Brown, Carlos; Browder, Timothy; Margulies, Daniel; Demetriades, Demetrios

    2008-10-01

    The present study examines the current management, closure rate, and complications of open abdomens in trauma patients admitted to an Academic Level I trauma center between May 2004 and April 2007. Variables examined include mechanism, injuries, use of antibiotics and paralytics, type of abdominal closure, days to closure, complications, ICU and hospital length of stay, and mortality. Stepwise logistic regression was performed to identify independent predictors of failed abdominal closure. Of 900 laparotomies, 93 (10%) were left open. Eighty-five (91%) patients survived for closure opportunity. Definitive fascial closure was achieved in 72 (85%) at 3.9 +/- 3.7 days (range 1-21 days). Of the remaining 13 patients, seven were closed with biologic material, five by skin grafting, and one had skin-only closure. Entero-atmospheric fistulas occurred in 14 (15%) patients. Two independent risk factors associated with failed abdominal closure were the presence of deep surgical site infection [odds ratio (OR) 17.4; 95% confidence interval (CI) 2.6-115.8, P = 0.003] and intra-abdominal abscess (OR 7.4; 95% CI 1.1-51.0, P = 0.04). In conclusion, open abdomens are commonly necessary after trauma laparotomies. Definitive fascial closure can be achieved in 85 per cent of cases. In conjunction with biologics, closure can be achieved in 93 per cent of cases. Failure to primarily close the abdomen is associated with a significantly higher risk for entero-atmospheric fistula occurrence. PMID:18942608

  6. The state of sleep and the current brain paradigm

    PubMed Central

    Pigarev, Ivan N.; Pigareva, Marina L.

    2015-01-01

    Up to the present time cerebral cortex was considered as substrate for realization of the highest psychical functions including consciousness. Cortical sensory areas were regarded as structures specialized for processing of information coming from one particular modality (visual, auditory, somatosensory, and so on). However, studies of cortical activity in sleep-wake cycle demonstrated that during sleep the same neurons in the same cortical areas switch to processing of signals coming from the various visceral systems. After awakening these visceral responses disappear and the neurons return to processing of the information coming from the exteroreceptors. These observations indicate that most likely cortical areas are universal processors, which perform particular operations with incoming information independent of its origin. During wakefulness, results of the information processing on the cortical level should be directed to structures connected with organization of behavior and consciousness, while during sleep cortical outputs should be redirected to structures performing integration of the visceral information. Thus, results of sleep studies indicate that current brain paradigm should be changed. PMID:26528146

  7. Guide to clinical practice guidelines: the current state of play

    PubMed Central

    Kredo, Tamara; Bernhardsson, Susanne; Machingaidze, Shingai; Young, Taryn; Louw, Quinette; Ochodo, Eleanor; Grimmer, Karen

    2016-01-01

    Introduction Extensive research has been undertaken over the last 30 years on the methods underpinning clinical practice guidelines (CPGs), including their development, updating, reporting, tailoring for specific purposes, implementation and evaluation. This has resulted in an increasing number of terms, tools and acronyms. Over time, CPGs have shifted from opinion-based to evidence-informed, including increasingly sophisticated methodologies and implementation strategies, and thus keeping abreast of evolution in this field of research can be challenging. Methods This article collates findings from an extensive document search, to provide a guide describing standards, methods and systems reported in the current CPG methodology and implementation literature. This guide is targeted at those working in health care quality and safety and responsible for either commissioning, researching or delivering health care. It is presented in a way that can be updated as the field expands. Conclusion CPG development and implementation have attracted the most international interest and activity, whilst CPG updating, adopting (with or without contextualization), adapting and impact evaluation are less well addressed. PMID:26796486

  8. Current state of web accessibility of Malaysian ministries websites

    NASA Astrophysics Data System (ADS)

    Ahmi, Aidi; Mohamad, Rosli

    2016-08-01

    Despite the fact that Malaysian public institutions have progressed considerably on website and portal usage, web accessibility has been reported as one of the issues deserves special attention. Consistent with the government moves to promote an effective use of web and portal, it is essential for the government institutions to ensure compliance with established standards and guidelines on web accessibility. This paper evaluates accessibility of 25 Malaysian ministries websites using automated tools i.e. WAVE and Achecker. Both tools are designed to objectively evaluate web accessibility in conformance with Web Content Accessibility Guidelines 2.0 (WCAG 2.0) and United States Rehabilitation Act 1973 (Section 508). The findings reported somewhat low compliance to web accessibility standard amongst the ministries. Further enhancement is needed in the aspect of input elements such as label and checkbox to be associated with text as well as image-related elements. This findings could be used as a mechanism for webmasters to locate and rectify errors pertaining to the web accessibility and to ensure equal access of the web information and services to all citizen.

