Systematic review of serum steroid reference intervals developed using mass spectrometry.

PubMed

Tavita, Nevada; Greaves, Ronda F

2017-12-01

The aim of this study was to perform a systematic review of the published literature to determine the available serum/plasma steroid reference intervals generated by mass spectrometry (MS) methods across all age groups in healthy subjects and to suggest recommendations to achieve common MS based reference intervals for serum steroids. MEDLINE, EMBASE and PubMed databases were used to conduct a comprehensive search for English language, MS-based reference interval studies for serum/plasma steroids. Selection of steroids to include was based on those listed in the Royal College of Pathologists of Australasia Quality Assurance Programs, Chemical Pathology, Endocrine Program. This methodology has been registered onto the PROSPERO International prospective register of systematic reviews (ID number: CRD42015029637). After accounting for duplicates, a total of 60 manuscripts were identified through the search strategy. Following critical evaluation, a total of 16 studies were selected. Of the 16 studies, 12 reported reference intervals for testosterone, 11 for 17 hydroxy-progesterone, nine for androstenedione, six for cortisol, three for progesterone, two for dihydrotestosterone and only one for aldosterone and dehydroepiandrosterone sulphate. No studies established MS-based reference intervals for oestradiol. As far as we are aware, this report provides the first comparison of the peer reviewed literature for serum/plasma steroid reference intervals generated by MS-based methods. The reference intervals based on these published studies can be used to inform the process to develop common reference intervals, and agreed reporting units for mass spectrometry based steroid methods. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Reprint of "pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data".

PubMed

Chi, Hao; He, Kun; Yang, Bing; Chen, Zhen; Sun, Rui-Xiang; Fan, Sheng-Bo; Zhang, Kun; Liu, Chao; Yuan, Zuo-Fei; Wang, Quan-Hui; Liu, Si-Qi; Dong, Meng-Qiu; He, Si-Min

2015-11-03

Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

MassSieve: Panning MS/MS peptide data for proteins

PubMed Central

Slotta, Douglas J.; McFarland, Melinda A.; Markey, Sanford P.

2010-01-01

We present MassSieve, a Java-based platform for visualization and parsimony analysis of single and comparative LC-MS/MS database search engine results. The success of mass spectrometric peptide sequence assignment algorithms has led to the need for a tool to merge and evaluate the increasing data set sizes that result from LC-MS/MS-based shotgun proteomic experiments. MassSieve supports reports from multiple search engines with differing search characteristics, which can increase peptide sequence coverage and/or identify conflicting or ambiguous spectral assignments. PMID:20564260

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library*

PubMed Central

Yen, Chia-Yu; Houel, Stephane; Ahn, Natalie G.; Old, William M.

2011-01-01

The unambiguous assignment of tandem mass spectra (MS/MS) to peptide sequences remains a key unsolved problem in proteomics. Spectral library search strategies have emerged as a promising alternative for peptide identification, in which MS/MS spectra are directly compared against a reference library of confidently assigned spectra. Two problems relate to library size. First, reference spectral libraries are limited to rediscovery of previously identified peptides and are not applicable to new peptides, because of their incomplete coverage of the human proteome. Second, problems arise when searching a spectral library the size of the entire human proteome. We observed that traditional dot product scoring methods do not scale well with spectral library size, showing reduction in sensitivity when library size is increased. We show that this problem can be addressed by optimizing scoring metrics for spectrum-to-spectrum searches with large spectral libraries. MS/MS spectra for the 1.3 million predicted tryptic peptides in the human proteome are simulated using a kinetic fragmentation model (MassAnalyzer version2.1) to create a proteome-wide simulated spectral library. Searches of the simulated library increase MS/MS assignments by 24% compared with Mascot, when using probabilistic and rank based scoring methods. The proteome-wide coverage of the simulated library leads to 11% increase in unique peptide assignments, compared with parallel searches of a reference spectral library. Further improvement is attained when reference spectra and simulated spectra are combined into a hybrid spectral library, yielding 52% increased MS/MS assignments compared with Mascot searches. Our study demonstrates the advantages of using probabilistic and rank based scores to improve performance of spectrum-to-spectrum search strategies. PMID:21532008

Origin of Disagreements in Tandem Mass Spectra Interpretation by Search Engines.

PubMed

Tessier, Dominique; Lollier, Virginie; Larré, Colette; Rogniaux, Hélène

2016-10-07

Several proteomic database search engines that interpret LC-MS/MS data do not identify the same set of peptides. These disagreements occur even when the scores of the peptide-to-spectrum matches suggest good confidence in the interpretation. Our study shows that these disagreements observed for the interpretations of a given spectrum are almost exclusively due to the variation of what we call the "peptide space", i.e., the set of peptides that are actually compared to the experimental spectra. We discuss the potential difficulties of precisely defining the "peptide space." Indeed, although several parameters that are generally reported in publications can easily be set to the same values, many additional parameters-with much less straightforward user access-might impact the "peptide space" used by each program. Moreover, in a configuration where each search engine identifies the same candidates for each spectrum, the inference of the proteins may remain quite different depending on the false discovery rate selected.

Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate.

PubMed

Park, Gun Wook; Hwang, Heeyoun; Kim, Kwang Hoe; Lee, Ju Yeon; Lee, Hyun Kyoung; Park, Ji Yeong; Ji, Eun Sun; Park, Sung-Kyu Robin; Yates, John R; Kwon, Kyung-Hoon; Park, Young Mok; Lee, Hyoung-Joo; Paik, Young-Ki; Kim, Jin Young; Yoo, Jong Shin

2016-11-04

In the Chromosome-Centric Human Proteome Project (C-HPP), false-positive identification by peptide spectrum matches (PSMs) after database searches is a major issue for proteogenomic studies using liquid-chromatography and mass-spectrometry-based large proteomic profiling. Here we developed a simple strategy for protein identification, with a controlled false discovery rate (FDR) at the protein level, using an integrated proteomic pipeline (IPP) that consists of four engrailed steps as follows. First, using three different search engines, SEQUEST, MASCOT, and MS-GF+, individual proteomic searches were performed against the neXtProt database. Second, the search results from the PSMs were combined using statistical evaluation tools including DTASelect and Percolator. Third, the peptide search scores were converted into E-scores normalized using an in-house program. Last, ProteinInferencer was used to filter the proteins containing two or more peptides with a controlled FDR of 1.0% at the protein level. Finally, we compared the performance of the IPP to a conventional proteomic pipeline (CPP) for protein identification using a controlled FDR of <1% at the protein level. Using the IPP, a total of 5756 proteins (vs 4453 using the CPP) including 477 alternative splicing variants (vs 182 using the CPP) were identified from human hippocampal tissue. In addition, a total of 10 missing proteins (vs 7 using the CPP) were identified with two or more unique peptides, and their tryptic peptides were validated using MS/MS spectral pattern from a repository database or their corresponding synthetic peptides. This study shows that the IPP effectively improved the identification of proteins, including alternative splicing variants and missing proteins, in human hippocampal tissues for the C-HPP. All RAW files used in this study were deposited in ProteomeXchange (PXD000395).

Prevalence of metabolic syndrome in Brazilian adults: a systematic review

PubMed Central

2013-01-01

Background The metabolic syndrome (MS) is a complex of risk factors for cardiovascular disease. This syndrome increases the risk of diabetes, cardiovascular disease and all-cause mortality. It has been demonstrated that the prevalence of MS is increasing worldwide. Despite the importance of MS in the context of metabolic and cardiovascular disease, few studies have described the prevalence of MS and its determinants in Latin America. The present study aims to assess studies describing the prevalence of MS in Brazil in order to determine the global prevalence of the syndrome and its components. Methods Systematic review. Searches were carried out in PubMed and Scielo from the earliest available online indexing year through May 2013. There were no restrictions on language. The search terms used to describe MS were taken from the PubMed (MeSH) dictionary: “metabolic syndrome x”, “prevalence” and “Brazil”. Studies were included if they were cross-sectional, described the prevalence of MS and were conducted in apparently healthy subjects, from the general population, 19-64 years old (adult and middle aged) of both genders. The titles and abstracts of all the articles identified were screened for eligibility. Results Ten cross-sectional studies were selected. The weighted mean for general prevalence of MS in Brazil was 29.6% (range: 14.9%-65.3%). Half of the studies used the criteria for clinical diagnosis of MS proposed by the National Cholesterol Education Program Adult Treatment Panel III (NCEP-ATP III) (2001). The highest prevalence of MS (65.3%) was found in a study conducted in an indigenous population, whereas the lowest prevalence of MS (14.9%) was reported in a rural area. The most frequent MS components were low HDL-cholesterol (59.3%) and hypertension (52.5%). Conclusions Despite methodological differences among the studies selected, our findings suggested a high prevalence of MS in the Brazilian adult population. PMID:24350922

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

PubMed

Chamrad, Daniel C; Körting, Gerhard; Schäfer, Heike; Stephan, Christian; Thiele, Herbert; Apweiler, Rolf; Meyer, Helmut E; Marcus, Katrin; Blüggel, Martin

2006-09-01

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night.

PubMed

Kiseleva, Olga; Poverennaya, Ekaterina; Shargunov, Alexander; Lisitsa, Andrey

2018-02-01

Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data. Nowadays, the routine manual search does not satisfy the "speed" of modern science any longer. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. We compared the contribution of each of the eight search engines (X!Tandem, MS-GF[Formula: see text], MS Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an open-source graphical user interface SearchGUI ( http://searchgui.googlecode.com ) into total result of proteoforms identification and optimized set of engines working simultaneously. We also compared the results of our search combination with Mascot results using protein kit UPS2, containing 48 human proteins. We selected combination of X!Tandem, MS-GF[Formula: see text] and OMMSA as the most time-efficient and productive combination of search. We added homemade java-script to automatize pipeline from file picking to report generation. These settings resulted in rise of the efficiency of our customized pipeline unobtainable by manual scouting: the analysis of 192 files searched against human proteome (42153 entries) downloaded from UniProt took 11[Formula: see text]h.

PIPI: PTM-Invariant Peptide Identification Using Coding Method.

PubMed

Yu, Fengchao; Li, Ning; Yu, Weichuan

2016-12-02

In computational proteomics, the identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost associated with database search increases exponentially with respect to the number of modified amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible PTM patterns. To address this issue, one group of methods named restricted tools (including Mascot, Comet, and MS-GF+) only allow a small number of PTM types in database search process. Alternatively, the other group of methods named unrestricted tools (including MS-Alignment, ProteinProspector, and MODa) avoids enumerating PTM patterns with an alignment-based approach to localizing and characterizing modified amino acids. However, because of the large search space and PTM localization issue, the sensitivity of these unrestricted tools is low. This paper proposes a novel method named PIPI to achieve PTM-invariant peptide identification. PIPI belongs to the category of unrestricted tools. It first codes peptide sequences into Boolean vectors and codes experimental spectra into real-valued vectors. For each coded spectrum, it then searches the coded sequence database to find the top scored peptide sequences as candidates. After that, PIPI uses dynamic programming to localize and characterize modified amino acids in each candidate. We used simulation experiments and real data experiments to evaluate the performance in comparison with restricted tools (i.e., Mascot, Comet, and MS-GF+) and unrestricted tools (i.e., Mascot with error tolerant search, MS-Alignment, ProteinProspector, and MODa). Comparison with restricted tools shows that PIPI has a close sensitivity and running speed. Comparison with unrestricted tools shows that PIPI has the highest sensitivity except for Mascot with error tolerant search and ProteinProspector. These two tools simplify the task by only considering up to one modified amino acid in each peptide, which results in a higher sensitivity but has difficulty in dealing with multiple modified amino acids. The simulation experiments also show that PIPI has the lowest false discovery proportion, the highest PTM characterization accuracy, and the shortest running time among the unrestricted tools.

Tempest: GPU-CPU computing for high-throughput database spectral matching.

PubMed

Milloy, Jeffrey A; Faherty, Brendan K; Gerber, Scott A

2012-07-06

Modern mass spectrometers are now capable of producing hundreds of thousands of tandem (MS/MS) spectra per experiment, making the translation of these fragmentation spectra into peptide matches a common bottleneck in proteomics research. When coupled with experimental designs that enrich for post-translational modifications such as phosphorylation and/or include isotopically labeled amino acids for quantification, additional burdens are placed on this computational infrastructure by shotgun sequencing. To address this issue, we have developed a new database searching program that utilizes the massively parallel compute capabilities of a graphical processing unit (GPU) to produce peptide spectral matches in a very high throughput fashion. Our program, named Tempest, combines efficient database digestion and MS/MS spectral indexing on a CPU with fast similarity scoring on a GPU. In our implementation, the entire similarity score, including the generation of full theoretical peptide candidate fragmentation spectra and its comparison to experimental spectra, is conducted on the GPU. Although Tempest uses the classical SEQUEST XCorr score as a primary metric for evaluating similarity for spectra collected at unit resolution, we have developed a new "Accelerated Score" for MS/MS spectra collected at high resolution that is based on a computationally inexpensive dot product but exhibits scoring accuracy similar to that of the classical XCorr. In our experience, Tempest provides compute-cluster level performance in an affordable desktop computer.

Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra*

PubMed Central

Jeong, Kyowon; Kim, Sangtae; Bandeira, Nuno; Pevzner, Pavel A.

2011-01-01

Generating all plausible de novo interpretations of a peptide tandem mass (MS/MS) spectrum (Spectral Dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification. However, the sizes of the Spectral Dictionaries quickly grow with the peptide length making their generation impractical for long peptides. We introduce Gapped Spectral Dictionaries (all plausible de novo interpretations with gaps) that can be easily generated for any peptide length thus addressing the limitation of the Spectral Dictionary approach. We show that Gapped Spectral Dictionaries are small thus opening a possibility of using them to speed-up MS/MS searches. Our MS-GappedDictionary algorithm (based on Gapped Spectral Dictionaries) enables proteogenomics applications (such as searches in the six-frame translation of the human genome) that are prohibitively time consuming with existing approaches. MS-GappedDictionary generates gapped peptides that occupy a niche between accurate but short peptide sequence tags and long but inaccurate full length peptide reconstructions. We show that, contrary to conventional wisdom, some high-quality spectra do not have good peptide sequence tags and introduce gapped tags that have advantages over the conventional peptide sequence tags in MS/MS database searches. PMID:21444829

Tempest: Accelerated MS/MS database search software for heterogeneous computing platforms

PubMed Central

Adamo, Mark E.; Gerber, Scott A.

2017-01-01

MS/MS database search algorithms derive a set of candidate peptide sequences from in-silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU generates peptide candidates that are asynchronously sent to a discrete GPU to be scored against experimental spectra in parallel (Milloy et al., 2012). The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. PMID:27603022

Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data.

PubMed

Tu, Chengjian; Sheng, Quanhu; Li, Jun; Ma, Danjun; Shen, Xiaomeng; Wang, Xue; Shyr, Yu; Yi, Zhengping; Qu, Jun

2015-11-06

The two key steps for analyzing proteomic data generated by high-resolution MS are database searching and postprocessing. While the two steps are interrelated, studies on their combinatory effects and the optimization of these procedures have not been adequately conducted. Here, we investigated the performance of three popular search engines (SEQUEST, Mascot, and MS Amanda) in conjunction with five filtering approaches, including respective score-based filtering, a group-based approach, local false discovery rate (LFDR), PeptideProphet, and Percolator. A total of eight data sets from various proteomes (e.g., E. coli, yeast, and human) produced by various instruments with high-accuracy survey scan (MS1) and high- or low-accuracy fragment ion scan (MS2) (LTQ-Orbitrap, Orbitrap-Velos, Orbitrap-Elite, Q-Exactive, Orbitrap-Fusion, and Q-TOF) were analyzed. It was found combinations involving Percolator achieved markedly more peptide and protein identifications at the same FDR level than the other 12 combinations for all data sets. Among these, combinations of SEQUEST-Percolator and MS Amanda-Percolator provided slightly better performances for data sets with low-accuracy MS2 (ion trap or IT) and high accuracy MS2 (Orbitrap or TOF), respectively, than did other methods. For approaches without Percolator, SEQUEST-group performs the best for data sets with MS2 produced by collision-induced dissociation (CID) and IT analysis; Mascot-LFDR gives more identifications for data sets generated by higher-energy collisional dissociation (HCD) and analyzed in Orbitrap (HCD-OT) and in Orbitrap Fusion (HCD-IT); MS Amanda-Group excels for the Q-TOF data set and the Orbitrap Velos HCD-OT data set. Therefore, if Percolator was not used, a specific combination should be applied for each type of data set. Moreover, a higher percentage of multiple-peptide proteins and lower variation of protein spectral counts were observed when analyzing technical replicates using Percolator-associated combinations; therefore, Percolator enhanced the reliability for both identification and quantification. The analyses were performed using the specific programs embedded in Proteome Discoverer, Scaffold, and an in-house algorithm (BuildSummary). These results provide valuable guidelines for the optimal interpretation of proteomic results and the development of fit-for-purpose protocols under different situations.

Comparison of peak-picking workflows for untargeted liquid chromatography/high-resolution mass spectrometry metabolomics data analysis.

PubMed

Rafiei, Atefeh; Sleno, Lekha

2015-01-15

Data analysis is a key step in mass spectrometry based untargeted metabolomics, starting with the generation of generic peak lists from raw liquid chromatography/mass spectrometry (LC/MS) data. Due to the use of various algorithms by different workflows, the results of different peak-picking strategies often differ widely. Raw LC/HRMS data from two types of biological samples (bile and urine), as well as a standard mixture of 84 metabolites, were processed with four peak-picking softwares: Peakview®, Markerview™, MetabolitePilot™ and XCMS Online. The overlaps between the results of each peak-generating method were then investigated. To gauge the relevance of peak lists, a database search using the METLIN online database was performed to determine which features had accurate masses matching known metabolites as well as a secondary filtering based on MS/MS spectral matching. In this study, only a small proportion of all peaks (less than 10%) were common to all four software programs. Comparison of database searching results showed peaks found uniquely by one workflow have less chance of being found in the METLIN metabolomics database and are even less likely to be confirmed by MS/MS. It was shown that the performance of peak-generating workflows has a direct impact on untargeted metabolomics results. As it was demonstrated that the peaks found in more than one peak detection workflow have higher potential to be identified by accurate mass as well as MS/MS spectrum matching, it is suggested to use the overlap of different peak-picking workflows as preliminary peak lists for more rugged statistical analysis in global metabolomics investigations. Copyright © 2014 John Wiley & Sons, Ltd.

A novel algorithm for validating peptide identification from a shotgun proteomics search engine.

PubMed

Jian, Ling; Niu, Xinnan; Xia, Zhonghang; Samir, Parimal; Sumanasekera, Chiranthani; Mu, Zheng; Jennings, Jennifer L; Hoek, Kristen L; Allos, Tara; Howard, Leigh M; Edwards, Kathryn M; Weil, P Anthony; Link, Andrew J

2013-03-01

Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has revolutionized the proteomics analysis of complexes, cells, and tissues. In a typical proteomic analysis, the tandem mass spectra from a LC-MS/MS experiment are assigned to a peptide by a search engine that compares the experimental MS/MS peptide data to theoretical peptide sequences in a protein database. The peptide spectra matches are then used to infer a list of identified proteins in the original sample. However, the search engines often fail to distinguish between correct and incorrect peptides assignments. In this study, we designed and implemented a novel algorithm called De-Noise to reduce the number of incorrect peptide matches and maximize the number of correct peptides at a fixed false discovery rate using a minimal number of scoring outputs from the SEQUEST search engine. The novel algorithm uses a three-step process: data cleaning, data refining through a SVM-based decision function, and a final data refining step based on proteolytic peptide patterns. Using proteomics data generated on different types of mass spectrometers, we optimized the De-Noise algorithm on the basis of the resolution and mass accuracy of the mass spectrometer employed in the LC-MS/MS experiment. Our results demonstrate De-Noise improves peptide identification compared to other methods used to process the peptide sequence matches assigned by SEQUEST. Because De-Noise uses a limited number of scoring attributes, it can be easily implemented with other search engines.

Fast and efficient search for MPEG-4 video using adjacent pixel intensity difference quantization histogram feature

NASA Astrophysics Data System (ADS)

Lee, Feifei; Kotani, Koji; Chen, Qiu; Ohmi, Tadahiro

2010-02-01

In this paper, a fast search algorithm for MPEG-4 video clips from video database is proposed. An adjacent pixel intensity difference quantization (APIDQ) histogram is utilized as the feature vector of VOP (video object plane), which had been reliably applied to human face recognition previously. Instead of fully decompressed video sequence, partially decoded data, namely DC sequence of the video object are extracted from the video sequence. Combined with active search, a temporal pruning algorithm, fast and robust video search can be realized. The proposed search algorithm has been evaluated by total 15 hours of video contained of TV programs such as drama, talk, news, etc. to search for given 200 MPEG-4 video clips which each length is 15 seconds. Experimental results show the proposed algorithm can detect the similar video clip in merely 80ms, and Equal Error Rate (ERR) of 2 % in drama and news categories are achieved, which are more accurately and robust than conventional fast video search algorithm.

Searching for X-ray Pulsations from Neutron Stars Using NICER

NASA Astrophysics Data System (ADS)

Ray, Paul S.; Arzoumanian, Zaven; Bogdanov, Slavko; Bult, Peter; Chakrabarty, Deepto; Guillot, Sebastien; Kust Harding, Alice; Ho, Wynn C. G.; Lamb, Frederick K.; Mahmoodifar, Simin; Miller, M. Coleman; Strohmayer, Tod E.; Wilson-Hodge, Colleen A.; Wolff, Michael Thomas

2017-08-01

The Neutron Star Interior Composition Explorer (NICER) presents an exciting new capability for discovering new modulation properties of X-ray emitting neutron stars, including large area, low background, extremely precise absolute time stamps, superb low-energy response and flexible scheduling. The Pulsation Searches and Multiwavelength Coordination working group has designed a 2.5 Ms observing program to search for pulsations and characterize the modulation properties of about 30 known or suspected neutron star sources across a number of source categories. A key early goal will be to search for pulsations from millisecond pulsars that might exhibit thermal pulsations from the surface suitable for pulse profile modeling to constrain the neutron star equation of state. In addition, we will search for pulsations from transitional millisecond pulsars, isolated neutron stars, LMXBs, accretion-powered millisecond pulsars, central compact objects and other sources. We will present our science plan and initial results from the first months of the NICER mission.

Searching for X-ray Pulsations from Neutron Stars Using NICER

NASA Astrophysics Data System (ADS)

Ray, Paul S.; Arzoumanian, Zaven; Gendreau, Keith C.; Bogdanov, Slavko; Bult, Peter; Chakrabarty, Deepto; Chakrabarty, Deepto; Guillot, Sebastien; Harding, Alice; Ho, Wynn C. G.; Lamb, Frederick; Mahmoodifar, Simin; Miller, Cole; Strohmayer, Tod; Wilson-Hodge, Colleen; Wolff, Michael T.; NICER Science Team Working Group on Pulsation Searches and Multiwavelength Coordination

2018-01-01

The Neutron Star Interior Composition Explorer (NICER) presents an exciting new capability for discovering new modulation properties of X-ray emitting neutron stars, including large area, low background, extremely precise absolute time stamps, superb low-energy response and flexible scheduling. The Pulsation Searches and Multiwavelength Coordination working group has designed a 2.5 Ms observing program to search for pulsations and characterize the modulation properties of about 30 known or suspected neutron star sources across a number of source categories. A key early goal will be to search for pulsations from millisecond pulsars that might exhibit thermal pulsations from the surface suitable for pulse profile modeling to constrain the neutron star equation of state. In addition, we will search for pulsations from transitional millisecond pulsars, isolated neutron stars, LMXBs, accretion-powered millisecond pulsars, central compact objects and other sources. We present our science plan and initial results from the first months of the NICER mission.

ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite

PubMed Central

2010-01-01

Background Successful application of crosslinking combined with mass spectrometry for studying proteins and protein complexes requires specifically-designed crosslinking reagents, experimental techniques, and data analysis software. Using isotopically-coded ("heavy and light") versions of the crosslinker and cleavable crosslinking reagents is analytically advantageous for mass spectrometric applications and provides a "handle" that can be used to distinguish crosslinked peptides of different types, and to increase the confidence of the identification of the crosslinks. Results Here, we describe a program suite designed for the analysis of mass spectrometric data obtained with isotopically-coded cleavable crosslinkers. The suite contains three programs called: DX, DXDX, and DXMSMS. DX searches the mass spectra for the presence of ion signal doublets resulting from the light and heavy isotopic forms of the isotopically-coded crosslinking reagent used. DXDX searches for possible mass matches between cleaved and uncleaved isotopically-coded crosslinks based on the established chemistry of the cleavage reaction for a given crosslinking reagent. DXMSMS assigns the crosslinks to the known protein sequences, based on the isotopically-coded and un-coded MS/MS fragmentation data of uncleaved and cleaved peptide crosslinks. Conclusion The combination of these three programs, which are tailored to the analytical features of the specific isotopically-coded cleavable crosslinking reagents used, represents a powerful software tool for automated high-accuracy peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm PMID:20109223

The Anglo-Australian Planet Search Legacy

NASA Astrophysics Data System (ADS)

Wittenmyer, Robert A.; Tinney, Christopher G.; Butler, Paul; Horner, Jonathan; Carter, Brad; Wright, Duncan; Jones, H. R. A.

2017-01-01

Radial velocity searches for exoplanets have undergone a revolution in recent years: now precisions of 1 m/s or better are being demonstrated by many instruments, and new purpose-built spectrographs hold the promise of bringing Earth-mass planets into the realm of secure detectability. In the "race to the bottom," it is critical not to overlook the impact of long-running planet search programs that continue to hold the advantage of time. We highlight the continuing impact of the 18-year Anglo-Australian Planet Search: the characterisation of long-period giant planets, and the insights into the occurrence rate of Jupiter and Saturn analogs. To fully understand the origins of planetary systems and the fundamental question of how common (or rare) the architecture of the Solar system is in the Galaxy, we must continue these "legacy" surveys to probe ever-larger orbital separations.

LC/QTOF-MS fragmentation of N-nitrosodimethylamine precursors in drinking water supplies is predictable and aids their identification.

PubMed

Hanigan, David; Ferrer, Imma; Thurman, E Michael; Herckes, Pierre; Westerhoff, Paul

2017-02-05

N-Nitrosodimethylamine (NDMA) is carcinogenic in rodents and occurs in chloraminated drinking water and wastewater effluents. NDMA forms via reactions between chloramines and mostly unidentified, N-containing organic matter. We developed a mass spectrometry technique to identify NDMA precursors by analyzing 25 model compounds with LC/QTOF-MS. We searched isolates of 11 drinking water sources and 1 wastewater using a custom MATLAB ® program and extracted ion chromatograms for two fragmentation patterns that were specific to the model compounds. Once a diagnostic fragment was discovered, we conducted MS/MS during a subsequent injection to confirm the precursor ion. Using non-target searches and two diagnostic fragmentation patterns, we discovered 158 potential NDMA precursors. Of these, 16 were identified using accurate mass combined with fragment and retention time matches of analytical standards when available. Five of these sixteen NDMA precursors were previously unidentified in the literature, three of which were metabolites of pharmaceuticals. Except methadone, the newly identified precursors all had NDMA molar yields of less than 5%, indicating that NDMA formation could be additive from multiple compounds, each with low yield. We demonstrate that the method is applicable to other disinfection by-product precursors by predicting and verifying the fragmentation patterns for one nitrosodiethylamine precursor. Copyright © 2016. Published by Elsevier B.V.

Tempest: Accelerated MS/MS Database Search Software for Heterogeneous Computing Platforms.

PubMed

Adamo, Mark E; Gerber, Scott A

2016-09-07

MS/MS database search algorithms derive a set of candidate peptide sequences from in silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU (central processing unit) generates peptide candidates that are asynchronously sent to a discrete GPU (graphics processing unit) to be scored against experimental spectra in parallel. The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment

PubMed Central

Dasari, Surendra; Chambers, Matthew C.; Martinez, Misti A.; Carpenter, Kristin L.; Ham, Amy-Joan L.; Vega-Montoto, Lorenzo J.; Tabb, David L.

2012-01-01

Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measuring the quality of a spectrum-spectrum match (SSM). This scoring system does not offer a clear statistical interpretation and ignores fragment ion m/z discrepancies in the scoring. We developed a new spectral library search engine, Pepitome, which employs statistical systems for scoring SSMs. Pepitome outperformed the leading library search tool, SpectraST, when analyzing data sets acquired on three different mass spectrometry platforms. We characterized the reliability of spectral library searches by confirming shotgun proteomics identifications through RNA-Seq data. Applying spectral library and database searches on the same sample revealed their complementary nature. Pepitome identifications enabled the automation of quality analysis and quality control (QA/QC) for shotgun proteomics data acquisition pipelines. PMID:22217208

Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass

PubMed Central

Figeys, Daniel; Fai, Stephen; Bennett, Steffany A. L.

2013-01-01

Motivation: Establishing phospholipid identities in large lipidomic datasets is a labour-intensive process. Where genomics and proteomics capitalize on sequence-based signatures, glycerophospholipids lack easily definable molecular fingerprints. Carbon chain length, degree of unsaturation, linkage, and polar head group identity must be calculated from mass to charge (m/z) ratios under defined mass spectrometry (MS) conditions. Given increasing MS sensitivity, many m/z values are not represented in existing prediction engines. To address this need, Visualization and Phospholipid Identification is a web-based application that returns all theoretically possible phospholipids for any m/z value and MS condition. Visualization algorithms produce multiple chemical structure files for each species. Curated lipids detected by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics are provided as high-resolution structures. Availability: VaLID is available through the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics resources web site at https://www.med.uottawa.ca/lipidomics/resources.html. Contacts: lipawrd@uottawa.ca Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23162086

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences.

PubMed

Padliya, Neerav D; Garrett, Wesley M; Campbell, Kimberly B; Tabb, David L; Cooper, Bret

2007-11-01

LC-MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC-MS/MS does not require pathogen-specific reagents for the detection of pathogen-specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database-search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC-MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database-search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross-species protein matches and misidentification of pathogens.

The Pulsar Search Collaboratory: Discovery and Timing of Five New Pulsars

NASA Astrophysics Data System (ADS)

Rosen, R.; Swiggum, J.; McLaughlin, M. A.; Lorimer, D. R.; Yun, M.; Heatherly, S. A.; Boyles, J.; Lynch, R.; Kondratiev, V. I.; Scoles, S.; Ransom, S. M.; Moniot, M. L.; Cottrill, A.; Weaver, M.; Snider, A.; Thompson, C.; Raycraft, M.; Dudenhoefer, J.; Allphin, L.; Thorley, J.; Meadows, B.; Marchiny, G.; Liska, A.; O'Dwyer, A. M.; Butler, B.; Bloxton, S.; Mabry, H.; Abate, H.; Boothe, J.; Pritt, S.; Alberth, J.; Green, A.; Crowley, R. J.; Agee, A.; Nagley, S.; Sargent, N.; Hinson, E.; Smith, K.; McNeely, R.; Quigley, H.; Pennington, A.; Chen, S.; Maynard, T.; Loope, L.; Bielski, N.; McGough, J. R.; Gural, J. C.; Colvin, S.; Tso, S.; Ewen, Z.; Zhang, M.; Ciccarella, N.; Bukowski, B.; Novotny, C. B.; Gore, J.; Sarver, K.; Johnson, S.; Cunningham, H.; Collins, D.; Gardner, D.; Monteleone, A.; Hall, J.; Schweinhagen, R.; Ayers, J.; Jay, S.; Uosseph, B.; Dunkum, D.; Pal, J.; Dydiw, S.; Sterling, M.; Phan, E.

2013-05-01

We present the discovery and timing solutions of five new pulsars by students involved in the Pulsar Search Collaboratory, a NSF-funded joint program between the National Radio Astronomy Observatory and West Virginia University designed to excite and engage high-school students in Science, Technology, Engineering, and Mathematics (STEM) and related fields. We encourage students to pursue STEM fields by apprenticing them within a professional scientific community doing cutting edge research, specifically by teaching them to search for pulsars. The students are analyzing 300 hr of drift-scan survey data taken with the Green Bank Telescope at 350 MHz. These data cover 2876 deg2 of the sky. Over the course of five years, more than 700 students have inspected diagnostic plots through a web-based graphical interface designed for this project. The five pulsars discovered in the data have spin periods ranging from 3.1 ms to 4.8 s. Among the new discoveries are PSR J1926-1314, a long period, nulling pulsar; PSR J1821+0155, an isolated, partially recycled 33 ms pulsar; and PSR J1400-1438, a millisecond pulsar in a 9.5 day orbit whose companion is likely a white dwarf star.

Visual search for arbitrary objects in real scenes

PubMed Central

Alvarez, George A.; Rosenholtz, Ruth; Kuzmova, Yoana I.; Sherman, Ashley M.

2011-01-01

How efficient is visual search in real scenes? In searches for targets among arrays of randomly placed distractors, efficiency is often indexed by the slope of the reaction time (RT) × Set Size function. However, it may be impossible to define set size for real scenes. As an approximation, we hand-labeled 100 indoor scenes and used the number of labeled regions as a surrogate for set size. In Experiment 1, observers searched for named objects (a chair, bowl, etc.). With set size defined as the number of labeled regions, search was very efficient (~5 ms/item). When we controlled for a possible guessing strategy in Experiment 2, slopes increased somewhat (~15 ms/item), but they were much shallower than search for a random object among other distinctive objects outside of a scene setting (Exp. 3: ~40 ms/item). In Experiments 4–6, observers searched repeatedly through the same scene for different objects. Increased familiarity with scenes had modest effects on RTs, while repetition of target items had large effects (>500 ms). We propose that visual search in scenes is efficient because scene-specific forms of attentional guidance can eliminate most regions from the “functional set size” of items that could possibly be the target. PMID:21671156

Visual search for arbitrary objects in real scenes.

PubMed

Wolfe, Jeremy M; Alvarez, George A; Rosenholtz, Ruth; Kuzmova, Yoana I; Sherman, Ashley M

2011-08-01

How efficient is visual search in real scenes? In searches for targets among arrays of randomly placed distractors, efficiency is often indexed by the slope of the reaction time (RT) × Set Size function. However, it may be impossible to define set size for real scenes. As an approximation, we hand-labeled 100 indoor scenes and used the number of labeled regions as a surrogate for set size. In Experiment 1, observers searched for named objects (a chair, bowl, etc.). With set size defined as the number of labeled regions, search was very efficient (~5 ms/item). When we controlled for a possible guessing strategy in Experiment 2, slopes increased somewhat (~15 ms/item), but they were much shallower than search for a random object among other distinctive objects outside of a scene setting (Exp. 3: ~40 ms/item). In Experiments 4-6, observers searched repeatedly through the same scene for different objects. Increased familiarity with scenes had modest effects on RTs, while repetition of target items had large effects (>500 ms). We propose that visual search in scenes is efficient because scene-specific forms of attentional guidance can eliminate most regions from the "functional set size" of items that could possibly be the target.

MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

PubMed

Wang, Yingfeng; Kora, Guruprasad; Bowen, Benjamin P; Pan, Chongle

2014-10-07

A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a metabolite by systematic bond dissociation, then calculates the plausibility of the fragments based on their fragmentation pathways, and finally scores the MSM to assess how well the experimental MS/MS spectrum from collision-induced dissociation (CID) is explained by the metabolite's predicted CID MS/MS spectrum. MIDAS was designed to search high-resolution tandem mass spectra acquired on time-of-flight or Orbitrap mass spectrometer against a metabolite database in an automated and high-throughput manner. The accuracy of metabolite identification by MIDAS was benchmarked using four sets of standard tandem mass spectra from MassBank. On average, for 77% of original spectra and 84% of composite spectra, MIDAS correctly ranked the true compounds as the first MSMs out of all MetaCyc metabolites as decoys. MIDAS correctly identified 46% more original spectra and 59% more composite spectra at the first MSMs than an existing database-searching algorithm, MetFrag. MIDAS was showcased by searching a published real-world measurement of a metabolome from Synechococcus sp. PCC 7002 against the MetaCyc metabolite database. MIDAS identified many metabolites missed in the previous study. MIDAS identifications should be considered only as candidate metabolites, which need to be confirmed using standard compounds. To facilitate manual validation, MIDAS provides annotated spectra for MSMs and labels observed mass spectral peaks with predicted fragments. The database searching and manual validation can be performed online at http://midas.omicsbio.org.

[Progress in the spectral library based protein identification strategy].

PubMed

Yu, Derui; Ma, Jie; Xie, Zengyan; Bai, Mingze; Zhu, Yunping; Shu, Kunxian

2018-04-25

Exponential growth of the mass spectrometry (MS) data is exhibited when the mass spectrometry-based proteomics has been developing rapidly. It is a great challenge to develop some quick, accurate and repeatable methods to identify peptides and proteins. Nowadays, the spectral library searching has become a mature strategy for tandem mass spectra based proteins identification in proteomics, which searches the experiment spectra against a collection of confidently identified MS/MS spectra that have been observed previously, and fully utilizes the abundance in the spectrum, peaks from non-canonical fragment ions, and other features. This review provides an overview of the implement of spectral library search strategy, and two key steps, spectral library construction and spectral library searching comprehensively, and discusses the progress and challenge of the library search strategy.

Proteomic analysis of Pinus radiata needles: 2-DE map and protein identification by LC/MS/MS and substitution-tolerant database searching.

PubMed

Valledor, Luis; Castillejo, Maria A; Lenz, Christof; Rodríguez, Roberto; Cañal, Maria J; Jorrín, Jesús

2008-07-01

Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. To identify key proteins related to tree growth, productivity and responses to environmental factors, a proteomic approach is being utilized. In this paper, we present the first report of the 2-DE protein reference map of physiologically mature P. radiata needles, as a basis for subsequent differential expression proteomic studies related to growth, development, biomass production and responses to stresses. After TCA/acetone protein extraction of needle tissue, 549 +/- 21 well-resolved spots were detected in Coommassie-stained gels within the 5-8 pH and 10-100 kDa M(r) ranges. The analytical and biological variance determined for 450 spots were of 31 and 42%, respectively. After LC/MS/MS analysis of in-gel tryptic digested spots, proteins were identified by using the novel Paragon algorithm that tolerates amino acid substitution in the first-pass search. It allowed the confident identification of 115 out of the 150 protein spots subjected to MS, quite unusual high percentage for a poor sequence database, as is the case of P. radiata. Proteins were classified into 12 or 18 groups based on their corresponding cell component or biological process/pathway categories, respectively. Carbohydrate metabolism and photosynthetic enzymes predominate in the 2-DE protein profile of P. radiata needles.

MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research.

PubMed

Bueschl, Christoph; Kluger, Bernhard; Berthiller, Franz; Lirk, Gerald; Winkler, Stephan; Krska, Rudolf; Schuhmacher, Rainer

2012-03-01

Liquid chromatography-mass spectrometry (LC/MS) is a key technique in metabolomics. Since the efficient assignment of MS signals to true biological metabolites becomes feasible in combination with in vivo stable isotopic labelling, our aim was to provide a new software tool for this purpose. An algorithm and a program (MetExtract) have been developed to search for metabolites in in vivo labelled biological samples. The algorithm makes use of the chromatographic characteristics of the LC/MS data and detects MS peaks fulfilling the criteria of stable isotopic labelling. As a result of all calculations, the algorithm specifies a list of m/z values, the corresponding number of atoms of the labelling element (e.g. carbon) together with retention time and extracted adduct-, fragment- and polymer ions. Its function was evaluated using native (12)C- and uniformly (13)C-labelled standard substances. MetExtract is available free of charge and warranty at http://code.google.com/p/metextract/. Precompiled executables are available for Windows operating systems. Supplementary data are available at Bioinformatics online.

STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.

PubMed

Piehowski, Paul D; Petyuk, Vladislav A; Sandoval, John D; Burnum, Kristin E; Kiebel, Gary R; Monroe, Matthew E; Anderson, Gordon A; Camp, David G; Smith, Richard D

2013-03-01

For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Installation Restoration Program Records Search for Bergstrom Air Force Base, Texas.

DTIC Science & Technology

1983-07-01

August 1981. "Pilot Plant Study of Copper , Zinc, and Trivalent Chromium Removal by Adsorbing Colloid Foam Flotation ." M.S. Thesis, Vanderbilt...graduate school and one of his activities included researching the removal of heavy metals, including copper , zinc and trivalent chromium, using a large...scale adsorbing colloid foam flotation pilot plant. Professional Registration Engineer-In-Training, Florida % -7. GREGORY T. MCINTYRE Membership in

Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries.

PubMed

Horlacher, Oliver; Lisacek, Frederique; Müller, Markus

2016-03-04

Experimental improvements in post-translational modification (PTM) detection by tandem mass spectrometry (MS/MS) has allowed the identification of vast numbers of PTMs. Open modification searches (OMSs) of MS/MS data, which do not require prior knowledge of the modifications present in the sample, further increased the diversity of detected PTMs. Despite much effort, there is still a lack of functional annotation of PTMs. One possibility to narrow the annotation gap is to mine MS/MS data deposited in public repositories and to correlate the PTM presence with biological meta-information attached to the data. Since the data volume can be quite substantial and contain tens of millions of MS/MS spectra, the data mining tools must be able to cope with big data. Here, we present two tools, Liberator and MzMod, which are built using the MzJava class library and the Apache Spark large scale computing framework. Liberator builds large MS/MS spectrum libraries, and MzMod searches them in an OMS mode. We applied these tools to a recently published set of 25 million spectra from 30 human tissues and present tissue specific PTMs. We also compared the results to the ones obtained with the OMS tool MODa and the search engine X!Tandem.

Study of thermal behavior of vitamin D3 by pyrolysis-GC-MS in combination with boiling point-retention time correlation.

PubMed

Sun, Yu'an; Liu, Baoxia; Wang, Guoqing; Zhang, Rongjie; Xie, Bing

2005-01-01

The thermal behavior of vitamin D3 was studied based on pyrolysis-GC-MS technique. It was pyrolyzed at 600 degrees C, 750 degrees C, 900 degrees C, respectively. The pyrolysis product were separated With an HP-5 column and identified by the NIST mass spectral search program in combination with the correlation of boiling point and retention time (BP-RT). There are totally 50 components, including mono aromatics and polycyclic aromatic hydrocarbons (PAHs), were determined. It is shown that the contents of the PAHs are increasing with the increasing of the pyrolysis temperature. The contents of the determined components vary from 0.04% to 37.08%.

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

PubMed Central

Sample, Paul J.; Gaston, Kirk W.; Alfonzo, Juan D.; Limbach, Patrick A.

2015-01-01

Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined ‘variable sequencing’, which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing. PMID:25820423

Speeding up the screening of steroids in urine: development of a user-friendly library.

PubMed

Galesio, M; López-Fdez, H; Reboiro-Jato, M; Gómez-Meire, Silvana; Glez-Peña, D; Fdez-Riverola, F; Lodeiro, Carlos; Diniz, M E; Capelo, J L

2013-12-11

This work presents a novel database search engine - MLibrary - designed to assist the user in the detection and identification of androgenic anabolic steroids (AAS) and its metabolites by matrix assisted laser desorption/ionization (MALDI) and mass spectrometry-based strategies. The detection of the AAS in the samples was accomplished by searching (i) the mass spectrometric (MS) spectra against the library developed to identify possible positives and (ii) by comparison of the tandem mass spectrometric (MS/MS) spectra produced after fragmentation of the possible positives with a complete set of spectra that have previously been assigned to the software. The urinary screening for anabolic agents plays a major role in anti-doping laboratories as they represent the most abused drug class in sports. With the help of the MLibrary software application, the use of MALDI techniques for doping control is simplified and the time for evaluation and interpretation of the results is reduced. To do so, the search engine takes as input several MALDI-TOF-MS and MALDI-TOF-MS/MS spectra. It aids the researcher in an automatic mode by identifying possible positives in a single MS analysis and then confirming their presence in tandem MS analysis by comparing the experimental tandem mass spectrometric data with the database. Furthermore, the search engine can, potentially, be further expanded to other compounds in addition to AASs. The applicability of the MLibrary tool is shown through the analysis of spiked urine samples. Copyright © 2013 Elsevier Inc. All rights reserved.

Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences.

PubMed Central

Myers, E W; Mount, D W

1986-01-01

We describe a program which may be used to find approximate matches to a short predefined DNA sequence in a larger target DNA sequence. The program predicts the usefulness of specific DNA probes and sequencing primers and finds nearly identical sequences that might represent the same regulatory signal. The program is written in the C programming language and will run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running under the MS/DOS and UNIX operating systems. The program has been integrated into an existing software package for the IBM personal computer (see article by Mount and Conrad, this volume). Some examples of its use are given. PMID:3753785

Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage.

PubMed

Zhao, Panpan; Zhong, Jiayong; Liu, Wanting; Zhao, Jing; Zhang, Gong

2017-12-01

Multiple search engines based on various models have been developed to search MS/MS spectra against a reference database, providing different results for the same data set. How to integrate these results efficiently with minimal compromise on false discoveries is an open question due to the lack of an independent, reliable, and highly sensitive standard. We took the advantage of the translating mRNA sequencing (RNC-seq) result as a standard to evaluate the integration strategies of the protein identifications from various search engines. We used seven mainstream search engines (Andromeda, Mascot, OMSSA, X!Tandem, pFind, InsPecT, and ProVerB) to search the same label-free MS data sets of human cell lines Hep3B, MHCCLM3, and MHCC97H from the Chinese C-HPP Consortium for Chromosomes 1, 8, and 20. As expected, the union of seven engines resulted in a boosted false identification, whereas the intersection of seven engines remarkably decreased the identification power. We found that identifications of at least two out of seven engines resulted in maximizing the protein identification power while minimizing the ratio of suspicious/translation-supported identifications (STR), as monitored by our STR index, based on RNC-Seq. Furthermore, this strategy also significantly improves the peptides coverage of the protein amino acid sequence. In summary, we demonstrated a simple strategy to significantly improve the performance for shotgun mass spectrometry by protein-level integrating multiple search engines, maximizing the utilization of the current MS spectra without additional experimental work.

Gas Chromatography-Tandem Mass Spectrometry of Lignin Pyrolyzates with Dopant-Assisted Atmospheric Pressure Chemical Ionization and Molecular Structure Search with CSI:FingerID

NASA Astrophysics Data System (ADS)

Larson, Evan A.; Hutchinson, Carolyn P.; Lee, Young Jin

2018-06-01

Dopant-assisted atmospheric pressure chemical ionization (dAPCI) is a soft ionization method rarely used for gas chromatography-mass spectrometry (GC-MS). The current study combines GC-dAPCI with tandem mass spectrometry (MS/MS) for analysis of a complex mixture such as lignin pyrolysis analysis. To identify the structures of volatile lignin pyrolysis products, collision-induced dissociation (CID) MS/MS using a quadrupole time-of-flight mass spectrometer (QTOFMS) and pseudo MS/MS through in-source collision-induced dissociation (ISCID) using a single stage TOFMS are utilized. To overcome the lack of MS/MS database, Compound Structure Identification (CSI):FingerID is used to interpret CID spectra and predict best matched structures from PubChem library. With this approach, a total of 59 compounds were positively identified in comparison to only 22 in NIST database search of GC-EI-MS dataset. This study demonstrates the effectiveness of GC-dAPCI-MS/MS to overcome the limitations of traditional GC-EI-MS analysis when EI-MS database is not sufficient. [Figure not available: see fulltext.

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

PubMed

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Paik, Young-Ki

2017-12-01

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information.

PubMed

Xiao, Chuan-Le; Chen, Xiao-Zhou; Du, Yang-Li; Sun, Xuesong; Zhang, Gong; He, Qing-Yu

2013-01-04

Mass spectrometry has become one of the most important technologies in proteomic analysis. Tandem mass spectrometry (LC-MS/MS) is a major tool for the analysis of peptide mixtures from protein samples. The key step of MS data processing is the identification of peptides from experimental spectra by searching public sequence databases. Although a number of algorithms to identify peptides from MS/MS data have been already proposed, e.g. Sequest, OMSSA, X!Tandem, Mascot, etc., they are mainly based on statistical models considering only peak-matches between experimental and theoretical spectra, but not peak intensity information. Moreover, different algorithms gave different results from the same MS data, implying their probable incompleteness and questionable reproducibility. We developed a novel peptide identification algorithm, ProVerB, based on a binomial probability distribution model of protein tandem mass spectrometry combined with a new scoring function, making full use of peak intensity information and, thus, enhancing the ability of identification. Compared with Mascot, Sequest, and SQID, ProVerB identified significantly more peptides from LC-MS/MS data sets than the current algorithms at 1% False Discovery Rate (FDR) and provided more confident peptide identifications. ProVerB is also compatible with various platforms and experimental data sets, showing its robustness and versatility. The open-source program ProVerB is available at http://bioinformatics.jnu.edu.cn/software/proverb/ .

TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University

PubMed Central

Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

2010-01-01

We developed, TNAURice: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx. PMID:21364829

TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University.

PubMed

Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

2010-11-27

WE DEVELOPED, TNAURICE: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx.

LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data.

PubMed

Zhang, Wei; Zhang, Jiyang; Xu, Changming; Li, Ning; Liu, Hui; Ma, Jie; Zhu, Yunping; Xie, Hongwei

2012-12-01

Database searching based methods for label-free quantification aim to reconstruct the peptide extracted ion chromatogram based on the identification information, which can limit the search space and thus make the data processing much faster. The random effect of the MS/MS sampling can be remedied by cross-assignment among different runs. Here, we present a new label-free fast quantitative analysis tool, LFQuant, for high-resolution LC-MS/MS proteomics data based on database searching. It is designed to accept raw data in two common formats (mzXML and Thermo RAW), and database search results from mainstream tools (MASCOT, SEQUEST, and X!Tandem), as input data. LFQuant can handle large-scale label-free data with fractionation such as SDS-PAGE and 2D LC. It is easy to use and provides handy user interfaces for data loading, parameter setting, quantitative analysis, and quantitative data visualization. LFQuant was compared with two common quantification software packages, MaxQuant and IDEAL-Q, on the replication data set and the UPS1 standard data set. The results show that LFQuant performs better than them in terms of both precision and accuracy, and consumes significantly less processing time. LFQuant is freely available under the GNU General Public License v3.0 at http://sourceforge.net/projects/lfquant/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Group Theoretic Approach to Metaheuristic Local Search for Partitioning Problems

DTIC Science & Technology

2005-05-01

Tabu Search. Mathematical and Computer Modeling 39: 599-616. 107 Daskin , M.S., E. Stern. 1981. A Hierarchical Objective Set Covering Model for EMS... A Group Theoretic Approach to Metaheuristic Local Search for Partitioning Problems by Gary W. Kinney Jr., B.G.S., M.S. Dissertation Presented to the...DISTRIBUTION STATEMENT A Approved for Public Release Distribution Unlimited The University of Texas at Austin May, 2005 20050504 002 REPORT

Installation Restoration Program. Phase I. Records Search, Plattsburgh AFB, New York

DTIC Science & Technology

1985-04-01

Storage Area (WSA) drainage to the Salmon River, the POL and housing area drainage to Lake Champlaln, and the golf course streams and ponds drain...Sanitary Engineering; 2. Michael A. Zapkln, Project Director, M. Eng. Environmental Engineering and M.S. Biology - Team Chief and Ecologlst; 3. Andrew...college courses were offered to World War II veterans. This center became part of the State University system in 1950 and was known as Champlain College

[Prevalence of metabolic syndrome in Argentina in the last 25 years: systematic review of population observational studies].

PubMed

Diaz, A; Espeche, W; March, C; Flores, R; Parodi, R; Genesio, M A; Sabio, R; Poppe, S

Metabolic syndrome (MS) comprises a set of risk factors for cardiovascular disease and diabetes. Argentina has numerous epidemiological studies on MS, however, there has been no systematic analysis of the prevalence of MS in our population. To estimate the prevalence of MS in the Argentine Republic, a systematic review of observational studies published during the period 1988-2014 was carried out. A bibliographic search was conducted in the MEDLINE (National Library of Medicine), SciELO (Scientific Electronic Library Online) and LILACS (Latin American and Caribbean Health Sciences Literature) databases on studies conducted in Argentina between January 1989 and December 2014. The following search terms were combined in English, Spanish and Portuguese: 'metabolic syndrome', 'insulin resistance', 'dysmetabolic syndrome', 'prevalence', 'epidemiology', and 'Argentina'. Epidemiological studies based on the adult population of Argentina with specific report of the prevalence of MS (according to the WHO, ATP III or IDF criteria) were included in the analysis. In the initial bibliographic search, 400 publications were identified. In the second phase of search, 296 titles and abstracts were excluded. In the third phase, the full text of 104 studies was analyzed. Finally, 6 publications were included in the analysis that reported the prevalence of MS in a total of 10,191 subjects (39.6% male). The average age of the population was 45.2 years. The prevalence of MS (random effects model) was 27.5% (95% CI: 21.3%-34.1%). The prevalence of MS was higher in men than in women (29.4% vs. 27.4%, respectively, P=.02). In order of frequency, the most common components of MS were dyslipidaemia (38.3%), hypertension (33.4%), obesity (32.1%) and diabetes (7.5%). Our data show that the prevalence of MS is high, which represents a very important public health problem in Argentina. Copyright © 2017 SEH-LELHA. Publicado por Elsevier España, S.L.U. All rights reserved.

Protocol for an electrospray ionization tandem mass spectral product ion library: development and application for identification of 240 pesticides in foods.

PubMed

Zhang, Kai; Wong, Jon W; Yang, Paul; Hayward, Douglas G; Sakuma, Takeo; Zou, Yunyun; Schreiber, André; Borton, Christopher; Nguyen, Tung-Vi; Kaushik, Banerjee; Oulkar, Dasharath

2012-07-03

Modern determination techniques for pesticides must yield identification quickly with high confidence for timely enforcement of tolerances. A protocol for the collection of liquid chromatography (LC) electrospray ionization (ESI)-quadruple linear ion trap (Q-LIT) mass spectrometry (MS) library spectra was developed. Following the protocol, an enhanced product ion (EPI) library of 240 pesticides was developed by use of spectra collected from two laboratories. A LC-Q-LIT-MS workflow using scheduled multiple reaction monitoring (sMRM) survey scan, information-dependent acquisition (IDA) triggered collection of EPI spectra, and library search was developed and tested to identify the 240 target pesticides in one single LC-Q-LIT MS analysis. By use of LC retention time, one sMRM survey scan transition, and a library search, 75-87% of the 240 pesticides were identified in a single LC/MS analysis at fortified concentrations of 10 ng/g in 18 different foods. A conventional approach with LC-MS/MS using two MRM transitions produced the same identifications and comparable quantitative results with the same incurred foods as the LC-Q-LIT using EPI library search, finding 1.2-49 ng/g of either carbaryl, carbendazim, fenbuconazole, propiconazole, or pyridaben in peaches; carbendazim, imazalil, terbutryn, and thiabendazole in oranges; terbutryn in salmon; and azoxystrobin in ginseng. Incurred broccoli, cabbage, and kale were screened with the same EPI library using three LC-Q-LIT and a LC-quadruple time-of-flight (Q-TOF) instruments. The library search identified azoxystrobin, cyprodinil, fludioxinil, imidacloprid, metalaxyl, spinosyn A, D, and J, amd spirotetramat with each instrument. The approach has a broad application in LC-MS/MS type targeted screening in food analysis.

[Nano-ESI-MS/MS identification on differentiation-associated proteins in M1 mouse myeloid leukemia cells induced by IL-6].

PubMed

Xia, Qing; Wang, Hong-xia; Wang, Jie; Liu, Bing-yu; Hu, Mei-ru; Zhang, Xue-min; Shen, Bei-fen

2004-10-01

To identify two differentiation-associated proteins induced by rhIL-6 in M1 mouse myeloid leukemia cells. Protein spots were excised from 2-D gels and digested in-gel with trypsin. The trypsin lysis products were first analyzed by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) through peptide mass fingerprinting and then performed peptide sequencing by nano-electrospray ionization mass spectrometry/mass spectrometry (nano-ESI-MS/MS). The database search was finished with the Mascot search engine (http://www.matrixscience.co.uk) using the data processed through MaxEnt3 and MasSeq. The two proteins were not revealed by peptide mass fingerprint using MALDI-TOF-MS, while they were respectively identified as Destrin and Putative protein after the sequence of their trypic peptides were obtained by the nano-ESI-MS/MS techniques. Nano-ESI-MS/MS technique can successfully identify the two differentiation-associated proteins induced by rhIL-6 and has great advantage in protein analysis.

Visual search guidance is best after a short delay.

PubMed

Schmidt, Joseph; Zelinsky, Gregory J

2011-03-25

Search displays are typically presented immediately after a target cue, but in the real-world, delays often exist between target designation and search. Experiments 1 and 2 asked how search guidance changes with delay. Targets were cued using a picture or text label, each for 3000ms, followed by a delay up to 9000ms before the search display. Search stimuli were realistic objects, and guidance was quantified using multiple eye movement measures. Text-based cues showed a non-significant trend towards greater guidance following any delay relative to a no-delay condition. However, guidance from a pictorial cue increased sharply 300-600ms after preview offset. Experiment 3 replicated this guidance enhancement using shorter preview durations while equating the time from cue onset to search onset, demonstrating that the guidance benefit is linked to preview offset rather than a more complete encoding of the target. Experiment 4 showed that enhanced guidance persists even with a mask flashed at preview offset, suggesting an explanation other than visual priming. We interpret our findings as evidence for the rapid consolidation of target information into a guiding representation, which attains its maximum effectiveness shortly after preview offset. Copyright © 2011 Elsevier Ltd. All rights reserved.

IESIP - AN IMPROVED EXPLORATORY SEARCH TECHNIQUE FOR PURE INTEGER LINEAR PROGRAMMING PROBLEMS

NASA Technical Reports Server (NTRS)

Fogle, F. R.

1994-01-01

IESIP, an Improved Exploratory Search Technique for Pure Integer Linear Programming Problems, addresses the problem of optimizing an objective function of one or more variables subject to a set of confining functions or constraints by a method called discrete optimization or integer programming. Integer programming is based on a specific form of the general linear programming problem in which all variables in the objective function and all variables in the constraints are integers. While more difficult, integer programming is required for accuracy when modeling systems with small numbers of components such as the distribution of goods, machine scheduling, and production scheduling. IESIP establishes a new methodology for solving pure integer programming problems by utilizing a modified version of the univariate exploratory move developed by Robert Hooke and T.A. Jeeves. IESIP also takes some of its technique from the greedy procedure and the idea of unit neighborhoods. A rounding scheme uses the continuous solution found by traditional methods (simplex or other suitable technique) and creates a feasible integer starting point. The Hook and Jeeves exploratory search is modified to accommodate integers and constraints and is then employed to determine an optimal integer solution from the feasible starting solution. The user-friendly IESIP allows for rapid solution of problems up to 10 variables in size (limited by DOS allocation). Sample problems compare IESIP solutions with the traditional branch-and-bound approach. IESIP is written in Borland's TURBO Pascal for IBM PC series computers and compatibles running DOS. Source code and an executable are provided. The main memory requirement for execution is 25K. This program is available on a 5.25 inch 360K MS DOS format diskette. IESIP was developed in 1990. IBM is a trademark of International Business Machines. TURBO Pascal is registered by Borland International.

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning.

PubMed

Zhou, Xie-Xuan; Zeng, Wen-Feng; Chi, Hao; Luo, Chunjie; Liu, Chao; Zhan, Jianfeng; He, Si-Min; Zhang, Zhifei

2017-12-05

In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides appears to be particularly important. Here, we present pDeep, a deep neural network-based model for the spectrum prediction of peptides. Using the bidirectional long short-term memory (BiLSTM), pDeep can predict higher-energy collisional dissociation, electron-transfer dissociation, and electron-transfer and higher-energy collision dissociation MS/MS spectra of peptides with >0.9 median Pearson correlation coefficients. Further, we showed that intermediate layer of the neural network could reveal physicochemical properties of amino acids, for example the similarities of fragmentation behaviors between amino acids. We also showed the potential of pDeep to distinguish extremely similar peptides (peptides that contain isobaric amino acids, for example, GG = N, AG = Q, or even I = L), which were very difficult to distinguish using traditional search engines.

Installation Restoration Program Records Search for Mather Air Force Base, California.

DTIC Science & Technology

1982-06-01

Board, Central Valley Region Sacramento, California Mr. Stan Phillippe, Mr. Tom Pinkos, Mr. Bob Matteoli, Ms. Liese Schadt, Mr. Gregory Vaughn 916/ 322 ...Grant Ardell 916/ 322 -7166 7. California Department of Fish and Game Sacramento, California Mr. Jack Linn 916/355-7030 8. U.S. Fish and Wildlife Service...34 " A23 " Fire bluea sar.d ... ." ".......443 " S gra vel If additional space is :equired, continue on DWR Form No. 246-Soppement. -ind attach to zesp :sive

High-throughput Database Search and Large-scale Negative Polarity Liquid Chromatography–Tandem Mass Spectrometry with Ultraviolet Photodissociation for Complex Proteomic Samples*

PubMed Central

Madsen, James A.; Xu, Hua; Robinson, Michelle R.; Horton, Andrew P.; Shaw, Jared B.; Giles, David K.; Kaoud, Tamer S.; Dalby, Kevin N.; Trent, M. Stephen; Brodbelt, Jennifer S.

2013-01-01

The use of ultraviolet photodissociation (UVPD) for the activation and dissociation of peptide anions is evaluated for broader coverage of the proteome. To facilitate interpretation and assignment of the resulting UVPD mass spectra of peptide anions, the MassMatrix database search algorithm was modified to allow automated analysis of negative polarity MS/MS spectra. The new UVPD algorithms were developed based on the MassMatrix database search engine by adding specific fragmentation pathways for UVPD. The new UVPD fragmentation pathways in MassMatrix were rigorously and statistically optimized using two large data sets with high mass accuracy and high mass resolution for both MS1 and MS2 data acquired on an Orbitrap mass spectrometer for complex Halobacterium and HeLa proteome samples. Negative mode UVPD led to the identification of 3663 and 2350 peptides for the Halo and HeLa tryptic digests, respectively, corresponding to 655 and 645 peptides that were unique when compared with electron transfer dissociation (ETD), higher energy collision-induced dissociation, and collision-induced dissociation results for the same digests analyzed in the positive mode. In sum, 805 and 619 proteins were identified via UVPD for the Halobacterium and HeLa samples, respectively, with 49 and 50 unique proteins identified in contrast to the more conventional MS/MS methods. The algorithm also features automated charge determination for low mass accuracy data, precursor filtering (including intact charge-reduced peaks), and the ability to combine both positive and negative MS/MS spectra into a single search, and it is freely open to the public. The accuracy and specificity of the MassMatrix UVPD search algorithm was also assessed for low resolution, low mass accuracy data on a linear ion trap. Analysis of a known mixture of three mitogen-activated kinases yielded similar sequence coverage percentages for UVPD of peptide anions versus conventional collision-induced dissociation of peptide cations, and when these methods were combined into a single search, an increase of up to 13% sequence coverage was observed for the kinases. The ability to sequence peptide anions and cations in alternating scans in the same chromatographic run was also demonstrated. Because ETD has a significant bias toward identifying highly basic peptides, negative UVPD was used to improve the identification of the more acidic peptides in conjunction with positive ETD for the more basic species. In this case, tryptic peptides from the cytosolic section of HeLa cells were analyzed by polarity switching nanoLC-MS/MS utilizing ETD for cation sequencing and UVPD for anion sequencing. Relative to searching using ETD alone, positive/negative polarity switching significantly improved sequence coverages across identified proteins, resulting in a 33% increase in unique peptide identifications and more than twice the number of peptide spectral matches. PMID:23695934

Simultaneous screening of targeted and non-targeted contaminants using an LC-QTOF-MS system and automated MS/MS library searching.

PubMed

Herrera-Lopez, S; Hernando, M D; García-Calvo, E; Fernández-Alba, A R; Ulaszewska, M M

2014-09-01

Simultaneous high-resolution full-scan and tandem mass spectrometry (MS/MS) analysis using time of flight mass spectrometry brings an answer for increasing demand of retrospective and non-targeted data analysis. Such analysis combined with spectral library searching is a promising tool for targeted and untargeted screening of small molecules. Despite considerable extension of the panel of compounds of tandem mass spectral libraries, the heterogeneity of spectral data poses a major challenge against the effective usage of spectral libraries. Performance evaluation of available LC-MS/MS libraries will significantly increase credibility in the search results. The present work was aimed to evaluate fluctuation of MS/MS pattern, in the peak intensities distribution together with mass accuracy measurements, and in consequence, performance compliant with ion ratio and mass error criteria as principles in identification processes for targeted and untargeted contaminants at trace levels. Matrix effect and ultra-trace levels of concentration (from 50 ng l(-1) to 1000 ng l(-1) were evaluated as potential source of inaccuracy in the performance of spectral matching. Matrix-matched samples and real samples were screened for proof of applicability. By manual review of data and application of ion ratio and ppm error criteria, false negatives were obtained; this number diminished when in-house library was used, while with on-line MS/MS databases 100% of positive samples were found. In our experience, intensity of peaks across spectra was highly correlated to the concentration effect and matrix complexity. In turn, analysis of spectra acquired at trace concentrations and in different matrices results in better performance in providing correct and reliable identification. Copyright © 2014 John Wiley & Sons, Ltd.

Web search behavior and information needs of people with multiple sclerosis: focus group study and analysis of online postings.

PubMed

Colombo, Cinzia; Mosconi, Paola; Confalonieri, Paolo; Baroni, Isabella; Traversa, Silvia; Hill, Sophie J; Synnot, Anneliese J; Oprandi, Nadia; Filippini, Graziella

2014-07-24

Multiple sclerosis (MS) patients and their family members increasingly seek health information on the Internet. There has been little exploration of how MS patients integrate health information with their needs, preferences, and values for decision making. The INtegrating and Deriving Evidence, Experiences, and Preferences (IN-DEEP) project is a collaboration between Italian and Australian researchers and MS patients, aimed to make high-quality evidence accessible and meaningful to MS patients and families, developing a Web-based resource of evidence-based information starting from their information needs. The objective of this study was to analyze MS patients and their family members' experience about the Web-based health information, to evaluate how they asses this information, and how they integrate health information with personal values. We organized 6 focus groups, 3 with MS patients and 3 with family members, in the Northern, Central, and Southern parts of Italy (April-June 2011). They included 40 MS patients aged between 18 and 60, diagnosed as having MS at least 3 months earlier, and 20 family members aged 18 and over, being relatives of a person with at least a 3-months MS diagnosis. The focus groups were audio-recorded and transcribed verbatim (Atlas software, V 6.0). Data were analyzed from a conceptual point of view through a coding system. An online forum was hosted by the Italian MS society on its Web platform to widen the collection of information. Nine questions were posted covering searching behavior, use of Web-based information, truthfulness of Web information. At the end, posts were downloaded and transcribed. Information needs covered a comprehensive communication of diagnosis, prognosis, and adverse events of treatments, MS causes or risk factors, new drugs, practical, and lifestyle-related information. The Internet is considered useful by MS patients, however, at the beginning or in a later stage of the disease a refusal to actively search for information could occur. Participants used to search on the Web before or after their neurologist's visit or when a new therapy was proposed. Social networks are widely used to read others' stories and retrieve information about daily management. A critical issue was the difficulty of recognizing reliable information on the Web. Many sources were used but the neurologist was mostly the final source of treatment decisions. MS patients used the Internet as a tool to integrate information about the illness. Information needs covered a wide spectrum, the searched topics changed with progression of the disease. Criteria for evaluating Internet accuracy and credibility of information were often lacking or generic. This may limit the empowerment of patients in health care choices.

Web Search Behavior and Information Needs of People With Multiple Sclerosis: Focus Group Study and Analysis of Online Postings

PubMed Central

Colombo, Cinzia; Confalonieri, Paolo; Baroni, Isabella; Traversa, Silvia; Hill, Sophie J; Synnot, Anneliese J; Oprandi, Nadia; Filippini, Graziella

2014-01-01

Background Multiple sclerosis (MS) patients and their family members increasingly seek health information on the Internet. There has been little exploration of how MS patients integrate health information with their needs, preferences, and values for decision making. The INtegrating and Deriving Evidence, Experiences, and Preferences (IN-DEEP) project is a collaboration between Italian and Australian researchers and MS patients, aimed to make high-quality evidence accessible and meaningful to MS patients and families, developing a Web-based resource of evidence-based information starting from their information needs. Objective The objective of this study was to analyze MS patients and their family members’ experience about the Web-based health information, to evaluate how they asses this information, and how they integrate health information with personal values. Methods We organized 6 focus groups, 3 with MS patients and 3 with family members, in the Northern, Central, and Southern parts of Italy (April-June 2011). They included 40 MS patients aged between 18 and 60, diagnosed as having MS at least 3 months earlier, and 20 family members aged 18 and over, being relatives of a person with at least a 3-months MS diagnosis. The focus groups were audio-recorded and transcribed verbatim (Atlas software, V 6.0). Data were analyzed from a conceptual point of view through a coding system. An online forum was hosted by the Italian MS society on its Web platform to widen the collection of information. Nine questions were posted covering searching behavior, use of Web-based information, truthfulness of Web information. At the end, posts were downloaded and transcribed. Results Information needs covered a comprehensive communication of diagnosis, prognosis, and adverse events of treatments, MS causes or risk factors, new drugs, practical, and lifestyle-related information. The Internet is considered useful by MS patients, however, at the beginning or in a later stage of the disease a refusal to actively search for information could occur. Participants used to search on the Web before or after their neurologist’s visit or when a new therapy was proposed. Social networks are widely used to read others’ stories and retrieve information about daily management. A critical issue was the difficulty of recognizing reliable information on the Web. Many sources were used but the neurologist was mostly the final source of treatment decisions. Conclusions MS patients used the Internet as a tool to integrate information about the illness. Information needs covered a wide spectrum, the searched topics changed with progression of the disease. Criteria for evaluating Internet accuracy and credibility of information were often lacking or generic. This may limit the empowerment of patients in health care choices. PMID:25093374

Computer Information Retrieval for Journalists.

ERIC Educational Resources Information Center

Rodewald, Pam

1989-01-01

Discusses the use of computer information retrieval (on-line electronic search methods). Examines advantages and disadvantages of on-line searching versus manual searching. Offers questions to help in the decision to purchase and use on-line searching with students. (MS)

A search asymmetry reversed by figure-ground assignment.

PubMed

Humphreys, G W; Müller, H

2000-05-01

We report evidence demonstrating that a search asymmetry favoring concave over convex targets can be reversed by altering the figure-ground assignment of edges in shapes. Visual search for a concave target among convex distractors is faster than search for a convex target among concave distractors (a search asymmetry). By using shapes with ambiguous local figure-ground relations, we demonstrated that search can be efficient (with search slopes around 10 ms/item) or inefficient (with search slopes around 30-40 ms/item) with the same stimuli, depending on whether edges are assigned to concave or convex "figures." This assignment process can operate in a top-down manner, according to the task set. The results suggest that attention is allocated to spatial regions following the computation of figure-ground relations in parallel across the elements present. This computation can also be modulated by top-down processes.

The effects of trait self-esteem and death cognitions on worldview defense and search for meaning.

PubMed

Juhl, Jacob; Routledge, Clay

2014-01-01

Terror management theory asserts that attaining self-esteem by adhering to the standards of meaning-providing worldviews helps manage death concerns. Research has shown that mortality salience (MS) increases worldview defense, however, there are conflicting results concerning how trait self-esteem moderates this effect. Studies 1 and 2 demonstrated that MS increases worldview defense for high, but not low, trait self-esteem individuals. These studies raised the question as to whether those with low trait self-esteem engage in efforts to find meaning in response to MS. Study 3 showed that MS increased the search for meaning for low, but not high, trait self-esteem individuals.

Disturbed Glucose Metabolism in Rat Neurons Exposed to Cerebrospinal Fluid Obtained from Multiple Sclerosis Subjects

PubMed Central

Mathur, Deepali; María-Lafuente, Eva; Ureña-Peralta, Juan R.; Sorribes, Lucas; Hernández, Alberto; Casanova, Bonaventura; López-Rodas, Gerardo; Coret-Ferrer, Francisco; Burgal-Marti, Maria

2017-01-01

Axonal damage is widely accepted as a major cause of permanent functional disability in Multiple Sclerosis (MS). In relapsing-remitting MS, there is a possibility of remyelination by myelin producing cells and restoration of neurological function. The purpose of this study was to delineate the pathophysiological mechanisms underpinning axonal injury through hitherto unknown factors present in cerebrospinal fluid (CSF) that may regulate axonal damage, remyelinate the axon and make functional recovery possible. We employed primary cultures of rat unmyelinated cerebellar granule neurons and treated them with CSF obtained from MS and Neuromyelitis optica (NMO) patients. We performed microarray gene expression profiling to study changes in gene expression in treated neurons as compared to controls. Additionally, we determined the influence of gene-gene interaction upon the whole metabolic network in our experimental conditions using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) program. Our findings revealed the downregulated expression of genes involved in glucose metabolism in MS-derived CSF-treated neurons and upregulated expression of genes in NMO-derived CSF-treated neurons. We conclude that factors in the CSF of these patients caused a perturbation in metabolic gene(s) expression and suggest that MS appears to be linked with metabolic deformity. PMID:29267205

Creative Thinking of Low Academic Student Undergoing Search Solve Create and Share Learning Integrated with Metacognitive Strategy

ERIC Educational Resources Information Center

Yusnaeni; Corebima, Aloysius Duran; Susilo, Herawati; Zubaidah, Siti

2017-01-01

This research was carried out to analyze the effectiveness of the Search Solve Create and Share learning integrated with metakognitive strategy [SSCS + MS] on the creative thinking ability of low academic students. A quasi experimental design has been used to compare the effect of traditional learning, SSCS, and SCCS + MS learning on the creative…

Use of high-performance liquid chromatography with diode array detection coupled to electrospray-Qq-time-of-flight mass spectrometry for the direct characterization of the phenolic fraction in organic commercial juices.

PubMed

Rodríguez-Medina, I C; Segura-Carretero, A; Fernández-Gutiérrez, A

2009-06-05

We have developed a direct method for the qualitative analysis of polyphenols in commercial organic fruit juices. The juices were diluted with water (50/50), filtered and directly injected. The analysis of phenolic compounds was carried out by reversed-phase high-performance liquid chromatography (RP-HPLC) coupled to photodiode array detection (DAD) and electrospray ionisation-Qq-time-of-flight mass spectrometry (ESI-Qq-TOF-MS). A unique gradient program has been optimized for the separation of several phenolic classes and the analysis time was only 5 min. The fruit juice samples were successfully analysed in positive and negative ionisation modes. In positive mode the anthocyanins were identified whereas the vast majority of polyphenols were identified using the negative ionisation mode. The sensitivity, together with mass accuracy and true isotopic pattern of the Qq-TOF-MS, allowed the identification of the phenolic compounds. Moreover, the advantage of the proposed method is the combined search of MS and MS/MS spectra, which improves the identification of compounds considerably, reducing ambiguities and false positive hits. Therefore the total fragmentation of the compound ion leading to the aglycone ion or other fragments was corroborated by MS-MS. The method was successfully employed to characterize diverse phenolic families in commercially available organic juices from four different fruits and consequently could be used in the future for the quantification purposes to compare different content of polyphenols in juices.

JTMIX - CRYOGENIC MIXED FLUID JOULE-THOMSON ANALYSIS PROGRAM

NASA Technical Reports Server (NTRS)

Jones, J. A.

1994-01-01

JTMIX was written to allow the prediction of both ideal and realistic properties of mixed gases in the 65-80K temperature range. It allows mixed gas J-T analysis for any fluid combination of neon, nitrogen, various hydrocarbons, argon, oxygen, carbon monoxide, carbon dioxide, and hydrogen sulfide. When used in conjunction with the NIST computer program DDMIX, JTMIX has accurately predicted order-of-magnitude increases in J-T cooling capacities when various hydrocarbons are added to nitrogen, and it predicts nitrogen normal boiling point depressions to as low as 60K when neon is added. JTMIX searches for heat exchanger "pinch points" that can result from insolubility of various components in each other. These points result in numerical solutions that cannot exist. The length of the heat exchanger is searched for such points and, if they exist, the user is warned and the temperatures and heat exchanger effectiveness are corrected to provide a real solution. JTMIX gives very good correlation (within data accuracy) to mixed gas data published by the USSR and data taken by APD for the U.S. Naval Weapons Lab. Data taken at JPL also confirms JTMIX for all cases tested. JTMIX is written in Turbo C for IBM PC compatible computers running MS-DOS. The National Institute of Standards and Technology's (NIST, Gaithersburg, MD, 301-975-2208) computer code DDMIX is required to provide mixed-fluid enthalpy data which is input into JTMIX. The standard distribution medium for this program is a 5.25 inch 360K MS-DOS format diskette. JTMIX was developed in 1991 and is a copyrighted work with all copyright vested in NASA.

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

PubMed Central

Jones, Andrew R.; Siepen, Jennifer A.; Hubbard, Simon J.; Paton, Norman W.

2010-01-01

Tandem mass spectrometry, run in combination with liquid chromatography (LC-MS/MS), can generate large numbers of peptide and protein identifications, for which a variety of database search engines are available. Distinguishing correct identifications from false positives is far from trivial because all data sets are noisy, and tend to be too large for manual inspection, therefore probabilistic methods must be employed to balance the trade-off between sensitivity and specificity. Decoy databases are becoming widely used to place statistical confidence in results sets, allowing the false discovery rate (FDR) to be estimated. It has previously been demonstrated that different MS search engines produce different peptide identification sets, and as such, employing more than one search engine could result in an increased number of peptides being identified. However, such efforts are hindered by the lack of a single scoring framework employed by all search engines. We have developed a search engine independent scoring framework based on FDR which allows peptide identifications from different search engines to be combined, called the FDRScore. We observe that peptide identifications made by three search engines are infrequently false positives, and identifications made by only a single search engine, even with a strong score from the source search engine, are significantly more likely to be false positives. We have developed a second score based on the FDR within peptide identifications grouped according to the set of search engines that have made the identification, called the combined FDRScore. We demonstrate by searching large publicly available data sets that the combined FDRScore can differentiate between between correct and incorrect peptide identifications with high accuracy, allowing on average 35% more peptide identifications to be made at a fixed FDR than using a single search engine. PMID:19253293

COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA

PubMed Central

Wenger, Craig D.; Phanstiel, Douglas H.; Lee, M. Violet; Bailey, Derek J.; Coon, Joshua J.

2011-01-01

Here we present the Coon OMSSA Proteomic Analysis Software Suite (COMPASS): a free and open-source software pipeline for high-throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. We detail a synergistic set of tools for protein database generation, spectral reduction, peptide false discovery rate analysis, peptide quantitation via isobaric labeling, protein parsimony and protein false discovery rate analysis, and protein quantitation. We strive for maximum ease of use, utilizing graphical user interfaces and working with data files in the original instrument vendor format. Results are stored in plain text comma-separated values files, which are easy to view and manipulate with a text editor or spreadsheet program. We illustrate the operation and efficacy of COMPASS through the use of two LC–MS/MS datasets. The first is a dataset of a highly annotated mixture of standard proteins and manually validated contaminants that exhibits the identification workflow. The second is a dataset of yeast peptides, labeled with isobaric stable isotope tags and mixed in known ratios, to demonstrate the quantitative workflow. For these two datasets, COMPASS performs equivalently or better than the current de facto standard, the Trans-Proteomic Pipeline. PMID:21298793

Measurement Standards " Commercial Vehicle Enforcement

Science.gov Websites

of Measurement Standards & Commercial Vehicle Enforcement Search DOT&PF State of Alaska DOT &PF> MS/CVE Home Director's Office Measurement Standards MS Home Chief Metrology Lab Commercial Admin Planning Contacts Welcome to MS/CVE Ensuring Accurate Trade Measurements and Enforcing Commercial

Matlab GUI for a Fluid Mixer

NASA Technical Reports Server (NTRS)

Barbieri, Enrique

2005-01-01

The Test and Engineering Directorate at NASA John C. Stennis Space Center developed an interest to study the modeling, evaluation, and control of a liquid hydrogen (LH2) and gas hydrogen (GH2) mixer subsystem of a ground test facility. This facility carries out comprehensive ground-based testing and certification of liquid rocket engines including the Space Shuttle Main engine. A software simulation environment developed in MATLAB/SIMULINK (M/S) will allow NASA engineers to test rocket engine systems at relatively no cost. In the progress report submitted in February 2004, we described the development of two foundation programs, a reverse look-up application using various interpolation algorithms, a variety of search and return methods, and self-checking methods to reduce the error in returned search results to increase the functionality of the program. The results showed that these efforts were successful. To transfer this technology to engineers who are not familiar with the M/S environment, a four-module GUI was implemented allowing the user to evaluate the mixer model under open-loop and closed-loop conditions. The progress report was based on an udergraduate Honors Thesis by Ms. Jamie Granger Austin in the Department of Electrical Engineering and Computer Science at Tulane University, during January-May 2003, and her continued efforts during August-December 2003. In collaboration with Dr. Hanz Richter and Dr. Fernando Figueroa we published these results in a NASA Tech Brief due to appear this year. Although the original proposal in 2003 did not address other components of the test facility, we decided in the last few months to extend our research and consider a related pressurization tank component as well. This report summarizes the results obtained towards a Graphical User Interface (GUI) for the evaluation and control of the hydrogen mixer subsystem model and for the pressurization tank each taken individually. Further research would combine the two components - mixer and tank, for a more realistic simulation tool.

Installation Restoration Program Records Search for McChord Air Force Base, Washington.

DTIC Science & Technology

1982-08-01

responsible for smoke testing for possi- ble outlets. g ŕ 115 0 V -j q * REFERENCES * .4 g SI * I w I WI j EU REFERENCES Brandin , R. M., and S. Sgt. S. A...Ms. R. Brandin . Griffin, W. C., et al. 1962. Water Resources of the Tacoma Area Washington. Geological Survey Water Supply Paper 1499-B. Prepared in...MEMBERS vS U STEVEN R. HOFFMAN Education B.S., Civil Engineering, South Dakota School of Mines and Technology, 1971 Experience - -. Mr. Hoffman is a

Why do people search Wikipedia for information on multiple sclerosis?

PubMed

Brigo, F; Lattanzi, S; Bragazzi, N; Nardone, R; Moccia, M; Lavorgna, L

2018-02-01

Wikipedia is a frequently-accessed online source of health-related information. In this study we evaluated the number of views of the Italian Wikipedia articles related to multiple sclerosis (MS) and its treatment. Using Pageviews Analysis we assessed the total views, and mean monthly and daily views of the Italian Wikipedia articles on MS and its treatments from 1 January 2015 to 31 October 2017. We compared the views of the article on MS with those for Alzheimer´s disease, epilepsy, migraine and stroke, and adjusted results for crude disease prevalence. The total views of the Italian Wikipedia article on MS was 929,983 (mean monthly views: 33,214; mean daily views: 1089). The adjusted views for the Italian Wikipedia article on MS were higher than those for the other neurological disorders. The normalized views for the MS article were 16, 7, 145 and 11 times higher than those of the articles on Alzheimer's disease, epilepsy, migraine and stroke, respectively. Peaks were temporally related to famous people with MS talking about their disease in talk shows on television or to news on novel treatments for MS. Wikipedia searches do not reliably reflect its actual epidemiology. Celebrities with MS acting as testimonials might effectively increase public knowledge on MS. Copyright © 2018 Elsevier B.V. All rights reserved.

Combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for qualitative analysis of drugs.

PubMed

Pavlic, Marion; Libiseller, Kathrin; Oberacher, Herbert

2006-09-01

The potential of the combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for the identification of therapeutic and illicit drugs has been evaluated. Reserpine was used for standardizing experimental conditions and for characterization of the performance of the applied mass spectrometric system. Experiments revealed that because of the mass accuracy, the stability of calibration, and the reproducibility of fragmentation, the QqTOF mass spectrometer is an appropriate platform for establishment of a tandem-mass-spectral library. Three-hundred and nineteen substances were used as reference samples to build the spectral library. For each reference compound, product-ion spectra were acquired at ten different collision-energy values between 5 eV and 50 eV. For identification of unknown compounds, a library search algorithm was developed. The closeness of matching between a measured product-ion spectrum and a spectrum stored in the library was characterized by a value called "match probability", which took into account the number of matched fragment ions, the number of fragment ions observed in the two spectra, and the sum of the intensity differences calculated for matching fragments. A large value for the match probability indicated a close match between the measured and the reference spectrum. A unique feature of the library search algorithm-an implemented spectral purification option-enables characterization of multi-contributor fragment-ion spectra. With the aid of this software feature, substances comprising only 1.0% of the total amount of binary mixtures were unequivocally assigned, in addition to the isobaric main contributors. The spectral library was successfully applied to the characterization of 39 forensic casework samples.

Efficient approach for the detection and identification of new androgenic metabolites by applying SRM GC-CI-MS/MS: a methandienone case study.

PubMed

Polet, Michael; Van Gansbeke, Wim; Van Eenoo, Peter; Deventer, Koen

2016-07-01

Identification of anabolic androgenic steroids (AAS) is a vital issue in doping control and toxicology, and searching for metabolites with longer detection times remains an important task. Recently, a gas chromatography chemical ionization triple quadrupole mass spectrometry (GC-CI-MS/MS) method was introduced, and CI, in comparison with electron ionization (EI), proved to be capable of increasing the sensitivity significantly. In addition, correlations between AAS structure and fragmentation behavior could be revealed. This enables the search for previously unknown but expected metabolites by selection of their predicted transitions. The combination of both factors allows the setup of an efficient approach to search for new metabolites. The approach uses selected reaction monitoring which is inherently more sensitive than full scan or precursor ion scan. Additionally, structural information obtained from the structure specific CI fragmentation pattern facilitates metabolite identification. The procedure was demonstrated by a methandienone case study. Its metabolites have been studied extensively in the past, and this allowed an adequate evaluation of the efficiency of the approach. Thirty three metabolites were detected, including all relevant previously discovered metabolites. In our study, the previously reported long-term metabolite (18-nor-17β-hydroxymethyl,17α-methyl-androst-1,4,13-trien-3-one) could be detected up to 26 days by using GC-CI-MS/MS. The study proves the validity of the approach to search for metabolites of new synthetic AAS and new long-term metabolites of less studied AAS and illustrates the increase in sensitivity by using CI. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Signals of threat do not capture, but prioritize, attention: a conditioning approach.

PubMed

Notebaert, Lies; Crombez, Geert; Van Damme, Stefaan; De Houwer, Jan; Theeuwes, Jan

2011-02-01

Research suggests that threatening information captures attention more rapidly than neutral information. However, in most studies threat stimuli differ perceptually from neutral stimuli and are instrumental to perform the task, leaving the question unanswered whether threat is sufficient to capture attention. In experiment 1, we designed a visual search task with stimuli of equal salience (colored circles) that have the potential to lead to efficient search (10 ms/item). In experiment 2, one of the colors (conditioned stimulus, CS+) was made threatening by means of fear conditioning. Participants responded to a target presented in one of the circles. Overall, the search was faster on congruent trials (where the target was presented in the CS+) than on baseline trials (where the CS + was absent). Furthermore, the search was slower on incongruent trials (where the target was presented in another color than the CS+) than on baseline trials. The search on congruent trials was affected by set size (90 ms/item), but to a lesser extent than on baseline trials (105 ms/item). We conclude that threat prioritizes, but does not capture attention. PsycINFO Database Record (c) 2011 APA, all rights reserved.

An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics

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

Wu, Chaochao; Monroe, Matthew E.; Xu, Zhe

2015-12-26

Comprehensive MS analysis of peptidome, the intracellular and intercellular products of protein degradation, has the potential to provide novel insights on endogenous proteolytic processing and their utility in disease diagnosis and prognosis. Along with the advances in MS instrumentation, a plethora of proteomics data analysis tools have been applied for direct use in peptidomics; however an evaluation of the currently available informatics pipelines for peptidomics data analysis has yet to be reported. In this study, we set off by evaluating the results of several popular MS/MS database search engines including MS-GF+, SEQUEST and MS-Align+ for peptidomics data analysis, followed bymore » identification and label-free quantification using the well-established accurate mass and time (AMT) tag and newly developed informed quantification (IQ) approaches, both based on direct LC-MS analysis. Our result demonstrated that MS-GF+ outperformed both SEQUEST and MS-Align+ in identifying peptidome peptides. Using a database established from the MS-GF+ peptide identifications, both the AMT tag and IQ approaches provided significantly deeper peptidome coverage and less missing value for each individual data set than the MS/MS methods, while achieving robust label-free quantification. Besides having an excellent correlation with the AMT tag quantification results, IQ also provided slightly higher peptidome coverage than AMT. Taken together, we propose an optimal informatics pipeline combining MS-GF+ for initial database searching with IQ (or AMT) for identification and label-free quantification for high-throughput, comprehensive and quantitative peptidomics analysis.« less

Dimension- and space-based intertrial effects in visual pop-out search: modulation by task demands for focal-attentional processing.

PubMed

Krummenacher, Joseph; Müller, Hermann J; Zehetleitner, Michael; Geyer, Thomas

2009-03-01

Two experiments compared reaction times (RTs) in visual search for singleton feature targets defined, variably across trials, in either the color or the orientation dimension. Experiment 1 required observers to simply discern target presence versus absence (simple-detection task); Experiment 2 required them to respond to a detection-irrelevant form attribute of the target (compound-search task). Experiment 1 revealed a marked dimensional intertrial effect of 34 ms for an target defined in a changed versus a repeated dimension, and an intertrial target distance effect, with an 4-ms increase in RTs (per unit of distance) as the separation of the current relative to the preceding target increased. Conversely, in Experiment 2, the dimension change effect was markedly reduced (11 ms), while the intertrial target distance effect was markedly increased (11 ms per unit of distance). The results suggest that dimension change/repetition effects are modulated by the amount of attentional focusing required by the task, with space-based attention altering the integration of dimension-specific feature contrast signals at the level of the overall-saliency map.

Separation and identification of mouse liver membrane proteins using a gel-based approach in combination with 2DnanoLC-Q-TOF-MS/MS

NASA Astrophysics Data System (ADS)

Thanh Tran, The; Phan, Van Chi

2010-03-01

In this work, we present results of membrane proteome profiling from mouse liver tissues using a gel-based approach in combination with 2DnanoLC-Q-TOF-MS/MS. Following purification of the membrane fraction, SDS-PAGE was carried out as a useful separation step. After staining, gels with protein bands were cut, reduced, alkylated and trypsin-digested. The peptide mixtures extracted from each gel slice were fractionated by two-dimensional nano liquid chromatography (2DnanoLC) coupled online with tandem mass spectrometry analysis (NanoESI-Q-TOF-MS/MS). The proteins were identified by MASCOT search against a mouse protein database using a peptide and fragment mass tolerance of ±0.5 Da. Protein identification was carried out using a Mowse scoring algorithm with a confidence level of 95% and processed by MSQuant v1.5 software for further validation. In total, 318 verified membrane proteins from mouse liver tissues were identified; 66.67% of them (212 proteins) contained at least one or more transmembrane domains predicted by the SOSUI program and 43 were found to be unique microsome membranes. Furthermore, GRAVY values of membrane proteins varied in the range -1.1276 to 0.9016 and only 31 (9.76%) membrane proteins had positive values. The functions and subcellular locations of the identified proteins were categorized as well, according to universal GO annotations.

Physical activity and cognitive function in adults with multiple sclerosis: an integrative review.

PubMed

Morrison, Janet D; Mayer, Lori

2017-09-01

To identify and synthesize the research evidence concerning (1) the relationship between physical activity and cognitive performance in persons with multiple sclerosis (MS) and (2) to review the reported effects of physical activity interventions on neurocognitive performance conducted in this population. Relevant peer-reviewed journal articles were identified by searching PubMed, PsychINFO, and SPORTDiscus through May 2016. Full-text articles meeting the inclusion criteria were evaluated for quality using tools developed by the National Institutes of Health. Studies deemed to be of poor quality were excluded from the review. Nineteen studies meeting the inclusion/exclusion criteria were analyzed. Nine studies reported significant relationships between higher levels of physical activity or cardiorespiratory fitness and measures of cognitive function. Data extracted from 10 physical activity intervention studies reported mixed results on the effectiveness of physical activity to improve selected domains of cognitive function in persons with MS. Although correlational studies provide evidence to support a linkage between physical activity and cognitive function in persons with MS, this linkage is confounded by factors that may have influenced the studies' results. Evidence derived from intervention studies that could support a positive effect of physical activity on cognition in persons with MS is equivocal. Implications for Rehabilitation Physical activity has numerous benefits for persons with multiple sclerosis (MS) including improvements in balance, ambulation, depression, fatigue, and quality of life. Structured physical activity programs may contribute to cognitive function stability or improvement in persons with MS.

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics.

PubMed

Joyce, Brendan; Lee, Danny; Rubio, Alex; Ogurtsov, Aleksey; Alves, Gelio; Yu, Yi-Kuo

2018-03-15

RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId's core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. We have constructed a graphical user interface to facilitate the use of RAId on users' local machines. Written in Java, RAId_GUI not only makes easy executions of RAId but also provides tools for data/spectra visualization, MS-product analysis, molecular isotopic distribution analysis, and graphing the retrieval versus the proportion of false discoveries. The results viewer displays and allows the users to download the analyses results. Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html .

The course of visual searching to a target in a fixed location: electrophysiological evidence from an emotional flanker task.

PubMed

Dong, Guangheng; Yang, Lizhu; Shen, Yue

2009-08-21

The present study investigated the course of visual searching to a target in a fixed location, using an emotional flanker task. Event-related potentials (ERPs) were recorded while participants performed the task. Emotional facial expressions were used as emotion-eliciting triggers. The course of visual searching was analyzed through the emotional effects arising from these emotion-eliciting stimuli. The flanker stimuli showed effects at about 150-250 ms following the stimulus onset, while the effect of target stimuli showed effects at about 300-400 ms. The visual search sequence in an emotional flanker task moved from a whole overview to a specific target, even if the target always appeared at a known location. The processing sequence was "parallel" in this task. The results supported the feature integration theory of visual search.

Identification of Poly(ethylene glycol) and Poly(ethylene glycol)-Based Detergents Using Peptide Search Engines.

PubMed

Ahmadi, Shiva; Winter, Dominic

2018-06-05

Poly(ethylene glycol) (PEG) is one of the most common polymer contaminations in mass spectrometry (MS) samples. At present, the detection of PEG and other polymers relies largely on manual inspection of raw data, which is laborious and frequently difficult due to sample complexity and retention characteristics of polymer species in reversed-phase chromatography. We developed a new strategy for the automated identification of PEG molecules from tandem mass spectrometry (MS/MS) data using protein identification algorithms in combination with a database containing "PEG-proteins". Through definition of variable modifications, we extend the approach for the identification of commonly used PEG-based detergents. We exemplify the identification of different types of polymers by static nanoelectrospray tandem mass spectrometry (nanoESI-MS/MS) analysis of pure detergent solutions and data analysis using Mascot. Analysis of liquid chromatography-tandem mass spectrometry (LC-MS/MS) runs of a PEG-contaminated sample by Mascot identified 806 PEG spectra originating from four PEG species using a defined set of modifications covering PEG and common PEG-based detergents. Further characterization of the sample for unidentified PEG species using error-tolerant and mass-tolerant searches resulted in identification of 3409 and 3187 PEG-related MS/MS spectra, respectively. We further demonstrate the applicability of the strategy for Protein Pilot and MaxQuant.

Detection and Identification of Heme c-Modified Peptides by Histidine Affinity Chromatography, High-Performance Liquid Chromatography-Mass Spectrometry, and Database Searching

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

Merkley, Eric D.; Anderson, Brian J.; Park, Jea H.

2012-12-07

Multiheme c-type cytochromes (proteins with covalently attached heme c moieties) play important roles in extracellular metal respiration in dissimilatory metal-reducing bacteria. Liquid chromatography-tandem mass spectrometry-(LC-MS/MS) characterization of c-type cytochromes is hindered by the presence of multiple heme groups, since the heme c modified peptides are typically not observed, or if observed, not identified. Using a recently reported histidine affinity chromatography (HAC) procedure, we enriched heme c tryptic peptides from purified bovine heart cytochrome c, a bacterial decaheme cytochrome, and subjected these samples to LC-MS/MS analysis. Enriched bovine cytochrome c samples yielded three- to six-fold more confident peptide-spectrum matches to heme-cmore » containing peptides than unenriched digests. In unenriched digests of the decaheme cytochrome MtoA from Sideroxydans lithotrophicus ES-1, heme c peptides for four of the ten expected sites were observed by LC-MS/MS; following HAC fractionation, peptides covering nine out of ten sites were obtained. Heme c peptide spiked into E. coli lysates at mass ratios as low as 10-4 was detected with good signal-to-noise after HAC and LC-MS/MS analysis. In addition to HAC, we have developed a proteomics database search strategy that takes into account the unique physicochemical properties of heme c peptides. The results suggest that accounting for the double thioether link between heme c and peptide, and the use of the labile heme fragment as a reporter ion, can improve database searching results. The combination of affinity chromatography and heme-specific informatics yielded increases in the number of peptide-spectrum matches of 20-100-fold for bovine cytochrome c.« less

LC-MS-Based Lipidomics and Automated Identification of Lipids Using the LipidBlast In-Silico MS/MS Library.

PubMed

Cajka, Tomas; Fiehn, Oliver

2017-01-01

This protocol describes the analysis, specifically the identification, of blood plasma lipids. Plasma lipids are extracted using methyl tert-butyl ether (MTBE), methanol, and water followed by separation and data acquisition of isolated lipids using reversed-phase liquid chromatography coupled to quadrupole/time-of-flight mass spectrometry (RPLC-QTOFMS) operated in MS/MS mode. For lipid identification, acquired MS/MS spectra are converted to the mascot generic format (MGF) followed by library search using the in-silico MS/MS library LipidBlast. Using this approach, lipid classes, carbon-chain lengths, and degree of unsaturation of fatty-acid components are annotated.

Dataset of breath research manuscripts curated using PubMed search strings from 1995-2016.

PubMed

Geer Wallace, M Ariel; Pleil, Joachim D

2018-06-01

The data contained in this article are PubMed search strings and search string builders used to curate breath research manuscripts published from 1995-2016 and the respective number of articles found that satisfied the search requirements for selected categories. Breath sampling represents a non-invasive technique that has gained usefulness for public health, clinical, diagnostic, and environmental exposure assessment applications over the years. This data article includes search strings that were utilized to retrieve publications through the PubMed database for different breath research-related topics that were related to the analysis of exhaled breath, exhaled breath condensate (EBC), and exhaled breath aerosol (EBA) as well as the analysis of cellular headspace. Manuscripts were curated for topics including EBC, EBA, Direct MS, GC-MS, LC-MS, alcohol, and sensors. A summary of the number of papers published per year for the data retrieved using each of the search strings is also included. These data can be utilized to discern trends in the number of breath research publications in each of the different topics over time. A supplementary Appendix A containing the titles, author lists, journal names, publication dates, PMID numbers, and EntrezUID numbers for each of the journal articles curated using the finalized search strings for the seven breath research-related topics can also be found within this article. The selected manuscripts can be used to explore the impact that breath research has had on expanding the scientific knowledge in each of the investigated topics.

Processing methods for differential analysis of LC/MS profile data

PubMed Central

Katajamaa, Mikko; Orešič, Matej

2005-01-01

Background Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data. Results We present a software package MZmine that enables differential LC/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards. Visualization tools enable comparative viewing of data across multiple samples. Peak lists can be exported into other data analysis programs. The toolbox has already been utilized in a wide range of applications. We demonstrate its utility on an example of metabolic profiling of Catharanthus roseus cell cultures. Conclusion The software is freely available under the GNU General Public License and it can be obtained from the project web page at: . PMID:16026613

Processing methods for differential analysis of LC/MS profile data.

PubMed

Katajamaa, Mikko; Oresic, Matej

2005-07-18

Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data. We present a software package MZmine that enables differential LC/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards. Visualization tools enable comparative viewing of data across multiple samples. Peak lists can be exported into other data analysis programs. The toolbox has already been utilized in a wide range of applications. We demonstrate its utility on an example of metabolic profiling of Catharanthus roseus cell cultures. The software is freely available under the GNU General Public License and it can be obtained from the project web page at: http://mzmine.sourceforge.net/.

Indoor air condensate as a novel matrix for monitoring inhalable organic contaminants.

PubMed

Roll, Isaac B; Halden, Rolf U; Pycke, Benny F G

2015-05-15

With the population of developed nations spending nearly 90% of their time indoors, indoor air quality (IAQ) is a critical indicator of human health risks from inhalation of airborne contaminants. We present a novel approach for qualitative monitoring of IAQ through the collection and analysis of indoor air condensate discharged from heat exchangers of heating, ventilation, and air conditioning (HVAC) systems. Condensate samples were collected from six suburban homes and one business in Maricopa County, Arizona, concentrated via solid-phase extraction, analyzed for 10 endocrine disrupting chemicals (EDCs) by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and screened for additional organic compounds by gas chromatography-mass spectrometry (GC-MS). All 10 EDCs were detected in at least one of the sampled buildings. More than 100 additional compounds were detected by GC-MS, of which 40 were tentatively identified using spectral database searches. Twelve compounds listed as designated chemicals for biomonitoring by the California Environmental Contaminant Biomonitoring Program were detected. Microfiltration of condensate samples prior to extraction had no discernable effect on contaminant concentration, suggesting that contaminants were freely dissolved or associated with inhalable, submicron particles. This study is the first to document the utility of HVAC condensate for the qualitative assessment of indoor air for pollutants. Copyright © 2015 Elsevier B.V. All rights reserved.

An integrated high resolution mass spectrometric and informatics approach for the rapid identification of phenolics in plant extract

USDA-ARS?s Scientific Manuscript database

An integrated approach based on high resolution MS analysis (orbitrap), database (db) searching and MS/MS fragmentation prediction for the rapid identification of plant phenols is reported. The approach was firstly validated by using a mixture of phenolic standards (phenolic acids, flavones, flavono...

False discovery rates in spectral identification.

PubMed

Jeong, Kyowon; Kim, Sangtae; Bandeira, Nuno

2012-01-01

Automated database search engines are one of the fundamental engines of high-throughput proteomics enabling daily identifications of hundreds of thousands of peptides and proteins from tandem mass (MS/MS) spectrometry data. Nevertheless, this automation also makes it humanly impossible to manually validate the vast lists of resulting identifications from such high-throughput searches. This challenge is usually addressed by using a Target-Decoy Approach (TDA) to impose an empirical False Discovery Rate (FDR) at a pre-determined threshold x% with the expectation that at most x% of the returned identifications would be false positives. But despite the fundamental importance of FDR estimates in ensuring the utility of large lists of identifications, there is surprisingly little consensus on exactly how TDA should be applied to minimize the chances of biased FDR estimates. In fact, since less rigorous TDA/FDR estimates tend to result in more identifications (at higher 'true' FDR), there is often little incentive to enforce strict TDA/FDR procedures in studies where the major metric of success is the size of the list of identifications and there are no follow up studies imposing hard cost constraints on the number of reported false positives. Here we address the problem of the accuracy of TDA estimates of empirical FDR. Using MS/MS spectra from samples where we were able to define a factual FDR estimator of 'true' FDR we evaluate several popular variants of the TDA procedure in a variety of database search contexts. We show that the fraction of false identifications can sometimes be over 10× higher than reported and may be unavoidably high for certain types of searches. In addition, we further report that the two-pass search strategy seems the most promising database search strategy. While unavoidably constrained by the particulars of any specific evaluation dataset, our observations support a series of recommendations towards maximizing the number of resulting identifications while controlling database searches with robust and reproducible TDA estimation of empirical FDR.