  9. The current state, challenges and perspectives of MR-PET.

    PubMed

    Herzog, Hans; Pietrzyk, Uwe; Shah, N Jon; Ziemons, Karl

    2010-02-01

    Following the success of PET/CT during the last decade and the recent increasing proliferation of SPECT/CT, another hybrid imaging instrument has been gaining more and more interest: MR-PET. First combined, simultaneous PET and MR studies carried out in small animals demonstrated the feasibility of the new approach. Concurrently, some prototypes of an MR-PET scanner for simultaneous human brain studies have been built, their performance is being tested and preliminary applications have already been shown. Through this pioneering work, it has become clear that advances in the detector design are necessary for further optimization. Recently, the different issues related to the present state and future prospects of MR-PET were presented and discussed during an international 2-day workshop at the Forschungszentrum Jülich, Germany, held after, and in conjunction with, the 2008 IEEE Nuclear Science Symposium and Medical Imaging Conference in Dresden, Germany on October 27-28, 2008. The topics ranged from small animal MR-PET imaging to human MR-BrainPET imaging, new detector developments, challenges/opportunities for ultra-high field MR-PET imaging and considerations of possible future research and clinical applications. This report presents a critical summary of the contributions made to the workshop. PMID:19853045

  10. Aggression in wild house mice: current state of affairs.

    PubMed

    Sluyter, F; van Oortmerssen, G A; de Ruiter, A J; Koolhaas, J M

    1996-09-01

    This paper reviews our present state of knowledge of genetic variation in (offensive) aggression in wild house mice. The basic tools in this research were lines bidirectionally selected for attack latency (fast attacking SAL and slow attacking LAL males), descended from a feral population. Using congenic lines for the nonpseudoautosomal region of the Y chromosome (YNPAR), reciprocal crosses between (parental) SAL and LAL, and crosses between parentals and congenics, an autosomally dependent Y chromosomal effect on aggression has been found. Both the pseudoautosomal (YPAK) region and the YNPAR play a role. As for environmental sources of variation, prenatal and postnatal maternal effects are of minor importance for the development of aggression differences. One of the physiological factors by which genetic effects may be mediated is testosterone (T). Besides quantitative aspects, the timing of T release seems crucial. Two important time frames are discussed: the perinatal and pubertal time periods. Finally, neurochemical and neuroanatomical correlates are considered. Differences in neostriatal dopaminergic activity, and sizes of the intra- and infrapyramidal mossy fiber terminal fields, as well as Y chromosomal effects on the latter two, are discussed. PMID:8917947

  11. Yeast as a cell factory: current state and perspectives.

    PubMed

    Kavšček, Martin; Stražar, Martin; Curk, Tomaž; Natter, Klaus; Petrovič, Uroš

    2015-01-01

    The yeast Saccharomyces cerevisiae is one of the oldest and most frequently used microorganisms in biotechnology with successful applications in the production of both bulk and fine chemicals. Yet, yeast researchers are faced with the challenge to further its transition from the old workhorse to a modern cell factory, fulfilling the requirements for next generation bioprocesses. Many of the principles and tools that are applied for this development originate from the field of synthetic biology and the engineered strains will indeed be synthetic organisms. We provide an overview of the most important aspects of this transition and highlight achievements in recent years as well as trends in which yeast currently lags behind. These aspects include: the enhancement of the substrate spectrum of yeast, with the focus on the efficient utilization of renewable feedstocks, the enhancement of the product spectrum through generation of independent circuits for the maintenance of redox balances and biosynthesis of common carbon building blocks, the requirement for accurate pathway control with improved genome editing and through orthogonal promoters, and improvement of the tolerance of yeast for specific stress conditions. The causative genetic elements for the required traits of the future yeast cell factories will be assembled into genetic modules for fast transfer between strains. These developments will benefit from progress in bio-computational methods, which allow for the integration of different kinds of data sets and algorithms, and from rapid advancement in genome editing, which will enable multiplexed targeted integration of whole heterologous pathways. The overall goal will be to provide a collection of modules and circuits that work independently and can be combined at will, depending on the individual conditions, and will result in an optimal synthetic host for a given production process. PMID:26122609

  12. Current state of development of the European Drought Observatory

    NASA Astrophysics Data System (ADS)

    Niemeyer, S.; de Jager, A.; Kurnik, B.; Laguardia, G.; Magni, D.; Nitcheva, O.; Rossi, S.; Weissteiner, C.