Results of a search for a new class of GRBS in the SMM data

NASA Technical Reports Server (NTRS)

Kouveliotou, C.; Cline, T. L.; Desai, U. D.; Dennis, B. R.; Orwig, L. E.

1986-01-01

The results of a search for the soft and short Gamma-Ray Bursts (GRBs) in the data of the Hard X-Ray Burst Spectrometer (HXRBS) on the Solar Maximum Mission (SMM) are presented. Data for four events are presented, including their time profiles and spectral characteristics. In one case the instrument time resolution reveals a total burst duration of 55 ms with rise and decay times of less than about 5 ms.

Detection of co-eluted peptides using database search methods

PubMed Central

Alves, Gelio; Ogurtsov, Aleksey Y; Kwok, Siwei; Wu, Wells W; Wang, Guanghui; Shen, Rong-Fong; Yu, Yi-Kuo

2008-01-01

Background Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost. Results We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods – SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS – in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides. Open peer review Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section. PMID:18597684

Assessment of Metabolome Annotation Quality: A Method for Evaluating the False Discovery Rate of Elemental Composition Searches

PubMed Central

Matsuda, Fumio; Shinbo, Yoko; Oikawa, Akira; Hirai, Masami Yokota; Fiehn, Oliver; Kanaya, Shigehiko; Saito, Kazuki

2009-01-01

Background In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed. Methodology/Principal Findings The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30–50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries. Conclusions/Significance High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data. PMID:19847304

Multiresidue pesticide analysis in ginseng and spinach by nontargeted and targeted screening procedures.

PubMed

Hayward, Douglas G; Wong, Jon W; Zhang, Kai; Chang, James; Shi, Feng; Banerjee, Kaushik; Yang, Paul

2011-01-01

Five different mass spectrometers interfaced to GC or LC were evaluated for their application to targeted and nontargeted screening of pesticides in two foods, spinach and ginseng. The five MS systems were capillary GC/MS/MS, GC-high resolution time-of-flight (GC/HR-TOF)-MS, TOF-MS interfaced with a comprehensive multidimensional GC (GCxGC/TOF-MS), an MS/MS ion trap hybrid mass (qTrap) system interfaced with an ultra-performance liquid chromatograph (UPLC-qTrap), and UPLC interfaced to an orbital trap high resolution mass spectrometer (UPLC/Orbitrap HR-MS). Each MS system was tested with spinach and ginseng extracts prepared through a modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) procedure. Each matrix was fortified at 10 and 50 ng/g for spinach or 25 and 100 ng/g for ginseng with subsets of 486 pesticides, isomers, and metabolites representing most pesticide classes. HR-TOF-MS was effective in a targeted search for characteristic accurate mass ions and identified 97% of 170 pesticides in ginseng at 25 ng/g. A targeted screen of either ginseng or spinach found 94-95% of pesticides fortified for analysis at 10 ng/g with GC/MS/MS or LC/MS/MS using multiple reaction monitoring (MRM) procedures. Orbitrap-MS successfully found 89% of 177 fortified pesticides in spinach at 25 ng/g using a targeted search of accurate mass pseudomolecular ions in the positive electrospray ionization mode. A comprehensive GCxGC/TOF-MS system provided separation and identification of 342 pesticides and metabolites in a single 32 min acquisition with standards. Only 67 or 81% of the pesticides were identified in ginseng and spinach matrixes at 25 ng/g or 10 ng/g, respectively. MS/MS or qTrap-MS operated in the MRM mode produced the lowest false-negative rates, at 10 ng/g. Improvements to instrumentation, methods, and software are needed for efficient use of nontargeted screens in parallel with triple quadrupole MS.

Expert system for computer-assisted annotation of MS/MS spectra.

PubMed

Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias

2012-11-01

An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions.

Expert System for Computer-assisted Annotation of MS/MS Spectra*

PubMed Central

Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias

2012-01-01

An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions. PMID:22888147

Detection and identification of drugs and toxicants in human body fluids by liquid chromatography-tandem mass spectrometry under data-dependent acquisition control and automated database search.

PubMed

Oberacher, Herbert; Schubert, Birthe; Libiseller, Kathrin; Schweissgut, Anna

2013-04-03

Systematic toxicological analysis (STA) is aimed at detecting and identifying all substances of toxicological relevance (i.e. drugs, drugs of abuse, poisons and/or their metabolites) in biological material. Particularly, gas chromatography-mass spectrometry (GC/MS) represents a competent and commonly applied screening and confirmation tool. Herein, we present an untargeted liquid chromatography-tandem mass spectrometry (LC/MS/MS) assay aimed to complement existing GC/MS screening for the detection and identification of drugs in blood, plasma and urine samples. Solid-phase extraction was accomplished on mixed-mode cartridges. LC was based on gradient elution in a miniaturized C18 column. High resolution electrospray ionization-MS/MS in positive ion mode with data-dependent acquisition control was used to generate tandem mass spectral information that enabled compound identification via automated library search in the "Wiley Registry of Tandem Mass Spectral Data, MSforID". Fitness of the developed LC/MS/MS method for application in STA in terms of selectivity, detection capability and reliability of identification (sensitivity/specificity) was demonstrated with blank samples, certified reference materials, proficiency test samples, and authentic casework samples. Copyright © 2013 Elsevier B.V. All rights reserved.

Effectiveness of vocational rehabilitation intervention on the return to work and employment of persons with multiple sclerosis.

PubMed

Khan, Fary; Ng, Louisa; Turner-Stokes, Lynne

2009-01-21

Multiple sclerosis is a neurological disease that frequently affects adults of working age, resulting in a range of physical, cognitive and psychosocial deficits that impact on workforce participation. Although, the literature supports vocational rehabilitation (VR) approaches in persons with multiple sclerosis (pwMS), the evidence for its effectiveness is yet to be established. To evaluate the effectiveness of VR programs compared to alternative programs or care as usual on return to work, workability and employment in pwMS; to evaluate the cost effectiveness of these programs. Electronic searches included: Cochrane Central Register of Controlled Trials "CENTRAL" 2008 issue 3, MEDLINE (PubMed) (1966- 2008), EMBASE (1988- 2008), CINAHL (1982- 2008), PEDro (1990- 2008), the Cochrane Rehabilitation and Related Therapies Field trials Register and the National Health Service National Research Register. Randomized and controlled clinical trials, including before - after controlled trials, that compare VR rehabilitation with alternative intervention such as standard or a lesser form of intervention or waitlist controls. Two reviewers selected trials and rated their methodological quality independently. A 'best evidence' synthesis was performed, based on methodological quality. Trials were grouped in terms of type and setting of VR programs. Two trials (one RCT and one CCT) (total 80 participants) met the review criteria. Both trials scored poorly on the methodological quality assessment. There was 'insufficient evidence' for VR programs for (a)'competitive employment', in altering rates of job retention, changes in employment, improvement in rates of re-entry into the labour force; (b) for altering 'work ability' by improving participants' confidence in the accommodation request process, or employability maturity or job seeking activity. No evidence could be assimilated for changes in proportions of persons in supported employment or on disability pensions, nor for cost-effectiveness. There was inconclusive evidence to support VR for pwMS. However, the review highlights some of the challenges in providing VR for pwMS. Clinicians need to be aware of vocational issues, and to understand and manage barriers for maintaining employment. Proactive and timely VR programs should incorporate practical solutions to deal with work disability, workplace accommodation and educate employers, and the wider community. Liaison with policy makers is imperative for government initiatives that encourage work focused VR programs. Future research in VR should focus on improving methodological and scientific rigour of clinical trials; on the development of appropriate and valid outcome measures; and on cost effectiveness of VR programs.

40 CFR 122.37 - Will the small MS4 storm water program regulations at §§ 122.32 through 122.36 and § 123.35 of...

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 23 2012-07-01 2012-07-01 false Will the small MS4 storm water program... Special NPDES Program Requirements § 122.37 Will the small MS4 storm water program regulations at §§ 122... evaluation of the NPDES MS4 storm water program. EPA will re-evaluate the regulations based on data from the...

40 CFR 122.37 - Will the small MS4 storm water program regulations at §§ 122.32 through 122.36 and § 123.35 of...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 23 2013-07-01 2013-07-01 false Will the small MS4 storm water program... Special NPDES Program Requirements § 122.37 Will the small MS4 storm water program regulations at §§ 122... evaluation of the NPDES MS4 storm water program. EPA will re-evaluate the regulations based on data from the...

40 CFR 122.37 - Will the small MS4 storm water program regulations at §§ 122.32 through 122.36 and § 123.35 of...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 22 2014-07-01 2013-07-01 true Will the small MS4 storm water program... Special NPDES Program Requirements § 122.37 Will the small MS4 storm water program regulations at §§ 122... evaluation of the NPDES MS4 storm water program. EPA will re-evaluate the regulations based on data from the...

IPeak: An open source tool to combine results from multiple MS/MS search engines.

PubMed

Wen, Bo; Du, Chaoqin; Li, Guilin; Ghali, Fawaz; Jones, Andrew R; Käll, Lukas; Xu, Shaohang; Zhou, Ruo; Ren, Zhe; Feng, Qiang; Xu, Xun; Wang, Jun

2015-09-01

Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Burden of neurological diseases in the US revealed by web searches.

PubMed

Baeza-Yates, Ricardo; Sangal, Puneet Mohan; Villoslada, Pablo

2017-01-01

Analyzing the disease-related web searches of Internet users provides insight into the interests of the general population as well as the healthcare industry, which can be used to shape health care policies. We analyzed the searches related to neurological diseases and drugs used in neurology using the most popular search engines in the US, Google and Bing/Yahoo. We found that the most frequently searched diseases were common diseases such as dementia or Attention Deficit/Hyperactivity Disorder (ADHD), as well as medium frequency diseases with high social impact such as Parkinson's disease, MS and ALS. The most frequently searched CNS drugs were generic drugs used for pain, followed by sleep disorders, dementia, ADHD, stroke and Parkinson's disease. Regarding the interests of the healthcare industry, ADHD, Alzheimer's disease, MS, ALS, meningitis, and hypersomnia received the higher advertising bids for neurological diseases, while painkillers and drugs for neuropathic pain, drugs for dementia or insomnia, and triptans had the highest advertising bidding prices. Web searches reflect the interest of people and the healthcare industry, and are based either on the frequency or social impact of the disease.

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

PubMed

Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver

2011-08-05

Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine. This approach allows the estimation of p-values for each candidate peptide and their combination across all search engines. The consensus approach works better than any single search engine across all different instrument types considered in this study. Improvements vary strongly from platform to platform and from search engine to search engine. Compared to the industry standard MASCOT, our approach can identify up to 60% more peptides. The software for consensus predictions is implemented in C++ as part of OpenMS, a software framework for mass spectrometry. The source code is available in the current development version of OpenMS and can easily be used as a command line application or via a graphical pipeline designer TOPPAS.

A collection of open source applications for mass spectrometry data mining.

PubMed

Gallardo, Óscar; Ovelleiro, David; Gay, Marina; Carrascal, Montserrat; Abian, Joaquin

2014-10-01

We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front-end graphical user interface that combines several Thermo RAW formats to MASCOT™ Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A theoretical search for supervelocity semiconductors

NASA Astrophysics Data System (ADS)

Littlejohn, M. A.; Kim, K. W.

1991-10-01

This document presents an annual report to the Office of Naval Research for a research program entitled 'A Theoretical Search for Supervelocity Semiconductors.' This program has been funded by ONR since 1974 in the Department of Electrical and Computer Engineering at N.C. State University. The research has resulted in more than 75 refereed publications and numerous conference presentations from its inception. Major contributions to the field of hot electron transport and semiconductor device modeling have been achieved, new computational methods have been developed (e.g., path integral Monte Carlo techniques), and the work has helped stimulate commercial ventures in the applications of quaternary semiconductor materials to electronic and optical devices. In addition, there have been twenty-six Ph.D. and M.S. students who have received degrees at N.C. State University with research support from this contract. Three visiting faculty members from Japan came to the university to work with the faculty investigators supported under this ONR contract during the 1979-1983 time period. A visiting professor from the French CNRS Microstructures and Microelectronics Laboratory in Bagneux (near Paris) spent a sabbatical year at N.C. State during 1988-89, and he devoted full-time working on this program at no cost to ONR. During the current funding period, a visiting scholar from China is a member of our research group working on projects which directly impact this ONR program.

Search Problems in Mission Planning and Navigation of Autonomous Aircraft. M.S. Thesis

NASA Technical Reports Server (NTRS)

Krozel, James A.

1988-01-01

An architecture for the control of an autonomous aircraft is presented. The architecture is a hierarchical system representing an anthropomorphic breakdown of the control problem into planner, navigator, and pilot systems. The planner system determines high level global plans from overall mission objectives. This abstract mission planning is investigated by focusing on the Traveling Salesman Problem with variations on local and global constraints. Tree search techniques are applied including the breadth first, depth first, and best first algorithms. The minimum-column and row entries for the Traveling Salesman Problem cost matrix provides a powerful heuristic to guide these search techniques. Mission planning subgoals are directed from the planner to the navigator for planning routes in mountainous terrain with threats. Terrain/threat information is abstracted into a graph of possible paths for which graph searches are performed. It is shown that paths can be well represented by a search graph based on the Voronoi diagram of points representing the vertices of mountain boundaries. A comparison of Dijkstra's dynamic programming algorithm and the A* graph search algorithm from artificial intelligence/operations research is performed for several navigation path planning examples. These examples illustrate paths that minimize a combination of distance and exposure to threats. Finally, the pilot system synthesizes the flight trajectory by creating the control commands to fly the aircraft.

Systematic review of the published data on the worldwide prevalence of John Cunningham virus in patients with multiple sclerosis and neuromyelitis optica.

PubMed

Paz, Sonia Patricia Castedo; Branco, Luciana; Pereira, Marina Alves de Camargo; Spessotto, Caroline; Fragoso, Yara Dadalti

2018-01-01

John Cunningham virus (JCV) is a polyoma virus that infects humans, mainly in childhood or adolescence, and presents no symptomatic manifestations. JCV can cause progressive multifocal leukoencephalopathy (PML) in immunosuppressed individuals, including those undergoing treatment for multiple sclerosis (MS) and neuromyelitis optica (NMO). PML is a severe and potentially fatal disease of the brain. The prevalence of JCV antibodies in human serum has been reported to be between 50.0 and 90.0%. The aim of the present study was to review worldwide data on populations of patients with MS and NMO in order to establish the rates of JCV seropositivity in these individuals. The present review followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines and used the following search terms: "JCV" OR "JC virus" AND "multiple sclerosis" OR "MS" OR "NMO" OR "neuromyelitis optica" AND "prevalence." These terms were searched for both in smaller and in larger clusters of words. The databases searched included PubMed, MEDLINE, SciELO, LILACS, Google Scholar, and Embase. After the initial selection, 18 papers were included in the review. These articles reported the prevalence of JCV antibodies in the serum of patients with MS or NMO living in 26 countries. The systematic review identified data on 29,319 patients with MS/NMO and found that 57.1% of them (16,730 individuals) were seropositive for the anti-JCV antibody (range, 40.0 to 69.0%). The median worldwide prevalence of JCV among adults with MS or NMO was found to be 57.1%.

A Research Program in Flight Sciences

NASA Technical Reports Server (NTRS)

Whitesides, John L.; Waggoner, Edgar G. (Technical Monitor)

2005-01-01

Since its inception in January 2003, thc program has provided support for 1 faculty and a total of 7 Graduate Research Scholar Assistants, of these all 7 have completed their MS degree program. The program has generated 5 MS thesis and 2 MS project reports. Attachment: Appendix A, B, C, and D.

Systematic Review: The Effectiveness of Interventions to Reduce Falls and Improve Balance in Adults With Multiple Sclerosis.

PubMed

Gunn, Hilary; Markevics, Sophie; Haas, Bernhard; Marsden, Jonathan; Freeman, Jennifer

2015-10-01

To evaluate the effectiveness of interventions in reducing falls and/or improving balance as a falls risk in multiple sclerosis (MS). Computer-based and manual searches included the following medical subject heading keywords: "Multiple Sclerosis AND accidental falls" OR "Multiple Sclerosis AND postural balance" OR "Multiple Sclerosis AND exercise" OR "Multiple Sclerosis AND physical/physio therapy" NOT animals. All literature published to November 2014 with available full-text details were included. Studies were reviewed against the PICO (participants, interventions, comparisons, outcomes) selection criteria: P, adults with MS; I, falls management/balance rehabilitation interventions; C, randomized/quasi-randomized studies comparing intervention with usual care or placebo control; O, falls outcomes and measures of balance. Fifteen articles of the original 529 search results were included. Two reviewers independently extracted data and assessed methodological quality using the Cochrane Risk of Bias tool. Random-effects meta-analysis indicated a small decrease in falls risk (risk ratio, .74), although the 95% confidence interval (CI) crossed 1 (95% CI, .12-4.38). The pooled standardized mean difference (SMD) for balance outcomes was .55 (95% CI, .35-.74). SMD varied significantly between exercise subgroupings; gait, balance, and functional training interventions yielded the greatest pooled effect size (ES) (SMD=.82; 95% CI, 0.55-1.10). There was a moderate positive correlation between program volume (min/wk) and ES (Cohen's d) (r=.70, P=.009), and a moderate negative correlation between program duration in weeks and ES (r=-.62, P=.03). Variations in interventions and outcomes and methodological limitations mean that results must be viewed with caution. This review suggests that balance may improve through exercise interventions, but that the magnitude of the improvements achieved in existing programs may not be sufficient to impact falls outcomes. Supporting participants to achieve an appropriate intensity of practice of highly challenging balance activities appears to be critical to maximizing effectiveness. Copyright © 2015 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Cognitive Motor Interference in Multiple Sclerosis: Insights From a Systematic Quantitative Review.

PubMed

Learmonth, Yvonne C; Ensari, Ipek; Motl, Robert W

2017-06-01

To synthesize the evidence for differences in cognitive motor interference (CMI) between persons with multiple sclerosis (MS) and those without MS by using systematic review and meta-analysis. EMBASE, PubMed, ScienceDirect, Scopus, SPORTDiscus, and Web of Science. Our focused literature search was informed by past systematic reviews of CMI during walking in MS. The key terms searched included Multiple sclerosis and synonyms of motor function (eg, Gait disorders, Gait, Walking, Balance, or Fall) and motor and cognitive functions (eg, Cognitive motor interference or Thinking). From the 116 abstract-identified articles, 13 experimental studies were selected for the final analysis and were rated using the Quality Assessment of Diagnostic Accuracy Studies tool. A meta-analysis was performed for all considered outcomes. The results yielded a small overall effect size (ES) of .08 (SE=.17; 95% confidence interval, -.25 to .40; z=.49; P>.05), which indicated a nonsignificant minimal difference in CMI between persons with MS and those without MS. The moderator analysis for motor task (mobility task: ES, .22; postural task: ES, -.11) was not significantly different between persons with MS and those without MS. The moderator analysis for cognitive task (verbal fluency task: ES, .66; mental tracking task: ES, .04; discrimination and decision-making task: ES, -.30) resulted in a significant difference in CMI between persons with MS and those without MS (P<.05). We provide evidence that overall there is a minimal difference in CMI between persons with MS and those without MS. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Rapid Resumption of Interrupted Search Is Independent of Age-Related Improvements in Visual Search

ERIC Educational Resources Information Center

Lleras, Alejandro; Porporino, Mafalda; Burack, Jacob A.; Enns, James T.

2011-01-01

In this study, 7-19-year-olds performed an interrupted visual search task in two experiments. Our question was whether the tendency to respond within 500 ms after a second glimpse of a display (the "rapid resumption" effect ["Psychological Science", 16 (2005) 684-688]) would increase with age in the same way as overall search efficiency. The…

On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm.

PubMed

Oberacher, Herbert; Pavlic, Marion; Libiseller, Kathrin; Schubert, Birthe; Sulyok, Michael; Schuhmacher, Rainer; Csaszar, Edina; Köfeler, Harald C

2009-04-01

A sophisticated matching algorithm developed for highly efficient identity search within tandem mass spectral libraries is presented. For the optimization of the search procedure a collection of 410 tandem mass spectra corresponding to 22 compounds was used. The spectra were acquired in three different laboratories on four different instruments. The following types of tandem mass spectrometric instruments were used: quadrupole-quadrupole-time-of-flight (QqTOF), quadrupole-quadrupole-linear ion trap (QqLIT), quadrupole-quadrupole-quadrupole (QqQ), and linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer (LIT-FTICR). The obtained spectra were matched to an established MS/MS-spectral library that contained 3759 MS/MS-spectra corresponding to 402 different reference compounds. All 22 test compounds were part of the library. A dynamic intensity cut-off, the search for neutral losses, and optimization of the formula used to calculate the match probability were shown to significantly enhance the performance of the presented library search approach. With the aid of these features the average number of correct assignments was increased to 98%. For statistical evaluation of the match reliability the set of fragment ion spectra was extended with 300 spectra corresponding to 100 compounds not included in the reference library. Performance was checked with the aid of receiver operating characteristic (ROC) curves. Using the magnitude of the match probability as well as the precursor ion mass as benchmarks to rate the obtained top hit, overall correct classification of a compound being included or not included in the mass spectrometric library, was obtained in more than 95% of cases clearly indicating a high predictive accuracy of the established matching procedure. Copyright (c) 2009 John Wiley & Sons, Ltd.

A combined de novo protein sequencing and cDNA library approach to the venomic analysis of Chinese spider Araneus ventricosus.

PubMed

Duan, Zhigui; Cao, Rui; Jiang, Liping; Liang, Songping

2013-01-14

In past years, spider venoms have attracted increasing attention due to their extraordinary chemical and pharmacological diversity. The recently popularized proteomic method highly improved our ability to analyze the proteins in the venom. However, the lack of information about isolated venom proteins sequences dramatically limits the ability to confidently identify venom proteins. In the present paper, the venom from Araneus ventricosus was analyzed using two complementary approaches: 2-DE/Shotgun-LC-MS/MS coupled to MASCOT search and 2-DE/Shotgun-LC-MS/MS coupled to manual de novo sequencing followed by local venom protein database (LVPD) search. The LVPD was constructed with toxin-like protein sequences obtained from the analysis of cDNA library from A. ventricosus venom glands. Our results indicate that a total of 130 toxin-like protein sequences were unambiguously identified by manual de novo sequencing coupled to LVPD search, accounting for 86.67% of all toxin-like proteins in LVPD. Thus manual de novo sequencing coupled to LVPD search was proved an extremely effective approach for the analysis of venom proteins. In addition, the approach displays impeccable advantage in validating mutant positions of isoforms from the same toxin-like family. Intriguingly, methyl esterifcation of glutamic acid was discovered for the first time in animal venom proteins by manual de novo sequencing. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Barriers and Facilitators Related to Participation in Aquafitness Programs for People with Multiple Sclerosis

PubMed Central

Kitchen, Kaitlyn; Nicoll, Kaley

2012-01-01

Exercise and leisure activities provide physical and psychosocial benefits to people with multiple sclerosis (MS) and can enhance their quality of life. In Winnipeg, Manitoba, Canada, people with MS have reported barriers to their participation in local MS-specific aquafitness (AF) programs. Therefore, a formal exploration of the accessibility of local AF programs for people with MS was undertaken. The purpose of this phenomenological study was to identify factors that facilitate or impede participation in AF programs by individuals with MS living in Winnipeg. Qualitative data were collected from a total of eight participants through one focus group (n = 7) and one in-depth interview (n = 1). The sample consisted of individuals with MS who were currently participating in AF programming as well as those who were not. Data were audio-recorded and transcribed verbatim, and thematic analysis was completed. Seven themes emerged regarding factors affecting participation in local AF programs. Barriers to participation included inadequate transportation, lack of one-on-one support, environmental inaccessibility, and fears associated with participation in the programs. Facilitators of participation included a knowledgeable instructor and experiencing physical and psychosocial benefits from the program. Information from this study was used locally to advocate for people with MS in order to increase participation in local AF programming. PMID:24453744

Use of ultra-high-pressure liquid chromatography-quadrupole time-of-flight MS to discover the presence of pesticide metabolites in food samples.

PubMed

Hernández, Félix; Grimalt, Susana; Pozo, Oscar J; Sancho, Juan V

2009-07-01

In this paper we illustrate the use of two different methodologies to investigate the presence of pesticide metabolites in parent pesticide-positive food samples, using ultra-high-pressure liquid chromatography coupled to hybrid quadrupole time-of-flight (UHPLC-QTOF) mass spectrometry. First, a common fragmentation pathway between the parent pesticide and its metabolites has been considered to search for metabolites in two positive market samples (imazalil in lemon, chlorpyrifos in grape). Secondly, olive oil samples from field residue trials were used for automated application of comparative software (MetaboLynx), which was used with treated and untreated samples to search for expected and unexpected metabolites of phosmet. One of the main objectives when using these approaches was to avoid the tedious manual searching for potential metabolites within the huge amount of information contained in the total ion chromatogram acquired by TOF MS. The common fragmentation approach applied to TOF MS full-acquisition data, considering an enhanced fragmentation in the collision cell, has allowed the discovery of two metabolites of imazalil (1-[2-(2,4-dichlorophenyl)-2-hydroxyethyl]-1H-imidazole and 1-[2-(2,4-dichlorophenyl)-2-oxoethyl]-1H-imidazole) in a lemon positive sample, as well as another two metabolites of chlorpyrifos (chlorpyrifos-oxon and 3,5,6-trichloro-2-pyridinol) in a grape positive sample. Moreover, MetaboLynx application to TOF MS data, without promoting fragmentation, from treated and untreated olive oil samples has been helpful in detecting the metabolite phosmet-oxon. In both strategies, every metabolite detected by TOF MS was confirmed using QTOF and/or triple quadrupole instruments. Accurate masses given by TOF MS together with the valuable information on product ions given by QTOF MS/MS experiments were crucial for the unambiguous identification of metabolites.

Towards a full reference library of MS(n) spectra. Testing of a library containing 3126 MS2 spectra of 1743 compounds.

PubMed

Milman, Boris L

2005-01-01

A library consisting of 3766 MS(n) spectra of 1743 compounds, including 3126 MS2 spectra acquired mainly using ion trap (IT) and triple-quadrupole (QqQ) instruments, was composed of numerous collections/sources. Ionization techniques were mainly electrospray ionization and also atmospheric pressure chemical ionization and chemical ionization. The library was tested for the performance in identification of unknowns, and in this context this work is believed to be the largest of all known tests of product-ion mass spectral libraries. The MS2 spectra of the same compounds from different collections were in turn divided into spectra of 'unknown' and reference compounds. For each particular compound, library searches were performed resulting in selection by taking into account the best matches for each spectral collection/source. Within each collection/source, replicate MS2 spectra differed in the collision energy used. Overall, there were up to 950 search results giving the best match factors and their ranks in corresponding hit lists. In general, the correct answers were obtained as the 1st rank in up to 60% of the search results when retrieved with (on average) 2.2 'unknown' and 6.2 reference replicates per compound. With two or more replicates of both 'unknown' and reference spectra (the average numbers of replicates were 4.0 and 7.8, respectively), the fraction of correct answers in the 1st rank increased to 77%. This value is close to the performance of established electron ionization mass spectra libraries (up to 79%) found by other workers. The hypothesis that MS2 spectra better match reference spectra acquired using the same type of tandem mass spectrometer (IT or QqQ) was neither strongly proved nor rejected here. The present work shows that MS2 spectral libraries containing sufficiently numerous different entries for each compound are sufficiently efficient for identification of unknowns and suitable for use with different tandem mass spectrometers. 2005 John Wiley & Sons, Ltd.

Changes of Metabolomic Profile in Helianthus annuus under Exposure to Chromium(VI) Studied by capHPLC-ESI-QTOF-MS and MS/MS

PubMed Central

Gonzalez Ibarra, Alan Alexander; Wrobel, Kazimierz; Yanez Barrientos, Eunice; Corrales Escobosa, Alma Rosa; Gutierrez Corona, J. Felix; Enciso Donis, Israel

2017-01-01

The application of capHPLC-ESI-QTOF-MS and MS/MS to study the impact of Cr(VI) on metabolites profile in Helianthus annuus is reported. Germinated seeds were grown hydroponically in the presence of Cr(VI) (25 mgCr/L) and root extracts of the exposed and control plants were analyzed by untargeted metabolomic approach. The main goal was to detect which metabolite groups were mostly affected by Cr(VI) stress; two data analysis tools (ProfileAnalysis, Bruker, and online XCMS) were used under criteria of intensity threshold 5 · 104 cps, fold change ≥ 5, and p ≤ 0.01, yielding precursor ions. Molecular formulas were assigned based on data processing with two computational tools (SIRIUS and MS-Finder); annotation of candidate structures was performed by database search using CSI:FingerID and MS-Finder. Even though ultimate identification has not been achieved, it was demonstrated that secondary metabolism became activated under Cr(VI) stress. Among 42 candidate compounds returned from database search for seven molecular formulas, ten structures corresponded to isocoumarin derivatives and eleven were sesquiterpenes or sesquiterpene lactones; three benzofurans and four glycoside or pyrane derivatives of phenolic compounds were also suggested. To gain further insight on the effect of Cr(VI) in sunflower, isocoumarins and sesquiterpenes were selected as the target compounds for future study. PMID:29359067

Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data.

PubMed

Nakayama, Hiroshi; Akiyama, Misaki; Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

2009-04-01

We present here a method to correlate tandem mass spectra of sample RNA nucleolytic fragments with an RNA nucleotide sequence in a DNA/RNA sequence database, thereby allowing tandem mass spectrometry (MS/MS)-based identification of RNA in biological samples. Ariadne, a unique web-based database search engine, identifies RNA by two probability-based evaluation steps of MS/MS data. In the first step, the software evaluates the matches between the masses of product ions generated by MS/MS of an RNase digest of sample RNA and those calculated from a candidate nucleotide sequence in a DNA/RNA sequence database, which then predicts the nucleotide sequences of these RNase fragments. In the second step, the candidate sequences are mapped for all RNA entries in the database, and each entry is scored for a function of occurrences of the candidate sequences to identify a particular RNA. Ariadne can also predict post-transcriptional modifications of RNA, such as methylation of nucleotide bases and/or ribose, by estimating mass shifts from the theoretical mass values. The method was validated with MS/MS data of RNase T1 digests of in vitro transcripts. It was applied successfully to identify an unknown RNA component in a tRNA mixture and to analyze post-transcriptional modification in yeast tRNA(Phe-1).

50 CFR 2.1 - Headquarters.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Pike, Falls Church, VA 22041-3803. Headquarters program Mail stop Business Management and Operations MS... Programs MS: FAC. International Affairs, including: • Division of Management Authority MS: IA. • Division of Scientific Authority Information Resource and Technology Management MS: IRTM. Migratory Birds...

Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines

PubMed Central

Chen, Yao-Yi; Dasari, Surendra; Ma, Ze-Qiang; Vega-Montoto, Lorenzo J.; Li, Ming

2013-01-01

Spectral counting has become a widely used approach for measuring and comparing protein abundance in label-free shotgun proteomics. However, when analyzing complex samples, the ambiguity of matching between peptides and proteins greatly affects the assessment of peptide and protein inventories, differentiation, and quantification. Meanwhile, the configuration of database searching algorithms that assign peptides to MS/MS spectra may produce different results in comparative proteomic analysis. Here, we present three strategies to improve comparative proteomics through spectral counting. We show that comparing spectral counts for peptide groups rather than for protein groups forestalls problems introduced by shared peptides. We demonstrate the advantage and flexibility of this new method in two datasets. We present four models to combine four popular search engines that lead to significant gains in spectral counting differentiation. Among these models, we demonstrate a powerful vote counting model that scales well for multiple search engines. We also show that semi-tryptic searching outperforms tryptic searching for comparative proteomics. Overall, these techniques considerably improve protein differentiation on the basis of spectral count tables. PMID:22552787

Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines.

PubMed

Chen, Yao-Yi; Dasari, Surendra; Ma, Ze-Qiang; Vega-Montoto, Lorenzo J; Li, Ming; Tabb, David L

2012-09-01

Spectral counting has become a widely used approach for measuring and comparing protein abundance in label-free shotgun proteomics. However, when analyzing complex samples, the ambiguity of matching between peptides and proteins greatly affects the assessment of peptide and protein inventories, differentiation, and quantification. Meanwhile, the configuration of database searching algorithms that assign peptides to MS/MS spectra may produce different results in comparative proteomic analysis. Here, we present three strategies to improve comparative proteomics through spectral counting. We show that comparing spectral counts for peptide groups rather than for protein groups forestalls problems introduced by shared peptides. We demonstrate the advantage and flexibility of this new method in two datasets. We present four models to combine four popular search engines that lead to significant gains in spectral counting differentiation. Among these models, we demonstrate a powerful vote counting model that scales well for multiple search engines. We also show that semi-tryptic searching outperforms tryptic searching for comparative proteomics. Overall, these techniques considerably improve protein differentiation on the basis of spectral count tables.

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

PubMed Central

Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

2015-01-01

Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

Unassigned MS/MS Spectra: Who Am I?

PubMed

Pathan, Mohashin; Samuel, Monisha; Keerthikumar, Shivakumar; Mathivanan, Suresh

2017-01-01

Recent advances in high resolution tandem mass spectrometry (MS) has resulted in the accumulation of high quality data. Paralleled with these advances in instrumentation, bioinformatics software have been developed to analyze such quality datasets. In spite of these advances, data analysis in mass spectrometry still remains critical for protein identification. In addition, the complexity of the generated MS/MS spectra, unpredictable nature of peptide fragmentation, sequence annotation errors, and posttranslational modifications has impeded the protein identification process. In a typical MS data analysis, about 60 % of the MS/MS spectra remains unassigned. While some of these could attribute to the low quality of the MS/MS spectra, a proportion can be classified as high quality. Further analysis may reveal how much of the unassigned MS spectra attribute to search space, sequence annotation errors, mutations, and/or posttranslational modifications. In this chapter, the tools used to identify proteins and ways to assign unassigned tandem MS spectra are discussed.

Combining Search Engines for Comparative Proteomics

PubMed Central

Tabb, David

2012-01-01

Many proteomics laboratories have found spectral counting to be an ideal way to recognize biomarkers that differentiate cohorts of samples. This approach assumes that proteins that differ in quantity between samples will generate different numbers of identifiable tandem mass spectra. Increasingly, researchers are employing multiple search engines to maximize the identifications generated from data collections. This talk evaluates four strategies to combine information from multiple search engines in comparative proteomics. The “Count Sum” model pools the spectra across search engines. The “Vote Counting” model combines the judgments from each search engine by protein. Two other models employ parametric and non-parametric analyses of protein-specific p-values from different search engines. We evaluated the four strategies in two different data sets. The ABRF iPRG 2009 study generated five LC-MS/MS analyses of “red” E. coli and five analyses of “yellow” E. coli. NCI CPTAC Study 6 generated five concentrations of Sigma UPS1 spiked into a yeast background. All data were identified with X!Tandem, Sequest, MyriMatch, and TagRecon. For both sample types, “Vote Counting” appeared to manage the diverse identification sets most effectively, yielding heightened discrimination as more search engines were added.

Burden of neurological diseases in the US revealed by web searches

PubMed Central

Baeza-Yates, Ricardo; Sangal, Puneet Mohan

2017-01-01

Background Analyzing the disease-related web searches of Internet users provides insight into the interests of the general population as well as the healthcare industry, which can be used to shape health care policies. Methods We analyzed the searches related to neurological diseases and drugs used in neurology using the most popular search engines in the US, Google and Bing/Yahoo. Results We found that the most frequently searched diseases were common diseases such as dementia or Attention Deficit/Hyperactivity Disorder (ADHD), as well as medium frequency diseases with high social impact such as Parkinson’s disease, MS and ALS. The most frequently searched CNS drugs were generic drugs used for pain, followed by sleep disorders, dementia, ADHD, stroke and Parkinson’s disease. Regarding the interests of the healthcare industry, ADHD, Alzheimer’s disease, MS, ALS, meningitis, and hypersomnia received the higher advertising bids for neurological diseases, while painkillers and drugs for neuropathic pain, drugs for dementia or insomnia, and triptans had the highest advertising bidding prices. Conclusions Web searches reflect the interest of people and the healthcare industry, and are based either on the frequency or social impact of the disease. PMID:28531237

Visual search guidance is best after a short delay

PubMed Central

Schmidt, Joseph; Zelinsky, Gregory J.

2011-01-01

Search displays are typically presented immediately after a target cue, but in the real-world, delays often exist between target designation and search. Experiments 1 and 2 asked how search guidance changes with delay. Targets were cued using a picture or text label, each for 3000ms, followed by a delay up to 9000ms before the search display. Search stimuli were realistic objects, and guidance was quantified using multiple eye movement measures. Text-based cues showed a non-significant trend towards greater guidance following any delay relative to a no-delay condition. However, guidance from a pictorial cue increased sharply 300–600 msec after preview offset. Experiment 3 replicated this guidance enhancement using shorter preview durations while equating the time from cue onset to search onset, demonstrating that the guidance benefit is linked to preview offset rather than a more complete encoding of the target. Experiment 4 showed that enhanced guidance persists even with a mask flashed at preview offset, suggesting an explanation other than visual priming. We interpret our findings as evidence for the rapid consolidation of target information into a guiding representation, which attains its maximum effectiveness shortly after preview offset. PMID:21295053

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching.

PubMed

Pai, Pei-Jing; Hu, Yingwei; Lam, Henry

2016-08-31

Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Exploring Site-Specific N-Glycosylation Microheterogeneity of Haptoglobin using Glycopeptide CID Tandem Mass Spectra and Glycan Database Search

PubMed Central

Chandler, Kevin Brown; Pompach, Petr; Goldman, Radoslav

2013-01-01

Glycosylation is a common protein modification with a significant role in many vital cellular processes and human diseases, making the characterization of protein-attached glycan structures important for understanding cell biology and disease processes. Direct analysis of protein N-glycosylation by tandem mass spectrometry of glycopeptides promises site-specific elucidation of N-glycan microheterogeneity, something which detached N-glycan and de-glycosylated peptide analyses cannot provide. However, successful implementation of direct N-glycopeptide analysis by tandem mass spectrometry remains a challenge. In this work, we consider algorithmic techniques for the analysis of LC-MS/MS data acquired from glycopeptide-enriched fractions of enzymatic digests of purified proteins. We implement a computational strategy which takes advantage of the properties of CID fragmentation spectra of N-glycopeptides, matching the MS/MS spectra to peptide-glycan pairs from protein sequences and glycan structure databases. Significantly, we also propose a novel false-discovery-rate estimation technique to estimate and manage the number of false identifications. We use a human glycoprotein standard, haptoglobin, digested with trypsin and GluC, enriched for glycopeptides using HILIC chromatography, and analyzed by LC-MS/MS to demonstrate our algorithmic strategy and evaluate its performance. Our software, GlycoPeptideSearch (GPS), assigned glycopeptide identifications to 246 of the spectra at false-discovery-rate 5.58%, identifying 42 distinct haptoglobin peptide-glycan pairs at each of the four haptoglobin N-linked glycosylation sites. We further demonstrate the effectiveness of this approach by analyzing plasma-derived haptoglobin, identifying 136 N-linked glycopeptide spectra at false-discovery-rate 0.4%, representing 15 distinct glycopeptides on at least three of the four N-linked glycosylation sites. The software, GlycoPeptideSearch, is available for download from http://edwardslab.bmcb.georgetown.edu/GPS. PMID:23829323

Online tools for individuals with depression and neurologic conditions: A scoping review.

PubMed

Lukmanji, Sara; Pham, Tram; Blaikie, Laura; Clark, Callie; Jetté, Nathalie; Wiebe, Samuel; Bulloch, Andrew; Holroyd-Leduc, Jayna; Macrodimitris, Sophia; Mackie, Aaron; Patten, Scott B

2017-08-01

Patients with neurologic conditions commonly have depression. Online tools have the potential to improve outcomes in these patients in an efficient and accessible manner. We aimed to identify evidence-informed online tools for patients with comorbid neurologic conditions and depression. A scoping review of online tools (free, publicly available, and not requiring a facilitator) for patients with depression and epilepsy, Parkinson disease (PD), multiple sclerosis (MS), traumatic brain injury (TBI), or migraine was conducted. MEDLINE, EMBASE, PsycINFO, Cochrane Database of Systematic Reviews, and Cochrane CENTRAL Register of Controlled Trials were searched from database inception to January 2017 for all 5 neurologic conditions. Gray literature using Google and Google Scholar as well as app stores for both Android and Apple devices were searched. Self-management or self-efficacy online tools were not included unless they were specifically targeted at depression and one of the neurologic conditions and met the other eligibility criteria. Only 4 online tools were identified. Of these 4 tools, 2 were web-based self-management programs for patients with migraine or MS and depression. The other 2 were mobile apps for patients with PD or TBI and depression. No online tools were found for epilepsy. There are limited depression tools for people with neurologic conditions that are evidence-informed, publicly available, and free. Future research should focus on the development of high-quality, evidence-based online tools targeted at neurologic patients.

Meaningful Engagement of Organizational and Agency Partnerships to Enhance Diversity within the Earth System Science Community: A Case Study

NASA Astrophysics Data System (ADS)

Pyrtle, A. J.; Whitney, V. W.; Powell, J. M.; Bailey, K. L.

2006-12-01

The Minorities Striving and Pursuing Higher Degrees of Success in Earth System Science Initiative (MS PHD'S) was established by and for underrepresented minorities to facilitate increased and sustained participation in Earth system science community. The MS PHD'S launched its pilot program in 2003 with twenty professional organizations, agencies and institutions as partners. Each year partnership alliances have grown. In the second year or programming, thirty-one partnering agencies/institutions supported involvement of MS PHD'S student participants and for 2005-2006, representatives from forty-five agencies and institutions have provided similar support and exposure to the third cohort of student participants. Nineteen scientists served as meeting mentors during the MS PHD'S pilot program in 2003. By the following year, twenty-two additional scientists partnered with MS PHD'S mentees. During 2005-2006, twenty-one new scientists served as program mentors. Thus far, the MS PHD'S program has successfully engaged sixty-two minority and non-minority scientists as mentors to MS PHD'S student participants. AGU, AMS, ASLO, ESA, TOS, NAS OSB and JOI continue to serve as MS PHD'S Society Partners and hosts for MS PHD'S student activities in conjunction with their meetings. Each of the five professional society partners provided assistance in identifying mentors, provided complimentary memberships and meeting registrations for MS PHD'S student participants. AGU, AMS, ASLO, JOI and TOS have sponsored more than 90 conference registration and travel awards for the purpose of student participants engaging in MS PHD'S Professional Development Program Phase 2 activities at their international meetings. How did MS PHD'S establish meaningful engagement of organizational and agency partnerships to enhance diversity within the Earth system science community? This case study reveals replicable processes and constructs to enhance the quality of meaningful collaboration and engagement. In addition, the study addresses frequently asked questions (FAQ's) on the formation and sustenance of partnerships among principal investigators and evaluators and the impact of this partnership on writing proposals, implementing and evaluating program activities and outcomes.

Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification.

PubMed

Khatun, Jainab; Hamlett, Eric; Giddings, Morgan C

2008-03-01

The identification of peptides by tandem mass spectrometry (MS/MS) is a central method of proteomics research, but due to the complexity of MS/MS data and the large databases searched, the accuracy of peptide identification algorithms remains limited. To improve the accuracy of identification we applied a machine-learning approach using a hidden Markov model (HMM) to capture the complex and often subtle links between a peptide sequence and its MS/MS spectrum. Our model, HMM_Score, represents ion types as HMM states and calculates the maximum joint probability for a peptide/spectrum pair using emission probabilities from three factors: the amino acids adjacent to each fragmentation site, the mass dependence of ion types and the intensity dependence of ion types. The Viterbi algorithm is used to calculate the most probable assignment between ion types in a spectrum and a peptide sequence, then a correction factor is added to account for the propensity of the model to favor longer peptides. An expectation value is calculated based on the model score to assess the significance of each peptide/spectrum match. We trained and tested HMM_Score on three data sets generated by two different mass spectrometer types. For a reference data set recently reported in the literature and validated using seven identification algorithms, HMM_Score produced 43% more positive identification results at a 1% false positive rate than the best of two other commonly used algorithms, Mascot and X!Tandem. HMM_Score is a highly accurate platform for peptide identification that works well for a variety of mass spectrometer and biological sample types. The program is freely available on ProteomeCommons via an OpenSource license. See http://bioinfo.unc.edu/downloads/ for the download link.

California State University Long Beach: Model for a Terminal Master's Program as a Bridge to PhD

NASA Astrophysics Data System (ADS)

Bill, Andreas; Kenealy, Patrick; Kwon, Chuhee; Papp, Zoltan; Pickett, Galen T.

The department of Physics & Astronomy at California State University Long Beach has redesigned its Master's program in 2008 with the goal to provide a true graduate experience in Physics. The hallmarks of the program are five core graduate courses and a research-based MS thesis. During the last five years, 42% of MS recipients (24 students) were accepted to PhD programs, 41% started private-sector STEM careers, and 17% decided on teaching and other paths. The program doubled in size during that period. In 2013 we also became one of six Bridge Sites and only non-PhD granting institution of the American Physical Society (APS). We will describe the structure of the MS program, its goals and its place in the University degree plan landscape. We will also discuss how the APS Bridge Program has been implemented in our institution and has influenced our MS program. We gratefully acknowledge support from a variety of sources that contributed to establish the MS program, including the APS Bridge Program, individual NSF and Army Research Laboratory Grants.

Customizing Process to Align with Purpose and Program: The 2003 MS PHD'S in Ocean Sciences Program Evaluative Case Study

NASA Astrophysics Data System (ADS)

Williamson, V. A.; Pyrtle, A. J.

2004-12-01

How did the 2003 Minorities Striving and Pursuing Higher Degrees of Success (MS PHD'S) in Ocean Sciences Program customize evaluative methodology and instruments to align with program goals and processes? How is data captured to document cognitive and affective impact? How are words and numbers utilized to accurately illustrate programmatic outcomes? How is compliance with implicit and explicit funding regulations demonstrated? The 2003 MS PHD'S in Ocean Sciences Program case study provides insightful responses to each of these questions. MS PHD'S was developed by and for underrepresented minorities to facilitate increased and sustained participation in Earth system science. Key components of this initiative include development of a community of scholars sustained by face-to-face and virtual mentoring partnerships; establishment of networking activities between and among undergraduate, graduate, postgraduate students, scientists, faculty, professional organization representatives, and federal program officers; and provision of forums to address real world issues as identified by each constituent group. The evaluative case study of the 2003 MS PHD'S in Ocean Sciences Program consists of an analysis of four data sets. Each data set was aligned to document progress in the achievement of the following program goals: Goal 1: The MS PHD'S Ocean Sciences Program will successfully market, recruit, select, and engage underrepresented student and non-student participants with interest/ involvement in Ocean Sciences; Goal 2: The MS PHD'S Ocean Sciences Program will provide meaningful engagement for participants as determined by quantitative analysis of user-feedback; Goal 3: The MS PHD'S Ocean Sciences Program will provide meaningful engagement for participants as determined by qualitative analysis of user-feedback, and; Goal 4: The MS PHD'S Ocean Sciences Program will develop a constituent base adequate to demonstrate evidence of interest, value, need and sustainability in its vision, mission, goals and activities. In addition to the documentation of evaluative process, the case study also provides insight on the establishment of mutually supportive principal investigator and evaluator partnerships as necessary foundations for building effective teams. The study addresses frequently asked questions (FAQ's) on the formation and sustenance of partnerships among visionaries and evaluators and the impact of this partnership on the achievement of program outcomes.

Proteome Speciation by Mass Spectrometry: Characterization of Composite Protein Mixtures in Milk Replacers.

PubMed

Gaspari, Marco; Chiesa, Luca; Nicastri, Annalisa; Gabriele, Caterina; Harper, Valeria; Britti, Domenico; Cuda, Giovanni; Procopio, Antonio

2016-12-06

The ability of tandem mass spectrometry to determine the primary structure of proteolytic peptides can be exploited to trace back the organisms from which the corresponding proteins were extracted. This information can be important when food products, such as protein powders, can be supplemented with lower-quality starting materials. In order to dissect the origin of proteinaceous material composing a given unknown mixture, a two-step database search strategy for bottom-up nanoscale liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) data was implemented. A single nanoLC-MS/MS analysis was sufficient not only to determine the qualitative composition of the mixtures under examination, but also to assess the relative percent composition of the various proteomes, if dedicated calibration curves were previously generated. The approach of two-step database search for qualitative analysis and proteome total ion current (pTIC) calculation for quantitative analysis was applied to several binary and ternary mixtures which mimic the composition of milk replacers typically used in calf feeding.

Protein Identification Using Top-Down Spectra*

PubMed Central

Liu, Xiaowen; Sirotkin, Yakov; Shen, Yufeng; Anderson, Gordon; Tsai, Yihsuan S.; Ting, Ying S.; Goodlett, David R.; Smith, Richard D.; Bafna, Vineet; Pevzner, Pavel A.

2012-01-01

In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set. PMID:22027200

Proteomic analysis of sweet algerian apricot kernels (Prunus armeniaca L.) by combinatorial peptide ligand libraries and LC-MS/MS.

PubMed

Ghorab, Hamida; Lammi, Carmen; Arnoldi, Anna; Kabouche, Zahia; Aiello, Gilda

2018-01-15

An investigation on the proteome of the sweet kernel of apricot, based on equalisation with combinatorial peptide ligand libraries (CPLLs), SDS-PAGE, nLC-ESI-MS/MS, and database search, permitted identifying 175 proteins. Gene ontology analysis indicated that their main molecular functions are in nucleotide binding (20.9%), hydrolase activities (10.6%), kinase activities (7%), and catalytic activity (5.6%). A protein-protein association network analysis using STRING software permitted to build an interactomic map of all detected proteins, characterised by 34 interactions. In order to forecast the potential health benefits deriving from the consumption of these proteins, the two most abundant, i.e. Prunin 1 and 2, were enzymatically digested in silico predicting 10 and 14 peptides, respectively. Searching their sequences in the database BIOPEP, it was possible to suggest a variety of bioactivities, including dipeptidyl peptidase-IV (DPP-IV) and angiotensin converting enzyme I (ACE) inhibition, glucose uptake stimulation and antioxidant properties. Copyright © 2017 Elsevier Ltd. All rights reserved.

rTANDEM, an R/Bioconductor package for MS/MS protein identification.

PubMed

Fournier, Frédéric; Joly Beauparlant, Charles; Paradis, René; Droit, Arnaud

2014-08-01

rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor. rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0). frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Limitations of Using Microsoft Excel Version 2016 (MS Excel 2016) for Statistical Analysis for Medical Research.

PubMed

Tanavalee, Chotetawan; Luksanapruksa, Panya; Singhatanadgige, Weerasak

2016-06-01

Microsoft Excel (MS Excel) is a commonly used program for data collection and statistical analysis in biomedical research. However, this program has many limitations, including fewer functions that can be used for analysis and a limited number of total cells compared with dedicated statistical programs. MS Excel cannot complete analyses with blank cells, and cells must be selected manually for analysis. In addition, it requires multiple steps of data transformation and formulas to plot survival analysis graphs, among others. The Megastat add-on program, which will be supported by MS Excel 2016 soon, would eliminate some limitations of using statistic formulas within MS Excel.

Antidepressant Drug Treatment in Association with Multiple Sclerosis Disease-Modifying Therapy: Using Explorys in the MS Population.

PubMed

Mirsky, Matthew M; Marrie, Ruth Ann; Rae-Grant, Alexander

2016-01-01

Background: The Explorys Enterprise Performance Management (EPM) database contains de-identified clinical data for 50 million patients. Multiple sclerosis (MS) disease-modifying therapies (DMTs), specifically interferon beta (IFNβ) treatments, may potentiate depression. Conflicting data have emerged, and a large-scale claims-based study by Patten et al. did not support such an association. This study compares the results of Patten et al. with those using the EPM database. Methods: "Power searches" were built to test the relationship between antidepressant drug use and DMT in the MS population. Searches were built to produce a cohort of individuals diagnosed as having MS in the past 3 years taking a specific DMT who were then given any antidepressant drug. The antidepressant drug therapy prevalence was tested in the MS population on the following DMTs: IFNβ-1a, IFNβ-1b, combined IFNβ, glatiramer acetate, natalizumab, fingolimod, and dimethyl fumarate. Results: In patients with MS, the rate of antidepressant drug use in those receiving DMTs was 40.60% to 44.57%. The rate of antidepressant drug use for combined IFNβ DMTs was 41.61% (males: 31.25%-39.62%; females: 43.10%-47.33%). Antidepressant drug use peaked in the group aged 45 to 54 years for five of six DMTs. Conclusions: We found no association between IFNβ treatment and antidepressant drug use in the MS population compared with other DMTs. The EPM database has been validated against the Patten et al. data for future use in the MS population.

A multi-level assessment of a program to teach medical students to teach.

PubMed

Blatt, Benjamin; Greenberg, Larrie

2007-02-01

Few longitudinal programs exist to teach senior students (MS4s) to be teachers, nor have there been any reports of comprehensive program evaluation in this area. The primary objectives of this study were to describe our ongoing faculty development effort and to develop a multi-level program evaluation, using Dixon's model. The TALKS (Teaching and Learning Communication Skills) program is a senior elective and open to all MS4s. We evaluated our program through assessment of its participants at three levels: level 1, opinion; level 2, competence; and level 3, performance; but not level 4, patient outcomes. The authors used a retrospective, pre-post questionnaire to assess MS4 attitudes about their educational experiences, a traditional instrument to assess their teaching, an interaction analysis technique using Bloom's taxonomy to assess MS4s' feedback skills, and a SP exam to assess MS4 communication skills. The authors hypothesized that MS4s participating in TALKS would view medical education more positively and informatively, would demonstrate important principles in giving feedback, would be assessed as excellent teachers, and would perform better than controls in an SP exam emphasizing communication skills. Results revealed that MS4s' ratings as teachers were very good to excellent, with the highest scores on the items "knowledgeable, supportive of me, and answering questions clearly." (Level 1, Opinion) MS4s' perceptions of their knowledge, attitudes and skills increased significantly from the pre to the post-questionnaire. (Level 2, Competence) MS4 feedback skills to MS2s revealed they did more talking than ideal, often at the lowest levels of Bloom's taxonomy. (Level 3, Performance) MS4s demonstrated better communication skills than controls on an evaluation by professional SPs. (Level 3, Performance).

Treatment Effects for Dysphagia in Adults with Multiple Sclerosis: A Systematic Review.

PubMed

Alali, Dalal; Ballard, Kirrie; Bogaardt, Hans

2016-10-01

Dysphagia or swallowing difficulties have been reported to be a concern in adults with multiple sclerosis (MS). This problem can result in several complications including aspiration pneumonia, reduced quality of life and an increase in mortality rate. No previous systematic reviews on treatment effects for dysphagia in MS have been published. The main objective of this study is to summarise and qualitatively analyse published studies on treatment effects for dysphagia in MS. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were applied to conduct a systematic search of seven databases, using relevant key words, and subsequent analysis of the identified studies. The studies were required to meet all three inclusion criteria of including a statement on intention to treat, or measure the effects of treatment for dysphagia in adults with MS and data on treatment outcomes for at least one adult diagnosed with MS. Retained studies were evaluated by two independent reviewers using a critical appraisal tool. This study has not been registered. A total of 563 studies were identified from the database searches. After screening and assessment of full articles for eligibility, five studies were included in the review. Three examined electrical stimulation and two examined the use of botulinum toxin. One study testing electrical stimulation was a randomised controlled trial, two were well-designed case series and two were case series lacking experimental control. All studies reported some positive effects on dysphagia; however, treatments that involved the use of electrical stimulation showed larger effect sizes. There is a paucity of evidence to guide treatment of dysphagia in MS, with only electrical stimulation and botulinum toxin treatment represented in the literature search conducted here. While both treatments show initial promise for reducing the swallowing impairment, they require further research using well-controlled experimental designs to determine their clinical applicability and long-term treatment effects for dysphagia across different types and severity of MS.

MS/MS fragmentation-guided search of TMG-chitooligomycins and their structure-activity relationship in specific β-N-acetylglucosaminidase inhibition.

PubMed

Usuki, Hirokazu; Yamamoto, Yukihiro; Kumagai, Yuya; Nitoda, Teruhiko; Kanzaki, Hiroshi; Hatanaka, Tadashi

2011-04-21

The reducing tetrasaccharide TMG-chitotriomycin (1) is an inhibitor of β-N-acetylglucosaminidase (GlcNAcase), produced by the actinomycete Streptomyces anulatus NBRC13369. The inhibitor shows a unique inhibitory spectrum, that is, selectivity toward enzymes from chitin-containing organisms such as insects and fungi. Nevertheless, its structure-selectivity relationship remains to be clarified. In this study, we conducted a structure-guided search of analogues of 1 in order to obtain diverse N,N,N-trimethylglucosaminium (TMG)-containing chitooligosaccharides. In this approach, the specific fragmentation profile of 1 on ESI-MS/MS analysis was used for the selective detection of desired compounds. As a result, two new analogues, named TMG-chitomonomycin (3) and TMG-chitobiomycin (2), were obtained from a culture filtrate of 1-producing Streptomyces. Their enzyme-inhibiting activity revealed that the potency and selectivity depended on the degree of polymerization of the reducing end GlcNAc units. Furthermore, a computational modeling study inspired the inhibitory mechanism of TMG-related compounds as a mimic of the substrate in the Michaelis complex of the GH20 enzyme. This study is an example of the successful application of a MS/MS experiment for structure-guided isolation of natural products.

Paresthesia: A Review of Its Definition, Etiology and Treatments in View of the Traditional Medicine.

PubMed

Emami, Seyed Ahmad; Sahebkar, Amirhossein; Javadi, Behjat

2016-01-01

To search major Islamic Traditional Medicine (ITM) textbooks for definition, etiology and medicinal plants used to manage 'khadar' or 'paresthesia', a common sensory symptom of multiple sclerosis (MS) and peripheral neuropathies. In addition, the conformity of the efficacy of ITM-suggested plants with the findings from modern pharmacological research on MS will be discussed. Data on the medicinal plants used to treat 'khadar' were obtained from major ITM texts. A detailed search in PubMed, ScienceDirect, Scopus and Google Scholar databases was performed to confirm the effects of ITM-mentioned medicinal plants on MS in view of identified pharmacological actions. Moringa oleifera Lam., Aloe vera (L.) Burm.f., Euphorbia species, Citrullus colocynthis (L.) Schrad., and Costus speciosus (Koen ex. Retz) Sm. are among the most effective ITM plants for the management of 'khadar'. Recent experimental evidence confirms the effectiveness of the mentioned plants in ameliorating MS symptoms. Moreover, according to ITM, prolonged exposure to cold and consuming foodstuff with cold temperament might be involved in the etiopathogenesis of MS. The use of traditional knowledge can help finding neglected risk factors as well as effective and safe therapeutic approaches, phytomedicines and dietary habits for the management of paresthesia and related disorders such as MS.

Computational search for rare-earth free hard-magnetic materials

NASA Astrophysics Data System (ADS)

Flores Livas, José A.; Sharma, Sangeeta; Dewhurst, John Kay; Gross, Eberhard; MagMat Team

2015-03-01

It is difficult to over state the importance of hard magnets for human life in modern times; they enter every walk of our life from medical equipments (NMR) to transport (trains, planes, cars, etc) to electronic appliances (for house hold use to computers). All the known hard magnets in use today contain rare-earth elements, extraction of which is expensive and environmentally harmful. Rare-earths are also instrumental in tipping the balance of world economy as most of them are mined in limited specific parts of the world. Hence it would be ideal to have similar characteristics as a hard magnet but without or at least with reduced amount of rare-earths. This is the main goal of our work: search for rare-earth-free magnets. To do so we employ a combination of density functional theory and crystal prediction methods. The quantities which define a hard magnet are magnetic anisotropy energy (MAE) and saturation magnetization (Ms), which are the quantities we maximize in search for an ideal magnet. In my talk I will present details of the computation search algorithm together with some potential newly discovered rare-earth free hard magnet. J.A.F.L. acknowledge financial support from EU's 7th Framework Marie-Curie scholarship program within the ``ExMaMa'' Project (329386).

Improved molecular level identification of organic compounds using comprehensive two-dimensional chromatography, dual ionization energies and high resolution mass spectrometry

DOE PAGES

Worton, David R.; Decker, Monika; Isaacman-VanWertz, Gabriel; ...

2017-05-22

A new analytical methodology combining comprehensive two-dimensional gas chromatography (GC×GC), dual ionization energies and high resolution time of flight mass spectrometry has been developed that improves molecular level identification of organic compounds in complex environmental samples. GC×GC maximizes compound separation providing cleaner mass spectra by minimizing erroneous fragments from interferences and co-eluting peaks. Traditional electron ionization (EI, 70 eV) provides MS fragmentation patterns that can be matched to published EI MS libraries while vacuum ultraviolet photoionization (VUV, 10.5 eV) yields MS with reduced fragmentation enhancing the abundance of the molecular ion providing molecular formulas when combined with high resolution massmore » spectrometry. We demonstrate this new approach by applying it to a sample of organic aerosol. In this sample, 238 peaks were matched to EI MS library data with FM ≥ 800 but a fifth (42 compounds) were determined to be incorrectly identified because the molecular formula was not confirmed by the VUV MS data. This highlights the importance of using a complementary technique to confirm compound identifications even for peaks with very good matching statistics. In total, 171 compounds were identified by EI MS matching to library spectra with confirmation of the molecular formula from the high resolution VUV MS data and were not dependent on the matching statistics being above a threshold value. A large number of unidentified peaks were still observed with FM < 800, which in routine analysis would typically be neglected. Where possible, these peaks were assigned molecular formulas from the VUV MS data (211 in total). In total, the combination of EI and VUV MS data provides more than twice as much molecular level peak information than traditional approaches and improves confidence in the identification of individual organic compounds. The molecular formula data from the VUV MS data was used, in conjunction with GC×GC retention times and the observed EI MS, to generate a new, searchable EI MS library compatible with the standard NIST MS search program. This library is deliberately dynamic and editable so that other end users can add new entries and update existing entries as new information becomes available.A new analytical methodology has been developed to improve molecular level identification of organic compounds in complex samples.« less

Improved molecular level identification of organic compounds using comprehensive two-dimensional chromatography, dual ionization energies and high resolution mass spectrometry

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

Worton, David R.; Decker, Monika; Isaacman-VanWertz, Gabriel

A new analytical methodology combining comprehensive two-dimensional gas chromatography (GC×GC), dual ionization energies and high resolution time of flight mass spectrometry has been developed that improves molecular level identification of organic compounds in complex environmental samples. GC×GC maximizes compound separation providing cleaner mass spectra by minimizing erroneous fragments from interferences and co-eluting peaks. Traditional electron ionization (EI, 70 eV) provides MS fragmentation patterns that can be matched to published EI MS libraries while vacuum ultraviolet photoionization (VUV, 10.5 eV) yields MS with reduced fragmentation enhancing the abundance of the molecular ion providing molecular formulas when combined with high resolution massmore » spectrometry. We demonstrate this new approach by applying it to a sample of organic aerosol. In this sample, 238 peaks were matched to EI MS library data with FM ≥ 800 but a fifth (42 compounds) were determined to be incorrectly identified because the molecular formula was not confirmed by the VUV MS data. This highlights the importance of using a complementary technique to confirm compound identifications even for peaks with very good matching statistics. In total, 171 compounds were identified by EI MS matching to library spectra with confirmation of the molecular formula from the high resolution VUV MS data and were not dependent on the matching statistics being above a threshold value. A large number of unidentified peaks were still observed with FM < 800, which in routine analysis would typically be neglected. Where possible, these peaks were assigned molecular formulas from the VUV MS data (211 in total). In total, the combination of EI and VUV MS data provides more than twice as much molecular level peak information than traditional approaches and improves confidence in the identification of individual organic compounds. The molecular formula data from the VUV MS data was used, in conjunction with GC×GC retention times and the observed EI MS, to generate a new, searchable EI MS library compatible with the standard NIST MS search program. This library is deliberately dynamic and editable so that other end users can add new entries and update existing entries as new information becomes available.A new analytical methodology has been developed to improve molecular level identification of organic compounds in complex samples.« less

ESI-MS2 and Anti-inflammatory Studies of Cyclopropanic Triterpenes. UPLC-ESI-MS and MS2 Search of Related Metabolites from Donella ubanguiensis.

PubMed

Sandjo, Louis P; Nascimento, Marcus V P Dos Santos; da Silva, Layzon A L; Munhoz, Antonio C M; Pollo, Luiz A E; Biavatti, Maique W; Ngadjui, Bonaventure T; Opatz, Till; Fröde, Tania S

2017-01-01

Triterpenes are one of the largest secondary metabolites groups spread in the plant kingdom with various skeletons. These metabolites have showed various bioactivities including anti-inflammatory activity. The study aims to explore the mass spectrometry fragmentation of donellanic acids A-C (DA A-C), three compounds identified from Donella ubanguiensis; in addition, the fragmentation behaviour of these metabolites will serve as a fingerprint to search and characterise triterpenes congeners in fruits, bark and wood crude extracts of D. ubanguiensis. This work was prompted by the anti-inflammatory activity on leukocyte migration, exudate concentrations and myeloperoxidase activity obtained for DA A-B. The bioactivity was performed on mouse model of pleurisy induced by carrageenan and the parameters were analysed by veterinarian automated cell counter and colorimetric assays. While the tandem mass analyses of DA A-C were carried out by a direct infusion ESI-QTOF-MS/MS, the extracts were studied by UPLC-ESI-QTOF-MS and UPLC-ESI-QTOF-MS/MS. DA A displayed interesting anti-inflammatory activity by inhibiting leukocyte migration, exudate concentrations and myeloperoxidase activity (p < 0.05) while DA B was weakly active (p > 0.05). Moreover, the diagnostic of the MS 2 behaviour of DA A-C in conjunction with the chromatograms and the obtained MS 2 data of the crude extract led to the characterisation of three cyclopropane triterpenes (T1-T3) and six saponins (T4-T9) from the fruits, the bark, and the wood extracts. Donella species deserve more investigation since metabolites related to the anti-inflammatory compound (DA A) could be identified. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Annotation: a computational solution for streamlining metabolomics analysis

PubMed Central

Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Benton, H. Paul; Siuzdak, Gary

2017-01-01

Metabolite identification is still considered an imposing bottleneck in liquid chromatography mass spectrometry (LC/MS) untargeted metabolomics. The identification workflow usually begins with detecting relevant LC/MS peaks via peak-picking algorithms and retrieving putative identities based on accurate mass searching. However, accurate mass search alone provides poor evidence for metabolite identification. For this reason, computational annotation is used to reveal the underlying metabolites monoisotopic masses, improving putative identification in addition to confirmation with tandem mass spectrometry. This review examines LC/MS data from a computational and analytical perspective, focusing on the occurrence of neutral losses and in-source fragments, to understand the challenges in computational annotation methodologies. Herein, we examine the state-of-the-art strategies for computational annotation including: (i) peak grouping or full scan (MS1) pseudo-spectra extraction, i.e., clustering all mass spectral signals stemming from each metabolite; (ii) annotation using ion adduction and mass distance among ion peaks; (iii) incorporation of biological knowledge such as biotransformations or pathways; (iv) tandem MS data; and (v) metabolite retention time calibration, usually achieved by prediction from molecular descriptors. Advantages and pitfalls of each of these strategies are discussed, as well as expected future trends in computational annotation. PMID:29039932

Working-memory capacity predicts the executive control of visual search among distractors: the influences of sustained and selective attention.

PubMed

Poole, Bradley J; Kane, Michael J

2009-07-01

Variation in working-memory capacity (WMC) predicts individual differences in only some attention-control capabilities. Whereas higher WMC subjects outperform lower WMC subjects in tasks requiring the restraint of prepotent but inappropriate responses, and the constraint of attentional focus to target stimuli against distractors, they do not differ in prototypical visual-search tasks, even those that yield steep search slopes and engender top-down control. The present three experiments tested whether WMC, as measured by complex memory span tasks, would predict search latencies when the 1-8 target locations to be searched appeared alone, versus appearing among distractor locations to be ignored, with the latter requiring selective attentional focus. Subjects viewed target-location cues and then fixated on those locations over either long (1,500-1,550 ms) or short (300 ms) delays. Higher WMC subjects identified targets faster than did lower WMC subjects only in the presence of distractors and only over long fixation delays. WMC thus appears to affect subjects' ability to maintain a constrained attentional focus over time.

YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

PubMed Central

Colangelo, Christopher M.; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L.; Carriero, Nicholas J.; Gulcicek, Erol E.; Lam, TuKiet T.; Wu, Terence; Bjornson, Robert D.; Bruce, Can; Nairn, Angus C.; Rinehart, Jesse; Miller, Perry L.; Williams, Kenneth R.

2015-01-01

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry (LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED’s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. PMID:25712262

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

PubMed

Colangelo, Christopher M; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L; Carriero, Nicholas J; Gulcicek, Erol E; Lam, TuKiet T; Wu, Terence; Bjornson, Robert D; Bruce, Can; Nairn, Angus C; Rinehart, Jesse; Miller, Perry L; Williams, Kenneth R

2015-02-01

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Stars of type MS with evidence of white dwarf companions. [IUE, Main Sequence (MS)

NASA Technical Reports Server (NTRS)

Peery, Benjamin F., Jr.

1986-01-01

A search for white dwarf companions of MS-type stars was conducted, using IUE. The overendowments of these stars in typical S-process nuclides suggest that they, like the Ba II stars, may owe their peculiar compositions to earlier mass transfer. Short-wavelength IUE spectra show striking emission line variability in HD35155, HD61913, and 4 Ori; HD35155 and 4 Ori show evidence of white dwarf companions.

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification.

PubMed

Li, Honglan; Joh, Yoon Sung; Kim, Hyunwoo; Paek, Eunok; Lee, Sang-Won; Hwang, Kyu-Baek

2016-12-22

Proteogenomics is a promising approach for various tasks ranging from gene annotation to cancer research. Databases for proteogenomic searches are often constructed by adding peptide sequences inferred from genomic or transcriptomic evidence to reference protein sequences. Such inflation of databases has potential of identifying novel peptides. However, it also raises concerns on sensitive and reliable peptide identification. Spurious peptides included in target databases may result in underestimated false discovery rate (FDR). On the other hand, inflation of decoy databases could decrease the sensitivity of peptide identification due to the increased number of high-scoring random hits. Although several studies have addressed these issues, widely applicable guidelines for sensitive and reliable proteogenomic search have hardly been available. To systematically evaluate the effect of database inflation in proteogenomic searches, we constructed a variety of real and simulated proteogenomic databases for yeast and human tandem mass spectrometry (MS/MS) data, respectively. Against these databases, we tested two popular database search tools with various approaches to search result validation: the target-decoy search strategy (with and without a refined scoring-metric) and a mixture model-based method. The effect of separate filtering of known and novel peptides was also examined. The results from real and simulated proteogenomic searches confirmed that separate filtering increases the sensitivity and reliability in proteogenomic search. However, no one method consistently identified the largest (or the smallest) number of novel peptides from real proteogenomic searches. We propose to use a set of search result validation methods with separate filtering, for sensitive and reliable identification of peptides in proteogenomic search.

Smoking and multiple sclerosis: A systematic review and meta-analysis using the Bradford Hill criteria for causation.

PubMed

Degelman, Michelle L; Herman, Katya M

2017-10-01

Despite being one of the most common neurological disorders globally, the cause(s) of multiple sclerosis (MS) remain unknown. Cigarette smoking has been studied with regards to both the development and progression of MS. The Bradford Hill criteria for causation can contribute to a more comprehensive evaluation of a potentially causal risk factor-disease outcome relationship. The objective of this systematic review and meta-analysis was to assess the relationship between smoking and both MS risk and MS progression, subsequently applying Hill's criteria to further evaluate the likelihood of causal associations. The Medline, EMBASE, CINAHL, PsycInfo, and Cochrane Library databases were searched for relevant studies up until July 28, 2015. A random-effects meta-analysis was conducted for three outcomes: MS risk, conversion from clinically isolated syndrome (CIS) to clinically definite multiple sclerosis (CDMS), and progression from relapsing-remitting multiple sclerosis (RRMS) to secondary-progressive multiple sclerosis (SPMS). Dose-response relationships and risk factor interactions, and discussions of mechanisms and analogous associations were noted. Hill's criteria were applied to assess causality of the relationships between smoking and each outcome. The effect of second-hand smoke exposure was also briefly reviewed. Smoking had a statistically significant association with both MS risk (conservative: OR/RR 1.54, 95% CI [1.46-1.63]) and SPMS risk (HR 1.80, 95% CI [1.04-3.10]), but the association with progression from CIS to CDMS was non-significant (HR 1.13, 95% CI [0.73-1.76]). Using Hill's criteria, there was strong evidence of a causal role of smoking in MS risk, but only moderate evidence of a causal association between smoking and MS progression. Heterogeneity in study designs and target populations, inconsistent results, and an overall scarcity of studies point to the need for more research on second-hand smoke exposure in relation to MS prior to conducting a detailed meta-analysis. This first review to supplement systematic review and meta-analytic methods with Hill's criteria to analyze the smoking-MS association provides evidence supporting the causal involvement of smoking in the development and progression of MS. Smoking prevention and cessation programs and policies should consider MS as an additional health risk when aiming to reduce smoking prevalence in the population. Copyright © 2017 Elsevier B.V. All rights reserved.

Meaningful Engagement to Enhance Diversity: Broadened Impact Actualized

NASA Astrophysics Data System (ADS)

Whitney, V. W.; Pyrtle, A. J.

2008-12-01

The MS PHD'S Professional Development Program was established by and for UR/US populations to facilitate increased and sustained participation within the Earth system science community. MS PHD'S is jointly funded by NSF and NASA. Fourteen (14) minority Earth system scientists served as Program mentors and one- hundred fifteen (115) minority and non-minority scientists served as Meeting Mentors to student participants. Representatives from fifty-six (56) agencies and institutions provided support and exposure to MS PHD'S student participants. Two hundred fifty-eight (258) highly qualified UR/US students completed on-line applications to participate in the MS PHD'S Professional Development Program. Because of funding limitations, slightly fewer than 50% of the applicants were selected to participate. One-hundred twenty-six (126) undergraduate and graduate students from 26 states and Puerto Rico participated in the MS PHD'S program. Sixty-eight (68) MS PHD'S student participants self-identified as African American; thirty-four (34) as Puerto Rican; nine (9) as Hispanic/Mexican American, ten (10) as Native American and one (1) each as African, Asian, Pacific Islander, Hispanic and Multi-Ethnic. During the five year span of MS PHD'S programming, sixteen (16) student participants completed BS degrees, twelve (12) completed MS degrees and ten (10) completed the Doctoral degrees. How did MS PHD'S establish meaningful engagement to enhance diversity within the Earth system science community? This case study reveals replicable processes and constructs to enhance the quality of meaningful collaboration and engagement. In addition, the study addresses frequently asked questions (FAQ's) on outreach, recruitment, engagement, retention and success of students from underrepresented populations within diversity-focused programs.

Chemometric Profile of Root Extracts of Rhodiola imbricata Edgew. with Hyphenated Gas Chromatography Mass Spectrometric Technique

PubMed Central

Tayade, Amol B.; Dhar, Priyanka; Kumar, Jatinder; Sharma, Manu; Chauhan, Rajinder S.; Chaurasia, Om P.; Srivastava, Ravi B.

2013-01-01

Rhodiola imbricata Edgew. (Rose root or Arctic root or Golden root or Shrolo), belonging to the family Crassulaceae, is an important food crop and medicinal plant in the Indian trans-Himalayan cold desert. Chemometric profile of the n-hexane, chloroform, dichloroethane, ethyl acetate, methanol, and 60% ethanol root extracts of R. imbricata were performed by hyphenated gas chromatography mass spectrometry (GC/MS) technique. GC/MS analysis was carried out using Thermo Finnigan PolarisQ Ion Trap GC/MS MS system comprising of an AS2000 liquid autosampler. Interpretation on mass spectrum of GC/MS was done using the NIST/EPA/NIH Mass Spectral Database, with NIST MS search program v.2.0g. Chemometric profile of root extracts revealed the presence of 63 phyto-chemotypes, among them, 1-pentacosanol; stigmast-5-en-3-ol, (3β,24S); 1-teracosanol; 1-henteracontanol; 17-pentatriacontene; 13-tetradecen-1-ol acetate; methyl tri-butyl ammonium chloride; bis(2-ethylhexyl) phthalate; 7,8-dimethylbenzocyclooctene; ethyl linoleate; 3-methoxy-5-methylphenol; hexadecanoic acid; camphor; 1,3-dimethoxybenzene; thujone; 1,3-benzenediol, 5-pentadecyl; benzenemethanol, 3-hydroxy, 5-methoxy; cholest-4-ene-3,6-dione; dodecanoic acid, 3-hydroxy; octadecane, 1-chloro; ethanone, 1-(4-hydroxyphenyl); α-tocopherol; ascaridole; campesterol; 1-dotriacontane; heptadecane, 9-hexyl were found to be present in major amount. Eventually, in the present study we have found phytosterols, terpenoids, fatty acids, fatty acid esters, alkyl halides, phenols, alcohols, ethers, alkanes, and alkenes as the major group of phyto-chemotypes in the different root extracts of R. imbricata. All these compounds identified by GC/MS analysis were further investigated for their biological activities and it was found that they possess a diverse range of positive pharmacological actions. In future, isolation of individual phyto-chemotypes and subjecting them to biological activity will definitely prove fruitful results in designing a novel drug. PMID:23326358

Extending a Tandem Mass Spectral Library to Include MS2 Spectra of Fragment Ions Produced In-Source and MSn Spectra.

PubMed

Yang, Xiaoyu; Neta, Pedatsur; Stein, Stephen E

2017-11-01

Tandem mass spectral library searching is finding increased use as an effective means of determining chemical identity in mass spectrometry-based omics studies. We previously reported on constructing a tandem mass spectral library that includes spectra for multiple precursor ions for each analyte. Here we report our method for expanding this library to include MS 2 spectra of fragment ions generated during the ionization process (in-source fragment ions) as well as MS 3 and MS 4 spectra. These can assist the chemical identification process. A simple density-based clustering algorithm was used to cluster all significant precursor ions from MS 1 scans for an analyte acquired during an infusion experiment. The MS 2 spectra associated with these precursor ions were grouped into the same precursor clusters. Subsequently, a new top-down hierarchical divisive clustering algorithm was developed for clustering the spectra from fragmentation of ions in each precursor cluster, including the MS 2 spectra of the original precursors and of the in-source fragments as well as the MS n spectra. This algorithm starts with all the spectra of one precursor in one cluster and then separates them into sub-clusters of similar spectra based on the fragment patterns. Herein, we describe the algorithms and spectral evaluation methods for extending the library. The new library features were demonstrated by searching the high resolution spectra of E. coli extracts against the extended library, allowing identification of compounds and their in-source fragment ions in a manner that was not possible before. Graphical Abstract ᅟ.

Brute-Force Approach for Mass Spectrometry-Based Variant Peptide Identification in Proteogenomics without Personalized Genomic Data

NASA Astrophysics Data System (ADS)

Ivanov, Mark V.; Lobas, Anna A.; Levitsky, Lev I.; Moshkovskii, Sergei A.; Gorshkov, Mikhail V.

2018-02-01

In a proteogenomic approach based on tandem mass spectrometry analysis of proteolytic peptide mixtures, customized exome or RNA-seq databases are employed for identifying protein sequence variants. However, the problem of variant peptide identification without personalized genomic data is important for a variety of applications. Following the recent proposal by Chick et al. (Nat. Biotechnol. 33, 743-749, 2015) on the feasibility of such variant peptide search, we evaluated two available approaches based on the previously suggested "open" search and the "brute-force" strategy. To improve the efficiency of these approaches, we propose an algorithm for exclusion of false variant identifications from the search results involving analysis of modifications mimicking single amino acid substitutions. Also, we propose a de novo based scoring scheme for assessment of identified point mutations. In the scheme, the search engine analyzes y-type fragment ions in MS/MS spectra to confirm the location of the mutation in the variant peptide sequence.

Establishing strategies for a transportation MS4.

DOT National Transportation Integrated Search

2015-05-01

The objective of this project has been to identify best practices and approaches to MS4 program planning for : the Iowa Department of Transportation. Information is primarily based on existing state MS4 programs as : examples and references for use a...

DECIDE: a software for computer-assisted evaluation of diagnostic test performance.

PubMed

Chiecchio, A; Bo, A; Manzone, P; Giglioli, F

1993-05-01

The evaluation of the performance of clinical tests is a complex problem involving different steps and many statistical tools, not always structured in an organic and rational system. This paper presents a software which provides an organic system of statistical tools helping evaluation of clinical test performance. The program allows (a) the building and the organization of a working database, (b) the selection of the minimal set of tests with the maximum information content, (c) the search of the model best fitting the distribution of the test values, (d) the selection of optimal diagnostic cut-off value of the test for every positive/negative situation, (e) the evaluation of performance of the combinations of correlated and uncorrelated tests. The uncertainty associated with all the variables involved is evaluated. The program works in a MS-DOS environment with EGA or higher performing graphic card.

Joint MS Degree Program between the Korea University of Technology and Education and the University of Kansas

NASA Astrophysics Data System (ADS)

Dougherty, R. L.; Kim, Kwang Su

This paper provides an overview of the Joint MS Degree Program between Korea University of Technology and Education’ s (KUT) Mechatronics Department and Kansas University’ s (KU) Mechanical Engineering Department. Discussions were initiated in early 2005 which resulted in a formal agreement being approved by both parties in mid-2007. The Joint MS Degree Program is composed of 30 semester credit hours, equally split between the two universities, with the actual degree being awarded by the institution at which the thesis work is performed. Issues addressed during the development of this Joint MS Program included: joint versus dual degrees, institutional acceptance of the transfer of fifteen hours of credit for an MS degree, different admissions requirements and procedures for the two institutions, financial support of the students, faculty advisors at each institution, Graduate Directors at each institution, transcript acknowledgement of the Joint Degree, residency requirements, English speaking requirements/abilities, thesis publication allowances/requirements, and time zone differences for virtual meetings. These issues have been addressed, and the Joint MS Degree Program is functioning with a small number of students having taken advantage of the opportunity since the Program’ s inception. Future considerations are: growing the number of students in the Program, expansion to other Departments besides KU-Mechanical Engineering and KUTMechatronics, including other universities in the Program, expansion to a Joint PhD Degree Program, and stronger funding resources.

Computational mass spectrometry for small molecules

PubMed Central

2013-01-01

The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline. PMID:23453222

Applicability of preparative overpressured layer chromatography and direct bioautography in search of antibacterial chamomile compounds.

PubMed

Móricz, Agnes M; Ott, Péter G; Alberti, Agnes; Böszörményi, Andrea; Lemberkovics, Eva; Szoke, Eva; Kéry, Agnes; Mincsovics, Emil

2013-01-01

In situ sample preparation and preparative overpressured layer chromatography (OPLC) fractionation on a 0.5 mm thick adsorbent layer of chamomile flower methanol extract prepurified by conventional gravitation accelerated column chromatography were applied in searching for bioactive components. Sample cleanup in situ on the adsorbent layer subsequent to sample application was performed using mobile phase flow in the opposite direction (the input and output of the eluent was exchanged). The antibacterial effect of the fractions obtained from the stepwise gradient OPLC separation with the flow in the normal direction was evaluated by direct bioautography against two Gram-negative bacteria: the luminescence gene tagged plant pathogenic Pseudomonas syringae pv. maculicola, and the naturally luminescent marine bacterium Vibrio fischeri. The fractions having strong activity were analyzed by SPME-GC/MS and HPLC/MS/MS. Mainly essential oil components, coumarins, flavonoids, phenolic acids, and fatty acids were tentatively identified in the fractions.

Music therapy in the treatment of multiple sclerosis: a comprehensive literature review.

PubMed

Ostermann, Thomas; Schmid, Wolfgang

2006-04-01

Coping with multiple sclerosis symptoms still remains a challenge for each patient suffering from this chronic inflammatory disease. Therefore, patients often turn to using complementary and alternative medicine (CAM). In this review, the authors aimed to investigate the current state of literature of music therapy in the treatment of multiple sclerosis (MS). Medline, PubMed, Embase, AMED, CAMbase and the Music Therapy World Journal Index were searched for the terms MS and 'music therapy'. In addition, an internet search using Google Scholar was performed. The authors found seven case-reports/series and seven studies on music therapy for MS-patients. Both the case reports and studies presented here are pioneer work. Most of the studies are naturally predominated by the use of qualitative and uncontrolled research designs. Nevertheless, the results of the studies as well as the case reports demonstrate patients' improvement in the domains of self-acceptance, anxiety and depression. The results of the studies as well as the case reports define a sufficient basis for further music therapeutical work as they show a variety of psychosocial and emotional benefits for MS patients.

Multi-mode acquisition (MMA): An MS/MS acquisition strategy for maximizing selectivity, specificity and sensitivity of DIA product ion spectra.

PubMed

Williams, Brad J; Ciavarini, Steve J; Devlin, Curt; Cohn, Steven M; Xie, Rong; Vissers, Johannes P C; Martin, LeRoy B; Caswell, Allen; Langridge, James I; Geromanos, Scott J

2016-08-01

In proteomics studies, it is generally accepted that depth of coverage and dynamic range is limited in data-directed acquisitions. The serial nature of the method limits both sensitivity and the number of precursor ions that can be sampled. To that end, a number of data-independent acquisition (DIA) strategies have been introduced with these methods, for the most part, immune to the sampling issue; nevertheless, some do have other limitations with respect to sensitivity. The major limitation with DIA approaches is interference, i.e., MS/MS spectra are highly chimeric and often incapable of being identified using conventional database search engines. Utilizing each available dimension of separation prior to ion detection, we present a new multi-mode acquisition (MMA) strategy multiplexing both narrowband and wideband DIA acquisitions in a single analytical workflow. The iterative nature of the MMA workflow limits the adverse effects of interference with minimal loss in sensitivity. Qualitative identification can be performed by selected ion chromatograms or conventional database search strategies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Disturbance of visual search by stimulating to posterior parietal cortex in the brain using transcranial magnetic stimulation

NASA Astrophysics Data System (ADS)

Iramina, Keiji; Ge, Sheng; Hyodo, Akira; Hayami, Takehito; Ueno, Shoogo

2009-04-01

In this study, we applied a transcranial magnetic stimulation (TMS) to investigate the temporal aspect for the functional processing of visual attention. Although it has been known that right posterior parietal cortex (PPC) in the brain has a role in certain visual search tasks, there is little knowledge about the temporal aspect of this area. Three visual search tasks that have different difficulties of task execution individually were carried out. These three visual search tasks are the "easy feature task," the "hard feature task," and the "conjunction task." To investigate the temporal aspect of the PPC involved in the visual search, we applied various stimulus onset asynchronies (SOAs) and measured the reaction time of the visual search. The magnetic stimulation was applied on the right PPC or the left PPC by the figure-eight coil. The results show that the reaction times of the hard feature task are longer than those of the easy feature task. When SOA=150 ms, compared with no-TMS condition, there was a significant increase in target-present reaction time when TMS pulses were applied. We considered that the right PPC was involved in the visual search at about SOA=150 ms after visual stimulus presentation. The magnetic stimulation to the right PPC disturbed the processing of the visual search. However, the magnetic stimulation to the left PPC gives no effect on the processing of the visual search.

Automated toxicological screening reports of modified Agilent MSD Chemstation combined with Microsoft Visual Basic application programs.

PubMed

Choe, Sanggil; Kim, Suncheun; Choi, Hyeyoung; Choi, Hwakyoung; Chung, Heesun; Hwang, Bangyeon

2010-06-15

Agilent GC-MS MSD Chemstation offers automated library search report for toxicological screening using total ion chromatogram (TIC) and mass spectroscopy in normal mode. Numerous peaks appear in the chromatogram of biological specimen such as blood or urine and often large migrating peaks obscure small target peaks, in addition, any target peaks of low abundance regularly give wrong library search result or low matching score. As a result, retention time and mass spectrum of all the peaks in the chromatogram have to be checked to see if they are relevant. These repeated actions are very tedious and time-consuming to toxicologists. MSD Chemstation software operates using a number of macro files which give commands and instructions on how to work on and extract data from the chromatogram and spectroscopy. These macro files are developed by the own compiler of the software. All the original macro files can be modified and new macro files can be added to the original software by users. To get more accurate results with more convenient method and to save time for data analysis, we developed new macro files for reports generation and inserted new menus in the Enhanced Data Analysis program. Toxicological screening reports generated by these new macro files are in text mode or graphic mode and these reports can be generated with three different automated subtraction options. Text reports have Brief mode and Full mode and graphic reports have the option with or without mass spectrum mode. Matched mass spectrum and matching score for detected compounds are printed in reports by modified library searching modules. We have also developed an independent application program named DrugMan. This program manages drug groups, lists and parameters that are in use in MSD Chemstation. The incorporation of DrugMan with modified macro modules provides a powerful tool for toxicological screening and save a lot of valuable time on toxicological work. (c) 2010 Elsevier Ireland Ltd. All rights reserved.

PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.

PubMed

Saeed, Fahad; Pisitkun, Trairak; Hoffert, Jason D; Rashidian, Sara; Wang, Guanghui; Gucek, Marjan; Knepper, Mark A

2013-11-07

Phosphorylation site assignment of high throughput tandem mass spectrometry (LC-MS/MS) data is one of the most common and critical aspects of phosphoproteomics. Correctly assigning phosphorylated residues helps us understand their biological significance. The design of common search algorithms (such as Sequest, Mascot etc.) do not incorporate site assignment; therefore additional algorithms are essential to assign phosphorylation sites for mass spectrometry data. The main contribution of this study is the design and implementation of a linear time and space dynamic programming strategy for phosphorylation site assignment referred to as PhosSA. The proposed algorithm uses summation of peak intensities associated with theoretical spectra as an objective function. Quality control of the assigned sites is achieved using a post-processing redundancy criteria that indicates the signal-to-noise ratio properties of the fragmented spectra. The quality assessment of the algorithm was determined using experimentally generated data sets using synthetic peptides for which phosphorylation sites were known. We report that PhosSA was able to achieve a high degree of accuracy and sensitivity with all the experimentally generated mass spectrometry data sets. The implemented algorithm is shown to be extremely fast and scalable with increasing number of spectra (we report up to 0.5 million spectra/hour on a moderate workstation). The algorithm is designed to accept results from both Sequest and Mascot search engines. An executable is freely available at http://helixweb.nih.gov/ESBL/PhosSA/ for academic research purposes.

Post Milestone B Funding Climate and Cost Growth in Major Defense Acquisition Programs

DTIC Science & Technology

2017-03-01

by P-5126 supposes that most of the growth in unit cost shown by programs that pass MS B in a bust funding climate is “ baked into” the baselines...that most of the growth in unit cost shown by programs that pass MS B in a bust funding climate is “ baked into” the baselines established at MS B

A framework for intelligent data acquisition and real-time database searching for shotgun proteomics.

PubMed

Graumann, Johannes; Scheltema, Richard A; Zhang, Yong; Cox, Jürgen; Mann, Matthias

2012-03-01

In the analysis of complex peptide mixtures by MS-based proteomics, many more peptides elute at any given time than can be identified and quantified by the mass spectrometer. This makes it desirable to optimally allocate peptide sequencing and narrow mass range quantification events. In computer science, intelligent agents are frequently used to make autonomous decisions in complex environments. Here we develop and describe a framework for intelligent data acquisition and real-time database searching and showcase selected examples. The intelligent agent is implemented in the MaxQuant computational proteomics environment, termed MaxQuant Real-Time. It analyzes data as it is acquired on the mass spectrometer, constructs isotope patterns and SILAC pair information as well as controls MS and tandem MS events based on real-time and prior MS data or external knowledge. Re-implementing a top10 method in the intelligent agent yields similar performance to the data dependent methods running on the mass spectrometer itself. We demonstrate the capabilities of MaxQuant Real-Time by creating a real-time search engine capable of identifying peptides "on-the-fly" within 30 ms, well within the time constraints of a shotgun fragmentation "topN" method. The agent can focus sequencing events onto peptides of specific interest, such as those originating from a specific gene ontology (GO) term, or peptides that are likely modified versions of already identified peptides. Finally, we demonstrate enhanced quantification of SILAC pairs whose ratios were poorly defined in survey spectra. MaxQuant Real-Time is flexible and can be applied to a large number of scenarios that would benefit from intelligent, directed data acquisition. Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available.

A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics*

PubMed Central

Graumann, Johannes; Scheltema, Richard A.; Zhang, Yong; Cox, Jürgen; Mann, Matthias

2012-01-01

In the analysis of complex peptide mixtures by MS-based proteomics, many more peptides elute at any given time than can be identified and quantified by the mass spectrometer. This makes it desirable to optimally allocate peptide sequencing and narrow mass range quantification events. In computer science, intelligent agents are frequently used to make autonomous decisions in complex environments. Here we develop and describe a framework for intelligent data acquisition and real-time database searching and showcase selected examples. The intelligent agent is implemented in the MaxQuant computational proteomics environment, termed MaxQuant Real-Time. It analyzes data as it is acquired on the mass spectrometer, constructs isotope patterns and SILAC pair information as well as controls MS and tandem MS events based on real-time and prior MS data or external knowledge. Re-implementing a top10 method in the intelligent agent yields similar performance to the data dependent methods running on the mass spectrometer itself. We demonstrate the capabilities of MaxQuant Real-Time by creating a real-time search engine capable of identifying peptides “on-the-fly” within 30 ms, well within the time constraints of a shotgun fragmentation “topN” method. The agent can focus sequencing events onto peptides of specific interest, such as those originating from a specific gene ontology (GO) term, or peptides that are likely modified versions of already identified peptides. Finally, we demonstrate enhanced quantification of SILAC pairs whose ratios were poorly defined in survey spectra. MaxQuant Real-Time is flexible and can be applied to a large number of scenarios that would benefit from intelligent, directed data acquisition. Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available. PMID:22171319

20 CFR 617.49 - Job Search Program.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 20 Employees' Benefits 3 2014-04-01 2014-04-01 false Job Search Program. 617.49 Section 617.49... FOR WORKERS UNDER THE TRADE ACT OF 1974 Job Search Program § 617.49 Job Search Program. (a) Program... approved job search program (JSP), or have completed a JSP, as a condition for receiving TRA, except where...

20 CFR 617.49 - Job Search Program.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Job Search Program. 617.49 Section 617.49... FOR WORKERS UNDER THE TRADE ACT OF 1974 Job Search Program § 617.49 Job Search Program. (a) Program... approved job search program (JSP), or have completed a JSP, as a condition for receiving TRA, except where...

20 CFR 617.49 - Job Search Program.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 20 Employees' Benefits 3 2011-04-01 2011-04-01 false Job Search Program. 617.49 Section 617.49... FOR WORKERS UNDER THE TRADE ACT OF 1974 Job Search Program § 617.49 Job Search Program. (a) Program... approved job search program (JSP), or have completed a JSP, as a condition for receiving TRA, except where...

20 CFR 617.49 - Job Search Program.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 20 Employees' Benefits 3 2012-04-01 2012-04-01 false Job Search Program. 617.49 Section 617.49... FOR WORKERS UNDER THE TRADE ACT OF 1974 Job Search Program § 617.49 Job Search Program. (a) Program... approved job search program (JSP), or have completed a JSP, as a condition for receiving TRA, except where...

20 CFR 617.49 - Job Search Program.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 20 Employees' Benefits 3 2013-04-01 2013-04-01 false Job Search Program. 617.49 Section 617.49... FOR WORKERS UNDER THE TRADE ACT OF 1974 Job Search Program § 617.49 Job Search Program. (a) Program... approved job search program (JSP), or have completed a JSP, as a condition for receiving TRA, except where...

Broader Impact Actualized: Collaborative Efforts that Facilitate Successful Movement of Underrepresented Students Through the Pipeline

NASA Astrophysics Data System (ADS)

Pyrtle, A. J.; Whitney, V. W.

2007-12-01

The Minorities Striving and Pursuing Higher Degrees of Success in Earth System Science Initiative \\(MS PHD'S)\\ was established by and for underrepresented minorities to facilitate increased and sustained participation in Earth system science community. Based on successful experiences of students within the SOARS program, the MS PHD'S 2003 pilot project incorporated a team mentoring structure. Student interaction with multiple mentors resulted in exposure to multiple learning perspectives and increased one-on-one, mentee/mentor interaction. Since program inception, eleven \\(11)\\ minority Earth system scientists have served as Program mentors and eighty-two (82) minority and non-minority scientists have served as Meeting Mentors to MS PHD'S student participants A total of ninety-nine \\(99)\\ undergraduate and graduate students from underrepresented populations have participated in the MS PHD'S program. Twenty-five undergraduate and graduate students participated in the MS PHD'S pilot program in 2003 as Cohort I. During FY 04-05, Cohort II consisted of twenty-seven students and twenty-three students formed Cohort III. FY 06-07, twenty-four (24) students formed Cohort IV. Of the ninety-nine \\(99)\\ student participants, fifty-four \\(54)\\ MS PHD'S student participants self-identified as African American, twenty-seven \\(27)\\ as Puerto Rican, six \\(6)\\ as Hispanic/Mexican American, eight \\(8)\\ as Native American and one \\(1)\\ each as African, Asian, Pacific Islander and Multi-Ethnic. During the five \\(5)\\ year span of MS PHD'S programming, fourteen \\(14)\\ student participants completed BS degrees, ten (10) completed MS degrees and seven \\(7\\ completed the Doctoral degrees. How did MS PHD'S establish meaningful engagement of the science community to enhance diversity within the Earth system science community? This case study reveals replicable processes and constructs to enhance the quality of meaningful collaboration and engagement. In addition, the study addresses frequently asked questions \\ (FAQ's)\\ on outreach, recruitment, engagement, retention and success of students from underrepresented populations within diversity-focused programs.

Fermilab Today

Science.gov Websites

Search GO Special Result of the Week Toward a high-intensity muon source Impact of a single pulse of 12 x moment of impact (T=0); b) 9ms after impact; c) 15ms after impact. To solve the mysteries of nature 1012 protons at 14 GeV on a 1cm-wide jet of mercury flowing at 15m/s in a 10T solenoid field: a) at the

LC-IMS-MS Feature Finder

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

2013-03-07

LC-IMS-MS Feature Finder is a command line software application which searches for possible molecular ion signatures in multidimensional liquid chromatography, ion mobility spectrometry, and mass spectrometry data by clustering deisotoped peaks with similar monoisotopic mass values, charge states, elution times, and drift times. The software application includes an algorithm for detecting multiple conformations and co-eluting species in the ion mobility dimension. LC-IMS-MS Feature Finder is designed to create an output file with detected features that includes associated information about the detected features.

Online Depressive Symptom Self-Management: Comparing Program Outcomes for Adults With Multiple Sclerosis Versus Those With Other Chronic Diseases.

PubMed

Tietjen, Kiira; Wilson, Marian; Amiri, Solmaz; Dietz, Jeremy

2018-02-01

The goals of the study were to evaluate participant engagement and effects of an Internet-based, self-directed program for depressive symptoms. We compared outcomes of adults with multiple sclerosis (MS) with those of adults with other chronic diseases. This was a secondary analysis of a randomized controlled pilot study. Data were explored for differences between people diagnosed with MS and those with other chronic disease diagnoses. Data were obtained from 47 participants who participated in the original parent study (11 had MS). Participants with at least a moderate preexisting depressive symptom burden on the Patient Health Questionnaire (PHQ) were randomly divided into either a control group or the 8-week "Think Clearly About Depression" online depression self-management program. Study tools were administered at baseline, week 4, and week 8 to evaluate whether the online program improved depressive symptom self-management. Analysis examined differences between participants with and without an MS diagnosis in the treatment and control groups. Average baseline depressive symptom burdens were severe for those with MS and those without MS as measured by the PHQ. Number needed to treat analysis indicated that 1 in every 2 treatment group participants with MS found clinically significant reductions in depressive symptoms by week 8. All participants with MS completed all online program modules. When compared with those with other chronic diseases, participants with MS showed a trend toward greater improvements in the PHQ and health distress scores in addition to self-efficacy in exercising regularly, social/recreational activities, and controlling/managing depression at the end of 8 weeks. An online depressive symptom self-management program is acceptable to people with MS and may be helpful to address undertreated depressive symptoms. The number of participants limits available statistics and ability to generalize results.

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines.

PubMed

Yu, Wen; Taylor, J Alex; Davis, Michael T; Bonilla, Leo E; Lee, Kimberly A; Auger, Paul L; Farnsworth, Chris C; Welcher, Andrew A; Patterson, Scott D

2010-03-01

Despite recent advances in qualitative proteomics, the automatic identification of peptides with optimal sensitivity and accuracy remains a difficult goal. To address this deficiency, a novel algorithm, Multiple Search Engines, Normalization and Consensus is described. The method employs six search engines and a re-scoring engine to search MS/MS spectra against protein and decoy sequences. After the peptide hits from each engine are normalized to error rates estimated from the decoy hits, peptide assignments are then deduced using a minimum consensus model. These assignments are produced in a series of progressively relaxed false-discovery rates, thus enabling a comprehensive interpretation of the data set. Additionally, the estimated false-discovery rate was found to have good concordance with the observed false-positive rate calculated from known identities. Benchmarking against standard proteins data sets (ISBv1, sPRG2006) and their published analysis, demonstrated that the Multiple Search Engines, Normalization and Consensus algorithm consistently achieved significantly higher sensitivity in peptide identifications, which led to increased or more robust protein identifications in all data sets compared with prior methods. The sensitivity and the false-positive rate of peptide identification exhibit an inverse-proportional and linear relationship with the number of participating search engines.

Search for and detection of pulsars inmonitoring observations at 111 MHz

NASA Astrophysics Data System (ADS)

Tyul'bashev, S. A.; Tyul'bashev, V. S.; Kitaeva, M. A.; Chernyshova, A. I.; Malofeev, V. M.; Chashei, I. V.; Shishov, V. I.; Dagkesamanskii, R. D.; Klimenko, S. V.; Nikitin, I. N.; Nikitina, L. D.

2017-10-01

In the course of monitoring interplanetary scintillations of a large number of sources using the Big Scanning Antenna of the Lebedev Physical Institute, a search for pulsars with periods ≥0.4 s at declinations -9◦ < δ < 42◦ and right ascensions 0h < α < 24h was simultaneously carried out. The search was conducted using four years of observations carried out at 110.25MHz in six frequency channels making up a 2.5 MHz band and having a time resolution of 100 ms. The initial identification of pulsar candidates was done using Fourier power spectra averaged over the entire observational period; the pulsar candidates were then verified using observations with higher frequency and time resolution: 32 frequency channels and a time resolution of 12.5 ms. Eighteen new pulsars were discovered in the studied area, whose main characteristics are presented.

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

PubMed

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

2010-02-05

Major plasma protein families play different roles in blood physiology and hemostasis and in immunodefense. Other proteins in plasma can be involved in signaling as chemical messengers or constitute biological markers of the status of distant tissues. In this respect, the plasma phosphoproteome holds potentially relevant information on the mechanisms modulating these processes through the regulation of protein activity. In this work we describe for the first time a collection of phosphopeptides identified in human plasma using immunoaffinity separation of the seven major serum protein families from other plasma proteins, SCX fractionation, and TiO(2) purification prior to LC-MS/MS analysis. One-hundred and twenty-seven phosphosites in 138 phosphopeptides mapping 70 phosphoproteins were identified with FDR < 1%. A high-confidence collection of phosphosites was obtained using a combined search with the OMSSA, SEQUEST, and Phenyx search engines.