    2009-04-01

    The Joint Research Centre of the European Commission (JRC) is developing the prototype of the European Drought Observatory (EDO) for drought forecasting, detection, and monitoring in Europe. EDO is conceived as a web-based information system (http://edo.jrc.ec.europa.eu), integrating information from various sources and disciplines relevant to monitor and detect droughts throughout Europe. The prototype is currently performing the pre-operational production of drought indices using meteorological information, modelled hydrological parameters, and remote sensing data. In particular, the Standardized Precipitation Index (SPI) shows the general precipitation status according to the historical average in the predefined period. SPI in monthly step is calculated for the 1, 3, 6, 9 and 12 months averaging periods. Soil moisture estimations are produced daily by the LISFLOOD hydrological model, along with their anomalies and seven days forecasts. Two satellite remote sensing drought indicators are produced: Normalized Difference Water Index (NDWI) and Fraction of Absorbed Photosynthetic Active Radiation (fAPAR) anomalies. NDWI 10-day composites are obtained daily from Moderate Resolution Imaging Spectroradiometer (MODIS) data, while fAPAR anomalies are calculated from 10-day composites delivered by the European Space Agency (ESA) and estimated from Medium Resolution Imaging Spectrometer Instrument (MERIS) data. All these drought indicators are made available online for visualization and querying by means of a map viewer based on University of Minnesota MapServer and Oracle. The tool generates maps of the different indicators and provides functionalities to browse the maps, query the data, produce graphs, and output the maps in various formats.

  13. Circulating vaccine-derived polioviruses: current state of knowledge.

    PubMed Central

    Kew, Olen M.; Wright, Peter F.; Agol, Vadim I.; Delpeyroux, Francis; Shimizu, Hiroyuki; Nathanson, Neal; Pallansch, Mark A.

    2004-01-01

    Within the past 4 years, poliomyelitis outbreaks associated with circulating vaccine-derived polioviruses (cVDPVs) have occurred in Hispaniola (2000-01), the Philippines (2001), and Madagascar (2001-02). Retrospective studies have also detected the circulation of endemic cVDPV in Egypt (1988-93) and the likely localized spread of oral poliovirus vaccine (OPV)-derived virus in Belarus (1965-66). Gaps in OPV coverage and the previous eradication of the corresponding serotype of indigenous wild poliovirus were the critical risk factors for all cVDPV outbreaks. The cVDPV outbreaks were stopped by mass immunization campaigns using OPV. To increase sensitivity for detecting vaccine-derived polioviruses (VDPVs), in 2001 the Global Polio Laboratory Network implemented additional testing requirements for all poliovirus isolates under investigation. This approach quickly led to the recognition of the Philippines and Madagascar cVDPV outbreaks, but of no other current outbreaks. The potential risk of cVDPV emergence has increased dramatically in recent years as wild poliovirus circulation has ceased in most of the world. The risk appears highest for the type 2 OPV strain because of its greater tendency to spread to contacts. The emergence of cVDPVs underscores the critical importance of eliminating the last pockets of wild poliovirus circulation, maintaining universally high levels of polio vaccine coverage, stopping OPV use as soon as it is safely possible to do so, and continuing sensitive poliovirus surveillance into the foreseeable future. Particular attention must be given to areas where the risks for wild poliovirus circulation have been highest, and where the highest rates of polio vaccine coverage must be maintained to suppress cVDPV emergence. PMID:15106296