Time trends in the incidence and prevalence of multiple sclerosis in Norway during eight decades

PubMed Central

Grytten, N; Torkildsen, Ø; Myhr, K-M

2015-01-01

Norway has been subjected to numerous epidemiological investigations on the prevalence and incidence of multiple sclerosis (MS), dating back to 1935. The objective of this study was to review the studies on the prevalence and incidence of MS in Norway, provide an update on the prevalence of MS in Norway, and describe the time trends in the prevalence and incidence of MS in relation to risk factors, case ascertainment, and data. We performed a systematic search on PubMed and MEDLINE up to November 2014 using the search string ‘multiple sclerosis prevalence in Norway’ or ‘multiple sclerosis incidence in Norway’. In addition, we scrutinized the reference lists of the publications identified for relevant citations. We retrieved data on the distribution of MS in Norway on December 31, 2013 from the Norwegian Multiple Sclerosis Registry and Biobank and the Norwegian Patient Registry. We identified 29 articles. From 1961 to 2014, the reported prevalence of MS increased from 20 to 203 per 100,000 inhabitants, and the incidence increased from 1.9 to 8.0 per 100,000. The nationwide crude prevalence in Norway, based on the Norwegian Patient Registry, was 208 per 100,000 on December 31, 2013. The reported prevalence of MS in Norway has increased 10-fold, with several possible causes. During eight decades, neurological health services have generally become more accessible to the population, and transforming diagnostic criteria has made the diagnosis of MS more precise and valid. There have also been changes in lifestyle behavior and known risk factors, such as vitamin D and smoking, that might have contributed to the increased incidence of MS. A possible role of increased survival in MS needs to be examined further. This article is commented on by Berg-Hansen et al, published in 132: 364–367 (DOI: 10.1111/ane.12489). PMID:26046556

Botulinum Toxin Treatment in Multiple Sclerosis-a Review.

PubMed

Safarpour, Yasaman; Mousavi, Tahereh; Jabbari, Bahman

2017-08-17

Purpose of review The purpose of this review is to provide updated information on the role of botulinum neurotoxin (BoNT) therapy in multiple sclerosis (MS). This review aims to answer which symptoms of multiple sclerosis may be amenable to BoNT therapy. Recent findings We searched the literature on the efficacy of BoNTs for treatment of MS symptoms up to April 1st 2017 via the Yale University Library's search engine including but not limited to Pub Med and Ovis SP. The level of efficacy was defined according to the assessment's criteria set forth by the Subcommittee on Guideline Development of the American Academy of Neurology. Significant efficacy was found for two indications based on the available blinded studies (class I and II) and has been suggested for several others through open-label clinical trials. Summary There is level A evidence (effective- two or more class I) that injection of BoNT-A into the bladder's detrusor muscle improves MS-related neurogenic detrusor overactivity (NDO) and MS-related overactive (OA) bladder. There is level B evidence (probably effective- two class II studies) for utility of intramuscular BoNT-A injections for spasticity of multiple sclerosis. Emerging data based on retrospective class IV studies demonstrates that intramuscular injection of BoNTs may help other symptoms of MS such as focal tonic spasms, focal myokymia, spastic dysphagia, and double vision in internuclear ophthalmoplegia. There is no data on MS-related trigeminal neuralgia and sialorrhea, two conditions which have been shown to respond to BoNT therapy in non-MS population.

Extensive characterization of Tupaia belangeri neuropeptidome using an integrated mass spectrometric approach.

PubMed

Petruzziello, Filomena; Fouillen, Laetitia; Wadensten, Henrik; Kretz, Robert; Andren, Per E; Rainer, Gregor; Zhang, Xiaozhe

2012-02-03

Neuropeptidomics is used to characterize endogenous peptides in the brain of tree shrews (Tupaia belangeri). Tree shrews are small animals similar to rodents in size but close relatives of primates, and are excellent models for brain research. Currently, tree shrews have no complete proteome information available on which direct database search can be allowed for neuropeptide identification. To increase the capability in the identification of neuropeptides in tree shrews, we developed an integrated mass spectrometry (MS)-based approach that combines methods including data-dependent, directed, and targeted liquid chromatography (LC)-Fourier transform (FT)-tandem MS (MS/MS) analysis, database construction, de novo sequencing, precursor protein search, and homology analysis. Using this integrated approach, we identified 107 endogenous peptides that have sequences identical or similar to those from other mammalian species. High accuracy MS and tandem MS information, with BLAST analysis and chromatographic characteristics were used to confirm the sequences of all the identified peptides. Interestingly, further sequence homology analysis demonstrated that tree shrew peptides have a significantly higher degree of homology to equivalent sequences in humans than those in mice or rats, consistent with the close phylogenetic relationship between tree shrews and primates. Our results provide the first extensive characterization of the peptidome in tree shrews, which now permits characterization of their function in nervous and endocrine system. As the approach developed fully used the conservative properties of neuropeptides in evolution and the advantage of high accuracy MS, it can be portable for identification of neuropeptides in other species for which the fully sequenced genomes or proteomes are not available.

Carnitine for fatigue in multiple sclerosis.

PubMed

Tejani, Aaron M; Wasdell, Michael; Spiwak, Rae; Rowell, Greg; Nathwani, Shabita

2010-02-17

Fatigue is reported to occur in up to 92% of patients with multiple sclerosis (MS) and has been described as the most debilitating of all MS symptoms by 28% to 40% of MS patients. To assess whether carnitine (enteral or intravenous) supplementation can improve the quality of life and reduce the symptoms of fatigue in patients with MS-related fatigue and to identify any adverse effects of carnitine when used for this purpose. A literature search was performed using Cochrane MS Group Trials Register (21 May 2009), Cochrane Central Register of Controlled Trials (CENTRAL) "The Cochrane Library 2009, issue 2, MEDLINE (PubMed) (1966-21 May 2009), EMBASE (1974-21 May 2009). Reference lists of review articles and primary studies were also screened. A hand search of the abstract book of recent relevant conference symposia was also conducted. Personal contact with MS experts and a manufacturer (Source Naturals, United States) of carnitine formulation was contacted to determine if they knew of other clinical trials. No language restrictions were applied. Full reports of published and unpublished randomized controlled trials and quasi-randomized trials of any carnitine intervention in adults with a clinical diagnosis of fatigue associated with multiple sclerosis were included. Data from the eligible trials was extracted and coded using a standardized data extraction form and entered into RevMan 5. Discrepancies were to be resolved by discussion with a third reviewer however this was not necessary. The quality items to be assessed were method of randomization, allocation concealment, blinding (participants, investigators, outcome assessors and data analysis), intention-to-treat analysis and completeness of follow up. The search identified one randomized cross-over trial. In this study patients were exposed to both acetyl L-carnitine (ALCAR(tm)) 2 grams daily and amantadine 200 mg daily in adult patients with relapsing-remitting and secondary progressive MS. The effects of carnitine on fatigue are not clear based on the one included crossover RCT. There was no difference between carnitine and amantadine for the number of patients withdrawing from the study due to an adverse event (relative risk ratio 0.20; 95% confidence interval 0.03 to 1.55. Mortality, serious adverse events, total adverse events, and quality of life were not reported. There is insufficient evidence that carnitine for the treatment of MS-related fatigue offers a therapeutic advantage over placebo or active comparators.

Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments.

PubMed

Zani, Carlos L; Carroll, Anthony R

2017-06-23

The discovery of novel and/or new bioactive natural products from biota sources is often confounded by the reisolation of known natural products. Dereplication strategies that involve the analysis of NMR and MS spectroscopic data to infer structural features present in purified natural products in combination with database searches of these substructures provide an efficient method to rapidly identify known natural products. Unfortunately this strategy has been hampered by the lack of publically available and comprehensive natural product databases and open source cheminformatics tools. A new platform, DEREP-NP, has been developed to help solve this problem. DEREP-NP uses the open source cheminformatics program DataWarrior to generate a database containing counts of 65 structural fragments present in 229 358 natural product structures derived from plants, animals, and microorganisms, published before 2013 and freely available in the nonproprietary Universal Natural Products Database (UNPD). By counting the number of times one or more of these structural features occurs in an unknown compound, as deduced from the analysis of its NMR ( 1 H, HSQC, and/or HMBC) and/or MS data, matching structures carrying the same numeric combination of searched structural features can be retrieved from the database. Confirmation that the matching structure is the same compound can then be verified through literature comparison of spectroscopic data. This methodology can be applied to both purified natural products and fractions containing a small number of individual compounds that are often generated as screening libraries. The utility of DEREP-NP has been verified through the analysis of spectra derived from compounds (and fractions containing two or three compounds) isolated from plant, marine invertebrate, and fungal sources. DEREP-NP is freely available at https://github.com/clzani/DEREP-NP and will help to streamline the natural product discovery process.

Identification of volatile and semivolatile compounds in chemical ionization GC-MS using a mass-to-structure (MTS) Search Engine with integral isotope pattern ranking.

PubMed

Liao, Wenta; Draper, William M

2013-02-21

The mass-to-structure or MTS Search Engine is an Access 2010 database containing theoretical molecular mass information for 19,438 compounds assembled from common sources such as the Merck Index, pesticide and pharmaceutical compilations, and chemical catalogues. This database, which contains no experimental mass spectral data, was developed as an aid to identification of compounds in atmospheric pressure ionization (API)-LC-MS. This paper describes a powerful upgrade to this database, a fully integrated utility for filtering or ranking candidates based on isotope ratios and patterns. The new MTS Search Engine is applied here to the identification of volatile and semivolatile compounds including pesticides, nitrosoamines and other pollutants. Methane and isobutane chemical ionization (CI) GC-MS spectra were obtained from unit mass resolution mass spectrometers to determine MH(+) masses and isotope ratios. Isotopes were measured accurately with errors of <4% and <6%, respectively, for A + 1 and A + 2 peaks. Deconvolution of interfering isotope clusters (e.g., M(+) and [M - H](+)) was required for accurate determination of the A + 1 isotope in halogenated compounds. Integrating the isotope data greatly improved the speed and accuracy of the database identifications. The database accurately identified unknowns from isobutane CI spectra in 100% of cases where as many as 40 candidates satisfied the mass tolerance. The paper describes the development and basic operation of the new MTS Search Engine and details performance testing with over 50 model compounds.

Cooperative Program Providing Public and Private Sectors with Information for Use on Examination of Environmental Issues

DTIC Science & Technology

1997-12-22

Ms. Melinda Borel Mr. Scott Bosworth Ms. Bonnie Burgan Ms. April Burkett Ms. Cheryl Button Ms. Terri Cabbell Mr. Huadong Cao Mr. Jiamin Cao Ms...Ms. Dana Harrison Dr. Ennis Hawkins Mr. Eddie Haynes Mr. Yuhua He Dr. Jamie L. Hebert Mr. David R. Hoffpauir Ms. Shen Huang Mr. Phillip T

Improvement in visual search with practice: mapping learning-related changes in neurocognitive stages of processing.

PubMed

Clark, Kait; Appelbaum, L Gregory; van den Berg, Berry; Mitroff, Stephen R; Woldorff, Marty G

2015-04-01

Practice can improve performance on visual search tasks; the neural mechanisms underlying such improvements, however, are not clear. Response time typically shortens with practice, but which components of the stimulus-response processing chain facilitate this behavioral change? Improved search performance could result from enhancements in various cognitive processing stages, including (1) sensory processing, (2) attentional allocation, (3) target discrimination, (4) motor-response preparation, and/or (5) response execution. We measured event-related potentials (ERPs) as human participants completed a five-day visual-search protocol in which they reported the orientation of a color popout target within an array of ellipses. We assessed changes in behavioral performance and in ERP components associated with various stages of processing. After practice, response time decreased in all participants (while accuracy remained consistent), and electrophysiological measures revealed modulation of several ERP components. First, amplitudes of the early sensory-evoked N1 component at 150 ms increased bilaterally, indicating enhanced visual sensory processing of the array. Second, the negative-polarity posterior-contralateral component (N2pc, 170-250 ms) was earlier and larger, demonstrating enhanced attentional orienting. Third, the amplitude of the sustained posterior contralateral negativity component (SPCN, 300-400 ms) decreased, indicating facilitated target discrimination. Finally, faster motor-response preparation and execution were observed after practice, as indicated by latency changes in both the stimulus-locked and response-locked lateralized readiness potentials (LRPs). These electrophysiological results delineate the functional plasticity in key mechanisms underlying visual search with high temporal resolution and illustrate how practice influences various cognitive and neural processing stages leading to enhanced behavioral performance. Copyright © 2015 the authors 0270-6474/15/355351-09$15.00/0.

Breaking down the gut microbiome composition in multiple sclerosis.

PubMed

Budhram, Adrian; Parvathy, Seema; Kremenchutzky, Marcelo; Silverman, Michael

2017-04-01

The gut microbiome, which consists of a highly diverse ecologic community of micro-organisms, has increasingly been studied regarding its role in multiple sclerosis (MS) immunopathogenesis. This review critically examines the literature investigating the gut microbiome in MS. A comprehensive search was performed of PubMed databases and ECTRIMS meeting abstracts for literature relating to the gut microbiome in MS. Controlled studies examining the gut microbiome in patients with MS were included for review. Identified studies were predominantly case-control in their design and consistently found differences in the gut microbiome of MS patients compared to controls. We examine plausible mechanistic links between these differences and MS immunopathogenesis, and discuss the therapeutic implications of these findings. Review of the available literature reveals potential immunopathogenic links between the gut microbiome and MS, identifies avenues for therapeutic advancement, and emphasizes the need for further systematic study in this emerging field.

Broad screening and identification of β-agonists in feed and animal body fluid and tissues using ultra-high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry combined with spectra library search.

PubMed

Li, Tingting; Cao, Jingjing; Li, Zhen; Wang, Xian; He, Pingli

2016-02-01

Broad screening and identification of β-agonists in feed, serum, urine, muscle and liver samples was achieved in a quick and highly sensitive manner using ultra high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) combined with a spectra library search. Solid-phase extraction technology was employed for sample purification and enrichment. After extraction and purification, the samples were analyzed using a Q-Orbitrap high-resolution mass spectrometer under full-scan and data-dependent MS/MS mode. The acquired mass spectra were compared with an in-house library (compound library and MS/MS mass spectral library) built with TraceFinder Software which contained the M/Z of the precursor ion, chemical formula, retention time, character fragment ions and the entire MS/MS spectra of 32 β-agonist standards. Screening was achieved by comparing 5 key mass spectral results and positive matches were marked. Using the developed method, the identification results from 10 spiked samples and 238 actual samples indicated that only 2% of acquired mass spectra produced false identities. The method validation results showed that the limit of detection ranged from 0.021-3.854 μg kg(-1)and 0.015-1.198 ng mL(-1) for solid and liquid samples, respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

Application of LC/MS/MS Techniques to Development of US ...

EPA Pesticide Factsheets

This presentation will describe the U.S. EPA’s drinking water and ambient water method development program in relation to the process employed and the typical challenges encountered in developing standardized LC/MS/MS methods for chemicals of emerging concern. The EPA’s Drinking Water Contaminant Candidate List and Unregulated Contaminant Monitoring Regulations, which are the driving forces behind drinking water method development, will be introduced. Three drinking water LC/MS/MS methods (Methods 537, 544 and a new method for nonylphenol) and two ambient water LC/MS/MS methods for cyanotoxins will be described that highlight some of the challenges encountered during development of these methods. This presentation will provide the audience with basic understanding of EPA's drinking water method development program and an introduction to two new ambient water EPA methods.

SR-XFA as a method of choice in the search of signals of changing palaeoclimates in the sediments of Lake Baikal, compared to INAA and ICP-MS

NASA Astrophysics Data System (ADS)

Phedorin, M. A.; Bobrov, V. A.; Goldberg, E. L.; Navez, J.; Zolotaryov, K. V.; Grachev, M. A.

2000-06-01

Sediments of Lake Baikal obtained on top of the underwater Akademichesky Ridge for reconstruction of the palaeoclimates of Holocene and Upper Pleistocene were subjected to elemental analysis with three methods: (i) synchrotron radiation X-ray fluorescent analysis (SR-XFA); (ii) instrumental neutron activation analysis (INAA); (iii) induction-coupled plasma mass-spectrometry (ICP-MS). Comparison of the results obtained is accompanied by statistical tests and shows that, due to its high sensitivity, simplicity, and non-destructive nature, SR-XFA can be recommended as a method of choice in the search of geochemical signals of changing palaeoclimates.

Histoplasma capsulatum proteome response to decreased iron availability

PubMed Central

Winters, Michael S; Spellman, Daniel S; Chan, Qilin; Gomez, Francisco J; Hernandez, Margarita; Catron, Brittany; Smulian, Alan G; Neubert, Thomas A; Deepe, George S

2008-01-01

Background A fundamental pathogenic feature of the fungus Histoplasma capsulatum is its ability to evade innate and adaptive immune defenses. Once ingested by macrophages the organism is faced with several hostile environmental conditions including iron limitation. H. capsulatum can establish a persistent state within the macrophage. A gap in knowledge exists because the identities and number of proteins regulated by the organism under host conditions has yet to be defined. Lack of such knowledge is an important problem because until these proteins are identified it is unlikely that they can be targeted as new and innovative treatment for histoplasmosis. Results To investigate the proteomic response by H. capsulatum to decreasing iron availability we have created H. capsulatum protein/genomic databases compatible with current mass spectrometric (MS) search engines. Databases were assembled from the H. capsulatum G217B strain genome using gene prediction programs and expressed sequence tag (EST) libraries. Searching these databases with MS data generated from two dimensional (2D) in-gel digestions of proteins resulted in over 50% more proteins identified compared to searching the publicly available fungal databases alone. Using 2D gel electrophoresis combined with statistical analysis we discovered 42 H. capsulatum proteins whose abundance was significantly modulated when iron concentrations were lowered. Altered proteins were identified by mass spectrometry and database searching to be involved in glycolysis, the tricarboxylic acid cycle, lysine metabolism, protein synthesis, and one protein sequence whose function was unknown. Conclusion We have created a bioinformatics platform for H. capsulatum and demonstrated the utility of a proteomic approach by identifying a shift in metabolism the organism utilizes to cope with the hostile conditions provided by the host. We have shown that enzyme transcripts regulated by other fungal pathogens in response to lowering iron availability are also regulated in H. capsulatum at the protein level. We also identified H. capsulatum proteins sensitive to iron level reductions which have yet to be connected to iron availability in other pathogens. These data also indicate the complexity of the response by H. capsulatum to nutritional deprivation. Finally, we demonstrate the importance of a strain specific gene/protein database for H. capsulatum proteomic analysis. PMID:19108728

Inborn Error of Metabolism (IEM) screening in Singapore by electrospray ionization-tandem mass spectrometry (ESI/MS/MS): An 8 year journey from pilot to current program.

PubMed

Lim, J S; Tan, E S; John, C M; Poh, S; Yeo, S J; Ang, J S M; Adakalaisamy, P; Rozalli, R A; Hart, C; Tan, E T H; Ranieri, E; Rajadurai, V S; Cleary, M A; Goh, D L M

2014-01-01

IEM screening by ESI/MS/MS was introduced in Singapore in 2006. There were two phases; a pilot study followed by implementation of the current program. The pilot study was over a 4 year period. During the pilot study, a total of 61,313 newborns were screened, and 20 cases of IEM were diagnosed (detection rate of 1:3065; positive predictive value (PPV) of 11%). Regular self-review, participation in external quality assessment and the Region 4 Genetic collaborative programs (http://www.region4genetics.org/) had led to the robust development of our current NBS MS/MS program. Overall, from July 2006 to April 2014, we screened a total of 177,267 newborns. The mean age at the time of sampling was 47.9h. Transportation of samples to the testing laboratory averaged 0.92 day. Upon receipt of sample, the NBS result was available within 1.64 days and within 3.8 days if a second tier test was required. Using absolute cut-off values in place of the initial 99th percentile reference range for the analyte markers and the introduction of two 2nd tier tests (MMA and Succinylacetone) had significantly reduced the high recall rate from an initial 1.5% during the period 2006-07 to 0.12% in 2013. The NBS MS/MS program was supported by a centralized confirmatory/diagnostic testing laboratory and a rapid response team of metabolic specialists. The detection rate was 1: 3165 (1:2727 if maternal conditions were also included). There were 23 newborns affected with organic acidemias (incidence: 1:6565), 23 with fatty acid oxidation disorders (incidence: 1:6565), and 10 with amino acidopathies (incidence 1:17,726). The performance metrics for the screening test were acceptable (sensitivity: 95.59%, specificity: 99.85%, PPV: 20%, FPR: 0.15). Participation in the NBS MS/MS program by hospitals was voluntary, and in 2013, the uptake rate was 71% of the annual births. We hope that newborn screening by MS/MS will become a standard of care for all babies in Singapore. Copyright © 2014 Elsevier Inc. All rights reserved.

Energy-Efficient High-Performance Routers

DTIC Science & Technology

2012-02-01

award, the PI Dr. Sartaj Sahni, AFRL research scientist Dr. Gunasekaran Seetharaman, and University of Florida Ph.D. student Ms. Tania Banerjee...Sartaj Sahni, AFRL research scientist Dr. Gunasekaran Seetharaman, and University of Florida Ph.D. student Ms. Tania Banerjee-Mishra...Searching and Shift Redundancy Architecture, IJSSC, 40, 1, Jan 2005, 245-253. PC-DUOS+: A TCAM Architecture for Packet Classifiers Tania Banerjee

Application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in Alzheimer's disease.

PubMed

Grela, Agatha; Turek, Agata; Piekoszewski, Wojciech

2012-02-11

Alzheimer's disease is becoming an increasing problem in our aging society. According to our knowledge, so far, no effective pharmacotherapy to cure the cause of the disease has been developed. Therefore, early diagnosis is needed, which will result in implementation of a drug therapy aimed at decreasing and/or inhibiting disease development. Mass spectrometry techniques (MS) have a wide range of applications in proteomics and the search for biomarkers of neurodegenerative disorders, opening new possibilities in diagnostics. Identification of proteins in body fluids (like cerebrospinal fluid or blood) is possible due to MS spectra analysis. The detected changes in protein concentrations are connected with pathological states in an organism and, therefore, can be regarded as biomarkers. Developing procedures for proteome analysis might result in fast diagnosis, as well as creating better suited pharmaceuticals. This paper reviews the search of biomarkers in cerebrospinal fluid and blood. Later on, the use of matrix-assisted-laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in proteomics, focusing on blood-related biomarkers, is discussed. The aim of the work is also to highlight the advantages and disadvantages of MALDI-TOF-based analyses.

A proteomics study of barley powdery mildew haustoria.

PubMed

Godfrey, Dale; Zhang, Ziguo; Saalbach, Gerhard; Thordal-Christensen, Hans

2009-06-01

A number of fungal and oomycete plant pathogens of major economic importance feed on their hosts by means of haustoria, which they place inside living plant cells. The underlying mechanisms are poorly understood, partly due to difficulty in preparing haustoria. We have therefore developed a procedure for isolating haustoria from the barley powdery mildew fungus (Blumeria graminis f.sp. hordei, Bgh). We subsequently aimed to understand the molecular mechanisms of haustoria through a study of their proteome. Extracted proteins were digested using trypsin, separated by LC, and analysed by MS/MS. Searches of a custom Bgh EST sequence database and the NCBI-NR fungal protein database, using the MS/MS data, identified 204 haustoria proteins. The majority of the proteins appear to have roles in protein metabolic pathways and biological energy production. Surprisingly, pyruvate decarboxylase (PDC), involved in alcoholic fermentation and commonly abundant in fungi and plants, was absent in our Bgh proteome data set. A sequence encoding this enzyme was also absent in our EST sequence database. Significantly, BLAST searches of the recently available Bgh genome sequence data also failed to identify a sequence encoding this enzyme, strongly indicating that Bgh does not have a gene for PDC.

A Program of Research and Education to Advance the Design, Synthesis, and Optimization of Aero-Space System Concepts

NASA Technical Reports Server (NTRS)

Sandusky, Robert

2002-01-01

Since its inception in December 1999, the program has provided support for a total of 11 Graduate Research Scholar Assistants, of these, 6 have completed their MS degree program. The program has generated 3 MS theses and a total of 4 publications/presentations.

Early multisensory interactions affect the competition among multiple visual objects.

PubMed

Van der Burg, Erik; Talsma, Durk; Olivers, Christian N L; Hickey, Clayton; Theeuwes, Jan

2011-04-01

In dynamic cluttered environments, audition and vision may benefit from each other in determining what deserves further attention and what does not. We investigated the underlying neural mechanisms responsible for attentional guidance by audiovisual stimuli in such an environment. Event-related potentials (ERPs) were measured during visual search through dynamic displays consisting of line elements that randomly changed orientation. Search accuracy improved when a target orientation change was synchronized with an auditory signal as compared to when the auditory signal was absent or synchronized with a distractor orientation change. The ERP data show that behavioral benefits were related to an early multisensory interaction over left parieto-occipital cortex (50-60 ms post-stimulus onset), which was followed by an early positive modulation (80-100 ms) over occipital and temporal areas contralateral to the audiovisual event, an enhanced N2pc (210-250 ms), and a contralateral negative slow wave (CNSW). The early multisensory interaction was correlated with behavioral search benefits, indicating that participants with a strong multisensory interaction benefited the most from the synchronized auditory signal. We suggest that an auditory signal enhances the neural response to a synchronized visual event, which increases the chances of selection in a multiple object environment. Copyright © 2010 Elsevier Inc. All rights reserved.

Tandem mass spectrometry data quality assessment by self-convolution.

PubMed

Choo, Keng Wah; Tham, Wai Mun

2007-09-20

Many algorithms have been developed for deciphering the tandem mass spectrometry (MS) data sets. They can be essentially clustered into two classes. The first performs searches on theoretical mass spectrum database, while the second based itself on de novo sequencing from raw mass spectrometry data. It was noted that the quality of mass spectra affects significantly the protein identification processes in both instances. This prompted the authors to explore ways to measure the quality of MS data sets before subjecting them to the protein identification algorithms, thus allowing for more meaningful searches and increased confidence level of proteins identified. The proposed method measures the qualities of MS data sets based on the symmetric property of b- and y-ion peaks present in a MS spectrum. Self-convolution on MS data and its time-reversal copy was employed. Due to the symmetric nature of b-ions and y-ions peaks, the self-convolution result of a good spectrum would produce a highest mid point intensity peak. To reduce processing time, self-convolution was achieved using Fast Fourier Transform and its inverse transform, followed by the removal of the "DC" (Direct Current) component and the normalisation of the data set. The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result. The method was validated using both theoretical mass spectra, with various permutations, and several real MS data sets. The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores. We have demonstrated in this work a method for determining the quality of tandem MS data set. By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results. We conclude that the algorithm performs well and could potentially be used as a pre-processing for all mass spectrometry based protein identification tools.

An integrated software suite for surface-based analyses of cerebral cortex.

PubMed

Van Essen, D C; Drury, H A; Dickson, J; Harwell, J; Hanlon, D; Anderson, C H

2001-01-01

The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.

An integrated software suite for surface-based analyses of cerebral cortex

NASA Technical Reports Server (NTRS)

Van Essen, D. C.; Drury, H. A.; Dickson, J.; Harwell, J.; Hanlon, D.; Anderson, C. H.

2001-01-01

The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.

Science Education at Fermilab Program Search

Science.gov Websites

JavaScript is Turned Off or Not Supported in Your Browser. To search for programs go to the Non -Javascript Search or turn on Javascript and reload this page. Programs | Science Adventures | Calendar | Undergraduates Fermilab Ed Site Search Google Custom Search Programs: Introducing You to the World of Science

LC-IMS-MS Feature Finder. Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets

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

Crowell, Kevin L.; Slysz, Gordon W.; Baker, Erin Shammel

2013-09-05

We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time, and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension.

On-target digestion of collected bacteria for MALDI mass spectrometry.

PubMed

Dugas, Alton J; Murray, Kermit K

2008-10-03

An on-target protein digestion system was developed for the identification of microorganisms in collected bioaerosols using off-line matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Bacteria analysis techniques based on MALDI-MS were adapted for use with an orthogonal MALDI quadrupole-time-of-flight mass spectrometer. Bioaerosols were generated using a pneumatic nebulizer and infused into a chamber for sampling. An Andersen N6 single-stage impactor was used to collect the bioaerosols on a MALDI target. On-target digestion was carried out inside temporary mini-wells placed over the impacted samples. The wells served as miniature reactors for proteolysis. Collected test aerosol particles containing the protein cytochrome c and E. coli bacteria were proteolyzed in situ using trypsin or cyanogen bromide. A total of 19 unique proteins were identified for E. coli. Using the TOF-MS spectra of the digested samples, peptide mass mapping was performed using the MASCOT search engine and an iterative search technique.

Comprehensive gas chromatography coupled to mass spectrometry for the separation of pesticides in a very complex matrix.

PubMed

Mondello, Luigi; Casilli, Alessandro; Tranchida, Peter Quinto; Lo Presti, Maria; Dugo, Paola; Dugo, Giovanni

2007-11-01

The present research is focused on the development of a comprehensive two-dimensional gas chromatography-rapid scanning quadrupole mass spectrometric (GC x GC-qMS) methodology for the analysis of trace-amount pesticides contained in a complex real-world sample. Reliable peak assignment was carried out by using a recently developed, dedicated pesticide MS library (for comprehensive GC analysis), characterized by a twin-filter search procedure, the first based on a minimum degree of spectral similarity and the second on the interactive use of linear retention indices (LRI). The library was constructed by subjecting mixtures of commonly used pesticides to GC x GC-qMS analysis and then deriving their pure mass spectra and LRI values. In order to verify the effectiveness of the approach, a pesticide-contaminated red grapefruit extract was analysed. The certainty of peak assignment was attained by exploiting both the enhanced separation power of dual-oven GC x GC and the highly effective search procedure.

A search for optical bursts from the repeating fast radio burst FRB 121102

NASA Astrophysics Data System (ADS)

Hardy, L. K.; Dhillon, V. S.; Spitler, L. G.; Littlefair, S. P.; Ashley, R. P.; De Cia, A.; Green, M. J.; Jaroenjittichai, P.; Keane, E. F.; Kerry, P.; Kramer, M.; Malesani, D.; Marsh, T. R.; Parsons, S. G.; Possenti, A.; Rattanasoon, S.; Sahman, D. I.

2017-12-01

We present a search for optical bursts from the repeating fast radio burst FRB 121102 using simultaneous observations with the high-speed optical camera ULTRASPEC on the 2.4-m Thai National Telescope and radio observations with the 100-m Effelsberg Radio Telescope. A total of 13 radio bursts were detected, but we found no evidence for corresponding optical bursts in our 70.7-ms frames. The 5σ upper limit to the optical flux density during our observations is 0.33 mJy at 767 nm. This gives an upper limit for the optical burst fluence of 0.046 Jy ms, which constrains the broad-band spectral index of the burst emission to α ≤ -0.2. Two of the radio pulses are separated by just 34 ms, which may represent an upper limit on a possible underlying periodicity (a rotation period typical of pulsars), or these pulses may have come from a single emission window that is a small fraction of a possible period.

DARPA Antibody Technology Program Standardized Test Bed for Antibody Characterization: Characterization of an MS2 sdAb Produced by U.S. Naval Research Laboratory

DTIC Science & Technology

2016-10-01

Program (ATP) Quality MS2 coat protein (MS2CP) Enzyme-linked immunosorbent assay ( ELISA ) 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...3 2.6 Thermal Stress Test............................................................................................4 2.7 ELISA ...7 3.4 DSC Results .....................................................................................................10 3.5 ELISA

DARPA Antibody Technology Program Standardized Test Bed for Antibody Characterization: Characterization of an MS2 ScFv Antibody

DTIC Science & Technology

2016-03-01

performance in an enzyme-linked immunosorbent assay ( ELISA ), with little regard for quantification of the full spectrum of variables affecting antibody...Program (ATP) Quality MS2 coat protein (MS2CP) Enzyme-linked immunosorbent assay ( ELISA ) 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT...5 2.7 ELISA ................................................................................................................5

Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra*

PubMed Central

Richards, Alicia L.; Vincent, Catherine E.; Guthals, Adrian; Rose, Christopher M.; Westphall, Michael S.; Bandeira, Nuno; Coon, Joshua J.

2013-01-01

We report the use of neutron-encoded (NeuCode) stable isotope labeling of amino acids in cell culture for the purpose of C-terminal product ion annotation. Two NeuCode labeling isotopologues of lysine, 13C615N2 and 2H8, which differ by 36 mDa, were metabolically embedded in a sample proteome, and the resultant labeled proteins were combined, digested, and analyzed via liquid chromatography and mass spectrometry. With MS/MS scan resolving powers of ∼50,000 or higher, product ions containing the C terminus (i.e. lysine) appear as a doublet spaced by exactly 36 mDa, whereas N-terminal fragments exist as a single m/z peak. Through theory and experiment, we demonstrate that over 90% of all y-type product ions have detectable doublets. We report on an algorithm that can extract these neutron signatures with high sensitivity and specificity. In other words, of 15,503 y-type product ion peaks, the y-type ion identification algorithm correctly identified 14,552 (93.2%) based on detection of the NeuCode doublet; 6.8% were misclassified (i.e. other ion types that were assigned as y-type products). Searching NeuCode labeled yeast with PepNovo+ resulted in a 34% increase in correct de novo identifications relative to searching through MS/MS only. We use this tool to simplify spectra prior to database searching, to sort unmatched tandem mass spectra for spectral richness, for correlation of co-fragmented ions to their parent precursor, and for de novo sequence identification. PMID:24043425

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

PubMed

Shilov, Ignat V; Seymour, Sean L; Patel, Alpesh A; Loboda, Alex; Tang, Wilfred H; Keating, Sean P; Hunter, Christie L; Nuwaysir, Lydia M; Schaeffer, Daniel A

2007-09-01

The Paragon Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user-controlled settings to consider or not consider a feature. The use of feature probabilities in conjunction with Sequence Temperature Values allows for a very large increase in the effective search space with only a very small increase in the actual number of hypotheses that must be scored. The algorithm has a new kind of user interface that removes the user expertise requirement, presenting control settings in the language of the laboratory that are translated to optimal algorithmic settings. To validate this new algorithm, a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space probed with Mascot by relaxing the tryptic digestion conformance requirements from trypsin to semitrypsin to no enzyme and with the Paragon Algorithm using its Rapid mode and Thorough mode with and without tryptic specificity. Although they performed similarly for small search space, dramatic differences were observed in large search space. With the Paragon Algorithm, hundreds of biological and artifact modifications, all possible substitutions, and all levels of conformance to the expected digestion pattern can be searched in a single search step, yet the typical cost in search time is only 2-5 times that of conventional small search space. Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space.

Effects of a Training Program Involving Body Cooling on Physical and Cognitive Capacities and Quality of Life in Multiple Sclerosis Patients: A Pilot Study.

PubMed

Gonzales, Benoit; Chopard, Gilles; Charry, Benjamin; Berger, Eric; Tripard, Julien; Magnin, Eloi; Groslambert, Alain

2017-01-01

Two methods using exercise and body cooling could influence the well-being of patients with multiple sclerosis (PwMS). The aim of this study was to determine whether wearing a cooling vest during a physical training program could increase the cognitive and physical capacities and quality of life in PwMS. Eighteen PwMS (49.6 ± 8 years; Expanded Disability Status Score 5.0 ± 1.0) were randomly assigned to a cooling or control group. PwMS underwent a 7-week physical training program. In the cooling group, PwMS wore a cooling vest during each training session, whereas in the control group, PwMS wore a cotton T-shirt. Before and after the training program, both groups completed the Isaacs Set Test (IST), Trail Making Test A-B (TMT A-B), SEP-59, Multidimensional Fatigue Inventory and performed a 6-minute walk test (6MWT). The cooling group showed significantly (p < 0.05) improved performance for IST, TMT A and 6MWT. Their emotional well-being and cognitive functions investigated in SEP-59 were significantly (p < 0.05) improved, and general and physical fatigue significantly (p < 0.05) decreased. This physical training program combined with a cooling strategy could have a significant positive influence on both cognitive and physical performances, perceived fatigue and emotional well-being in heat-sensitive PwMS. © 2017 S. Karger AG, Basel.

New & Special Grad School Programs.

ERIC Educational Resources Information Center

Ross, Steven S.

1988-01-01

Discusses some special Master of Science in engineering (MS) programs including manufacturing and quality control, safety engineering, transportation engineering, and computer related areas. Gives a table showing MS degrees, institutions, and faculty. (YP)

National Cholesterol Educational Program and International Diabetes Federation diagnostic criteria for metabolic syndrome in an Italian cohort: results from the FIBAR Study.

PubMed

Mannucci, E; Monami, M; Bardini, G; Ognibene, A; Rotella, C M

2007-12-01

The adoption of the International Diabetes Federation (IDF) criteria for metabolic syndrome (MS), in comparison with the National Cholesterol Educational Program (NCEP) criteria, produces different changes in estimates of prevalence in diverse populations. Few data are available in Caucasian non-diabetic subjects. The prevalence of NCEP- and IDF-defined MS was assessed in a sample of 2,945 individuals, aged 55.2+/-11.5 yr, enrolled in a screening program for diabetes. Association of different definitions of MS with glucose intolerance (120-min glucose 7.8 mmol/l after a 75 g-oral glucose load) and hyperuricemia (>0.38 mmol/l) was also assessed. The prevalence of MS was 16.6% and 29.7% with NCEP and IDF definitions, respectively. The prevalence of NCEP-defined MS was higher than IDF-MS through all age ranges; among those aged >60 yr, the prevalence of IDF-MS reached 52.8% (vs 33.1% for NCEP-MS). Both NCEP- and IDF-MS were associated with glucose intolerance and hyperuricemia. Individuals fulfilling IDF, but not NCEP criteria for MS, showed a prevalence of glucose intolerance (22.7%) significantly (p<0.05) lower than those fulfilling NCEP criteria only (31.6%) or both sets of criteria (31.8%). In Caucasian subjects without known diabetes, IDF criteria produce a relevant increase in estimates of prevalence of MS, particularly in older subjects, when compared with NCEP criteria. NCEP-MS seems to be more effective than IDF-MS in the identification of glucose intolerant subjects.

Program of Research and Education in Aerospace Structures

NASA Technical Reports Server (NTRS)

Whitesides, John L.; Johansen, Laurie W.

2005-01-01

Since its inception in January 2003, the program has provided support for 1 research professor and a total of 10 Graduate Research Scholar Assistants of these all 10 have completed their MS degree program. The program has generated 10 MS thesis. Final report lists papers presented in seminars for the period January 1, 2003 through June 30, 2005.

Internet Medline providers.

PubMed

Vine, D L; Coady, T R

1998-01-01

Each database in this review has features that will appeal to some users. Each provides a credible interface to information available within the Medline database. The major differences are pricing and interface design. In this context, features that cost more and might seem trivial to the occasional searcher may actually save time and money when used by the professional. Internet Grateful Med is free, but Ms. Coady and I agree the availability of only three ANDable search fields is a major functional limitation. PubMed is also free but much more powerful. The command line interface that permits very sophisticated searches requires a commitment that casual users will find intimidating. Ms. Coady did not believe the feedback currently provided during a search was sufficient for sustained professional use. Paper Chase and Knowledge Finder are mature, modestly priced Medline search services. Paper Chase provides a menu-driven interface that is very easy to use, yet permits the user to search virtually all of Medline's data fields. Knowledge Finder emphasizes the use of natural language queries but fully supports more traditional search strategies. The impact of the tradeoff between fuzzy and Boolean strategies offered by Knowledge Finder is unclear and beyond the scope of this review. Additional software must be downloaded to use all of Knowledge Finders' features. Other providers required no software beyond the basic Internet browser, and this requirement prevented Ms. Coady from evaluating Knowledge Finder. Ovid and Silver Platter offer well-designed interfaces that simplify the construction of complex queries. These are clearly services designed for professional users. While pricing eliminates these for casual use, it should be emphasized that Medline citation access is only a portion of the service provided by these high-end vendors. Finally, we should comment that each of the vendors and government-sponsored services provided prompt and useful feedback to e-mail questions about usage. In conclusion, we would suggest you try the various services, determine which interface suits your style and budget, then perform simple searches until you learn the strengths and weaknesses of the service you select.

The Green Bank Northern Celestial Cap Pulsar Survey. II. The Discovery and Timing of 10 Pulsars

NASA Astrophysics Data System (ADS)

Kawash, A. M.; McLaughlin, M. A.; Kaplan, D. L.; DeCesar, M. E.; Levin, L.; Lorimer, D. R.; Lynch, R. S.; Stovall, K.; Swiggum, J. K.; Fonseca, E.; Archibald, A. M.; Banaszak, S.; Biwer, C. M.; Boyles, J.; Cui, B.; Dartez, L. P.; Day, D.; Ernst, S.; Ford, A. J.; Flanigan, J.; Heatherly, S. A.; Hessels, J. W. T.; Hinojosa, J.; Jenet, F. A.; Karako-Argaman, C.; Kaspi, V. M.; Kondratiev, V. I.; Leake, S.; Lunsford, G.; Martinez, J. G.; Mata, A.; Matheny, T. D.; Mcewen, A. E.; Mingyar, M. G.; Orsini, A. L.; Ransom, S. M.; Roberts, M. S. E.; Rohr, M. D.; Siemens, X.; Spiewak, R.; Stairs, I. H.; van Leeuwen, J.; Walker, A. N.; Wells, B. L.

2018-04-01

We present timing solutions for 10 pulsars discovered in 350 MHz searches with the Green Bank Telescope. Nine of these were discovered in the Green Bank Northern Celestial Cap survey and one was discovered by students in the Pulsar Search Collaboratory program during an analysis of drift-scan data. Following the discovery and confirmation with the Green Bank Telescope, timing has yielded phase-connected solutions with high-precision measurements of rotational and astrometric parameters. Eight of the pulsars are slow and isolated, including PSR J0930‑2301, a pulsar with a nulling fraction lower limit of ∼30% and a nulling timescale of seconds to minutes. This pulsar also shows evidence of mode changing. The remaining two pulsars have undergone recycling, accreting material from binary companions, resulting in higher spin frequencies. PSR J0557‑2948 is an isolated, 44 ms pulsar that has been partially recycled and is likely a former member of a binary system that was disrupted by a second supernova. The paucity of such so-called “disrupted binary pulsars” (DRPs) compared to double neutron star (DNS) binaries can be used to test current evolutionary scenarios, especially the kicks imparted on the neutron stars in the second supernova. There is some evidence that DRPs have larger space velocities, which could explain their small numbers. PSR J1806+2819 is a 15 ms pulsar in a 44-day orbit with a low-mass white dwarf companion. We did not detect the companion in archival optical data, indicating that it must be older than 1200 Myr.

Specializations for aerial hawking in the echolocation system of Molossus molossus (Molossidae, Chiroptera).

PubMed

Mora, E C; Macías, S; Vater, M; Coro, F; Kössl, M

2004-07-01

While searching for prey, Molossus molossus broadcasts narrow-band calls of 11.42 ms organized in pairs of pulses that alternate in frequency. The first signal of the pair is at 34.5 kHz, the second at 39.6 kHz. Pairs of calls with changing frequencies were only emitted when the interpulse intervals were below 200 ms. Maximum duty cycles during search phase are close to 20%. Frequency alternation of search calls is interpreted as a mechanism for increasing duty cycle and thus the temporal continuity of scanning, as well as increasing the detection range. A neurophysiological correlate for the processing of search calls was found in the inferior colliculus. 64% of neurons respond to frequencies in the 30- to 40-kHz range and only in this frequency range were closed tuning curves found for levels below 40 dB SPL. In addition, 15% of the neurons have double-tuned frequency-threshold curves with best thresholds at 34 and 39 kHz. Differing from observations in other bats, approach calls of M. molossus are longer and of higher frequencies than search calls. Close to the roost, the call frequency is increased to 45.0-49.8 kHz and, in addition, extremely broadband signals are emitted. This demonstrates high plasticity of call design.

Qualitative perspectives on aquatic exercise initiation and satisfaction among persons with multiple sclerosis.

PubMed

Chard, Sarah

2017-06-01

To identify the individual and social experiences underlying the initiation and satisfaction with aquatic exercise among persons with MS. A convenience sample (n = 45) of persons aged ≥18 with MS who had engaged in water-based exercise within the previous six months completed a 60-90 min semi-structured telephone interview regarding their aquatic exercise experiences. An aquatic exercise history was not a prerequisite for the adoption of aquatic exercise. Rather, participants described aquatic exercise routines as stemming from recognition of a decline in physical function combined with encouragement and invitations to join aquatic programs. Despite regular visits, health care providers were not a common source of information regarding the feasibility of aquatic exercise. Participants' aquatic activities included MS-specific and generalized aquatics courses, with class satisfaction resting on the instructor, class "fit" and a feeling of acceptance. Communication regarding local aquatic opportunities is critical for ensuring aquatics engagement among persons with MS. Providers could play a stronger role in emphasizing the feasibility and benefits of aquatic programs. In addition, persons with MS should be encouraged to try local MS and more generalized aquatic programs in order to identify a program matching their social and physical goals. Implications for Rehabilitation Directed communication regarding aquatic opportunities is essential to prompting the initiation of aquatic exercise Both MS-specific and general aquatics classes can provide positive exercise experiences for persons with MS A history of regular exercise or aquatic experiences is not a prerequisite for the initiation of aquatic exercise among persons with MS Health care provider visits may represent missed opportunities for promoting aquatics; providers should consider the suitability of aquatics for all patients with MS, regardless of the patient's exercise history.

40 CFR 122.34 - As an operator of a regulated small MS4, what will my NPDES MS4 storm water permit require?

Code of Federal Regulations, 2014 CFR

2014-07-01

... management program designed to reduce the discharge of pollutants from your MS4 to the maximum extent... Clean Water Act. Your storm water management program must include the minimum control measures described... (BMPs) are generally the most appropriate form of effluent limitations when designed to satisfy...

40 CFR 122.34 - As an operator of a regulated small MS4, what will my NPDES MS4 storm water permit require?

Code of Federal Regulations, 2013 CFR

2013-07-01

... management program designed to reduce the discharge of pollutants from your MS4 to the maximum extent... Clean Water Act. Your storm water management program must include the minimum control measures described... (BMPs) are generally the most appropriate form of effluent limitations when designed to satisfy...

40 CFR 122.34 - As an operator of a regulated small MS4, what will my NPDES MS4 storm water permit require?

Code of Federal Regulations, 2011 CFR

2011-07-01

... management program designed to reduce the discharge of pollutants from your MS4 to the maximum extent... Clean Water Act. Your storm water management program must include the minimum control measures described... (BMPs) are generally the most appropriate form of effluent limitations when designed to satisfy...

40 CFR 122.34 - As an operator of a regulated small MS4, what will my NPDES MS4 storm water permit require?

Code of Federal Regulations, 2012 CFR

2012-07-01

... management program designed to reduce the discharge of pollutants from your MS4 to the maximum extent... Clean Water Act. Your storm water management program must include the minimum control measures described... (BMPs) are generally the most appropriate form of effluent limitations when designed to satisfy...

40 CFR 122.34 - As an operator of a regulated small MS4, what will my NPDES MS4 storm water permit require?

Code of Federal Regulations, 2010 CFR

2010-07-01

..., accumulated sediments, floatables, and other debris); and ways to ensure that new flood management projects... management program designed to reduce the discharge of pollutants from your MS4 to the maximum extent... Clean Water Act. Your storm water management program must include the minimum control measures described...

Linear System of Equations, Matrix Inversion, and Linear Programming Using MS Excel

ERIC Educational Resources Information Center

El-Gebeily, M.; Yushau, B.

2008-01-01

In this note, we demonstrate with illustrations two different ways that MS Excel can be used to solve Linear Systems of Equation, Linear Programming Problems, and Matrix Inversion Problems. The advantage of using MS Excel is its availability and transparency (the user is responsible for most of the details of how a problem is solved). Further, we…

40 CFR 123.35 - As the NPDES Permitting Authority for regulated small MS4s, what is my role?

Code of Federal Regulations, 2013 CFR

2013-07-01

... MS4 storm water program.) (b) You must develop a process, as well as criteria, to designate small MS4s... under the NPDES storm water discharge control program. This process must include the authority to... storm water discharge results in or has the potential to result in exceedances of water quality...

40 CFR 123.35 - As the NPDES Permitting Authority for regulated small MS4s, what is my role?

Code of Federal Regulations, 2012 CFR

2012-07-01

... MS4 storm water program.) (b) You must develop a process, as well as criteria, to designate small MS4s... under the NPDES storm water discharge control program. This process must include the authority to... storm water discharge results in or has the potential to result in exceedances of water quality...

40 CFR 123.35 - As the NPDES Permitting Authority for regulated small MS4s, what is my role?

Code of Federal Regulations, 2014 CFR

2014-07-01

... MS4 storm water program.) (b) You must develop a process, as well as criteria, to designate small MS4s... under the NPDES storm water discharge control program. This process must include the authority to... storm water discharge results in or has the potential to result in exceedances of water quality...

DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets

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

Petyuk, Vladislav A.; Mayampurath, Anoop M.; Monroe, Matthew E.

2009-12-16

Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and MS/MS fragmentation have become widely available in recent years and have allowed for sig-nificantly better discrimination between true and false MS/MS pep-tide identifications by applying relatively narrow windows for maxi-mum allowable deviations for parent ion mass measurements. To fully gain the advantage of highly accurate parent ion mass meas-urements, it is important to limit systematic mass measurement errors. The DtaRefinery software tool can correct systematic errors in parent ion masses by reading a set of fragmentation spectra, searching for MS/MS peptide identifications, then fitting a model that canmore » estimate systematic errors, and removing them. This results in a new fragmentation spectrum file with updated parent ion masses.« less

50 CFR 660.150 - Mothership (MS) Coop Program.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Accumulation limits—(i) MS permit usage limit. No person who owns an MS permit(s) may register the MS permit(s... permit owner complies with the accumulation limits. (ii) Catcher vessel usage limit. No vessel may catch...

Fat-soluble vitamins as disease modulators in multiple sclerosis.

PubMed

Torkildsen, Ø; Løken-Amsrud, K I; Wergeland, S; Myhr, K-M; Holmøy, T

2013-01-01

Fat-soluble vitamins (A, D, E and K) have properties that could be relevant as modulators of disease activity in multiple sclerosis (MS). We performed a systematic search on PubMed and Medline up to May 2012, using the search strings 'vitamin A', 'retinol', 'retinal', 'carotenoids', 'vitamin D', 'vitamin E', 'alpha-tocopherol', 'vitamin K' in conjunction with 'multiple sclerosis', 'animal model' and 'experimental autoimmune encephalitis (EAE)'. In addition, the reference lists of the publications identified were examined for further citations of relevance. There is comprehensive evidence from epidemiological, observational, and experimental studies that vitamin D may be beneficial in MS. Results from small-scale clinical studies are inconclusive, and large-scale, adequately powered, randomized, controlled trials are still lacking. For vitamin D, Oxford Centre for Evidence-Based Medicine level 2c evidence exists for a positive therapeutic effect. Evidence from animal models indicates that all the examined fat-soluble vitamins could have potential as modulators of disease activity in MS. For vitamin A and E, level 4 and 5 evidence exists for a modulatory effect in MS; for vitamin K, too few studies have been conducted to indicate an effect in humans. Vitamin D is a promising candidate as modulator of disease activity in MS, and controlled studies are currently being conducted. All the fat-soluble vitamins have, however, been demonstrated to be effective in different animal models for the disease, and vitamin A and E have biological properties that could be relevant for MS pathogenesis. Thus, vitamin A and E seem to be promising candidates for future case-control and cohort studies. © 2012 John Wiley & Sons A/S.