  14. Current state of the art of medical foods.

    PubMed

    Blum, Stephanie; Brito, Fernando

    2014-01-01

    Inflammatory bowel disease (IBD) is one of the five most prevalent gastrointestinal disease burdens in the US, with an overall health care cost of more than USD 1.7 billion. It commonly requires a lifetime of care, and accounts for more than 700,000 physician visits, 100,000 hospitalizations, and disability in 119,000 patients each year. IBD is a multifactorial disease and comprises genetic susceptibility, uncontrolled immune responses, and environmental factors which play a role in the pathogenesis and course of the disease. IBD patients are lifelong on medication, either for induction or maintenance therapy. Current treatment option (corticosteroids, immune suppressants, biologics), administered in mono- or combination therapy, are still unsatisfactory. Due to the nature of disease, 20-40% of patients relapse within the first 12 months. Although modern treatment algorithms have diminished the risk of surgery, the treatments harbor significant side effects, which impacts patients' quality of life. The role of nutrition in IBD has gathered high interest, especially in pediatric Crohn's disease, where studies have shown that exclusive enteral nutrition can induce remission in mild-to-moderate disease comparable to corticosteroids. Thus, gastroenterologists and patients become increasingly aware that specific nutritional interventions offered in addition to the standard of care are an appealing option for a safe long-term disease management. Such specific nutritional solutions should be based on scientific/clinical evidence and specifically designed to address the patients' distinct nutritional requirements. As per definition, these nutrition products fall under the regulatory framework of a Medical Food (Foods for Special Medical Purposes in Europe). PMID:25227302

  15. United States refugee and asylum policy: history and current approaches.

    PubMed

    Stein, B N

    1986-01-01

    For most of the 4 decades since World War II, US refugee and asylum policy has been generous but ad hoc, discretionary, and highly variable favoring some refugee groups and discriminating against or ignoring others. This paper: 1) tries to clarify some of the terminology of the refugee field and explains the distinctions between asylum and resettlement, 2) provides some of the historical background that has brought the US to its present condition and chronicles the US overseas refugee admission policy, and 3) examines some asylum issues and other refugee issues. Asylum is far more difficult to control than refugee resettlement. As a result of what is perceived to be abuse of the asylum system, the US has joined the growing tendency of states to treat asylum-seekers as illegal migrants. The greatest problem with American asylum policy is its lack of fairness of application; many critics believe that foreign policy factors dominate asylum hearings rather than the individual merits of the case. The 3 classic solutions to this problem are resettlement, voluntary repatriation, and settlement in a country of 1st asylum. Only in the Indochinese refugee crisis has resettlement been widely used as a solution for 3rd World refugees. Nationalism and nation-building conflicts are at the root of many refugee movements; hosts are often no less nationalistic than source countries, thus many non-integrated refugees live in peril. Developed country political will and statesmanship are needed to revive resettlement as a durable solution. Resettlement may be difficult and costly, but the pluralistic western societies do offer an integrated new life. PMID:12178938

  16. Current cigarette smoking among adults - United States, 2005-2014.

    PubMed

    Jamal, Ahmed; Homa, David M; O'Connor, Erin; Babb, Stephen D; Caraballo, Ralph S; Singh, Tushar; Hu, S Sean; King, Brian A

    2015-11-13

    Tobacco smoking is the leading cause of preventable disease and death in the United States, resulting in approximately 480,000 premature deaths and more than $300 billion in direct health care expenditures and productivity losses each year (1). To assess progress toward achieving the Healthy People 2020 objective of reducing the percentage of U.S. adults who smoke cigarettes to ≤12.0%,* CDC assessed the most recent national estimates of smoking prevalence among adults aged ≥18 years using data from the 2014 National Health Interview Survey (NHIS). The percentage of U.S. adults who smoke cigarettes declined from 20.9% in 2005 to 16.8% in 2014. Among daily cigarette smokers, declines were observed in the percentage who smoked 20–29 cigarettes per day (from 34.9% to 27.4%) or ≥30 cigarettes per day (from 12.7% to 6.9%). In 2014, prevalence of cigarette smoking was higher among males, adults aged 25–44 years, multiracial persons and American Indian/Alaska Natives, persons who have a General Education Development certificate, live below the federal poverty level, live in the Midwest, are insured through Medicaid or are uninsured, have a disability or limitation, or are lesbian, gay, or bisexual. Proven population-based interventions, including tobacco price increases, comprehensive smoke-free laws, high impact mass media campaigns, and barrier-free access to quitting assistance, are critical to reduce cigarette smoking and smoking-related disease and death among U.S. adults. PMID:26562061

  17. Current State of the Art in High Brightness LEDs

    NASA Astrophysics Data System (ADS)