Quality evaluation of LC-MS/MS-based E. coli H antigen typing (MS-H) through label-free quantitative data analysis in a clinical sample setup.

PubMed

Cheng, Keding; Sloan, Angela; McCorrister, Stuart; Peterson, Lorea; Chui, Huixia; Drebot, Mike; Nadon, Celine; Knox, J David; Wang, Gehua

2014-12-01

The need for rapid and accurate H typing is evident during Escherichia coli outbreak situations. This study explores the transition of MS-H, a method originally developed for rapid H antigen typing of E. coli using LC-MS/MS of flagella digest of reference strains and some clinical strains, to E. coli isolates in clinical scenario through quantitative analysis and method validation. Motile and nonmotile strains were examined in batches to simulate clinical sample scenario. Various LC-MS/MS batch run procedures and MS-H typing rules were compared and summarized through quantitative analysis of MS-H data output for a standard method development. Label-free quantitative data analysis of MS-H typing was proven very useful for examining the quality of MS-H result and the effects of some sample carryovers from motile E. coli isolates. Based on this, a refined procedure and protein identification rule specific for clinical MS-H typing was established and validated. With LC-MS/MS batch run procedure and database search parameter unique for E. coli MS-H typing, the standard procedure maintained high accuracy and specificity in clinical situations, and its potential to be used in a clinical setting was clearly established. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Arabidopsis MALE STERILITY1 Encodes a PHD-Type Transcription Factor and Regulates Pollen and Tapetum Development[W

PubMed Central

Ito, Takuya; Nagata, Noriko; Yoshiba, Yoshu; Ohme-Takagi, Masaru; Ma, Hong; Shinozaki, Kazuo

2007-01-01

The Arabidopsis thaliana MALE STERILITY1 (MS1) gene encodes a nuclear protein with Leu zipper–like and PHD-finger motifs and is important for postmeiotic pollen development. Here, we examined MS1 function using both cell biological and molecular biological approaches. We introduced a fusion construct of MS1 and a transcriptional repression domain (MS1-SRDX) into wild-type Arabidopsis, and the transgenic plants showed a semisterile phenotype similar to that of ms1. Since the repression domain can convert various kinds of transcriptional activators to dominant repressors, this suggested that MS1 functioned as a transcriptional activator. The Leu zipper–like region and the PHD motif were required for the MS1 function. Phenotypic analysis of the ms1 mutant and the MS1-SRDX transgenic Arabidopsis indicated that MS1 was involved in formation of pollen exine and pollen cytosolic components as well as tapetum development. Next, we searched for MS1 downstream genes by analyzing publicly available microarray data and identified 95 genes affected by MS1. Using a transgenic ms1 plant showing dexamethasone-inducible recovery of fertility, we further examined whether these genes were immediately downstream of MS1. From these results, we discuss a role of MS1 in pollen and tapetum development and the conservation of MS1 function in flowering plants. PMID:18032630

EndNote 7.0.

PubMed

Eapen, Bell Raj

2006-01-01

EndNote is a useful software for online literature search and efficient bibliography management. It helps to format the bibliography according to the citation style of each journal. EndNote stores references in a library file, which can be shared with others. It can connect to online resources like PubMed and retrieve search results as per the search criteria. It can also effortlessly integrate with popular word processors like MS Word. The Indian Journal of Dermatology, Venereology and Leprology website has a provision to import references to EndNote.

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

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

Omenn, Gilbert; States, David J.; Adamski, Marcin

2005-08-13

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasetsmore » had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.« less

Carnitine for fatigue in multiple sclerosis.

PubMed

Tejani, Aaron M; Wasdell, Michael; Spiwak, Rae; Rowell, Greg; Nathwani, Shabita

2012-05-16

Fatigue is reported to occur in up to 92% of patients with multiple sclerosis (MS) and has been described as the most debilitating of all MS symptoms by 28% to 40% of MS patients. To assess whether carnitine (enteral or intravenous) supplementation can improve the quality of life and reduce the symptoms of fatigue in patients with MS-related fatigue and to identify any adverse effects of carnitine when used for this purpose. A literature search was performed using Cochrane MS Group Trials Register (09 September 2011), Cochrane Central Register of Controlled Trials (CENTRAL) "The Cochrane Library 2011, issue 3", MEDLINE (PubMed) (1966-09 September 2011), EMBASE (1974-09 September 2011), and www.clinicaltrials.gov for ongoing trials retrieval. Reference lists of review articles and primary studies were also screened. A hand search of the abstract book of recent relevant conference symposia was also conducted. Personal contact with MS experts and a manufacturer (Source Naturals, United States) of carnitine formulation was contacted to determine if they knew of other clinical trials. No language restrictions were applied. Full reports of published and unpublished randomized controlled trials and quasi-randomized trials of any carnitine intervention in adults affected by multiple sclerosis with a clinical diagnosis of fatigue associated with multiple sclerosis were included. Data from the eligible trials was extracted and coded using a standardized data extraction form and entered into RevMan 5. Discrepancies were to be resolved by discussion with a third reviewer, however this was not necessary.The quality items to be assessed were method of randomization, allocation concealment, blinding (participants, investigators, outcome assessors and data analysis), intention-to-treat analysis and completeness of follow up. The search identified one ongoing randomized, placebo-controlled, cross-over trial (expected completion 2013) and one completed randomized, active-comparator, cross-over trial. In the completed study, adult patients with relapsing-remitting and secondary progressive MS were exposed to both acetyl L-carnitine 2 grams daily and amantadine 200 mg daily The effects of carnitine on fatigue are unclear. There was no difference between carnitine and amantadine for the number of patients withdrawing from the study due to an adverse event (relative risk ratio 0.20; 95% confidence interval 0.03 to 1.55) and no patients experienced a serious adverse event in either treatment group. Mortality and quality of life were not reported. There is insufficient evidence that carnitine for the treatment of MS-related fatigue offers a therapeutic advantage over placebo or active comparators. Results of the ongoing trial are eagerly anticipated in order to provide clarity.

Improvement of fatigue in multiple sclerosis by physical exercise is associated to modulation of systemic interferon response.

PubMed

Mulero, Patricia; Almansa, Raquel; Neri, María José; Bermejo-Martin, Jesús Francisco; Archanco, Miguel; Arenillas, Juan Francisco; Téllez, Nieves

2015-03-15

Mechanisms underlying multiple sclerosis (MS) fatigue and the causes of the beneficial effect of exercise on this symptom are not clarified. Our aim was to evaluate gene expression profiles in MS patients who improved their fatigue status after an exercise program and to compare them with healthy controls (HC). Gene expression in whole blood was profiled at baseline in 7 HC and also in 7 fatigued-MS patients. Patients underwent an exercise program for 6 months, and their fatigue status and gene expression profiles were again analyzed. MS patients showed a significant activation of genes participating in the systemic interferon response in comparison with HC that disappeared at the end of the program. Our results provide a biological basis for the observed benefit of exercise in MS. Copyright © 2015 Elsevier B.V. All rights reserved.

Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You Tropical Warnings Naval Meteorology and Oceanography Command, 1100 Balch Blvd, Stennis Space Center, MS

Feasibility of a 6-Month Yoga Program to Improve the Physical and Psychosocial Status of Persons with Multiple Sclerosis and their Family Members.

PubMed

Kahraman, Turhan; Ozdogar, Asiye Tuba; Yigit, Pinar; Hosgel, Ilknur; Mehdiyev, Zaur; Ertekin, Ozge; Ozakbas, Serkan

To the best of our knowledge, there has been no study on yoga that includes both persons with multiple sclerosis (MS) and their family members. Because yoga has therapeutic effects in both persons with MS and healthy persons, we hypothesized that it would be an effective method to improve not only the physical and psychosocial status but also the time persons with MS and their family members spend together. To examine the feasibility of a 6-month (long-term) yoga program to improve the physical and psychosocial status of persons with MS and their family members. Uncontrolled clinical trial. The protocol was developed at the Department of Neurology, Faculty of Medicine, and School of Physical Therapy and Rehabilitation, Dokuz Eylül University, Izmir, Turkey. Persons with MS and healthy family members. Walking, balance, fatigue, health-related quality of life, depression, pain, and kinesiophobia. Yoga training was given once a week (at least 1h) for 6 months. The same assessors who assessed at baseline also performed the same assessments immediately after the end of the training (i.e., after 6 months). In total, 44 participants (27 persons with MS and 17 healthy family members) participated in the study. Twelve persons with MS and three healthy family members completed the 6-month yoga intervention. The completion rate for persons with MS and healthy subjects was 44.4% and 17.6%, respectively. In persons with MS, the mental dimension of health-related quality of life, walking speed, fatigue, and depression levels significantly improved after the yoga program (p < .05). However, there was no significant change in the self-reported walking impact, balance, pain, physical dimension of health-related quality of life, and kinesiophobia levels in the persons with MS (p > .05). This study suggests that a 6-month yoga program can improve the mental dimension of health-related quality of life, walking speed, fatigue, and depression in the persons with MS. However, the 6-month yoga program does not appear to be a feasible method to increase the time that persons with MS spend together with their family members. Copyright © 2018 Elsevier Inc. All rights reserved.

Status and plans of NASA's Materials Science and Manufacturing in Space (MS/MS) program

NASA Technical Reports Server (NTRS)

Armstrong, W. O.; Bredt, J. H.

1972-01-01

A description is given of a research and development program on the space shuttle mission designed to prepare the way for possible commercial manufacturing operations on permanently orbiting space stations.

LESSONS IN DE NOVO PEPTIDE SEQUENCING BY TANDEM MASS SPECTROMETRY

PubMed Central

Medzihradszky, Katalin F.; Chalkley, Robert J.

2015-01-01

Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are “translated” into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general. PMID:25667941

Mapping the primary structure of copper/topaquinone-containing methylamine oxidase from Aspergillus niger.

PubMed

Lenobel, R; Sebela, M; Frébort, I

2005-01-01

The amino acid sequence of methylamine oxidase (MeAO) from the fungus Aspergillus niger was analyzed using mass spectrometry (MS). First, MeAO was characterized by an accurate molar mass of 72.4 kDa of the monomer measured using MALDI-TOF-MS and by a pI value of 5.8 determined by isoelectric focusing. MALDI-TOF-MS revealed a clear peptide mass fingerprint after tryptic digestion, which did not provide any relevant hit when searched against a nonredundant protein database and was different from that of A. niger amine oxidase AO-I. Tandem mass spectrometry with electrospray ionization coupled to liquid chromatography allowed unambiguous reading of six peptide sequences (11-19 amino acids) and seven sequence tags (4-15 amino acids), which were used for MS BLAST homology searching. MeAO was found to be largely homologous to a hypothetical protein AN7641.2 (EMBL/GenBank protein-accession code EAA61827) from Aspergillus nidulans FGSC A4 with a theoretical molar mass of 76.46 kDa and pI 6.14, which belongs to the superfamily of copper amine oxidases. The protein AN7641.2 is only little homologous to the amine oxidase AO-I (32% identity, 49 % similarity).

Chemical markers for bacteria in extraterrestrial samples.

PubMed

Fox, Alvin

2002-11-01

Interplanetary missions to collect pristine Martian surface samples for analysis of organic molecules, and to search for evidence of life, are in the planning phases. The only extraterrestrial samples currently on Earth are lunar dust and rocks, brought back by the Apollo (U.S.) and Luna (Soviet Union) missions to the moon, and meteorites. Meteorites are contaminated when they pass through the Earth's atmosphere, and during environmental exposure on Earth. Lunar fines have been stored on Earth for over 30 years under conditions designed to avoid chemical but not microbiological contamination. It has been extremely difficult to draw firm conclusions about the origin of chemicals (including amino acids) in extraterrestrial samples. Of particular concern has been the possibility of bacterial contamination. Recent work using state-of-the-art gas chromatography tandem mass spectrometry (GC-MS/MS) has dramatically lowered the chemical background, allowing a clear demonstration that lunar fines are remarkably different from terrestrial dust in that they generally lack certain chemical markers (muramic acid and 3-hydroxy fatty acids) characteristic of Earth's bacteria. Thus, lunar dust might be used as a negative control, in conjunction with GC-MS/MS analyses, in future analytical studies of lunar dust and meteorites. Such analyses may also be important in studies designed to search for the presence of life on Mars. Copyright 2002 Wiley-Liss, Inc.

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes.

PubMed

Jin, Ya; Yuan, Qi; Zhang, Jun; Manabe, Takashi; Tan, Wen

2015-09-01

Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an "overlap score," (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 "overlap factors," (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Perspectives of Medieval Persian Medicine on Multiple Sclerosis.

PubMed

Sahraian, Mohammad Ali; Parviz, Mohsen; Sheibani, Behnam; Schiess, Nicoline; Ghorbanifar, Zahra; Kamalinejad, Mohammad; Nazem, Esmail; Sadeghpour, Omid; Rezaeizadeh, Hossein

2018-01-01

Traditional Persian Medicine (TPM) was the prevailing practice of medicine in the Eurasia region up through the 18th century, a practice of medicine stemming back to Hippocrates and to the 5000 year old civilization of the region. It is a school of medicine which touches on many a delicate points which may seem unimaginable within the realm of modern allopathic medicine. This practice of ancient medicine besides shedding light on various possible theoretical modern day disorders serves as a vast resource for therapeutics. In this paper, we present study of the manuscripts of this ancient medical practice in search of symptom presentations coinciding with presentation of multiple sclerosis (MS). This paper represents a comprehensive search through TPM texts and manuscripts with the intention to seek possible clues on MS from potentially valuable age-old resources. We predominantly focused our search on the works of five eminent physicians of Medieval Persia: Avicenna (980-1037 AD), Haly Abbas (949-982 AD), Rhazes (865-925 AD), Averroes (1126-1198 AD) and Jorjani (1042-1137 AD). In this paper, the authors attempt a theory and conclude with high probability that a conjunction of a series of signs, symptoms found in TPM texts under the terms khadar, isterkha and falej form the symptoms and the disease pattern of modern day MS. This theory draws upon existent similarities in terms of disease pathology, disease patterns and predisposing factors seen between MS and the related morbidities within Persian Medicine. We recommend further examinations of such potentially valuable long-standing resources, examining the diagnoses and treatments as set forth by Persian Medicine through international collaboration within the global scientific community. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

40 CFR 122.32 - As an operator of a small MS4, am I regulated under the NPDES storm water program?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 21 2010-07-01 2010-07-01 false As an operator of a small MS4, am I regulated under the NPDES storm water program? 122.32 Section 122.32 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS EPA ADMINISTERED PERMIT PROGRAMS: THE NATIONAL POLLUTANT DISCHARGE ELIMINATION SYSTEM Permit...

40 CFR 122.32 - As an operator of a small MS4, am I regulated under the NPDES storm water program?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 22 2011-07-01 2011-07-01 false As an operator of a small MS4, am I regulated under the NPDES storm water program? 122.32 Section 122.32 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS EPA ADMINISTERED PERMIT PROGRAMS: THE NATIONAL POLLUTANT DISCHARGE ELIMINATION SYSTEM Permit...

Interim Report on the Truancy Court Diversion Program in the District of Columbia, 2011-12

ERIC Educational Resources Information Center

Cahill, Meagan; Liberman, Akiva; Cramer, Lindsey

2012-01-01

The Truancy Court Diversion Program (TCDP) is a voluntary program for at risk students and their parents. It combines involvement of a Family Court judge in group and individual sessions with service provision. During the 2011-12 school year, a pilot TCDP was implemented at Kramer Middle School (M.S.) and at Johnson M.S. The program attempts to…

Non-Lethal Weapons Program

Science.gov Websites

), 26th Marine Expeditionary Unit (MEU), practice non-lethal control techniques during a non-lethal Skip to main content (Press Enter). Toggle navigation Non-Lethal Weapons Program Search Search JNLWP: Search Search JNLWP: Search Non-Lethal Weapons Program U.S. Department of Defense Non-Lethal

Botulinum toxin therapy for treatment of spasticity in multiple sclerosis: review and recommendations of the IAB-Interdisciplinary Working Group for Movement Disorders task force.

PubMed

Dressler, Dirk; Bhidayasiri, Roongroj; Bohlega, Saeed; Chahidi, Abderrahmane; Chung, Tae Mo; Ebke, Markus; Jacinto, L Jorge; Kaji, Ryuji; Koçer, Serdar; Kanovsky, Petr; Micheli, Federico; Orlova, Olga; Paus, Sebastian; Pirtosek, Zvezdan; Relja, Maja; Rosales, Raymond L; Sagástegui-Rodríguez, José Alberto; Schoenle, Paul W; Shahidi, Gholam Ali; Timerbaeva, Sofia; Walter, Uwe; Saberi, Fereshte Adib

2017-01-01

Botulinum toxin (BT) therapy is an established treatment of spasticity due to stroke. For multiple sclerosis (MS) spasticity this is not the case. IAB-Interdisciplinary Working Group for Movement Disorders formed a task force to explore the use of BT therapy for treatment of MS spasticity. A formalised PubMed literature search produced 55 publications (3 randomised controlled trials, 3 interventional studies, 11 observational studies, 2 case studies, 35 reviews, 1 guideline) all unanimously favouring the use of BT therapy for MS spasticity. There is no reason to believe that BT should be less effective and safe in MS spasticity than it is in stroke spasticity. Recommendations include an update of the current prevalence of MS spasticity and its clinical features according to classifications used in movement disorders. Immunological data on MS patients already treated should be analysed with respect to frequencies of MS relapses and BT antibody formation. Registration authorities should expand registration of BT therapy for spasticity regardless of its aetiology. MS specialists should consider BT therapy for symptomatic treatment of spasticity.

Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument

PubMed Central

Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun

2016-01-01

The recently-introduced Orbitrap Fusion mass spectrometry permits various types of MS2 acquisition methods. To date, these different MS2 strategies and the optimal data interpretation approach for each have not been adequately evaluated. This study comprehensively investigated the four MS2 strategies: HCD-OT (higher-energy-collisional-dissociation with Orbitrap detection), HCD-IT (HCD with ion trap, IT), CID-IT (collision-induced-dissociation with IT) and CID-OT on Orbitrap Fusion. To achieve extensive comparison and identify the optimal data interpretation method for each technique, several search engines (SEQUEST and Mascot) and post-processing methods (score-based, PeptideProphet, and Percolator) were assessed for all techniques for the analysis of a human cell proteome. It was found that divergent conclusions could be made from the same dataset when different data interpretation approaches were used and therefore requiring a relatively fair comparison among techniques. Percolator was chosen for comparison of techniques because it performs the best among all search engines and MS2 strategies. For the analysis of human cell proteome using individual MS2 strategies, the highest number of identifications was achieved by HCD-OT, followed by HCD-IT and CID-IT. Based on these results, we concluded that a relatively fair platform for data interpretation is necessary to avoid divergent conclusions from the same dataset, and HCD-OT and HCD-IT may be preferable for protein/peptide identification using Orbitrap Fusion. PMID:27472422

MALDI-TOF MS Distinctly Differentiates Nontypable Haemophilus influenzae from Haemophilus haemolyticus

PubMed Central

Zhang, Huifang; Zhang, Yongchan; Gao, Yuan; Xu, Li; Lv, Jing; Wang, Yingtong; Zhang, Jianzhong; Shao, Zhujun

2013-01-01

Nontypable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus exhibit different pathogenicities, but to date, there remains no definitive and reliable strategy for differentiating these strains. In this study, we evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a potential method for differentiating NTHi and H. haemolyticus. The phylogenetic analysis of concatenated 16S rRNA and recombinase A (recA) gene sequences, outer membrane protein P6 gene sequencing and single-gene PCR were used as reference methods. The original reference database (ORD, provided with the Biotyper software) and new reference database (NRD, extended with Chinese strains) were compared for the evaluation of MALDI-TOF MS. Through a search of the ORD, 76.9% of the NTHi (40/52) and none of the H. haemolyticus (0/20) strains were identified at the species level. However, all NTHi and H. haemolyticus strains used for identification were accurately recognized at the species level when searching the NRD. From the dendrogram clustering of the main spectra projections, the Chinese and foreign H. influenzae reference strains were categorized into two distinct groups, and H. influenzae and H. haemolyticus were also separated into two categories. Compared to the existing methods, MALDI-TOF MS has the advantage of integrating high throughput, accuracy and speed. In conclusion, MALDI-TOF MS is an excellent method for differentiating NTHi and H. haemolyticus. This method can be recommended for use in appropriately equipped laboratories. PMID:23457514

Multiplexed Post-Experimental Monoisotopic Mass Refinement ( m PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation

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

Madar, Inamul Hasan; Ko, Seung-Ik; Kim, Hokeun

Mass spectrometry (MS)-based proteomics, which uses high-resolution hybrid mass spectrometers such as the quadrupole-orbitrap mass spectrometer, can yield tens of thousands of tandem mass (MS/MS) spectra of high resolution during a routine bottom-up experiment. Despite being a fundamental and key step in MS-based proteomics, the accurate determination and assignment of precursor monoisotopic masses to the MS/MS spectra remains difficult. The difficulties stem from imperfect isotopic envelopes of precursor ions, inaccurate charge states for precursor ions, and cofragmentation. We describe a composite method of utilizing MS data to assign accurate monoisotopic masses to MS/MS spectra, including those subject to cofragmentation. Themore » method, “multiplexed post-experiment monoisotopic mass refinement” (mPE-MMR), consists of the following: multiplexing of precursor masses to assign multiple monoisotopic masses of cofragmented peptides to the corresponding multiplexed MS/MS spectra, multiplexing of charge states to assign correct charges to the precursor ions of MS/ MS spectra with no charge information, and mass correction for inaccurate monoisotopic peak picking. When combined with MS-GF+, a database search algorithm based on fragment mass difference, mPE-MMR effectively increases both sensitivity and accuracy in peptide identification from complex high-throughput proteomics data compared to conventional methods.« less

Evolving Concepts in Posterior Subthalamic Area Deep Brain Stimulation for Treatment of Tremor: Surgical Neuroanatomy and Practical Considerations.

PubMed

Ramirez-Zamora, Adolfo; Smith, Heather; Kumar, Vignessh; Prusik, Julia; Phookan, Sujoy; Pilitsis, Julie G

2016-01-01

Although thalamic deep brain stimulation (DBS) has been established as an effective therapy for refractory tremor in Parkinson's disease and essential tremor, reports investigating the efficacy of posterior subthalamic area (PSA) DBS for severe, debilitating tremors continue to emerge. However, questions regarding the optimal anatomical target, surgical approach, programming paradigms and effectiveness compared to other targets remain. In this report, we aimed to review the current literature to assess different stereotactic techniques, anatomical considerations, adverse effects and stimulation settings in PSA DBS. A comprehensive literature review was performed searching for articles discussing tremors and PSA stimulation. We performed a quantitative analysis comparing different DBS tremor targets. Tremor improvement is consistently documented in most reports with an average reduction in tremor of 79% depending on the specific tremor syndrome. Tremor benefit in patients with multiple sclerosis (MS) tremor was significantly higher than for other stimulation targets. Transient paresthesias, imbalance, dizziness and dysarthria are the most common side effects with PSA DBS. PSA DBS is an effective and safe treatment for tremor control and should be considered in patients with refractory tremors with associated cerebellar or dystonic features, proximal tremors and MS tremor. © 2016 S. Karger AG, Basel.

Development of High-Performance Chemical Isotope Labeling LC-MS for Profiling the Carbonyl Submetabolome.

PubMed

Zhao, Shuang; Dawe, Margot; Guo, Kevin; Li, Liang

2017-06-20

Metabolites containing a carbonyl group represent several important classes of molecules including various forms of ketones and aldehydes such as steroids and sugars. We report a high-performance chemical isotope labeling (CIL) LC-MS method for profiling the carbonyl submetabolome with high coverage and high accuracy and precision of relative quantification. This method is based on the use of dansylhydrazine (DnsHz) labeling of carbonyl metabolites to change their chemical and physical properties to such an extent that the labeled metabolites can be efficiently separated by reversed phase LC and ionized by electrospray ionization MS. In the analysis of six standards representing different carbonyl classes, acetaldehyde could be ionized only after labeling and MS signals were significantly increased for other 5 standards with an enhancement factor ranging from ∼15-fold for androsterone to ∼940-fold for 2-butanone. Differential 12 C- and 13 C-DnsHz labeling was developed for quantifying metabolic differences in comparative samples where individual samples were separately labeled with 12 C-labeling and spiked with a 13 C-labeled pooled sample, followed by LC-MS analysis, peak pair picking, and peak intensity ratio measurement. In the replicate analysis of a 1:1 12 C-/ 13 C-labeled human urine mixture (n = 6), an average of 2030 ± 39 pairs per run were detected with 1737 pairs in common, indicating the possibility of detecting a large number of carbonyl metabolites as well as high reproducibility of peak pair detection. The average RSD of the peak pair ratios was 7.6%, and 95.6% of the pairs had a RSD value of less than 20%, demonstrating high precision for peak ratio measurement. In addition, the ratios of most peak pairs were close to the expected value of 1.0 (e.g., 95.5% of them had ratios of between 0.67 and 1.5), showing the high accuracy of the method. For metabolite identification, a library of DnsHz-labeled standards was constructed, including 78 carbonyl metabolites with each containing MS, retention time (RT), and MS/MS information. This library and an online search program for labeled carbonyl metabolite identification based on MS, RT, and MS/MS matches have been implemented in a freely available Website, www.mycompoundid.org . Using this library, out of the 1737 peak pairs detected in urine, 33 metabolites were positively identified. In addition, 1333 peak pairs could be matched to the metabolome databases with most of them belonging to the carbonyl metabolites. These results show that 12 C-/ 13 C-DnsHz labeling LC-MS is a useful tool for profiling the carbonyl submetabolome of complex samples with high coverage.

An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex

PubMed Central

Van Essen, David C.; Drury, Heather A.; Dickson, James; Harwell, John; Hanlon, Donna; Anderson, Charles H.

2001-01-01

The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database. PMID:11522765

Supply and Demand in mHealth Apps for Persons With Multiple Sclerosis: Systematic Search in App Stores and Scoping Literature Review.

PubMed

Giunti, Guido; Guisado Fernández, Estefanía; Dorronzoro Zubiete, Enrique; Rivera Romero, Octavio

2018-05-23

Multiple sclerosis (MS) is a non-curable chronic inflammatory disease of the central nervous system that affects more than 2 million people worldwide. MS-related symptoms impact negatively on the quality of life of persons with MS, who need to be active in the management of their health. mHealth apps could support these patient groups by offering useful tools, providing reliable information, and monitoring symptoms. A previous study from this group identified needs, barriers, and facilitators for the use of mHealth solutions among persons with MS. It is unknown how commercially available health apps meet these needs. The main objective of this review was to assess how the features present in MS apps meet the reported needs of persons with MS. We followed a combination of scoping review methodology and systematic assessment of features and content of mHealth apps. A search strategy was defined for the two most popular app stores (Google Play and Apple App Store) to identify relevant apps. Reviewers independently conducted a screening process to filter apps according to the selection criteria. Interrater reliability was assessed through the Fleiss-Cohen coefficient (k=.885). Data from the included MS apps were extracted and explored according to classification criteria. An initial total of 581 potentially relevant apps was found. After removing duplicates and applying inclusion and exclusion criteria, 30 unique apps were included in the study. A similar number of apps was found in both stores. The majority of the apps dealt with disease management and disease and treatment information. Most apps were developed by small and medium-sized enterprises, followed by pharmaceutical companies. Patient education and personal data management were among the most frequently included features in these apps. Energy management and remote monitoring were often not present in MS apps. Very few contained gamification elements. Currently available MS apps fail to meet the needs and demands of persons with MS. There is a need for health professionals, researchers, and industry partners to collaborate in the design of mHealth solutions for persons with MS to increase adoption and engagement. ©Guido Giunti, Estefanía Guisado Fernández, Enrique Dorronzoro Zubiete, Octavio Rivera Romero. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 23.05.2018.

A Graduate Program in Institutional Pharmacy Management Leading to an MS in Hospital Pharmacy, MBA and Residency.

ERIC Educational Resources Information Center

Blair, Jan N.; Lipman, Arthur G.

1981-01-01

A combined program leading to the MS in Hospital Pharmacy, MBA, and Certificate of Residency in Hospital Pharmacy established at the University of Utah in 1978 is described. The program provides coursework in both hospital pharmacy and management plus practical experience in hospital pharmacy practice management. (Author/MLW)

MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

PubMed Central

2015-01-01

Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae. PMID:25263576

Limits to the usability of iconic memory

PubMed Central

Rensink, Ronald A.

2014-01-01

Human vision briefly retains a trace of a stimulus after it disappears. This trace—iconic memory—is often believed to be a surrogate for the original stimulus, a representational structure that can be used as if the original stimulus were still present. To investigate its nature, a flicker-search paradigm was developed that relied upon a full scan (rather than partial report) of its contents. Results show that for visual search it can indeed act as a surrogate, with little cost for alternating between visible and iconic representations. However, the duration over which it can be used depends on the type of task: some tasks can use iconic memory for at least 240 ms, others for only about 190 ms, while others for no more than about 120 ms. The existence of these different limits suggests that iconic memory may have multiple layers, each corresponding to a particular level of the visual hierarchy. In this view, the inability to use a layer of iconic memory may reflect an inability to maintain feedback connections to the corresponding representation. PMID:25221539

Limits to the usability of iconic memory.

PubMed

Rensink, Ronald A

2014-01-01

Human vision briefly retains a trace of a stimulus after it disappears. This trace-iconic memory-is often believed to be a surrogate for the original stimulus, a representational structure that can be used as if the original stimulus were still present. To investigate its nature, a flicker-search paradigm was developed that relied upon a full scan (rather than partial report) of its contents. Results show that for visual search it can indeed act as a surrogate, with little cost for alternating between visible and iconic representations. However, the duration over which it can be used depends on the type of task: some tasks can use iconic memory for at least 240 ms, others for only about 190 ms, while others for no more than about 120 ms. The existence of these different limits suggests that iconic memory may have multiple layers, each corresponding to a particular level of the visual hierarchy. In this view, the inability to use a layer of iconic memory may reflect an inability to maintain feedback connections to the corresponding representation.

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

PubMed

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

2017-07-07

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

SLiMSearch 2.0: biological context for short linear motifs in proteins

PubMed Central

Davey, Norman E.; Haslam, Niall J.; Shields, Denis C.

2011-01-01

Short, linear motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences. User-friendly output and visualizations of motif context allow the user to quickly gain insight into the validity of a putatively functional motif occurrence. For each motif occurrence, overlapping UniProt features and annotated SLiMs are displayed. Visualization also includes annotated multiple sequence alignments surrounding each occurrence, showing conservation and protein disorder statistics in addition to known and predicted SLiMs, protein domains and known post-translational modifications. In addition, enrichment of Gene Ontology terms and protein interaction partners are provided as indicators of possible motif function. All web server results are available for download. Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html. PMID:21622654

Comprehensive identification and structural characterization of target components from Gelsemium elegans by high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry based on accurate mass databases combined with MS/MS spectra.

PubMed

Liu, Yan-Chun; Xiao, Sa; Yang, Kun; Ling, Li; Sun, Zhi-Liang; Liu, Zhao-Ying

2017-06-01

This study reports an applicable analytical strategy of comprehensive identification and structure characterization of target components from Gelsemium elegans by using high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QqTOF MS) based on the use of accurate mass databases combined with MS/MS spectra. The databases created included accurate masses and elemental compositions of 204 components from Gelsemium and their structural data. The accurate MS and MS/MS spectra were acquired through data-dependent auto MS/MS mode followed by an extraction of the potential compounds from the LC-QqTOF MS raw data of the sample. The same was matched using the databases to search for targeted components in the sample. The structures for detected components were tentatively characterized by manually interpreting the accurate MS/MS spectra for the first time. A total of 57 components have been successfully detected and structurally characterized from the crude extracts of G. elegans, but has failed to differentiate some isomers. This analytical strategy is generic and efficient, avoids isolation and purification procedures, enables a comprehensive structure characterization of target components of Gelsemium and would be widely applicable for complicated mixtures that are derived from Gelsemium preparations. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Assess, Coordinate, Execute: How to ACE an Executive Director Search. Issue Brief

ERIC Educational Resources Information Center

Mitchell, Mollie

2011-01-01

This issue brief presents a meaningful strategy for how charter school boards can hire top-notch, well-suited leaders for their schools. Written by Mollie Mitchell, founder and president of The K12 Search Group, this brief is a how-to guide for managing the process of bringing on a new charter school leader. As Ms. Mitchell notes, the only thing…

ms2: A molecular simulation tool for thermodynamic properties

NASA Astrophysics Data System (ADS)

Deublein, Stephan; Eckl, Bernhard; Stoll, Jürgen; Lishchuk, Sergey V.; Guevara-Carrion, Gabriela; Glass, Colin W.; Merker, Thorsten; Bernreuther, Martin; Hasse, Hans; Vrabec, Jadran

2011-11-01

This work presents the molecular simulation program ms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules. ms2 features the two main molecular simulation techniques, molecular dynamics (MD) and Monte-Carlo. It supports the calculation of vapor-liquid equilibria of pure fluids and multi-component mixtures described by rigid molecular models on the basis of the grand equilibrium method. Furthermore, it is capable of sampling various classical ensembles and yields numerous thermodynamic properties. To evaluate the chemical potential, Widom's test molecule method and gradual insertion are implemented. Transport properties are determined by equilibrium MD simulations following the Green-Kubo formalism. ms2 is designed to meet the requirements of academia and industry, particularly achieving short response times and straightforward handling. It is written in Fortran90 and optimized for a fast execution on a broad range of computer architectures, spanning from single processor PCs over PC-clusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable to different computing platforms. Feature tools facilitate the interaction with the code and the interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work. Program summaryProgram title:ms2 Catalogue identifier: AEJF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Special Licence supplied by the authors No. of lines in distributed program, including test data, etc.: 82 794 No. of bytes in distributed program, including test data, etc.: 793 705 Distribution format: tar.gz Programming language: Fortran90 Computer: The simulation tool ms2 is usable on a wide variety of platforms, from single processor machines over PC-clusters and vector computers to vector-parallel architectures. (Tested with Fortran compilers: gfortran, Intel, PathScale, Portland Group and Sun Studio.) Operating system: Unix/Linux, Windows Has the code been vectorized or parallelized?: Yes. Message Passing Interface (MPI) protocol Scalability. Excellent scalability up to 16 processors for molecular dynamics and >512 processors for Monte-Carlo simulations. RAM:ms2 runs on single processors with 512 MB RAM. The memory demand rises with increasing number of processors used per node and increasing number of molecules. Classification: 7.7, 7.9, 12 External routines: Message Passing Interface (MPI) Nature of problem: Calculation of application oriented thermodynamic properties for rigid electro-neutral molecules: vapor-liquid equilibria, thermal and caloric data as well as transport properties of pure fluids and multi-component mixtures. Solution method: Molecular dynamics, Monte-Carlo, various classical ensembles, grand equilibrium method, Green-Kubo formalism. Restrictions: No. The system size is user-defined. Typical problems addressed by ms2 can be solved by simulating systems containing typically 2000 molecules or less. Unusual features: Feature tools are available for creating input files, analyzing simulation results and visualizing molecular trajectories. Additional comments: Sample makefiles for multiple operation platforms are provided. Documentation is provided with the installation package and is available at http://www.ms-2.de. Running time: The running time of ms2 depends on the problem set, the system size and the number of processes used in the simulation. Running four processes on a "Nehalem" processor, simulations calculating VLE data take between two and twelve hours, calculating transport properties between six and 24 hours.

Application of HRAM screening and LC-MS/MS confirmation of active pharmaceutical ingredient in "natural" herbal supplements.

PubMed

Pascali, Jennifer P; Fais, Paolo; Vaiano, Fabio; Bertol, Elisabetta

2018-05-01

The growing market of herbal remedies worldwide could pose severe problems to consumers' health due to the possible presence of potentially harmful, undeclared synthetic substances or analogues of prescription drugs. The present work shows a simple but effective approach to unequivocally identify synthetic anorectic compounds in allegedly 'natural' herbal extracts, by exploiting liquid chromatography/time of flight (Q-TOF LC/MS) technology coupled to liquid chromatography/triple quadrupole (LC-MS/MS) confirmation and quantitation. The procedure was applied to five tea herbal extracts and pills sold as coadjutant for weigh loss. The method exploited liquid-liquid sample extraction (LLE) and separation in a C18 (2.1mm×150mm, 1.8μm) column. QTOF acquisitions were carried out both in scan mode and all ion MS/MS mode and results were obtained after search against ad hoc prepared library. Sibutramine, 4-hydroxyamphetamine, caffeine and theophylline were preliminary identified samples. Confirmation and quantitation of the preliminary identified compounds were obtained in LC-MS/MS after preparation of appropriated standards. Sibutramine, caffeine and theophylline were finally confirmed and quantitate. Copyright © 2018 Elsevier B.V. All rights reserved.

The ACCEND program: a combined BS and MS program in environmental engineering that includes co-operative work experience.

PubMed

Bishop, P L; Keener, T C; Kukreti, A R; Kowel, S T

2004-01-01

Environmental engineering education has rapidly expanded in recent years and new teaching methods are needed. Many professionals and educators believe that a MS degree in environmental engineering should be the minimum in order to practice the profession, along with practical training. This paper describes an innovative program being offered at the University of Cincinnati that combines an integrated BS in civil engineering and an MS in environmental engineering with extensive practical co-operative education (co-op) experience, all within a five-year period. The program includes distance learning opportunities during the co-op periods. The result is a well-trained graduate who will receive higher pay and more challenging career opportunities, and who will have developed professionalism and maturity beyond that from traditional engineering programs.

Managing Neuropsychological Impairment in Multiple Sclerosis

PubMed Central

Lau, Stephanie; Penner, Iris; Heesen, Christoph; Moritz, Steffen

2015-01-01

Background: Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease of the central nervous system of potential autoimmune origin that is frequently associated with psychological disorders and cognitive deficits, as well as with fatigue, stress, and psychosocial burden. These factors often cause decreased quality of life, social withdrawal, and unemployment. We describe the development of a cognitive-behavioral group intervention based on the concept of metacognition and evaluation of the feasibility and acceptance of the program as a rehabilitation tool. Methods: Metacognitive Training in MS (MaTiMS) consists of six modules, each 90 minutes in duration. We tested acceptance and design of the program in six focus groups (entire sample, n = 27). Framework analysis of transcripts was used to identify key topics and categories. Program modules were revised in accordance with appropriate recommendations of focus group members. We subsequently evaluated MaTiMS in two groups (n = 5, n = 6) in a rehabilitation center. Neuropsychological functioning as well as coping self-efficacy, depression, stress, perceived cognitive deficit, fatigue, and quality of life were assessed. Acceptance of MaTiMS from the patient perspective was also studied. Results: The modules were highly accepted by patients. Pre-post assessments showed significant improvements in the Coping Self Efficacy Scale (P = .007), the Würzburger Fatigue Inventory for MS Score (P = .028), and the Hamburg Quality of Life Questionnaire in Multiple Sclerosis Mood subscale (P = .046). Conclusions: These preliminary results suggest that MaTiMS represents a feasible psychological group training program that may foster improvements in self-efficacy, fatigue, and mood. The next step will be an evaluation of the program in a randomized controlled trial. PMID:26052258

PepArML: A Meta-Search Peptide Identification Platform

PubMed Central

Edwards, Nathan J.

2014-01-01

The PepArML meta-search peptide identification platform provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score, and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores — reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies 2–3 times more spectra than individual search engines at 10% FDR. PMID:25663956

A Study of the National Upward Bound and Talent Search Programs. Final Report. Volume III: Descriptive Study of the Talent Search Program.

ERIC Educational Resources Information Center

Pyecha, J. N.; And Others

The Office of Education's Talent Search program is designed to: (a) identify needy youths with exceptional potential and encourage them to complete secondary school and undertake further education; (b) publicize student financial aid; and (c) encourage dropouts of demonstrated aptitude to reenter educational programs. The Talent Search program…

Automated Literature Searches for Longitudinal Tracking of Cancer Research Training Program Graduates.

PubMed

Padilla, Luz A; Desmond, Renee A; Brooks, C Michael; Waterbor, John W

2018-06-01

A key outcome measure of cancer research training programs is the number of cancer-related peer-reviewed publications after training. Because program graduates do not routinely report their publications, staff must periodically conduct electronic literature searches on each graduate. The purpose of this study is to compare findings of an innovative computer-based automated search program versus repeated manual literature searches to identify post-training peer-reviewed publications. In late 2014, manual searches for publications by former R25 students identified 232 cancer-related articles published by 112 of 543 program graduates. In 2016, a research assistant was instructed in performing Scopus literature searches for comparison with individual PubMed searches on our 543 program graduates. Through 2014, Scopus found 304 cancer publications, 220 of that had been retrieved manually plus an additional 84 papers. However, Scopus missed 12 publications found manually. Together, both methods found 316 publications. The automated method found 96.2 % of the 316 publications while individual searches found only 73.4 %. An automated search method such as using the Scopus database is a key tool for conducting comprehensive literature searches, but it must be supplemented with periodic manual searches to find the initial publications of program graduates. A time-saving feature of Scopus is the periodic automatic alerts of new publications. Although a training period is needed and initial costs can be high, an automated search method is worthwhile due to its high sensitivity and efficiency in the long term.

Vogt Koyanagi Harada Syndrome mimicking multiple sclerosis: A case report and review of the literature.

PubMed

Algahtani, Hussein; Shirah, Bader; Algahtani, Raghad; Alkahtani, Abdulah; Alwadie, Saeed

2017-02-01

Vogt Koyanagi Harada (VKH) Syndrome, also called uveomeningioencephalitis, is a chronic disorder characterized by inflammation of the uvea, meninges, auditory system, and integumentary system. The association between VKH syndrome and multiple sclerosis (MS) has been reported only once in the literature in a patient who developed VKH syndrome after two years of the diagnosis of MS. In this article, we report a case who was misdiagnosed and treated as MS until she was proven to have VKH syndrome, and a diagnosis of MS was excluded. VKH syndrome is a systemic disorder that may present with clinical and/or radiological features mimicking MS. Applying diagnostic criteria is extremely important for confirming or excluding the diagnosis. Detailed history and physical examination are of paramount importance to score the final diagnosis. Rigorous search for red flags for both conditions is very helpful. Copyright © 2017 Elsevier B.V. All rights reserved.

Using ProHits to store, annotate and analyze affinity purification - mass spectrometry (AP-MS) data

PubMed Central

Liu, Guomin; Zhang, Jianping; Choi, Hyungwon; Lambert, Jean-Philippe; Srikumar, Tharan; Larsen, Brett; Nesvizhskii, Alexey I.; Raught, Brian; Tyers, Mike; Gingras, Anne-Claude

2012-01-01

Affinity purification coupled with mass spectrometry (AP-MS) is a robust technique used to identify protein-protein interactions. With recent improvements in sample preparation, and dramatic advances in MS instrumentation speed and sensitivity, this technique is becoming more widely used throughout the scientific community. To meet the needs of research groups both large and small, we have developed software solutions for tracking, scoring and analyzing AP-MS data. Here, we provide details for the installation and utilization of ProHits, a Laboratory Information Management System designed specifically for AP-MS interaction proteomics. This protocol explains: (i) how to install the complete ProHits system, including modules for the management of mass spectrometry files and the analysis of interaction data, and (ii) alternative options for the use of pre-existing search results in simpler versions of ProHits, including a virtual machine implementation of our ProHits Lite software. We also describe how to use the main features of the software to analyze AP-MS data. PMID:22948730

X-Ray Gas Temperatures in the Arc Clusters MS0440+204 and MS0302+1658

NASA Technical Reports Server (NTRS)

Gioia, Isabella M.; White, Nicholas

1997-01-01

The cluster of galaxies MS0440+02, originally discovered through its X-ray emission, was part of an optical observational program to search for arcs and arclets in a complete sample of X-ray luminous, medium-distant clusters of galaxies. Mauna Kea CCD images of MS0440+02 showed a remarkable optical morphology. The core of the cluster contains 6 bright galaxies and numerous fainter ones embedded in a low surface brightness halo. Besides, MS0440+02 is the most spectacular example that we have found of an arc system in a compact condensed cluster, with arcs symmetrically distributed to draw almost perfect circles around the cluster center. Giant arcs are magnified images of distant galaxies, gravitationally distorted by massive foreground clusters. It is of great importance to compare the results of the lensing studies with those derived from X-ray observations, as the two are independent methods of studying the mass distribution. Thus MS0440+02 was the ideal target to obtain temperature measurement with ASCA and good spatial resolution X-ray observations with ROSAT. The X-ray data have been used in conjunction with Hubble Space Telescope observations to put more stringent constrains on the mass estimates. Most of the different wavelength datasets have been reduced and analyzed. Mass determinations have been separately obtained from galaxy virial motions and X-ray profile fitting using the cluster gas temperature as measured by the ASCA satellite. Assuming that the hot gas is in hydrostatic equilibrium and in a spherical potential, we find from the X-ray data a mass distribution profile that is well described by a Beta model. From the multiple images formed by gravitational lensing (HST data) using the modelling of the gravitational lensed arcs, we have derived Beta model. To reconcile the mass estimates we have explored the possibility of having a supercluster surrounding the MOS0440 cluster, that is a model with two isothermal spheres, one embedded inside the other. These results have been published or are in press.

DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry*

PubMed Central

Zhang, Bo; Pirmoradian, Mohammad; Chernobrovkin, Alexey; Zubarev, Roman A.

2014-01-01

Based on conventional data-dependent acquisition strategy of shotgun proteomics, we present a new workflow DeMix, which significantly increases the efficiency of peptide identification for in-depth shotgun analysis of complex proteomes. Capitalizing on the high resolution and mass accuracy of Orbitrap-based tandem mass spectrometry, we developed a simple deconvolution method of “cloning” chimeric tandem spectra for cofragmented peptides. Additional to a database search, a simple rescoring scheme utilizes mass accuracy and converts the unwanted cofragmenting events into a surprising advantage of multiplexing. With the combination of cloning and rescoring, we obtained on average nine peptide-spectrum matches per second on a Q-Exactive workbench, whereas the actual MS/MS acquisition rate was close to seven spectra per second. This efficiency boost to 1.24 identified peptides per MS/MS spectrum enabled analysis of over 5000 human proteins in single-dimensional LC-MS/MS shotgun experiments with an only two-hour gradient. These findings suggest a change in the dominant “one MS/MS spectrum - one peptide” paradigm for data acquisition and analysis in shotgun data-dependent proteomics. DeMix also demonstrated higher robustness than conventional approaches in terms of lower variation among the results of consecutive LC-MS/MS runs. PMID:25100859

TUBEs-Mass Spectrometry for Identification and Analysis of the Ubiquitin-Proteome.

PubMed

Azkargorta, Mikel; Escobes, Iraide; Elortza, Felix; Matthiesen, Rune; Rodríguez, Manuel S

2016-01-01

Mass spectrometry (MS) has become the method of choice for the large-scale analysis of protein ubiquitylation. There exist a number of proposed methods for mapping ubiquitin sites, each with different pros and cons. We present here a protocol for the MS analysis of the ubiquitin-proteome captured by TUBEs and subsequent data analysis. Using dedicated software and algorithms, specific information on the presence of ubiquitylated peptides can be obtained from the MS search results. In addition, a quantitative and functional analysis of the ubiquitylated proteins and their interacting partners helps to unravel the biological and molecular processes they are involved in.

Living with Advanced MS

MedlinePlus

... whose health and safety are compromised by limited knowledge, understanding, and/or ability to access programs and benefits. Read More Read More Publication Managing Progressive MS An overview of symptom management, coping strategies when progressive MS makes the road ...

News! from the Naval Observatory - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You More... Naval Meteorology and Oceanography Command, 1100 Balch Blvd, Stennis Space Center, MS 39529

Ask the Librarian - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You Oceanography Command, 1100 Balch Blvd, Stennis Space Center, MS 39529 Fleet Forces Command | navy.com | Freedom

Age-dependent change in urine proteome of healthy individuals

NASA Astrophysics Data System (ADS)

Dobrokhotov, Igor; Liudmila Pastushkova, MRS.; Larina, Irina; Kononikhin, Alexey

It was analyzed the protein composition of urine samples obtained from twenty Russian cosmonauts and thirty-eight healthy volunteers, that have been selected for the experiments simulating the physiological effects of microgravity. The special sample preparation was performed, followed by liquid chromatography-mass spectrometry. Liquid chromatography-mass spectrometry of the minor proteins was performed on a nano-HPLC Agilent 1100 system (Agilent Technologies Inc., USA) in combination with a LTQ-FT Ultra mass spectrometer (Thermo Electron, Germany). List of masses derived peptides and they fragments have used for search and identification of proteins by database IPI-human (international index of protein) using the program Mascot (MS version 2.0.04 , UK) according to the following criteria: 1 - enzyme-trypsin; 2 - peptide tol. ± 5 ppm; 3 - MS / MS tol. 0.5Da. From list of proteins obtained as a result Mascot-search it was selected only those proteins that were identified based on 2 or more peptides with the rating more than 24. Analysis of the list of proteins was performed using software developed in the laboratory of VA Ivanisenko (ICG SB RAS) Age of healthy individuals was ranged from 18 to 54 years. Depending on the age, the data were divided into three groups: those relating to the group of persons under 25 years (youth and mature age 1), 25-40 years (mature age 2) and 40-54 years (mature age 3) It was detected reliable changes in the number of proteins among groups depending of the age. It was found that the minimum number of different proteins were detected in the urine of the group of young patients (under 25 years old) , and the maximum - was observed in the group of middle-aged persons (25 to 40 years). When the proteins were compared according to their molecular mass it was revealed that in the older group (40-54 years ) there is noticeably smaller percentage of high molecular weight proteins than in groups of young and middle aged persons. Thus, proteomic studies of urine samples can detect reliable age differences between groups of subjects, reflecting both age-specific features of processes of protein reabsorption by the kidneys, and the aging process in general.

Multiple sclerosis pathways: an innovative nursing role in disease management.

PubMed

Madonna, M G; Keating, M M

1999-12-01

Multiple sclerosis (MS), a chronic disease of the central nervous system, is characterized by a variable and unpredictable course. The most common pattern of the disease is the relapsing-remitting form in which clearly defined relapses (also called exacerbations) are followed by complete or incomplete recovery. Interferon beta-1b (Betaseron), a drug that affects the natural course of the disease, was developed for the treatment of relapsing-remitting MS. Multiple Sclerosis Pathways (MSP), a disease management program, was developed to provide comprehensive and personal support to MS patients taking interferon beta-1b and to serve as an information resource for all people with MS, their families, and healthcare professionals. The MSP program includes personal patient assistance, reimbursement services, a 24-hour nurse hotline, training program, educational resources, and injection supplies. The nurse hotline counselor (NHC) utilizes the nursing process in a unique telephone nursing practice in this program. The positive impact of education and support on adherence to therapy has been validated by training and nurse hotline data.

Timing and context of dolphin clicks during and after mine simulator detection and marking in the open ocean

PubMed Central

Dibble, Dianna S.; Kennemer, Jaime A.

2018-01-01

ABSTRACT Two dolphins carrying cameras swam in the ocean as they searched for and marked mine simulators – buried, proud or moored. As the animals swam ahead of a boat they searched the ocean. Cameras on their harness recorded continuous sound and video. Once a target was detected, the dolphins received a marker to take to the simulator's location. During search and detection, dolphins made almost continuous trains of varying interval clicks. During the marking phase, shorter click trains were interrupted by periods of silence. As the dolphins marked simulators, they often produced victory squeals – pulse bursts that vary in duration, peak frequency and amplitude. Victory squeals were produced on 72% of marks. Sometimes after marking, or at other times during their long swims, the dolphins produced click packets. Packets typically consisted of two to 10 clicks with inter-click intervals of 7-117 ms followed by a silence of 223-983 ms. Click packets appeared unrelated with searching or marking. We suggest that the packets were used to improve signal to noise ratios for locating a boat or other distant object. Victory squeals produced when marking the targets suggest to us that the dolphins know when they have succeeded in this multipart task. PMID:29463515

Timing and context of dolphin clicks during and after mine simulator detection and marking in the open ocean.

PubMed

Ridgway, Sam H; Dibble, Dianna S; Kennemer, Jaime A

2018-02-20

Two dolphins carrying cameras swam in the ocean as they searched for and marked mine simulators - buried, proud or moored. As the animals swam ahead of a boat they searched the ocean. Cameras on their harness recorded continuous sound and video. Once a target was detected, the dolphins received a marker to take to the simulator's location. During search and detection, dolphins made almost continuous trains of varying interval clicks. During the marking phase, shorter click trains were interrupted by periods of silence. As the dolphins marked simulators, they often produced victory squeals - pulse bursts that vary in duration, peak frequency and amplitude. Victory squeals were produced on 72% of marks. Sometimes after marking, or at other times during their long swims, the dolphins produced click packets. Packets typically consisted of two to 10 clicks with inter-click intervals of 7-117 ms followed by a silence of 223-983 ms. Click packets appeared unrelated with searching or marking. We suggest that the packets were used to improve signal to noise ratios for locating a boat or other distant object. Victory squeals produced when marking the targets suggest to us that the dolphins know when they have succeeded in this multipart task. © 2018. Published by The Company of Biologists Ltd.

Storage and retrieval of digital images in dermatology.

PubMed

Bittorf, A; Krejci-Papa, N C; Diepgen, T L

1995-11-01

Differential diagnosis in dermatology relies on the interpretation of visual information in the form of clinical and histopathological images. Up until now, reference images have had to be retrieved from textbooks and/or appropriate journals. To overcome inherent limitations of those storage media with respect to the number of images stored, display, and search parameters available, we designed a computer-based database of digitized dermatologic images. Images were taken from the photo archive of the Dermatological Clinic of the University of Erlangen. A database was designed using the Entity-Relationship approach. It was implemented on a PC-Windows platform using MS Access* and MS Visual Basic®. As WWW-server a Sparc 10 workstation was used with the CERN Hypertext-Transfer-Protocol-Daemon (httpd) 3.0 pre 6 software running. For compressed storage on a hard drive, a quality factor of 60 allowed on-screen differential diagnosis and corresponded to a compression factor of 1:35 for clinical images and 1:40 for histopathological images. Hierarchical keys of clinical or histopathological criteria permitted multi-criteria searches. A script using the Common Gateway Interface (CGI) enabled remote search and image retrieval via the World-Wide-Web (W3). A dermatologic image database, featurig clinical and histopathological images was constructed which allows for multi-parameter searches and world-wide remote access.

A master-slave parallel hybrid multi-objective evolutionary algorithm for groundwater remediation design under general hydrogeological conditions

NASA Astrophysics Data System (ADS)

Wu, J.; Yang, Y.; Luo, Q.; Wu, J.

2012-12-01

This study presents a new hybrid multi-objective evolutionary algorithm, the niched Pareto tabu search combined with a genetic algorithm (NPTSGA), whereby the global search ability of niched Pareto tabu search (NPTS) is improved by the diversification of candidate solutions arose from the evolving nondominated sorting genetic algorithm II (NSGA-II) population. Also, the NPTSGA coupled with the commonly used groundwater flow and transport codes, MODFLOW and MT3DMS, is developed for multi-objective optimal design of groundwater remediation systems. The proposed methodology is then applied to a large-scale field groundwater remediation system for cleanup of large trichloroethylene (TCE) plume at the Massachusetts Military Reservation (MMR) in Cape Cod, Massachusetts. Furthermore, a master-slave (MS) parallelization scheme based on the Message Passing Interface (MPI) is incorporated into the NPTSGA to implement objective function evaluations in distributed processor environment, which can greatly improve the efficiency of the NPTSGA in finding Pareto-optimal solutions to the real-world application. This study shows that the MS parallel NPTSGA in comparison with the original NPTS and NSGA-II can balance the tradeoff between diversity and optimality of solutions during the search process and is an efficient and effective tool for optimizing the multi-objective design of groundwater remediation systems under complicated hydrogeologic conditions.

Use of an informed search space maximizes confidence of site-specific assignment of glycoprotein glycosylation.

PubMed

Khatri, Kshitij; Klein, Joshua A; Zaia, Joseph

2017-01-01

In order to interpret glycopeptide tandem mass spectra, it is necessary to estimate the theoretical glycan compositions and peptide sequences, known as the search space. The simplest way to do this is to build a naïve search space from sets of glycan compositions from public databases and to assume that the target glycoprotein is pure. Often, however, purified glycoproteins contain co-purified glycoprotein contaminants that have the potential to confound assignment of tandem mass spectra based on naïve assumptions. In addition, there is increasing need to characterize glycopeptides from complex biological mixtures. Fortunately, liquid chromatography-mass spectrometry (LC-MS) methods for glycomics and proteomics are now mature and accessible. We demonstrate the value of using an informed search space built from measured glycomes and proteomes to define the search space for interpretation of glycoproteomics data. We show this using α-1-acid glycoprotein (AGP) mixed into a set of increasingly complex matrices. As the mixture complexity increases, the naïve search space balloons and the ability to assign glycopeptides with acceptable confidence diminishes. In addition, it is not possible to identify glycopeptides not foreseen as part of the naïve search space. A search space built from released glycan glycomics and proteomics data is smaller than its naïve counterpart while including the full range of proteins detected in the mixture. This maximizes the ability to assign glycopeptide tandem mass spectra with confidence. As the mixture complexity increases, the number of tandem mass spectra per glycopeptide precursor ion decreases, resulting in lower overall scores and reduced depth of coverage for the target glycoprotein. We suggest use of α-1-acid glycoprotein as a standard to gauge effectiveness of analytical methods and bioinformatics search parameters for glycoproteomics studies. Graphical Abstract Assignment of site specific glycosylation from LC-tandemMS data.

Multiple Sclerosis Epidemiology in East Asia, South East Asia and South Asia: A Systematic Review.

PubMed

Eskandarieh, Sharareh; Heydarpour, Pouria; Minagar, Alireza; Pourmand, Shadi; Sahraian, Mohammad Ali

2016-01-01

Multiple sclerosis (MS) is one of the most common chronic immune-mediated diseases of the human central nervous system and an important cause of non-traumatic neurologic disability among young population in several countries. Recent reports from East Asia, South East Asia and South Asia have proposed a low to moderate prevalence of MS in these countries. A literature review search was carried out in December 2014 in Medline, Embase, Scopus and Cochrane library to recover original population-based studies on MS epidemiology in East Asia, South East Asia and South Asia countries published between January 1, 1950 and December 30, 2014. We intended search strategies using the key words: multiple sclerosis, prevalence, incidence and epidemiology. Based on our inclusion criteria, 68 epidemiologic studies were included in this systematic review. The most extensively used diagnostic criteria in the studies were McDonald's criteria. Most studies were performed in a multi-center hospital setting. The female to male ratio varied and ranged from 0.7 in India to 9.0 in China. The mean age at disease onset ranged from the lowest age of 25.3 in Iran to the highest age of 46.4 in China. MS prevalence ranged from 0.77 in 100,000 populations in Hong Kong (1999) to 85.80 in 100,000 in Iran (2013). Advances in MS registries around the globe allow nationwide population-based studies and will allow worldly comparisons between the prevalence and incidence in different regions that are provided to monitor estimation. © 2016 S. Karger AG, Basel.

Untargeted metabolomic profiling plasma samples of patients with lung cancer for searching significant metabolites by HPLC-MS method

NASA Astrophysics Data System (ADS)

Dementeva, N.; Ivanova, K.; Kokova, D.; Kurzina, I.; Ponomaryova, A.; Kzhyshkowska, J.

2017-09-01

Lung cancer is one of the most common types of cancer leading to death. Consequently, the search and the identification of the metabolites associated with the risk of developing cancer are very valuable. For the purpose, untargeted metabolic profiling of the plasma samples collected from the patients with lung cancer (n = 100) and the control group (n = 100) was conducted. After sample preparation, the plasma samples were analyzed using LC-MS method. Biostatistics methods were applied to pre-process the data for elicitation of dominating metabolites which responded to the difference between the case and the control groups. At least seven significant metabolites were evaluated and annotated. The most part of identified metabolites are connected with lipid metabolism and their combination could be useful for follow-up studies of lung cancer pathogenesis.

Profiling of Histone Post-Translational Modifications in Mouse Brain with High-Resolution Top-Down Mass Spectrometry

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

Zhou, Mowei; Paša-Tolić, Ljiljana; Stenoien, David L.

Histones play central roles in most chromosomal functions and both their basic biology and roles in disease have been the subject of intense study. Since multiple PTMs along the entire protein sequence are potential regulators of histones, a top-down approach, where intact proteins are analyzed, is ultimately required for complete characterization of proteoforms. However, significant challenges remain for top-down histone analysis primarily because of deficiencies in separation/resolving power and effective identification algorithms. Here, we used state of the art mass spectrometry and a bioinformatics workflow for targeted data analysis and visualization. The workflow uses ProMex for intact mass deconvolution, MSPathFindermore » as search engine, and LcMsSpectator as a data visualization tool. ProMex sums across retention time to maximize sensitivity and accuracy for low abundance species in MS1deconvolution. MSPathFinder searches the MS2 data against protein sequence databases with user-defined modifications. LcMsSpectator presents the results from ProMex and MSPathFinder in a format that allows quick manual evaluation of critical attributes for high-confidence identifications. When complemented with the open-modification tool TopPIC, this workflow enabled identification of novel histone PTMs including tyrosine bromination on histone H4 and H2A, H3 glutathionylation, and mapping of conventional PTMs along the entire protein for many histone subunits.« less

Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei.

PubMed

Cassidy, Liam; Prasse, Daniela; Linke, Dennis; Schmitz, Ruth A; Tholey, Andreas

2016-10-07

The recent discovery of an increasing number of small open reading frames (sORF) creates the need for suitable analytical technologies for the comprehensive identification of the corresponding gene products. For biological and functional studies the knowledge of the entire set of proteins and sORF gene products is essential. Consequently in the present study we evaluated analytical approaches that will allow for simultaneous analysis of widest parts of the proteome together with the predicted sORF. We performed a full proteome analysis of the methane producing archaeon Methanosarcina mazei strain Gö1 cytosolic proteome using a high/low pH reversed phase LC-MS bottom-up approach. The second analytical approach was based on semi-top-down strategy, encompassing a separation at intact protein level using a GelFree system, followed by digestion and LC-MS analysis. A high overlap in identified proteins was found for both approaches yielding the most comprehensive coverage of the cytosolic proteome of this organism achieved so far. The application of the second approach in combination with an adjustment of the search criteria for database searches further led to a significant increase of sORF peptide identifications, finally allowing to detect and identify 28 sORF gene products.

Preprocessing Significantly Improves the Peptide/Protein Identification Sensitivity of High-resolution Isobarically Labeled Tandem Mass Spectrometry Data*

PubMed Central

Sheng, Quanhu; Li, Rongxia; Dai, Jie; Li, Qingrun; Su, Zhiduan; Guo, Yan; Li, Chen; Shyr, Yu; Zeng, Rong

2015-01-01

Isobaric labeling techniques coupled with high-resolution mass spectrometry have been widely employed in proteomic workflows requiring relative quantification. For each high-resolution tandem mass spectrum (MS/MS), isobaric labeling techniques can be used not only to quantify the peptide from different samples by reporter ions, but also to identify the peptide it is derived from. Because the ions related to isobaric labeling may act as noise in database searching, the MS/MS spectrum should be preprocessed before peptide or protein identification. In this article, we demonstrate that there are a lot of high-frequency, high-abundance isobaric related ions in the MS/MS spectrum, and removing isobaric related ions combined with deisotoping and deconvolution in MS/MS preprocessing procedures significantly improves the peptide/protein identification sensitivity. The user-friendly software package TurboRaw2MGF (v2.0) has been implemented for converting raw TIC data files to mascot generic format files and can be downloaded for free from https://github.com/shengqh/RCPA.Tools/releases as part of the software suite ProteomicsTools. The data have been deposited to the ProteomeXchange with identifier PXD000994. PMID:25435543

Microdose clinical trial: quantitative determination of nicardipine and prediction of metabolites in human plasma.

PubMed

Yamane, Naoe; Takami, Tomonori; Tozuka, Zenzaburo; Sugiyama, Yuichi; Yamazaki, Akira; Kumagai, Yuji

2009-01-01

A sample treatment procedure and high-sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for quantitative determination of nicardipine in human plasma were developed for a microdose clinical trial with nicardipine, a non-radioisotope labeled drug. The calibration curve was linear in the range of 1-500 pg/mL using 1 mL of plasma. Analytical method validation for the clinical dose, for which the calibration curve was linear in the range of 0.2-100 ng/mL using 20 microL of plasma, was also conducted. Each method was successfully applied to making determinations in plasma using LC/MS/MS after administration of a microdose (100 microg) and clinical dose (20 mg) to each of six healthy volunteers. We tested new approaches in the search for metabolites in plasma after microdosing. In vitro metabolites of nicardipine were characterized using linear ion trap-fourier transform ion cyclotron resonance mass spectrometry (LIT-FTICRMS) and the nine metabolites predicted to be in plasma were analyzed using LC/MS/MS. There is a strong possibility that analysis of metabolites by LC/MS/MS may advance to utilization in microdose clinical trials with non-radioisotope labeled drugs.

Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry.

PubMed

Huan, Tao; Li, Liang

2015-07-21

Generating precise and accurate quantitative information on metabolomic changes in comparative samples is important for metabolomics research where technical variations in the metabolomic data should be minimized in order to reveal biological changes. We report a method and software program, IsoMS-Quant, for extracting quantitative information from a metabolomic data set generated by chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS). Unlike previous work of relying on mass spectral peak ratio of the highest intensity peak pair to measure relative quantity difference of a differentially labeled metabolite, this new program reconstructs the chromatographic peaks of the light- and heavy-labeled metabolite pair and then calculates the ratio of their peak areas to represent the relative concentration difference in two comparative samples. Using chromatographic peaks to perform relative quantification is shown to be more precise and accurate. IsoMS-Quant is integrated with IsoMS for picking peak pairs and Zero-fill for retrieving missing peak pairs in the initial peak pairs table generated by IsoMS to form a complete tool for processing CIL LC-MS data. This program can be freely downloaded from the www.MyCompoundID.org web site for noncommercial use.

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2014-07-01 2014-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2011-07-01 2011-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

37 CFR 1.96 - Submission of computer program listings.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Apple Macintosh; (ii) Operating System Compatibility: MS-DOS, MS-Windows, Unix, or Macintosh; (iii) Line... 37 Patents, Trademarks, and Copyrights 1 2012-07-01 2012-07-01 false Submission of computer... Models, Exhibits, Specimens § 1.96 Submission of computer program listings. (a) General. Descriptions of...

Joint Services Electronics Program

DTIC Science & Technology

1990-07-31

Raghunath , Mandayam M.S. 88 Raman, Shankar M.S. 88 Scheckler, Ed M.S. 88 Song. Joon Ph. D. 88 Tsay, Jcnngang M.S. 89 Tsay, Rcn-Song Ph.D. 89 Vakhshoori...from Planar Resonators," submitted for publication to IEEE Trans. on Microwave Theory and Techniques, on April 17, 1990. Ranade M.T. Raghunath and A.G

Application of LC/MS/MS Techniques to Development of US EPA Standardized Methods for Chemicals of Emerging Concern

EPA Science Inventory

This presentation will describe the U.S. EPA’s drinking water and ambient water method development program in relation to the process employed and the typical challenges encountered in developing standardized LC/MS/MS methods for chemicals of emerging concern. The EPA&rsquo...

40 CFR 122.32 - As an operator of a small MS4, am I regulated under the NPDES storm water program?

Code of Federal Regulations, 2014 CFR

2014-07-01

... regulated under the NPDES storm water program? 122.32 Section 122.32 Protection of Environment ENVIRONMENTAL... operator of a small MS4, am I regulated under the NPDES storm water program? (a) Unless you qualify for a... a petition to the NPDES permitting authority to require an NPDES permit for your discharge of storm...

40 CFR 122.32 - As an operator of a small MS4, am I regulated under the NPDES storm water program?

Code of Federal Regulations, 2012 CFR

2012-07-01

... regulated under the NPDES storm water program? 122.32 Section 122.32 Protection of Environment ENVIRONMENTAL... operator of a small MS4, am I regulated under the NPDES storm water program? (a) Unless you qualify for a... a petition to the NPDES permitting authority to require an NPDES permit for your discharge of storm...

40 CFR 122.32 - As an operator of a small MS4, am I regulated under the NPDES storm water program?

Code of Federal Regulations, 2013 CFR

2013-07-01

... regulated under the NPDES storm water program? 122.32 Section 122.32 Protection of Environment ENVIRONMENTAL... operator of a small MS4, am I regulated under the NPDES storm water program? (a) Unless you qualify for a... a petition to the NPDES permitting authority to require an NPDES permit for your discharge of storm...

Use and acceptance of electronic communication by patients with multiple sclerosis: a multicenter questionnaire study.

PubMed

Haase, Rocco; Schultheiss, Thorsten; Kempcke, Raimar; Thomas, Katja; Ziemssen, Tjalf

2012-10-15

The number of multiple sclerosis (MS) information websites, online communities, and Web-based health education programs has been increasing. However, MS patients' willingness to use new ways of communication, such as websites, mobile phone application, short message service, or email with their physician, remains unknown. We designed a questionnaire to evaluate the a priori use of electronic communication methods by MS patients and to assess their acceptance of such tools for communication with their health care providers. We received complete data from 586 MS patients aged between 17 and 73 years. Respondents were surveyed in outpatient clinics across Germany using a novel paper-and-pencil questionnaire. In addition to demographics, the survey items queried frequency of use of, familiarity with, and comfort with using computers, websites, email, and mobile phones. About 90% of all MS patients used a personal computer (534/586) and the Internet (527/586) at least once a week, 87.0% (510/586) communicated by email, and 85.6% (488/570) communicated by mobile phone. When asked about their comfort with using electronic communication methods for communication with health care providers, 20.5% (120/586) accepted communication by mobile Internet application or short message service via mobile phone, 41.0% (240/586) by websites, 54.3% (318/586) by email service, and 67.8% (397/586) by at least one type of electronic communication. The level of a priori use was the best predictor for the acceptance of electronic communication with health care providers. Patients who reported already searching online for health information (odds ratio 2.4, P < .001) and who had already communicated with a physician through a website (odds ratio 3.3, P = .03) reported higher acceptance for Web-based communication. Patients who already scheduled appointments with their mobile phones (odds ratio 2.1, P = .002) were more likely to accept the use of mobile phone applications or short message service for communicating with their physician. The majority of MS patients seen at specialist centers already use modern communication technology regularly. New forms of electronic communication appear to have high levels of acceptance for exchanging information about MS between patients and health care providers. Such methods should be integrated into eHealth services such as electronic health records and patient relationship management systems.

Individual and Collective Protection Program

DTIC Science & Technology

2007-11-30

98 8.2.1 PREPARATION OF STOCK SUSPENSION OF MS2 COLIPHAGE ...103 8.3.1 PROCEDURE FOR ASSAYING MS2 COLIPHAGE ...CHALLENGE NUMBER OF TEST MICROORGANISMS..................106 8.4.1 METHOD FOR DETERMINATION OF CHALLENGE NUMBER OF MS2 COLIPHAGE

VizieR Online Data Catalog: Pan-Pacific Planet Search (PPPS) I. 7 CMa (Wittenmyer+, 2011)

NASA Astrophysics Data System (ADS)

Wittenmyer, R. A.; Endl, M.; Wang, L.; Johnson, J. A.; Tinney, C. G.; O'Toole, S. J.

2013-05-01

The "Pan-Pacific Planet Search" (PPPS) originated as a Southern Hemisphere extension of the established Lick & Keck Observatory survey for planets orbiting Northern "retired A stars" (Johnson et al. 2006ApJ...652.1724J, 2007ApJ...665..785J, 2010PASP..122..905J). This program is using the 3.9m Anglo-Australian Telescope (AAT) to observe a metal-rich sample of Southern Hemisphere subgiants. Observations for the PPPS began at the AAT in 2009 February. Observing time is scheduled such that each target should receive 4-6 observations per year. PPPS Doppler measurements are made with the UCLES echelle spectrograph (at the 3.9m AAT) which achieves a resolution of 45000 with a 1 arcsec slit. We have observed 7 CMa on 21 epochs, and an iodine-free template observation was obtained on 2010 January 30. Since 7 CMa is an extremely bright star, exposure times ranged from 100 to 500s, with a resulting S/N of ~200-300/pixel each epoch. The data span a total of 917 days and have a mean internal velocity uncertainty of 6.5m/s. (2 data files).

Liquid chromatography with high resolution mass spectrometry for identification of organic contaminants in fish fillet: screening and quantification assessment using two scan modes for data acquisition.

PubMed

Munaretto, Juliana S; May, Marília M; Saibt, Nathália; Zanella, Renato

2016-07-22

This study proposed a strategy to identify and quantify 182 organic contaminants from different chemical classes, as for instance pesticides, veterinary drug and personal care products, in fish fillet using liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QToF/MS). For this purpose, two different scan methods (full scan and all ions MS/MS) were evaluated to assess the best option for screening analysis in spiked fish fillet samples. In general, full scan acquisition was found to be more reliable (84%) in the automatic identification and quantification when compared to all ions MS/MS with 72% of the compounds detected. Additionally, a qualitative automatic search showed a mass accuracy error below 5ppm for 77% of the compounds in full scan mode compared to only 52% in all ions MS/MS scan. However, all ions MS/MS provides fragmentation information of the target compounds. Undoubtedly, structural information of a wide number of compounds can be obtained using high resolution mass spectrometry (HRMS), but it is necessary thoroughly assess it, in order to choose the best scan mode. Copyright © 2016 Elsevier B.V. All rights reserved.

Georgetown University and Hampton University Prostate Cancer Undergraduate Fellowship Program

DTIC Science & Technology

2015-10-01

Tyanna Jones-Gray (Dr. Vicente Notario), Ms. Damara Miller (Dr. Eliot Rosen), Ms. Jasmine Hatcher-Moorman (Dr. MaryBeth Martin), and Mr. Isaiah Brown...undergraduate students: 1. The Hampton University undergraduates (Ms. Tyanna Jones-Gray, Ms. Damara Miller, Ms. Jasmine Hatcher-Moorman, and Mr...cancer progression. Dr. Martin’s lab has identified the environmental hormones referred to as metallo- hormones. In Dr. Martin’s laboratory, Jasmine

40 CFR 122.37 - Will the small MS4 storm water program regulations at §§ 122.32 through 122.36 and § 123.35 of...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 21 2010-07-01 2010-07-01 false Will the small MS4 storm water program regulations at §§ 122.32 through 122.36 and § 123.35 of this chapter change in the future? 122.37 Section 122.37 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS EPA ADMINISTERED PERMIT PROGRAMS: THE NATIONAL...

40 CFR 122.37 - Will the small MS4 storm water program regulations at §§ 122.32 through 122.36 and § 123.35 of...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 22 2011-07-01 2011-07-01 false Will the small MS4 storm water program regulations at §§ 122.32 through 122.36 and § 123.35 of this chapter change in the future? 122.37 Section 122.37 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS EPA ADMINISTERED PERMIT PROGRAMS: THE NATIONAL...

Urine Multi-drug Screening with GC-MS or LC-MS-MS Using SALLE-hybrid PPT/SPE.

PubMed

Lee, Junhui; Park, Jiwon; Go, Ahra; Moon, Heesung; Kim, Sujin; Jung, Sohee; Jeong, Wonjoon; Chung, Heesun

2018-05-14

To intoxicated patients in the emergency room, toxicological analysis can be considerably helpful for identifying the involved toxicants. In order to develop a urine multi-drug screening (UmDS) method, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS-MS) were used to determine targeted and unknown toxicants in urine. A GC-MS method in scan mode was validated for selectivity, limit of detection (LOD) and recovery. An LC-MS-MS multiple reaction monitoring (MRM) method was validated for lower LOD, recovery and matrix effect. The results of the screening analysis were compared with patient medical records to check the reliability of the screen. Urine samples collected from an emergency room were extracted through a combination of salting-out assisted liquid-liquid extraction (SALLE) and hybrid protein precipitation/solid phase extraction (hybrid PPT/SPE) plates and examined by GC-MS and LC-MS-MS. GC-MS analysis was performed as unknown drug screen and LC-MS-MS analysis was conducted as targeted drug screen. After analysis by GC-MS, a library search was conducted using an in-house library established with the automated mass spectral deconvolution and identification system (AMDISTM). LC-MS-MS used Cliquid®2.0 software for data processing and acquisition in MRM mode. An UmDS method by GC-MS and LC-MS-MS was developed by using a SALLE-hybrid PPT/SPE and in-house library. The results of UmDS by GC-MS and LC-MS-MS showed that toxicants could be identified from 185 emergency room patient samples containing unknown toxicants. Zolpidem, acetaminophen and citalopram were the most frequently encountered drugs in emergency room patients. The UmDS analysis developed in this study can be used effectively to detect toxic substances in a short time. Hence, it could be utilized in clinical and forensic toxicology practices.

The role of exercise in modifying outcomes for people with multiple sclerosis: a randomized trial

PubMed Central

2013-01-01

Background Despite the commonly known benefits of exercise and physical activity evidence shows that persons Multiple Sclerosis (MS) are relatively inactive yet physical activity may be even more important in a population facing functional deterioration. No exercise is effective if it is not done and people with MS face unique barriers to exercise engagement which need to be overcome. We have developed and pilot tested a Multiple Sclerosis Tailored Exercise Program (MSTEP) and it is ready to be tested against general guidelines for superiority and ultimately for its impact on MS relevant outcomes. The primary research question is to what extent does an MS Tailored Exercise Program (MSTEP) result in greater improvements in exercise capacity and related outcomes over a one year period in comparison to a program based on general guidelines for exercise among people with MS who are sedentary and wish to engage in exercise as part of MS self-management. Methods/Design The proposed study is an assessor-blind, parallel-group, randomized controlled trial (RCT). The duration of the intervention will be one year with follow-up to year two. The targeted outcomes are exercise capacity, functional ambulation, strength, and components of quality of life including frequency and intensity of fatigue symptoms, mood, global physical function, health perception, and objective measures of activity level. Logistic regression will be used to test the main hypothesis related to the superiority of the MSTEP program based on a greater proportion of people making a clinically relevant gain in exercise capacity at 1 year and at 2 years, using an intention-to-treat approach. Sample size will be 240 (120 per group). Discussion The MS community is clearly looking for interventions to help alleviate the disabling sequelae of MS and promote health. Exercise is a well-known intervention which has known benefits to all, yet few exercise regularly. For people with MS, the role of exercise in MS management needs to be rigorously assessed to inform people as to how best to use exercise to reduce disability and promote health. Trial registration Clinical Trials.gov: NCT01611987 PMID:23809312

Modeling and Simulation Verification, Validation and Accreditation (VV&A): A New Undertaking for the Exploration Systems Mission Directorate

NASA Technical Reports Server (NTRS)

Prill, Mark E.

2005-01-01

and Accreditation (VV&A) session audience, a snapshot review of the Exploration Space Mission Directorate s (ESMD) investigation into implementation of a modeling and simulation (M&S) VV&A program. The presentation provides some legacy ESMD reference material, including information on the then-current organizational structure, and M&S (Simulation Based Acquisition (SBA)) focus contained therein, to provide a context for the proposed M&S VV&A approach. This reference material briefly highlights the SBA goals and objectives, and outlines FY05 M&S development and implementation consistent with the Subjective Assessment, Constructive Assessment, Operator-in-the-Loop Assessment, Hardware-in-the-Loop Assessment, and In Service Operations Assessment M&S construct, the NASA Exploration Information Ontology Model (NExIOM) data model, and integration with the Windchill-based Integrated Collaborative Environment (ICE). The presentation then addresses the ESMD team s initial conclusions regarding an M&S VV&A program, summarizes the general VV&A implementation approach anticipated, and outlines some of the recognized VV&A program challenges, all within a broader context of the overarching Integrated Modeling and Simulation (IM&S) environment at both the ESMD and Agency (NASA) levels. The presentation concludes with a status on the current M&S organization s progress to date relative to the recommended IM&S implementation activity. The overall presentation was focused to provide, for the Verification, Validation,

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

PubMed

Peterson, Elena S; McCue, Lee Ann; Schrimpe-Rutledge, Alexandra C; Jensen, Jeffrey L; Walker, Hyunjoo; Kobold, Markus A; Webb, Samantha R; Payne, Samuel H; Ansong, Charles; Adkins, Joshua N; Cannon, William R; Webb-Robertson, Bobbie-Jo M

2012-04-05

The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

PubMed Central

2012-01-01

Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php. PMID:22480257

Characterization of Vertical Impact Device Acceleration Pulses Using Parametric Assessment: Phase IV Dual Impact Pulses

DTIC Science & Technology

2017-01-04

response, including the time for reviewing instructions, searching existing data sources, searching existing data sources, gathering and maintaining...configurations with a restrained manikin, was evaluated in four different test series . Test Series 1 was conducted to determine the materials and...5 ms TTP. Test Series 2 was conducted to determine the materials and drop heights required for energy attenuation of the seat pan to generate a 4 m

Assessment of potential false positives via orbitrap-based untargeted lipidomics from rat tissues.

PubMed

Xu, Lina; Wang, Xueying; Jiao, Yupei; Liu, Xiaohui

2018-02-01

Untargeted lipidomics is increasingly popular due to the broad coverage of lipid species. Data dependent MS/MS acquisition is commonly used in order to acquire sufficient information for confident lipid assignment. However, although lipids are identified based on MS/MS confirmation, a number of false positives are still observed. Here, we discuss several causes of introducing lipid false identifications in untargeted analysis. Phosphotidylcholines and cholesteryl esters generate in-source fragmentation to produce dimethylated phosphotidylethanolamine and free cholesterol. Dimerization of fatty acid results in false identification of fatty acid ester of hydroxyl fatty acid. Realizing these false positives is able to improve confidence of results acquired from untargeted analysis. Besides, thresholds are established for lipids identified using LipidSearch v4.1.16 software to reduce unreliable results. Copyright © 2017 Elsevier B.V. All rights reserved.

Mind-Body Medicine for Multiple Sclerosis: A Systematic Review

PubMed Central

Senders, Angela; Wahbeh, Helané; Spain, Rebecca; Shinto, Lynne

2012-01-01

Background. Mind-body therapies are used to manage physical and psychological symptoms in many chronic health conditions. Objective. To assess the published evidence for using mind-body techniques for symptom management of multiple sclerosis. Methods. MEDLINE, PsycINFO, and Cochrane Clinical Trials Register were searched from inception to March 24, 2012. Eleven mind-body studies were reviewed (meditation, yoga, biofeedback, hypnosis, relaxation, and imagery). Results. Four high quality trials (yoga, mindfulness, relaxation, and biofeedback) were found helpful for a variety of MS symptoms. Conclusions. The evidence for mind-body medicine in MS is limited, yet mind-body therapies are relatively safe and may provide a nonpharmacological benefit for MS symptoms. PMID:23227313

75 FR 35962 - Special Evaluation Assistance for Rural Communities and Households Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-24

... and Households (SEARCH) Program as authorized by Section 306(a)(2) of the Consolidated Farm and Rural Development Act (CONACT) (7 U.S.C. 1926(a)(2)). The amendment added the new SEARCH grant program under which... Assistance for Rural Communities and Households Program (SEARCH). This catalog is available on a subscription...

50 CFR 660.150 - Mothership (MS) Coop Program.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Mothership (MS) Coop Program. 660.150 Section 660.150 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES West Coast Groundfish-Limited Entry Trawl Fisheries § 660.15...

PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences.

PubMed

Ferro, Myriam; Tardif, Marianne; Reguer, Erwan; Cahuzac, Romain; Bruley, Christophe; Vermat, Thierry; Nugues, Estelle; Vigouroux, Marielle; Vandenbrouck, Yves; Garin, Jérôme; Viari, Alain

2008-05-01

PepLine is a fully automated software which maps MS/MS fragmentation spectra of trypsic peptides to genomic DNA sequences. The approach is based on Peptide Sequence Tags (PSTs) obtained from partial interpretation of QTOF MS/MS spectra (first module). PSTs are then mapped on the six-frame translations of genomic sequences (second module) giving hits. Hits are then clustered to detect potential coding regions (third module). Our work aimed at optimizing the algorithms of each component to allow the whole pipeline to proceed in a fully automated manner using raw nucleic acid sequences (i.e., genomes that have not been "reduced" to a database of ORFs or putative exons sequences). The whole pipeline was tested on controlled MS/MS spectra sets from standard proteins and from Arabidopsis thaliana envelope chloroplast samples. Our results demonstrate that PepLine competed with protein database searching softwares and was fast enough to potentially tackle large data sets and/or high size genomes. We also illustrate the potential of this approach for the detection of the intron/exon structure of genes.

Proteomic analysis of bovine nucleolus.

PubMed

Patel, Amrutlal K; Olson, Doug; Tikoo, Suresh K

2010-09-01

Nucleolus is the most prominent subnuclear structure, which performs a wide variety of functions in the eukaryotic cellular processes. In order to understand the structural and functional role of the nucleoli in bovine cells, we analyzed the proteomic composition of the bovine nucleoli. The nucleoli were isolated from Madin Darby bovine kidney cells and subjected to proteomic analysis by LC-MS/MS after fractionation by SDS-PAGE and strong cation exchange chromatography. Analysis of the data using the Mascot database search and the GPM database search identified 311 proteins in the bovine nucleoli, which contained 22 proteins previously not identified in the proteomic analysis of human nucleoli. Analysis of the identified proteins using the GoMiner software suggested that the bovine nucleoli contained proteins involved in ribosomal biogenesis, cell cycle control, transcriptional, translational and post-translational regulation, transport, and structural organization. Copyright © 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

Minorities Striving and Pursuing Higher Degrees of Success in Earth System Science (MS PHD'S) Beyond the PhD Professional Development Program: A Pilot Project

NASA Astrophysics Data System (ADS)

Johnson, A.; Jearld, A.; Williamson Whitney, V.; Huggans, M.; Ricciardi, L.; Thomas, S. H.; Jansma, P. E.

2012-12-01

In 2011 the Minorities Striving and Pursuing Higher Degrees of Success in Earth System Science (MS PHD'S)® initiative launched its newest activity entitled the MS PHD'S "Beyond the PhD (B-PhD) Professional Development Program." This exciting new program was designed to facilitate the development of a new community of underrepresented minority (URM) doctoral candidates and recent doctorate degree recipients in Earth system science (ESS)-related fields. The MS PHD'S B-PhD provides customized support and advocacy for MS PHD'S B-PhD participants in order to facilitate smoother and informed transitions from graduate school, to postdoctoral and tenure-track positions, as well as other "first" jobs in government, industry, and non-profit organizations. In November 2011 the first cohort of MS PHD'S B-PhD participants engaged in intensive sessions on the following topics: "Toolkits for Success for Academia, Business/Industry, Federal Government and Non-Profits", "Defining Short, Mid and Long Term Career Goals", "Accessing and Refining Skill Sets and Other Door Openers", "International Preparation and Opportunities", "Paying it Forward/Lifting as You Climb", and "Customized Strategies for Next Steps". This pilot event, which was hosted by the University of Texas at Arlington's (UTA) College of Science, also provided opportunities for participants to serve as guest lecturers in the UTA's Colleges of Science and Engineering and included one-on-one discussions with MS PHD'S B-PhD mentors and guest speakers who are well established within their individual ESS fields. Insights regarding opportunities, challenges and obstacles commonly faced by URMs within the ESS fields, as well as strategies for success were shared by MS PHD'S B-PhD mentors and guest speakers. Survey results indicate that MS PHD'S B-PhD participants appreciated not only the material covered during this pilot activity, but also appreciated the opportunity to become part of a community of young URM ESS professionals who are committed to achieving successful careers and supporting one another. This presentation will discuss outcomes from this pilot project, the use of social media to track and support ongoing MS PHD'S B-PhD activities, and "next steps" for the MS PHD'S B-PhD Professional Development Program.

Virtual reality in multiple sclerosis - A systematic review.

PubMed

Massetti, Thais; Trevizan, Isabela Lopes; Arab, Claudia; Favero, Francis Meire; Ribeiro-Papa, Denise Cardoso; de Mello Monteiro, Carlos Bandeira

2016-07-01

Multiple sclerosis (MS) is an inflammatory disease in which the insulating cover of nerve cells in the brain and spinal cord are damaged. The methods used for motor rehabilitation of patients with neurological problems require the performance of several rehabilitation exercises. Recently, studies related to the use of video game consoles have proliferated in the field of motor rehabilitation. Virtual reality (VR) has been proposed as a potentially useful tool for motoring assessment and rehabilitation. The purpose of this study was to investigate the results shown in previous studies on "Multiple Sclerosis" and "Virtual Reality". A bibliographic review was performed without time limitations. The research was carried out using PubMed and BVS databases. Considering keywords, we included articles that showed the terms "Multiple Sclerosis" and "Virtual Reality". The review was according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines The initial search yielded 41 articles. After the duplicates were removed, two authors independently evaluated the title and abstract of each of the articles with the study inclusion criteria. From these, 31 articles were excluded based on the title and abstract. Finally, 10 articles were isolated that met the inclusion criteria. VR represents a motivational and effective alternative to traditional motor rehabilitation for MS patients. The results showed that VR programs could be an effective method of patients with MS rehabilitation in multiple cognitive and / or motor deficits. Additional research is needed to support the rehabilitation protocols with VR and increase the effects of treatment. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of a virtual reality and treadmill training on gait of subjects with multiple sclerosis: a pilot study.

PubMed

Peruzzi, Agnese; Cereatti, Andrea; Della Croce, Ugo; Mirelman, Anat

2016-01-01

Gait and cognitive deficits are common in multiple sclerosis (MS) and are negatively affected during dual-task walking. Treadmill (TM) training has been previously used to preserve locomotor activity in MS. Virtual reality (VR) engages the user in cognitive and motor activities simultaneously. A training combining TM and VR has been successfully adopted in several neurological diseases, but not in MS. This study aims at investigating the feasibility of a VR-based TM training program on gait of subjects with MS. Eight persons with relapsing-remitting MS were recruited to participate in a six-week VR-based TM training program. Gait analysis was performed both in single and dual task conditions. Clinical tests were used to assess walking endurance and obstacle negotiation. All the evaluations were performed before, immediately and one month after the training. Gait speed and stride length improved in dual task post-intervention and were retained at follow-up. An improved ability in negotiating obstacles was found across the evaluations. VR-based TM training program is feasible and safe for MS subjects with moderate disabilities and may positively affect gait under complex conditions, such as dual tasking and obstacle negotiation. Copyright © 2015. Published by Elsevier B.V.

MS PHD'S: A Synergistic Model for Diversifying the Earth Science Community

NASA Astrophysics Data System (ADS)

Ricciardi, L.; Johnson, A.; Williamson Whitney, V.; Ithier-Guzman, W.; Braxton, L.; Johnson, A.

2013-05-01

The Minorities Striving and Pursuing Higher Degrees of Success in Earth System Science (MS PHD'S) program focuses on increasing the number of underrepresented minorities (URM) receiving advanced degrees in Earth system sciences (ESS). Subscribing to Aristotle's philosophy that the "whole is greater than the sum of its parts", MS PHD'S uses a synergistic model of tiered mentoring practices, successful minority scientist role models, peer-to-peer community building activities, professional development training techniques, networking opportunities, and state of the art virtual communication tools to facilitate the retention and advancement of underrepresented ESS scientists. Using a three-phase program structure supported by a virtual community, URM students in ESS are afforded opportunities to establish mentoring relationships with successful scientists, build meaningful ties with URM peers and future colleagues, strengthen oral and written communication skills, engage in networking opportunities within premier scientific venues, and maintain continuity of networks formed through program participation. Established in 2003, MS PHD'S is now in its ninth cohort. From the original cohort of 24 participants, the program has grown to support 213 participants. Of these 213 participants, 42 have obtained the doctorate and are employed within the ESS workforce. Another 71 are enrolled in doctoral programs. Looking to the future with the purpose of continually furthering its synergistic philosophy, MS PHD'S has developed a new initiative, Beyond the PhD, designed to support and advance the representation of URM scientists within a global workforce.

Managing the oral side-effects of medications used to treat multiple sclerosis.

PubMed

Cockburn, N; Pateman, K; Taing, M W; Pradhan, A; Ford, P J

2017-09-01

Many medications used to manage multiple sclerosis (MS) affect oral health. This review aimed to identify the oral side-effects of the current drugs recommended in Australia to treat MS and make dental practitioners aware of the range of symptoms. The Australian Therapeutic Guidelines and the Australian Medicines Handbook were searched for medications used to treat MS. For each medication, the generic name, class, route of administration, dosage and drug company reported side-effects were extracted from the online Monthly Index of Medical Specialties (MIMs) database. Meyler's Side-effect of Drugs Encyclopaedia was used to identify any additional oral adverse reactions to medications used to treat MS. Fourteen drugs were identified for the treatment of MS progression and 13 drugs for the treatment of MS symptoms. For these medications, 18 oral side-effects were documented: xerostomia was the most common, followed by dysgeusia, dysphagia, mouth ulceration and sinusitis. Anticholinergic drugs caused xerostomia while immunosuppressants resulted in more infection-related side-effects. Dental practitioners should be aware of the range of symptoms likely to be reported by this population. Clinicians are encouraged to continue providing dental care for their patients who develop MS and refer complex cases to specialists. © 2017 Australian Dental Association.

An Updated Meta-Analysis of Risk of Multiple Sclerosis following Infectious Mononucleosis

PubMed Central

Handel, Adam E.; Williamson, Alexander J.; Disanto, Giulio; Handunnetthi, Lahiru; Giovannoni, Gavin; Ramagopalan, Sreeram V.

2010-01-01

Background Multiple sclerosis (MS) appears to develop in genetically susceptible individuals as a result of environmental exposures. Epstein-Barr virus (EBV) infection is an almost universal finding among individuals with MS. Symptomatic EBV infection as manifested by infectious mononucleosis (IM) has been shown in a previous meta-analysis to be associated with the risk of MS, however a number of much larger studies have since been published. Methods/Principal Findings We performed a Medline search to identify articles published since the original meta-analysis investigating MS risk following IM. A total of 18 articles were included in this study, including 19390 MS patients and 16007 controls. We calculated the relative risk of MS following IM using a generic inverse variance with random effects model. This showed that the risk of MS was strongly associated with IM (relative risk (RR) 2.17; 95% confidence interval 1.97–2.39; p<10−54). Discussion Our results establish firmly that a history of infectious mononucleosis significantly increases the risk of multiple sclerosis. Future work should focus on the mechanism of this association and interaction with other risk factors. PMID:20824132

Decision-Making in Multiple Sclerosis Patients: A Systematic Review.

PubMed

Neuhaus, Mireille; Calabrese, Pasquale; Annoni, Jean-Marie

2018-01-01

Multiple sclerosis (MS) is frequently associated with cognitive and behavioural deficits. A growing number of studies suggest an impact of MS on decision-making abilities. The aim of this systematic review was to assess if (1) performance of MS patients in decision-making tasks was consistently different from controls and (2) whether this modification was associated with cognitive dysfunction and emotional alterations. The search was conducted on Pubmed/Medline database. 12 studies evaluating the difference between MS patients and healthy controls using validated decision-making tasks were included. Outcomes considered were quantitative (net scores) and qualitative measurements (deliberation time and learning from feedback). Quantitative and qualitative decision-making impairment in MS was present in 64.7% of measurements. Patients were equally impaired in tasks for decision-making under risk and ambiguity. A correlation to other cognitive functions was present in 50% of cases, with the highest associations in the domains of processing speed and attentional capacity. In MS patients, qualitative and quantitative modifications may be present in any kind of decision-making task and can appear independently of other cognitive measures. Since decision-making abilities have a significant impact on everyday life, this cognitive aspect has an influential importance in various MS-related treatment settings.

Johns Hopkins University Announces Frederick CREST Classes for Fall 2016 | Poster

Cancer.gov

Johns Hopkins University’s (JHU) Advanced Academic Programs (AAP) division recently announced two classes that will be hosted at the Frederick Center for Research and Education in Science and Technology (CREST) this fall. According to a JHU press release, the classes are Biochemistry, which is part of the M.S. in Biotechnology program at JHU AAP, and Molecular Biology, a part of the M.S. in Bioinformatics program at JHU AAP.

Rosmarinus Officinalis Leaves as a Natural Source of Bioactive Compounds

PubMed Central

Borrás-Linares, Isabel; Stojanović, Zorica; Quirantes-Piné, Rosa; Arráez-Román, David; Švarc-Gajić, Jaroslava; Fernández-Gutiérrez, Alberto; Segura-Carretero, Antonio

2014-01-01

In an extensive search for bioactive compounds from plant sources, the composition of different extracts of rosemary leaves collected from different geographical zones of Serbia was studied. The qualitative and quantitative characterization of 20 rosemary (Rosmarinus officinalis) samples, obtained by microwave-assisted extraction (MAE), was determined by high performance liquid chromatography coupled to electrospray quadrupole-time of flight mass spectrometry (HPLC–ESI-QTOF-MS). The high mass accuracy and true isotopic pattern in both MS and MS/MS spectra provided by the QTOF-MS analyzer enabled the characterization of a wide range of phenolic compounds in the extracts, including flavonoids, phenolic diterpenes and abietan-type triterpenoids, among others. According to the data compiled, rosemary samples from Sokobanja presented the highest levels in flavonoids and other compounds such as carnosol, rosmaridiphenol, rosmadial, rosmarinic acid, and carnosic acid. On the other hand, higher contents in triterpenes were found in the extracts of rosemary from Gložan (Vojvodina). PMID:25391044

Spectral Archives: Extending Spectral Libraries to Analyze both Identified and Unidentified Spectra

PubMed Central

Frank, Ari M.; Monroe, Matthew E.; Shah, Anuj R.; Carver, Jeremy J.; Bandeira, Nuno F.; Moore, Ronald J.; Anderson, Gordon A.; Smith, Richard D.; Pevzner, Pavel A.

2011-01-01

MS/MS experiments generate multiple, nearly identical spectra of the same peptide in various laboratories, but proteomics researchers typically do not leverage the unidentified spectra produced in other labs to decode spectra generated in their own labs. We propose a spectral archives approach that clusters MS/MS datasets, representing similar spectra by a single consensus spectrum. Spectral archives extend spectral libraries by analyzing both identified and unidentified spectra in the same way and maintaining information about spectra of peptides shared across species and conditions. Thus archives offer both traditional library spectrum similarity-based search capabilities along with novel ways to analyze the data. By developing a clustering tool, MS-Cluster, we generated a spectral archive from ~1.18 billion spectra that greatly exceeds the size of existing spectral repositories. We advocate that publicly available data should be organized into spectral archives, rather than be analyzed as disparate datasets, as is mostly the case today. PMID:21572408

Characterizing Vaccinium berry Standard Reference Materials by GC-MS using NIST spectral libraries.

PubMed

Lowenthal, Mark S; Andriamaharavo, Nirina R; Stein, Stephen E; Phinney, Karen W

2013-05-01

A gas chromatography-mass spectrometry (GC-MS)-based method was developed for qualitative characterization of metabolites found in Vaccinium fruit (berry) dietary supplement Standard Reference Materials (SRMs). Definitive identifications are provided for 98 unique metabolites determined among six Vaccinium-related SRMs. Metabolites were enriched using an organic liquid/liquid extraction, and derivatized prior to GC-MS analysis. Electron ionization (EI) fragmentation spectra were searched against EI spectra of authentic standards compiled in the National Institute of Standards and Technology's mass spectral libraries, as well as spectra selected from the literature. Metabolite identifications were further validated using a retention index match along with prior probabilities and were compared with results obtained in a previous effort using collision-induced dissociation (CID) MS/MS datasets from liquid chromatography coupled to mass spectrometry experiments. This manuscript describes a nontargeted metabolite profile of Vaccinium materials, compares results among related materials and from orthogonal experimental platforms, and discusses the feasibility and development of using mass spectral library matching for nontargeted metabolite identification.

One-Year Outcomes of an Integrated Multiple Sclerosis Disease Management Program.

PubMed

Groeneweg, Marti; Forrester, Sara H; Arnold, Beth; Palazzo, Lorella; Zhu, Weiwei; Yoon, Paul; Scearce, Tim

2018-05-01

Multiple sclerosis (MS) is associated with high total health care cost, the majority of which is attributable to medications. Patients with MS are less likely to experience relapses, emergency department (ED) visits, and hospitalizations when they are adherent to disease-modifying treatments. Disease management programs are hypothesized to improve medication adherence thereby improving clinical and economic outcomes. To evaluate the clinical and economic effects of a specialty pharmacy and chronic disease management program for patients with MS from a health plan perspective. This study was a retrospective analysis using prescription drug claims, medical claims, and electronic medical record information (2013-2015) 1 year before and after enrollment in the disease management program for members with 24 months of continuous health plan coverage. Medication adherence was calculated using proportion of days covered (PDC). Relapse rate was defined as an MS outpatient visit associated with a corticosteroid dispense within 7 days of the visit or an MS hospitalization. Disease progression was assessed using the Modified Expanded Disability Status Scale (mEDSS). Resource use included outpatient visits, ED visits, and hospitalizations. Cost information was collected as health plan-paid amount and was reported in 2013 U.S. dollars. The analysis included 377 patients (mean age 55 years, 76.4% female). After enrollment in the program, 78.7% of the study group had a PDC of ≥ 0.80 compared with 70.0% before enrollment (P < 0.001). There was no difference in MS relapse rate (0.25 after vs. 0.45 before, P = 0.11) or mEDSS score (3.77 after vs. 3.76 before, P = 0.19). Health care resource utilization was minimal and did not change significantly throughout the study period: mean outpatient visits (13.09 after vs. 13.78 before, P = 0.69); mean ED visits (0.18 after vs. 0.16 before, P = 0.60); and mean hospitalizations (0.12 after vs. 0.12 before, P = 1.00). This nonsignificant finding remained when the analysis was limited to MS-related visits only. Average annual health plan spend per patient on MS medications significantly increased ($55,835 after vs. $40,883 before, P < 0.001). Specialty pharmacy and chronic disease management for patients with MS can increase the proportion of patients adherent to medication. The increase in health plan spend on MS medications is not offset by savings in health care resource utilization. This study was funded by Kaiser Permanente Washington Health Research Institute and Kaiser Permanente Washington Pharmacy Administration. The authors have no disclosures to report.

A Longitudinal Study of the Talent Search Program

ERIC Educational Resources Information Center

Brewer, Ernest W.; Landers, Jama McMahan

2005-01-01

This longitudinal study examined the impact of participation in the federally funded Talent Search program at The University of Tennessee, Knoxville. The Talent Search program provides career exploration and counseling services to low-income students with the potential to be first-generation college graduates. Postsecondary education enrollment…

Mass Spectral Enhanced Detection of Ubls Using SWATH Acquisition: MEDUSA—Simultaneous Quantification of SUMO and Ubiquitin-Derived Isopeptides

NASA Astrophysics Data System (ADS)

Griffiths, John R.; Chicooree, Navin; Connolly, Yvonne; Neffling, Milla; Lane, Catherine S.; Knapman, Thomas; Smith, Duncan L.