    Craford, George

    2007-03-01

    LED's have been commercially available since the 1960's. For many years they were used primarily for indicator applications. The remarkable increase in materials technology and efficiency that has been achieved since the early 1990's for AlInGaP red and amber LEDs, and InGaN green and blue LEDs, has enabled the penetration of markets such as outdoor display, signaling, and automotive brake light and turn signal applications. White LEDs, which are either blue LEDs combined with a phosphor, or a combination of red, green, and blue LEDs, are being used in emerging applications such as cell phone flash, television backlights, projection, and automotive headlights. In addition, to efficiency improvements these applications have required the development of higher power packages and, in some of these applications which are etendue limited, higher luminance devices. High power devices are commercially available which are capable of 140 lumens output and have an efficacy of around 70 lm/W for white emission. New package and chip technologies have been demonstrated which have a luminance of 38 mega nits (Mcd/m^2), approximately 50% more luminance than that of an automotive headlamp halogen bulb (˜25 mega nits). The recent progress in materials technology, packaging, and chip technology makes it clear that LED's will become important for general illumination applications. The rate of LED penetration of this market will depend upon continued increases in performance and lower costs as well as better control of the white spectral emission. Efficiency, current density, and costs are closely linked because the cost in dollars/lumen is inversely proportional to how many lumens can be realized from each unit of device area for a given device type. Performance as high as 138 lm/W, and over 40% wall plug efficiency, has been reported for low power research devices and over 90 lm/W for high power research devices. It is clear that high power commercial products with performance in

  18. The current state of seismic monitoring in Switzerland

    NASA Astrophysics Data System (ADS)

    Clinton, J. F.; Haslinger, F.; Diehl, T.; Cauzzi, C.; Plenkers, K.; Kästli, P.; Fäh, D.; Wiemer, S.

    2013-12-01

    The Swiss Seismological Service at ETH Zurich (SED) operates both the national strong motion and broadband permanent seismic networks in Switzerland, as well as supporting local real-time densifications related to projects (such as geothermal explorations and major tunneling) and a mobile pool for national and international deployments related to research and aftershock studies. This submission provides an overview of the current status of network monitoring in Switzerland. A digital high gain network has been operating since 1974 and was upgraded to a continuously recording realtime modern 24 bit broadband network comprising 30 stations from 1999-2002, with station spacing averaging ~30km across the nation. Various improvements and densifications since then have raised the number of broadband sensors to 45 and added co-located strong motion sensors at 13 sites. A notable recent densification is in the NE of Switzerland, where the Swiss National Cooperative for the Disposal of Radioactive Waste (Nagra) have funded an additional 10 broadband stations (including 3 100-200m deep borehole short period stations) in order to reduce the earthquake detection threshold and increase location accuracy in regions that are identified as potential deep nuclear waste storage sites. A strong motion network has been maintained since 1990, comprising 70 12-16 bit triggered sensors located predominantly in free-field urban sites but also including arrays on dams. The free-field network is in the midst of an upgrade (2009-2018), with 30 new stations already installed from the eventual 100 new free-field 24-bit real-time continuous stations. A project has just begun to upgrade the Swiss broadband network, which will co-locate strong-motion sensors at existing broadband sites; assess and implement improvements of installation quality, e.g. by shallow post-hole installations rather than surface vaults; and potentially fill remaining gaps in station coverage. The seismic network has

  19. Biological therapies in the spondyloarthritides--the current state.

    PubMed

    Braun, J; Sieper, J

    2004-09-01

    Therapeutic options for patients suffering from the more severe spondyloarthritides (SpA) have been rather limited in the last decades. Evidence is now accumulating that anti-tumour necrosis factor (TNF) therapy is highly effective in SpA, especially in ankylosing spondylitis (AS) and psoriatic arthritis (PsA). Based on the data recently published concerning more than 1000 patients with AS and PsA, this treatment seems to be even more effective than in rheumatoid arthritis (RA). The anti-TNFalpha agents currently available, infliximab (Remicade), etanercept (Enbrel) and adalimumab (Humira), are approved for the treatment of RA in the USA and Europe. The situation for SpA is different from RA because there is an unmet medical need, especially in AS, since no therapies with disease-modifying anti-rheumatic drugs (DMARDs) are available for severely affected patients, especially those with spinal disease. Thus, TNF blockers may even be considered a first-line treatment in a patient with active AS and PsA whose condition is not sufficiently controlled with non-steroidal anti-inflammatory drugs (NSAIDs) in the case of axial disease, and sulphasalazine or methotrexate in the case of peripheral arthritis. For infliximab, a dose of 5 mg/kg is required, and intervals of between 6 and 12 weeks are necessary to constantly suppress disease activity-also a major aim for long-term treatment. The standard dosage of etanercept is 2 x 25 mg subcutaneously per week. There are almost no studies yet on adalimumab (standard dose in RA, 20-40 mg subcutaneously every 1-2 weeks) in SpA. Infliximab and etanercept are now both approved for AS in Europe. The efficacy of etanercept was first demonstrated in PsA, and it is now approved for this indication in the USA and Europe. There is preliminary evidence that both agents also work in other SpA, such as undifferentiated SpA (uSpA). Studies should be performed to document the long-term efficacy of this treatment. There is hope that ankylosis

  20. [Malaria in Hungary: origin, current state and principles of prevention].

    PubMed

    Szénási, Zsuzsanna; Vass, Adám; Melles, Márta; Kucsera, István; Danka, József; Csohán, Agnes; Krisztalovics, Katalin

    2003-05-25

    Malaria was an endemic disease in Hungary for many centuries. A country-wide survey of the epidemiologic situation on malaria started in the year of 1927. That was done by the Department of Parasitology of the Royal State Institute of Hygiene (presently: Johan Béla National Center for Epidemiology). The notification of malaria was made compulsory in 1930. Free of charge laboratory examination of the blood of persons suffering from malaria or suspected of an infection have been carried out. Anti-malarial drugs were also distributed free of charge, together with appropriate medical advise given at the anti-malarial sanitary stations. Between 1933 and 1943, the actual number of malaria cases was estimated as high as 10-100,000 per year. The major breakthrough came in 1949 by the organized antimalarial campaign applying DDT for mosquito eradication. The drastic reduction of the vectors resulted in the rapid decline of malaria cases. Since 1956, there have not been reported any indigenous case in Hungary. In 1963, Hungary entered on the Official Register of the WHO to the areas where malaria eradication has been achieved. During the period of 1963-2001, 169 Hungarians acquired the malaria in abroad and 263 foreigners infected in abroad were registered in Hungary. More than half of the cases (230) were caused by Plasmodium falciparum. Further 178 cases were caused by Plasmodium vivax and 24 cases by other Plasmodium species. During that period, 7 fatal cases were reported (Plasmodium falciparum). The expansion of migration (both the increase of the number of foreigners travelling into Hungary and of Hungarians travelling abroad) favours to the appearance of imported cases. Attention is called of all the persons travelling to malaria endemic countries to the importance of malaria prevention by the International Vaccination Stations located in the National Center for Epidemiology and in the Public Health Institutes of 19 counties and of Budapest. The Johan Béla National

  1. 78 FR 9929 - Current Traumatic Brain Injury State Implementation Partnership Grantees; Non-Competitive One...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-12

    ... HUMAN SERVICES Health Resources and Services Administration Current Traumatic Brain Injury State... Services Administration (HRSA), Department of Health and Human Services (HHS). ACTION: Notice of Non-Competitive One-Year Extension Funds for Current Traumatic Brain Injury (TBI) State Implementation...

  2. 75 FR 7284 - NIOSH Current Intelligence Bulletin-Asbestos Fibers and Other Elongate Mineral Particles: State...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-18

    ... HUMAN SERVICES Centers for Disease Control and Prevention NIOSH Current Intelligence Bulletin--Asbestos... available for public comment entitled ``NIOSH Current Intelligence Bulletin--Asbestos Fibers and Other..., ``NIOSH Current Intelligence Bulletin--Asbestos Fibers and Other Elongate Mineral Particles: State of...

  3. Proteomics Analysis of the Causative Agent of Typhoid Fever

    SciTech Connect

    Ansong, Charles; Yoon, Hyunjin; Norbeck, Angela D.; Gustin, Jean K.; McDermott, Jason E.; Mottaz, Heather M.; Rue, Joanne; Adkins, Joshua N.; Heffron, Fred; Smith, Richard D.

    2008-02-01

    Typhoid fever is a potentially fatal disease caused by the bacterial pathogen Salmonella enterica serovar Typhi (S. typhi). S. typhi infection is a complex process that involves numerous bacterially-encoded virulence determinants, and these are thought to confer both stringent human host specificity and a high mortality rate. In the present study we used a liquid chromatography-mass spectrometry (LC-MS) based proteomics strategy to investigate the proteome of logarithmic, stationary phase, and low pH/low magnesium (MgM) S. typhi cultures. This represents the first large scale comprehensive characterization of the S. typhi proteome. Our analysis identified a total of 2066 S. typhi proteins. In an effort to identify putative S. typhi-specific virulence factors, we then compared our S. typhi results to those obtained in a previously published study of the S. typhimurium proteome under similar conditions (Adkins J.N. et al (2006) Mol Cell Prot). Comparative proteomic analysis of S. typhi (strain Ty2) and S. typhimurium (strains LT2 and 14028) revealed a subset of highly expressed proteins unique to S. typhi that were exclusively detected under conditions that mimic the infective state in macrophage cells. These proteins included CdtB, HlyE, and a conserved protein encoded by t1476. The differential expression of selected proteins was confirmed by Western blot analysis. Taken together with the current literature, our observations suggest that this subset of proteins may play a role in S. typhi pathogenesis and human host specificity. In addition, we observed products of the biotin (bio) operon displayed a higher abundance in the more virulent strains S. typhi-Ty2 and S. typhimurium-14028 compared to the virulence attenuated S. typhimurium strain LT2, suggesting bio proteins may contribute to Salmonella pathogenesis.

  4. Current Control in ITER Steady State Plasmas With Neutral Beam Steering

    SciTech Connect

    R.V. Budny

    2009-09-10

    Predictions of quasi steady state DT plasmas in ITER are generated using the PTRANSP code. The plasma temperatures, densities, boundary shape, and total current (9 - 10 MA) anticipated for ITER steady state plasmas are specified. Current drive by negative ion neutral beam injection, lower-hybrid, and electron cyclotron resonance are calculated. Four modes of operation with different combinations of current drive are studied. For each mode, scans with the NNBI aimed at differing heights in the plasma are performed to study effects of current control on the q profile. The timeevolution of the currents and q are calculated to evaluate long duration transients. Quasi steady state, strongly reversed q profiles are predicted for some beam injection angles if the current drive and bootstrap currents are sufficiently large.

  5. Polyploidy and the proteome.

    PubMed

    Soltis, Douglas E; Misra, Biswapriya B; Shan, Shengchen; Chen, Sixue; Soltis, Pamela S

    2016-08-01

    Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26993527

  6. Selective equilibration among the current-carrying states in the quantum Hall regime

    NASA Technical Reports Server (NTRS)

    Alphenaar, B. W.; Mceuen, P. L.; Wheeler, R. G.; Sacks, R. N.

    1990-01-01

    The Hall resistance of a two-dimensional electron gas is measured with gated probes to determine the extent of equilibration among the N current-carrying states in the quantum Hall regime. After traveling macroscopic distances, current injected into the first state is equilibrated among the N - 1 lowest states but equilibration into the highest state varies strongly across the Hall plateau. This is attributed to a change in the Nth state from being localized within a magnetic length of the edge to substantially extending into the sample.

  7. 42 CFR 457.80 - Current State child health insurance coverage and coordination.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 4 2012-10-01 2012-10-01 false Current State child health insurance coverage and coordination. 457.80 Section 457.80 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) STATE CHILDREN'S HEALTH INSURANCE PROGRAMS (SCHIPs) ALLOTMENTS AND GRANTS TO STATES Introduction;...

  8. 42 CFR 457.80 - Current State child health insurance coverage and coordination.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 4 2014-10-01 2014-10-01 false Current State child health insurance coverage and coordination. 457.80 Section 457.80 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) STATE CHILDREN'S HEALTH INSURANCE PROGRAMS (SCHIPs) ALLOTMENTS AND GRANTS TO STATES Introduction;...

  9. 42 CFR 457.80 - Current State child health insurance coverage and coordination.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 4 2013-10-01 2013-10-01 false Current State child health insurance coverage and coordination. 457.80 Section 457.80 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) STATE CHILDREN'S HEALTH INSURANCE PROGRAMS (SCHIPs) ALLOTMENTS AND GRANTS TO STATES Introduction;...

  10. 42 CFR 457.80 - Current State child health insurance coverage and coordination.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Current State child health insurance coverage and coordination. 457.80 Section 457.80 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) STATE CHILDREN'S HEALTH INSURANCE PROGRAMS (SCHIPs) ALLOTMENTS AND GRANTS TO STATES Introduction;...