2014-05-01

Protein modification by ubiquitination and SUMOylation occur throughout the cell and are responsible for numerous cellular functions such as apoptosis, DNA replication and repair, and gene transcription. Current methods for the identification of such modifications using mass spectrometry predominantly rely upon tryptic isopeptide tag generation followed by database searching with in vitro genetic mutation of SUMO routinely required. We have recently described a novel approach to ubiquitin and SUMO modification detection based upon the diagnostic a' and b' ions released from the isopeptide tags upon collision-induced dissociation of reductively methylated Ubl isopeptides (RUbI) using formaldehyde. Here, we significantly extend those studies by combining data-independent acquisition (DIA) with alternative labeling reagents to improve diagnostic ion coverage and enable relative quantification of modified peptides from both MS and MS/MS signals. Model synthetic ubiquitin and SUMO-derived isopeptides were labeled with mTRAQ reagents (Δ0, Δ4, and Δ8) and subjected to LC-MS/MS with SWATH acquisition. Novel diagnostic ions were generated upon CID, which facilitated the selective detection of these modified peptides. Simultaneous MS-based and MS/MS-based relative quantification was demonstrated for both Ub and SUMO-derived isopeptides across three channels in a background of mTRAQ-labeled Escherichia coli digest.

Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer.

PubMed

Ferries, Samantha; Perkins, Simon; Brownridge, Philip J; Campbell, Amy; Eyers, Patrick A; Jones, Andrew R; Eyers, Claire E

2017-09-01

Confident identification of sites of protein phosphorylation by mass spectrometry (MS) is essential to advance understanding of phosphorylation-mediated signaling events. However, the development of novel instrumentation requires that methods for MS data acquisition and its interrogation be evaluated and optimized for high-throughput phosphoproteomics. Here we compare and contrast eight MS acquisition methods on the novel tribrid Orbitrap Fusion MS platform using both a synthetic phosphopeptide library and a complex phosphopeptide-enriched cell lysate. In addition to evaluating multiple fragmentation regimes (HCD, EThcD, and neutral-loss-triggered ET(ca/hc)D) and analyzers for MS/MS (orbitrap (OT) versus ion trap (IT)), we also compare two commonly used bioinformatics platforms, Andromeda with PTM-score, and MASCOT with ptmRS for confident phosphopeptide identification and, crucially, phosphosite localization. Our findings demonstrate that optimal phosphosite identification is achieved using HCD fragmentation and high-resolution orbitrap-based MS/MS analysis, employing MASCOT/ptmRS for data interrogation. Although EThcD is optimal for confident site localization for a given PSM, the increased duty cycle compared with HCD compromises the numbers of phosphosites identified. Finally, our data highlight that a charge-state-dependent fragmentation regime and a multiple algorithm search strategy are likely to be of benefit for confident large-scale phosphosite localization.

Recruiting for Caregiver Education Research

PubMed Central

Finlayson, Marcia; Henkel, Christin

2012-01-01

Caregiver education programs can support participants in a role that is often challenging. Research is needed to determine the effectiveness of these programs; however, recruitment for such studies can be difficult. The objectives of this study were to explore 1) how multiple sclerosis (MS) caregivers respond to recruitment materials for a research study evaluating a caregiver education program, including aspects of the materials that encourage or discourage their interest in participation; and 2) what recommendations MS caregivers have for improving study recruitment advertising. Qualitative interviews were conducted with seven MS caregivers. Participants were asked about their reactions to advertisements for a pilot study intended to evaluate an MS caregiver education program. Participants were also asked to reflect on factors that would influence their decision to participate in the program and to provide suggestions to improve recruitment materials. Data were analyzed using a constant-comparative approach. Study findings indicated that the language and visual design of the advertisements influenced the participants' initial responses. Some caregivers first responded to the fact that the program was part of a research study, and these caregivers had overall negative responses to the advertising, such as concern that the program was being “tested.” Other caregivers first considered the personal relevance of the program. These caregivers had neutral-to-positive responses to the flyers and weighed the relevance of the program against the research and logistical aspects. Participants provided recommendations to improve the recruitment materials. While recruiting for caregiver education research can be challenging, piloting recruitment materials and using a variety of advertising options may improve response. PMID:24453751

Treatment adherence and other patient-reported outcomes as cost determinants in multiple sclerosis: a review of the literature.

PubMed

Lizán, Luis; Comellas, Marta; Paz, Silvia; Poveda, José Luis; Meletiche, Dennis M; Polanco, Carlos

2014-01-01

Treatment adherence is one of the key factors for achieving optimal clinical outcomes. In order to assess costs related to adherence to, and persistence and compliance with, disease-modifying therapies (DMTs) in patients with multiple sclerosis (MS), a narrative review of the literature was performed. Satisfaction with and preference for DMTs and their delivery devices were also assessed, as both can have an influence on patients' adherence and persistence. Electronic databases (MEDLINE, PubMed, Google Scholar, congress proceedings) were searched to identify publications analyzing MS costs related to adherence, persistence, satisfaction, and preferences for MS treatments. Bibliographic references were hand searched. English or Spanish studies published between January 2007 and January 2013 were selected. A total of 398 titles were identified, of which 12 met the inclusion criteria. Six studies evaluated the impact of adherence, persistence, and compliance on treatment costs; four publications analyzed satisfaction with DMTs; and two assessed treatment preferences based on attributes of the delivery device. Increased adherence and persistence were associated with better clinical outcomes, leading to lower relapse risk (odds ratio [OR]: 0.71; 95% confidence interval [CI]: 0.59-0.85) and a decrease in health care resource use, such as MS-related hospitalizations (OR: 0.63; 95% CI: 0.47-0.83) and emergency department visits (OR: 0.80; 95% CI: 0.60-1.07). This reduction in resource use led to a patient/year total cost reduction (excluding DMT costs) of up to 22%. This review highlights the importance of ensuring adequate adherence in MS patients through treatments and devices better tailored to patients' needs that could enhance clinical outcomes and reduce MS costs. Understanding the factors underlying satisfaction and compliance with treatment and patients' preference for certain therapies could help in the development of strategies that can improve adherence.

Image Processing for Educators in Global Hands-On Universe

NASA Astrophysics Data System (ADS)

Miller, J. P.; Pennypacker, C. R.; White, G. L.

2006-08-01

A method of image processing to find time-varying objects is being developed for the National Virtual Observatory as part of Global Hands-On Universe(tm) (Lawrence Hall of Science; University of California, Berkeley). Objects that vary in space or time are of prime importance in modern astronomy and astrophysics. Such objects include active galactic nuclei, variable stars, supernovae, or moving objects across a field of view such as an asteroid, comet, or extrasolar planet transiting its parent star. The search for these objects is undertaken by acquiring an image of the region of the sky where they occur followed by a second image taken at a later time. Ideally, both images are taken with the same telescope using the same filter and charge-coupled device. The two images are aligned and subtracted with the subtracted image revealing any changes in light during the time period between the two images. We have used a method of Christophe Alard using the image processing software IDL Version 6.2 (Research Systems, Inc.) with the exception of the background correction, which is done on the two images prior to the subtraction. Testing has been extensive, using images provided by a number of National Virtual Observatory and collaborating projects. They include the Supernovae Trace Cosmic Expansion (Cerro Tololo Inter-American Observatory), Supernovae/ Acceleration Program (Lawrence Berkeley National Laboratory), Lowell Observatory Near-Earth Object Search (Lowell Observatory), and the Centre National de la Recherche Scientifique (Paris, France). Further testing has been done with students, including a May 2006 two week program at the Lawrence Berkeley National Laboratory. Students from Hardin-Simmons University (Abilene, TX) and Jackson State University (Jackson, MS) used the subtraction method to analyze images from the Cerro Tololo Inter-American Observatory (CTIO) searching for new asteroids and Kuiper Belt objects. In October 2006 students from five U.S. high schools will use the subtraction method in an asteroid search campaign using CTIO images with 7-day follow-up images to be provided by the Las Cumbres Observatory (Santa Barbara, CA). During the Spring 2006 semester, students from Cape Fear High School used the method to search for near-Earth objects and supernovae. Using images from the Astronomical Research Institute (Charleston, IL) the method contributed to the original discovery of two supernovae, SN 2006al and SN 2006bi.

Contaminant screening of wastewater with HPLC-IM-qTOF-MS and LC+LC-IM-qTOF-MS using a CCS database.

PubMed

Stephan, Susanne; Hippler, Joerg; Köhler, Timo; Deeb, Ahmad A; Schmidt, Torsten C; Schmitz, Oliver J

2016-09-01

Non-target analysis has become an important tool in the field of water analysis since a broad variety of pollutants from different sources are released to the water cycle. For identification of compounds in such complex samples, liquid chromatography coupled to high resolution mass spectrometry are often used. The introduction of ion mobility spectrometry provides an additional separation dimension and allows determining collision cross sections (CCS) of the analytes as a further physicochemical constant supporting the identification. A CCS database with more than 500 standard substances including drug-like compounds and pesticides was used for CCS data base search in this work. A non-target analysis of a wastewater sample was initially performed with high performance liquid chromatography (HPLC) coupled to an ion mobility-quadrupole-time of flight mass spectrometer (IM-qTOF-MS). A database search including exact mass (±5 ppm) and CCS (±1 %) delivered 22 different compounds. Furthermore, the same sample was analyzed with a two-dimensional LC method, called LC+LC, developed in our group for the coupling to IM-qTOF-MS. This four dimensional separation platform revealed 53 different compounds, identified over exact mass and CCS, in the examined wastewater sample. It is demonstrated that the CCS database can also help to distinguish between isobaric structures exemplified for cyclophosphamide and ifosfamide. Graphical Abstract Scheme of sample analysis and database screening.

A National Picture of Talent Search and Talent Search Educational Programs

ERIC Educational Resources Information Center

Lee, Seon-Young; Matthews, Michael S.; Olszewski-Kubilius, Paula

2008-01-01

This article presents a comprehensive portrait of talent search testing and associated educational programs in the United States, now some 35 years after Dr. Julian Stanley originated the concept. Survey data from the six major talent search centers in the United States were used to examine the scope of talent search educational offerings,…

75 FR 3642 - Special Evaluation Assistance for Rural Communities and Households Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-22

... the Special Evaluation Assistance for Rural Communities and Households (SEARCH) Program as authorized.... 1926 (a)(2)). The amendment added the new SEARCH grant program under which the Secretary is authorized... following methods: Federal eRulemaking Portal: Go to http://www.regulations.gov and in the ``Search...

A multicenter, prospective, quasi-experimental evaluation study of a patient education program to foster multiple sclerosis self-management competencies.

PubMed

Feicke, Janine; Spörhase, Ulrike; Köhler, Jürgen; Busch, Claudia; Wirtz, Markus

2014-12-01

To determine the impact of the self-management training program "S.MS" for new multiple sclerosis (MS) patients. Multicenter, prospective, quasi-experimental study with 31 MS patients in the intervention group (training program) and 33 participants in the control group (CG) (brochures). Data were collected before, after and 6 months after the interventions. Analysis of change was done by ANCOVA with repeated measurements. At baseline, participants in CG were younger at the time of diagnosis, suffered more frequently from relapsing-remitting MS and took more MS-medication on a permanent basis. The intervention had a stable significant effect on each dimension of self-management ability, on total self-management ability (ES=0.194, p<0.001), on anxiety (ES=0.193, p=0.001), and on disease-specific quality of life (ES=0.120, p=0.007). Regarding depression, a significant interaction effect of time and intervention could be observed (ES=0.106, p=0.011). No effect was found on disease-specific knowledge. High participant acceptance was reported. "S.MS" participation was associated with a significant and sustained improvement of self-management abilities, anxiety and disease-specific quality of life in a quasi-experimental study design. Using RCT or CRT-designs would be desirable to further improve the evidence of treatment effectiveness. This study provides substantial evidence that "S.MS" fosters patients' self-management ability. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

The Relational Impact of Multiple Sclerosis: An Integrative Review of the Literature Using a Cognitive Analytic Framework.

PubMed

Blundell Jones, Joanna; Walsh, Sue; Isaac, Claire

2017-12-01

This integrative literature review uses cognitive analytic therapy (CAT) theory to examine the impact of a chronic illness, multiple sclerosis (MS), on relationships and mental health. Electronic searches were conducted in six medical and social science databases. Thirty-eight articles met inclusion criteria, and also satisfied quality criteria. Articles revealed that MS-related demands change care needs and alter relationships. Using a CAT framework, the MS literature was analysed, and five key patterns of relating to oneself and to others were identified. A diagrammatic formulation is proposed that interconnects these patterns with wellbeing and suggests potential "exits" to improve mental health, for example, assisting families to minimise overprotection. Application of CAT analysis to the literature clarifies relational processes that may affect mental health among individuals with MS, which hopefully will inform how services assist in reducing unhelpful patterns and improve coping. Further investigation of the identified patterns is needed.

Electrically programmable-erasable In-Ga-Zn-O thin-film transistor memory with atomic-layer-deposited Al{sub 2}O{sub 3}/Pt nanocrystals/Al{sub 2}O{sub 3} gate stack

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

Qian, Shi-Bing; Zhang, Wen-Peng; Liu, Wen-Jun

Amorphous indium-gallium-zinc oxide (a-IGZO) thin-film transistor (TFT) memory is very promising for transparent and flexible system-on-panel displays; however, electrical erasability has always been a severe challenge for this memory. In this article, we demonstrated successfully an electrically programmable-erasable memory with atomic-layer-deposited Al{sub 2}O{sub 3}/Pt nanocrystals/Al{sub 2}O{sub 3} gate stack under a maximal processing temperature of 300 {sup o}C. As the programming voltage was enhanced from 14 to 19 V for a constant pulse of 0.2 ms, the threshold voltage shift increased significantly from 0.89 to 4.67 V. When the programmed device was subjected to an appropriate pulse under negative gatemore » bias, it could return to the original state with a superior erasing efficiency. The above phenomena could be attributed to Fowler-Nordheim tunnelling of electrons from the IGZO channel to the Pt nanocrystals during programming, and inverse tunnelling of the trapped electrons during erasing. In terms of 0.2-ms programming at 16 V and 350-ms erasing at −17 V, a large memory window of 3.03 V was achieved successfully. Furthermore, the memory exhibited stable repeated programming/erasing (P/E) characteristics and good data retention, i.e., for 2-ms programming at 14 V and 250-ms erasing at −14 V, a memory window of 2.08 V was still maintained after 10{sup 3} P/E cycles, and a memory window of 1.1 V was retained after 10{sup 5} s retention time.« less

Harmonisation of serum dihydrotestosterone analysis: establishment of an external quality assurance program.

PubMed

Greaves, Ronda F; Jolly, Lisa; Hartmann, Michaela F; Ho, Chung Shun; Kam, Richard K T; Joseph, John; Boyder, Conchita; Wudy, Stefan A

2017-03-01

Serum dihydrotestosterone (DHT) is an important analyte for the clinical assessment of disorders of sex development. It is also reportedly a difficult analyte to measure. Currently, there are significant gaps in the standardisation of this analyte, including no external quality assurance (EQA) program available worldwide to allow for peer review performance of DHT. We therefore proposed to establish a pilot EQA program for serum DHT. DHT was assessed in the 2015 Royal College of Pathologists of Australasia Quality Assurance Programs' Endocrine program material. The material's target (i.e. "true") values were established using a measurement procedure based on isotope dilution gas chromatography (GC) tandem mass spectrometry (MS/MS). DHT calibrator values were based on weighed values of pure DHT material (>97.5% purity) from Sigma. The allowable limits of performance (ALP) were established as ±0.1 up to 0.5 nmol/L and ±15% for targets >0.5 nmol/L. Target values for the six levels of RCPAQAP material for DHT ranged from 0.02 to 0.43 nmol/L (0.01-0.12 ng/mL). The material demonstrated linearity across the six levels. There were seven participating laboratories for this pilot study. Results of the liquid chromatography (LC) MS/MS methods were within the ALP; whereas the results from the immunoassay methods were consistently higher than the target values and outside the ALP. This report provides the first peer comparison of serum DHT measured by mass spectrometry (MS) and immunoassay laboratories. Establishment of this program provides one of the pillars to achieve method harmonisation. This supports accurate clinical decisions where DHT measurement is required.

Academic dreamers to leaders: The emergence of the mathematics and science for minority students ((MS)(2)) program at Philips Academy Andover

NASA Astrophysics Data System (ADS)

Beckham, Jerrell K.

(MS)2 is a summer program for high achieving minority students interested in math and science careers. It was started in 1977. The Program is located at Phillips Academy in Andover Massachusetts. Phillips Academy is one of the nation's oldest college preparatory schools. The school was founded in 1778. Current U.S. President George Bush attended Phillips Academy and his father before him. The students in (MS)2 attend Phillips Academy in the summertime, along with regular Summer Session students. The (MS)2 Program represents about a fifth of the students at Phillips Academy Summer Session. At present the program is made up of African Americans, Latinos, and Native American students who attend a number of different public schools throughout the nation. This dissertation explores the experiences of students in this program spanning nearly a quarter of a central. My research seeks to understand and shred additional light on how certain outreach programs might help along the pipeline in regard to improving minority representation in mathematics and science fields. Also, this narrative hopes to not only paints a more complex pictures of the experiences of minorities in schools, but seeks to serve the larger public interest by challenging some of the popular renditions and myths of the failure of Blacks, Latino/as, and Native Americans in schooling (Ogbu 2003), as oppose to certain aspects of schooling and society continuing to failing them.

Expectations from Rehabilitation of Children with Cerebral Palsy: The Agreement between the Physiotherapists and Mothers

PubMed Central

Kavlak, Erdoğan; Altuğ, Filiz; Cavlak, Uğur; Kavlak, Havva Aylin; Şenol, Hande

2014-01-01

[Purpose] The aim of this study was to examine the agreement between physiotherapists (PTs) and mothers (Ms) about the treatment of children with cerebral palsy (CP) who received treatment in special education and rehabilitation centers. [Subjects] Ms of 130 children with CP (75 boys, 55 girls) and 130 PTs who applied rehabilitation programs were interviewed. [Methods] Clinical types and gross motor function levels of the children were recorded. A questionnaire consisting of 6 open-ended questions was used to describe the expectations and views of the PTs and Ms about the physiotherapy and rehabilitation programs for the children. [Results] The mean age of the children was 89.80±52.05 months. The mean treatment period for the children was 73.62±42.11 months. The mean age of the mothers was 35.47±5.79 years, and the mean age of the PTs was 28.07±7.28 years. We found a statistically moderate level of agreement between the PTs and Ms regarding the appropriateness of the treatment provided to the children. There was statistically insignificant agreement regarding the applied treatment methods and the appropriateness of the applied rehabilitation programs. [Conclusion] We believe that the views and expectations of the Ms should be taken into account by the PTs when preparing a treatment program for children with CP. PMID:25202182

Goals Set After Completing a Teleconference-Delivered Program for Managing Multiple Sclerosis Fatigue

PubMed Central

Asano, Miho; Preissner, Katharine; Duffy, Rose; Meixell, Maggie

2015-01-01

Setting goals can be a valuable skill to self-manage multiple sclerosis (MS) fatigue. A better understanding of the goals set by people with MS after completing a fatigue management program can assist health care professionals with tailoring interventions for clients. This study aimed to describe the focus of goals set by people with MS after a teleconference-delivered fatigue management program and to evaluate the extent to which participants were able to achieve their goals over time. In total, 485 goals were set by 81 participants. Over a follow-up period, 64 participants rated 284 goals regarding progress made toward goal achievement. Approximately 50% of the rated goals were considered achieved. The most common type of goal achieved was that of instrumental activities of daily living. Short-term goals were more likely to be achieved. This study highlights the need for and importance of promoting and teaching goal-setting skills to people with MS. PMID:25871602

2011 Women in Defense (WID) National Fall Conference

DTIC Science & Technology

2011-10-19

UCLA. She is also a graduate of the UCLA Executive Management Course and the University of Chicago Business Leadership Program. A member of the Air...Supercircuits Ms. Beth A. Shepard -Savery Cox Communications Hampton Roads, LLC Ms. Erin B. Sheppard McKenna Long & Aldridge, LLP Ms. Heidi L Shyu

Students helping students: vertical peer mentoring to enhance the medical school experience.

PubMed

Andre, Christine; Deerin, Jessica; Leykum, Luci

2017-05-02

Effective mentoring is an important component of medical student professional development. We provide a description of the mentoring program at our institution. Our institution UTHSCSA implemented a student-advising program (Veritas) with clinical faculty mentors and senior students (MiMs). The MiMs provided vertical peer mentoring to more junior students as an adjunct to faculty advising. The MiMs lead small group discussions that foster camaraderie, share academic and career information and promote professional identity. An optional MiM elective more intensively develops mentorship and leadership skills through a formal curriculum. The authors used annual survey data of all students as well as student mentors to evaluate program effectiveness. Overall, student perception of the program improved each year across multiple domains, including feeling more prepared, supported and satisfied with their overall experience in medical school. Student mentors also found the process rewarding and helpful to their future careers as physicians. The authors suggest implementing a vertical peer-mentoring program can be an effective adjunct to faculty mentoring.

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

PubMed

Goloborodko, Anton A; Levitsky, Lev I; Ivanov, Mark V; Gorshkov, Mikhail V

2013-02-01

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.

MixGF: spectral probabilities for mixture spectra from more than one peptide.

PubMed

Wang, Jian; Bourne, Philip E; Bandeira, Nuno

2014-12-01

In large-scale proteomic experiments, multiple peptide precursors are often cofragmented simultaneously in the same mixture tandem mass (MS/MS) spectrum. These spectra tend to elude current computational tools because of the ubiquitous assumption that each spectrum is generated from only one peptide. Therefore, tools that consider multiple peptide matches to each MS/MS spectrum can potentially improve the relatively low spectrum identification rate often observed in proteomics experiments. More importantly, data independent acquisition protocols promoting the cofragmentation of multiple precursors are emerging as alternative methods that can greatly improve the throughput of peptide identifications but their success also depends on the availability of algorithms to identify multiple peptides from each MS/MS spectrum. Here we address a fundamental question in the identification of mixture MS/MS spectra: determining the statistical significance of multiple peptides matched to a given MS/MS spectrum. We propose the MixGF generating function model to rigorously compute the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30-390%. Analysis of multiple data sets with MixGF reveals that in complex biological samples the number of identified mixture spectra can be as high as 20% of all the identified spectra and the number of unique peptides identified only in mixture spectra can be up to 35.4% of those identified in single-peptide spectra. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

The efficacy of vitamin D in multiple sclerosis: A meta-analysis.

PubMed

Zheng, Chao; He, Liang; Liu, Lingling; Zhu, Jie; Jin, Tao

2018-05-12

Multiple sclerosis (MS) is a chronic inflammatory demyelination disorder in the central nervous system (CNS) leading to a high level of neurological disability. The pathogenesis of MS remains largely unknown, which explains the lack of significant efficacy of therapy in MS. Vitamin D deficiency is widely considered to be an environmental risk factor for MS. Many studies investigating the therapeutic effects of vitamin D on MS have been applied. The objective of this systematic review and meta-analysis was to evaluate the effectiveness of vitamin D in MS patients. To obtain a more comprehensive estimate of the efficacy of vitamin D on MS patients, we conducted a meta-analysis to determine the role of vitamin D in MS. The PubMed, EMBASE and Cochrane databases were searched in October 2017. Randomized, double-blind, placebo-controlled clinical trials recorded within the three main databases were considered. The analysis was conducted for two specific outcomes: Expanded Disability Status Scale (EDSS) score and annual relapse rate (ARR). Vitamin D 3 as add-on treatment had no significant therapeutic effect on MS according to EDSS score (mean difference -0.01 [95% CI -0.34 to 0.33]). The ARR was higher in the vitamin D group than in the placebo group (mean difference 0.05 [95% CI 0.01 to 0.1]). Our findings suggest that vitamin D appeared to have no therapeutic effect on EDSS score or ARR in the patients with MS. Copyright © 2018 Elsevier B.V. All rights reserved.

MixGF: Spectral Probabilities for Mixture Spectra from more than One Peptide*

PubMed Central

Wang, Jian; Bourne, Philip E.; Bandeira, Nuno

2014-01-01

In large-scale proteomic experiments, multiple peptide precursors are often cofragmented simultaneously in the same mixture tandem mass (MS/MS) spectrum. These spectra tend to elude current computational tools because of the ubiquitous assumption that each spectrum is generated from only one peptide. Therefore, tools that consider multiple peptide matches to each MS/MS spectrum can potentially improve the relatively low spectrum identification rate often observed in proteomics experiments. More importantly, data independent acquisition protocols promoting the cofragmentation of multiple precursors are emerging as alternative methods that can greatly improve the throughput of peptide identifications but their success also depends on the availability of algorithms to identify multiple peptides from each MS/MS spectrum. Here we address a fundamental question in the identification of mixture MS/MS spectra: determining the statistical significance of multiple peptides matched to a given MS/MS spectrum. We propose the MixGF generating function model to rigorously compute the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30–390%. Analysis of multiple data sets with MixGF reveals that in complex biological samples the number of identified mixture spectra can be as high as 20% of all the identified spectra and the number of unique peptides identified only in mixture spectra can be up to 35.4% of those identified in single-peptide spectra. PMID:25225354

THE ROLE OF SEARCHING SERVICES IN AN ACQUISITIONS PROGRAM.

ERIC Educational Resources Information Center

LUECK, ANTOINETTE L.; AND OTHERS

A USER PRESENTS HIS POINT OF VIEW ON LITERATURE SEARCHING THROUGH THE MAJOR SEARCHING SERVICES IN THE OVERALL PROGRAM OF ACQUISITIONS FOR THE ENGINEERING STAFF OF THE AIR FORCE AERO PROPULSION LABORATORY. THESE MAJOR SEARCHING SERVICES INCLUDE THE DEFENSE DOCUMENTATION CENTER (DDC), THE NATIONAL AERONAUTICS AND SPACE ADMINISTRATION (NASA), THE…

Effectiveness of and User Experience With Web-Based Interventions in Increasing Physical Activity Levels in People With Multiple Sclerosis: A Systematic Review.

PubMed

Dennett, Rachel; Gunn, Hilary; Freeman, Jennifer A

2018-05-15

Supporting people with multiple sclerosis (MS) to achieve and maintain recommended levels of physical activity is important but challenging. Web-based interventions are increasingly being used to deliver targeted exercise programs and promote physical activity. The purpose of this study was to systematically review current evidence regarding the effectiveness and user experience of web-based interventions in increasing physical activity in people with MS. MEDLINE, EMBASE, CINAHL, AMED, PEDro, PsychInfo, Web of Sciences, The Cochrane Library, and gray literature were searched from 1990 to September 2016. English language articles reporting the use of web-based interventions to increase physical activity in adults with MS were included. Eligible quantitative studies were of any design and reported a measure of physical activity. Qualitative studies exploring users' experiences in any context were included. Of the 881 articles identified, 9 met the inclusion criteria. Two reviewers independently assessed methodological quality and extracted data using standardized critical appraisal and data extraction tools from the Joanna Briggs Institute Meta Analysis of Statistics Assessment and Review Instrument (JBI-MAStARI). Meta-analysis of self-reported physical activity questionnaire data from 4 studies demonstrated a standardized mean difference of 0.67 (95% CI = 0.43-0.92), indicating a positive effect in favor of the web-based interventions. Narrative review of accelerometry data from 3 studies indicated increases in objectively measured physical activity. No qualitative studies met the inclusion criteria. In the 9 included articles, only 2 different interventions (used with people who were ambulant) were reported. Web-based interventions had a short-term positive effect on self-reported physical activity in people who had MS and were ambulant. Evidence is not currently available to support or refute their use in the long-term or with people who are not ambulant.

Promoting Knowledge to Action through the Study of Environmental Arctic Change (SEARCH) Program

NASA Astrophysics Data System (ADS)

Myers, B.; Wiggins, H. V.

2016-12-01

The Study of Environmental Arctic Change (SEARCH) is a multi-institutional collaborative U.S. program that advances scientific knowledge to inform societal responses to Arctic change. Currently, SEARCH focuses on how diminishing Arctic sea ice, thawing permafrost, and shrinking land ice impact both Arctic and global systems. Emphasizing "knowledge to action", SEARCH promotes collaborative research, synthesizes research findings, and broadly communicates the resulting knowledge to Arctic researchers, stakeholders, policy-makers, and the public. This poster presentation will highlight recent program products and findings; best practices and challenges for managing a distributed, interdisciplinary program; and plans for cross-disciplinary working groups focused on Arctic coastal erosion, synthesis of methane budgets, and development of Arctic scenarios. A specific focus will include how members of the broader research community can participate in SEARCH activities. http://www.arcus.org/search

Comparison of aerobic versus resistance exercise training effects on metabolic syndrome (from the Studies of a Targeted Risk Reduction Intervention Through Defined Exercise - STRRIDE-AT/RT).

PubMed

Bateman, Lori A; Slentz, Cris A; Willis, Leslie H; Shields, A Tamlyn; Piner, Lucy W; Bales, Connie W; Houmard, Joseph A; Kraus, William E

2011-09-15

Aerobic training (AT) improves the metabolic syndrome (MS) and its component risk factors; however, to our knowledge, no randomized clinical studies have addressed whether resistance training (RT) improves the MS when performed alone or combined with AT. Sedentary, overweight dyslipidemic men and women, aged 18 to 70 years completed a 4-month inactive run-in period and were randomized to 1 of 3 eight-month exercise programs (n = 196). The exercise programs were (1) RT (3 days/week, 3 sets/day of 8 to 12 repetitions of 8 different exercises targeting all major muscle groups); (2) AT (∼120 minutes/week at 75% of the maximum oxygen uptake), and (3) AT and RT combined (AT/RT) (exact combination of AT and RT). Of the 196 randomized patients, 144 completed 1 of the 3 exercise programs. The 86 participants with complete data for all 5 MS criteria were used in the present analysis, and a continuous MS z score was calculated. Eight months of RT did not change the MS score. AT improved the MS score (p <0.07) and showed a trend toward significance compared to RT (p <0.10). AT/RT significantly decreased the MS score and was significantly different from RT alone. In conclusion, RT was not effective at improving the MS score; however, AT was effective. Combined AT and RT was similarly effective but not different from AT alone. When weighing the time commitment versus health benefit, the data suggest that AT alone was the most efficient mode of exercise for improving cardiometabolic health. Published by Elsevier Inc.

A continuing search for companions to PRG stars

NASA Technical Reports Server (NTRS)

Johnson, Hollis R.; Ake, Thomas B.; Ameen, Mudhaffer M.; Brown, Jeffery A.

1990-01-01

Results are presented from observations, made with the SWP spectrograph at low resolution, of Tc-deficient S and C members of the group of chemically peculiar red giant (PRG) stars, which were carried out to search for possible companions to these stars. The results support the hypothesis of Little et al. (1987) and Smith and Lambert (1987, 1988) that the chemical peculiarities of T-deficient S and MS PRG stars have arisen due to mass transfer from white dwarf companions.

Vertical Root Fracture Detection Using Limited-FOV Cone-Beam Computed Tomography

DTIC Science & Technology

2012-06-01

A thesis submitted to the Faculty of the Endodontics Graduate Program Naval Postgraduate Dental School Uniformed Services...Dental Program Navy Medicine Professional Development Center Terry D. Webb, DDS, MS CAPT, DC, USN Chairman, Endodontics Dept. Glen M. Imamura, S...Computed Tomography Geoffrey McMurray, DDS, MS ABSTRACT Introduction: Vertical root fractures (VRF) often occur in endodontically treated teeth

40 CFR 122.30 - What are the objectives of the storm water regulations for small MS4s?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 22 2011-07-01 2011-07-01 false What are the objectives of the storm water regulations for small MS4s? 122.30 Section 122.30 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS EPA ADMINISTERED PERMIT PROGRAMS: THE NATIONAL POLLUTANT DISCHARGE ELIMINATION SYSTEM Permit Application and...

40 CFR 122.30 - What are the objectives of the storm water regulations for small MS4s?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 21 2010-07-01 2010-07-01 false What are the objectives of the storm water regulations for small MS4s? 122.30 Section 122.30 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS EPA ADMINISTERED PERMIT PROGRAMS: THE NATIONAL POLLUTANT DISCHARGE ELIMINATION SYSTEM Permit Application and...

Site-specific N-glycosylation analysis: matrix-assisted laser desorption/ionization quadrupole-quadrupole time-of-flight tandem mass spectral signatures for recognition and identification of glycopeptides.

PubMed

Krokhin, Oleg; Ens, Werner; Standing, Kenneth G; Wilkins, John; Perreault, Hélène

2004-01-01

The identification of glycosylation sites in proteins is often possible through a combination of proteolytic digestion, separation, mass spectrometry (MS) and tandem MS (MS/MS). Liquid chromatography (LC) in combination with MS/MS has been a reliable method for detecting glycopeptides in digestion mixtures, and for assigning glycosylation sites and glycopeptide sequences. Direct interfacing of LC with MS relies on electrospray ionization, which produces ions with two, three or four charges for most proteolytic peptides and glycopeptides. MS/MS spectra of such glycopeptide ions often lead to ambiguous interpretation if deconvolution to the singly charged level is not used. In contrast, the matrix-assisted laser desorption/ionization (MALDI) technique usually produces singly charged peptide and glycopeptide ions. These ions require an extended m/z range, as provided by the quadrupole-quadrupole time-of-flight (QqTOF) instrument used in these experiments, but the main advantages of studying singly charged ions are the simplicity and consistency of the MS/MS spectra. A first aim of the present study is to develop methods to recognize and use glycopeptide [M+H]+ ions as precursors for MS/MS, and thus for glycopeptide/glycoprotein identification as part of wider proteomics studies. Secondly, this article aims at demonstrating the usefulness of MALDI-MS/MS spectra of N-glycopeptides. Mixtures of diverse types of proteins, obtained commercially, were prepared and subjected to reduction, alkylation and tryptic digestion. Micro-column reversed-phase separation allowed deposition of several fractions on MALDI plates, followed by MS and MS/MS analysis of all peptides. Glycopeptide fractions were identified after MS by their specific m/z spacing patterns (162, 203, 291 u) between glycoforms, and then analyzed by MS/MS. In most cases, MS/MS spectra of [M+H]+ ions of glycopeptides featured peaks useful for determining sugar composition, peptide sequence, and thus probable glycosylation site. Peptide-related product ions could be used in database search procedures and allowed the identification of the glycoproteins. Copyright 2004 John Wiley & Sons, Ltd.

Feasibility study design and methods for a home-based, square-stepping exercise program among older adults with multiple sclerosis: The SSE-MS project.

PubMed

Sebastião, Emerson; McAuley, Edward; Shigematsu, Ryosuke; Motl, Robert W

2017-09-01

We propose a randomized controlled trial (RCT) examining the feasibility of square-stepping exercise (SSE) delivered as a home-based program for older adults with multiple sclerosis (MS). We will assess feasibility in the four domains of process, resources, management and scientific outcomes. The trial will recruit older adults (aged 60 years and older) with mild-to-moderate MS-related disability who will be randomized into intervention or attention control conditions. Participants will complete assessments before and after completion of the conditions delivered over a 12-week period. Participants in the intervention group will have biweekly meetings with an exercise trainer in the Exercise Neuroscience Research Laboratory and receive verbal and visual instruction on step patterns for the SSE program. Participants will receive a mat for home-based practice of the step patterns, an instruction manual, and a logbook and pedometer for monitoring compliance. Compliance will be further monitored through weekly scheduled Skype calls. This feasibility study will inform future phase II and III RCTs that determine the actual efficacy and effectiveness of a home-based exercise program for older adults with MS.

Comparing routine neurorehabilitation program with trunk exercises based on Bobath concept in multiple sclerosis: pilot study.

PubMed

Keser, Ilke; Kirdi, Nuray; Meric, Aydin; Kurne, Asli Tuncer; Karabudak, Rana

2013-01-01

This study compared trunk exercises based on the Bobath concept with routine neurorehabilitation approaches in multiple sclerosis (MS). Bobath and routine neurorehabilitation exercises groups were evaluated. MS cases were divided into two groups. Both groups joined a 3 d/wk rehabilitation program for 8 wk. The experimental group performed trunk exercises based on the Bobath concept, and the control group performed routine neurorehabilitation exercises. Additionally, both groups performed balance and coordination exercises. All patients were evaluated with the Trunk Impairment Scale (TIS), Berg Balance Scale (BBS), International Cooperative Ataxia Rating Scale (ICARS), and Multiple Sclerosis Functional Composite (MSFC) before and after the physiotherapy program. In group analysis, TIS, BBS, ICARS, and MSFC scores and strength of abdominal muscles were significantly different after treatment in both groups (p < 0.05). When the groups were compared, no significant differences were found in any parameters (p > 0.05). Although trunk exercises based on the Bobath concept are rarely applied in MS rehabilitation, the results of this study show that they are as effective as routine neurorehabilitation exercises. Therefore, trunk exercises based on the Bobath concept can be beneficial in MS rehabilitation programs.

DARPA Antibody Technology Program Standardized Test Bed for Antibody Characterization: Characterization of an MS2 Human IgG Antibody Produced by AnaptysBio, Inc.

DTIC Science & Technology

2016-02-01

Enzyme-linked immunosorbent assay ( ELISA ) Quality Testing MS2 coat protein (MS2CP) 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF... ELISA ................................................................................................................4 2.8 SPR Method...3.5 ELISA Results .................................................................................................11 3.6 SPR Results

Decision-Making in Multiple Sclerosis Patients: A Systematic Review

PubMed Central

2018-01-01

Background Multiple sclerosis (MS) is frequently associated with cognitive and behavioural deficits. A growing number of studies suggest an impact of MS on decision-making abilities. The aim of this systematic review was to assess if (1) performance of MS patients in decision-making tasks was consistently different from controls and (2) whether this modification was associated with cognitive dysfunction and emotional alterations. Methods The search was conducted on Pubmed/Medline database. 12 studies evaluating the difference between MS patients and healthy controls using validated decision-making tasks were included. Outcomes considered were quantitative (net scores) and qualitative measurements (deliberation time and learning from feedback). Results Quantitative and qualitative decision-making impairment in MS was present in 64.7% of measurements. Patients were equally impaired in tasks for decision-making under risk and ambiguity. A correlation to other cognitive functions was present in 50% of cases, with the highest associations in the domains of processing speed and attentional capacity. Conclusions In MS patients, qualitative and quantitative modifications may be present in any kind of decision-making task and can appear independently of other cognitive measures. Since decision-making abilities have a significant impact on everyday life, this cognitive aspect has an influential importance in various MS-related treatment settings. PMID:29721338

Study of rat hypothalamic proteome by HPLC/ESI ion trap and HPLC/ESI-Q-TOF MS.

PubMed

Iqbal, Javed; Li, Wang; Ullah, Kaleem; Hasan, Murtaza; Linna, Guo; Awan, Umer; Zhang, Yongqian; Batool, Sajida; Qing, Hong; Deng, Yulin

2013-08-01

The proteomic profile of hypothalamus, a key organ of CNS, is explored here by employing two widely used MS techniques, i.e. HPLC/ESI-ion trap and HPLC/ESI-quadrupole-TOF MS. Strong cation exchange is used for the fractionation of peptides and protein search engine MASCOT is employed for data query. One hundred and thirty six proteins with 10 973 peptides were identified by HPLC/ESI-ion trap MS, while 140 proteins with 32 183 peptides were characterized by HPLC/ESI-quadrupole-TOF MS. Among the total 198 proteins identified in both experiments, 78 proteins were common in both sets of conditions. The rest of the 120 proteins were identified distinctly in both MS strategies, i.e. 58 unique proteins were found using the quadrupole-TOF while 62 were found with the HPLC/ESI-ion trap. Moreover, these proteins were classified into groups based on their functions performed in the body. Results presented here identified some important signal and cellular defense proteins inevitable for survival in stressed conditions. Additionally, it is also shown that any single MS strategy is not reliable for good results due to loss of data depending on sensitivity of the instrument used. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

'The surface management system' (SuMS) database: a surface-based database to aid cortical surface reconstruction, visualization and analysis

NASA Technical Reports Server (NTRS)

Dickson, J.; Drury, H.; Van Essen, D. C.

2001-01-01

Surface reconstructions of the cerebral cortex are increasingly widely used in the analysis and visualization of cortical structure, function and connectivity. From a neuroinformatics perspective, dealing with surface-related data poses a number of challenges. These include the multiplicity of configurations in which surfaces are routinely viewed (e.g. inflated maps, spheres and flat maps), plus the diversity of experimental data that can be represented on any given surface. To address these challenges, we have developed a surface management system (SuMS) that allows automated storage and retrieval of complex surface-related datasets. SuMS provides a systematic framework for the classification, storage and retrieval of many types of surface-related data and associated volume data. Within this classification framework, it serves as a version-control system capable of handling large numbers of surface and volume datasets. With built-in database management system support, SuMS provides rapid search and retrieval capabilities across all the datasets, while also incorporating multiple security levels to regulate access. SuMS is implemented in Java and can be accessed via a Web interface (WebSuMS) or using downloaded client software. Thus, SuMS is well positioned to act as a multiplatform, multi-user 'surface request broker' for the neuroscience community.

Demographics and clinical characteristics of episodic hypothermia in multiple sclerosis.

PubMed

Toledano, Michel; Weinshenker, Brian G; Kaufmann, Timothy J; Parisi, Joseph E; Paz Soldán, M Mateo

2018-03-01

Episodic hypothermia (EH) can occur in multiple sclerosis (MS). The putative mechanism is impairment of thermoregulation due to a presumed demyelinating hypothalamic lesion. To describe a cohort of patients with MS, who developed EH. Patients were identified through review of the Mayo Clinic electronic medical record (1996 to July 2015). Search terms were [multiple sclerosis] or [MS] within the diagnoses field and [hypothermia] within any field. We reviewed records for accuracy of diagnoses and abstracted relevant data. Magnetic resonance imaging (MRI) was reviewed for presence of hypothalamic lesions. Of 156 patients, 34 had concurrent MS and hypothermia. Thirty-two (94%) had progressive disease at EH onset. Median MS duration was 19.9 years, and median expanded disability status scale (EDSS) was 8.0. Most patients presented with alterations in consciousness. Infection was suspected as the precipitating factor in 19 (56%), but clinically/laboratory supported in only 9 (28%). MRI lesions were evident within the hypothalamus in only 4 (14%). EH occurs predominantly in patients with advanced secondary progressive MS. The major manifestation is altered consciousness. Infection is often suspected as causal, but infrequently confirmed. Although commonly implicated, hypothalamic lesions were rarely evident on MRI and were absent in two post-mortem evaluations.

Analysis of metal-binding proteins separated by non-denaturating gel electrophoresis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS).

PubMed

Becker, J Susanne; Mounicou, Sandra; Zoriy, Miroslav V; Becker, J Sabine; Lobinski, Ryszard

2008-09-15

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) have become established as very efficient and sensitive biopolymer and elemental mass spectrometric techniques for studying metal-binding proteins (metalloproteins) in life sciences. Protein complexes present in rat tissues (liver and kidney) were separated in their native state in the first dimension by blue native gel electrophoresis (BN-PAGE). Essential and toxic metals, such as zinc, copper, iron, nickel, chromium, cadmium and lead, were detected by scanning the gel bands using quadrupole LA-ICP-MS with and without collision cell as a microanalytical technique. Several proteins were identified by using MALDI-TOF-MS together with a database search. For example, on one protein band cut from the BN-PAGE gel and digested with the enzyme trypsin, two different proteins - protein FAM44B and cathepsin B precursor - were identified. By combining biomolecular and elemental mass spectrometry, it was possible to characterize and identify selected metal-binding rat liver and kidney tissue proteins.

Navigator program risk management

NASA Technical Reports Server (NTRS)

Wessen, Randii R.; Padilla, Deborah A.

2004-01-01

In this paper, program risk management as applied to the Navigator Program: In Search of New Worlds will be discussed. The Navigator Program's goals are to learn how planetary systems form and to search for those worlds that could or do harbor life.

Meteorology Products - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You Oceanography Products Tropical Applications Climatology and Archived Data Info Meteorology Products Global Tropical Warnings Naval Meteorology and Oceanography Command, 1100 Balch Blvd, Stennis Space Center, MS

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

PubMed Central

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

2016-01-01

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics datasets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and non-reference markers of cancer. The CPTAC labs have focused on colon, breast, and ovarian tissues in the first round of analyses; spectra from these datasets were produced from 2D LC-MS/MS analyses and represent deep coverage. To reduce the variability introduced by disparate data analysis platforms (e.g., software packages, versions, parameters, sequence databases, etc.), the CPTAC Common Data Analysis Platform (CDAP) was created. The CDAP produces both peptide-spectrum-match (PSM) reports and gene-level reports. The pipeline processes raw mass spectrometry data according to the following: (1) Peak-picking and quantitative data extraction, (2) database searching, (3) gene-based protein parsimony, and (4) false discovery rate (FDR)-based filtering. The pipeline also produces localization scores for the phosphopeptide enrichment studies using the PhosphoRS program. Quantitative information for each of the datasets is specific to the sample processing, with PSM and protein reports containing the spectrum-level or gene-level (“rolled-up”) precursor peak areas and spectral counts for label-free or reporter ion log-ratios for 4plex iTRAQ™. The reports are available in simple tab-delimited formats and, for the PSM-reports, in mzIdentML. The goal of the CDAP is to provide standard, uniform reports for all of the CPTAC data, enabling comparisons between different samples and cancer types as well as across the major ‘omics fields. PMID:26860878

Novel software for data analysis of Fourier transform ion cyclotron resonance mass spectra applied to natural organic matter.

PubMed

Grinhut, Tzafrir; Lansky, Dedy; Gaspar, Andras; Hertkorn, Norbert; Schmitt-Kopplin, Philippe; Hadar, Yitzhak; Chen, Yona

2010-10-15

Natural organic matter (NOM) occurs as an extremely complex mixture of large, charged molecules that are formed by secondary synthesis reactions. Due to their nature, their full characterization is an important challenge to scientists specializing in NOM as well as analytical chemistry. Ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis enables the identification of thousands of masses in a single measurement. A major challenge in the data analysis process of NOM using the FT-ICR MS technique is the need to sort the entire data set and to present it in an accessible mode. Here we present a simple targeted algorithm called the David Mass Sort (DMS) algorithm which facilitates the detection and counting of consecutive series of masses correlated to any selected mass spacing. This program searches for specific mass differences among all of the masses in a single spectrum against all of the masses in the same spectrum. As a representative case, the current study focuses on the analysis of the well-characterized Suwannee River humic and fulvic acid (SRHA and SRFA, respectively). By applying this algorithm, we were able to find and assess the amount of singly and doubly charged molecules. In addition we present the capabilities of the program to detect any series of consecutive masses correlated to specific mass spacing, e.g. COO, H(2), OCH(2) and O(2). Under several limitations, these mass spacings may be correlated to both chemical and biochemical changes which occur simultaneously during the formation and/or degradation of large mixtures of compounds. Copyright © 2010 John Wiley & Sons, Ltd.

Image analysis tools and emerging algorithms for expression proteomics

PubMed Central

English, Jane A.; Lisacek, Frederique; Morris, Jeffrey S.; Yang, Guang-Zhong; Dunn, Michael J.

2012-01-01

Since their origins in academic endeavours in the 1970s, computational analysis tools have matured into a number of established commercial packages that underpin research in expression proteomics. In this paper we describe the image analysis pipeline for the established 2-D Gel Electrophoresis (2-DE) technique of protein separation, and by first covering signal analysis for Mass Spectrometry (MS), we also explain the current image analysis workflow for the emerging high-throughput ‘shotgun’ proteomics platform of Liquid Chromatography coupled to MS (LC/MS). The bioinformatics challenges for both methods are illustrated and compared, whilst existing commercial and academic packages and their workflows are described from both a user’s and a technical perspective. Attention is given to the importance of sound statistical treatment of the resultant quantifications in the search for differential expression. Despite wide availability of proteomics software, a number of challenges have yet to be overcome regarding algorithm accuracy, objectivity and automation, generally due to deterministic spot-centric approaches that discard information early in the pipeline, propagating errors. We review recent advances in signal and image analysis algorithms in 2-DE, MS, LC/MS and Imaging MS. Particular attention is given to wavelet techniques, automated image-based alignment and differential analysis in 2-DE, Bayesian peak mixture models and functional mixed modelling in MS, and group-wise consensus alignment methods for LC/MS. PMID:21046614

SEARCH: Study of Environmental Arctic Change—A System-scale, Cross-disciplinary Arctic Research Program

NASA Astrophysics Data System (ADS)

Wiggins, H. V.; Eicken, H.; Fox, S. E.; Search Science Steering Committee

2010-12-01

The Study of Environmental Arctic Change (SEARCH) is a multi-agency effort to understand system-scale arctic change. Interrelated environmental changes in the Arctic are affecting ecosystems and living resources and are impacting local and global communities. The SEARCH program is guided by the Science Steering Committee (SSC), the Interagency Program Management Committee (IPMC), and focused panels. Over 150 projects and activities contribute to SEARCH implementation. The Observing Change component is underway through the National Science Foundation’s (NSF) Arctic Observing Network (AON), NOAA-sponsored atmospheric and sea ice observations, and other relevant national and international efforts. The Understanding Change component of SEARCH consists of modeling and analysis efforts, with strong linkages to relevant programs such as NSF’s Arctic System Science (ARCSS) Program. The SEARCH Sea Ice Outlook (http://www.arcus.org/search/seaiceoutlook/index.php) is an "Understanding Change" synthesis effort that aims to advance our understanding of the arctic sea ice system. The Responding to Change element currently includes initial planning efforts by the International Study of Arctic Change (ISAC) program as well as a newly-launched "Sea Ice for Walrus Outlook," which is a weekly report of sea ice conditions geared to Alaska Native walrus subsistence hunters, coastal communities, and others interested in sea ice and walrus (http://www.arcus.org/search/siwo). SEARCH is sponsored by eight U.S. agencies, including: the National Science Foundation (NSF), the National Oceanic and Atmospheric Administration (NOAA), the National Aeronautics and Space Administration (NASA), the Department of Defense (DOD), the Department of Energy (DOE), the Department of the Interior (DOI), the Smithsonian Institution, and the U.S. Department of Agriculture (USDA). The U.S. Arctic Research Commission participates as an IPMC observer. For further information, please visit the website: http://www.arcus.org/search or contact: Helen V. Wiggins: helen@arcus.org, SEARCH Project Office, Arctic Research Consortium of the U.S. (ARCUS); or Hajo Eicken, hajo.eicken@gi.alaska.edu, SEARCH SSC Chair.

Memory rehabilitation for the working memory of patients with multiple sclerosis (MS).

PubMed

Mousavi, Shokoufeh; Zare, Hossein; Etemadifar, Masoud; Taher Neshatdoost, Hamid

2018-05-01

The main cognitive impairments in multiple sclerosis (MS) affect the working memory, processing speed, and performances that are in close interaction with one another. Cognitive problems in MS are influenced to a lesser degree by disease recovery medications or treatments,but cognitive rehabilitation is considered one of the promising methods for cure. There is evidence regarding the effectiveness of cognitive rehabilitation for MS patients in various stages of the disease. Since the impairment in working memory is one of the main MS deficits, a particular training that affects this cognitive domain can be of a great value. This study aims to determine the effectiveness of memory rehabilitation on the working memory performance of MS patients. Sixty MS patients with cognitive impairment and similar in terms of demographic characteristics, duration of disease, neurological problems, and mental health were randomly assigned to three groups: namely, experimental, placebo, and control. Patients' cognitive evaluation incorporated baseline assessments immediately post-intervention and 5 weeks post-intervention. The experimental group received a cognitive rehabilitation program in one-hour sessions on a weekly basis for 8 weeks. The placebo group received relaxation techniques on a weekly basis; the control group received no intervention. The results of this study showed that the cognitive rehabilitation program had a positive effect on the working memory performance of patients with MS in the experimental group. These results were achieved in immediate evaluation (post-test) and follow-up 5 weeks after intervention. There was no significant difference in working memory performance between the placebo group and the control group. According to the study, there is evidence for the effectiveness of a memory rehabilitation program for the working memory of patients with MS. Cognitive rehabilitation can improve working memory disorders and have a positive effect on the working memory performance of these patients.

New FDA-Approved Disease-Modifying Therapies for Multiple Sclerosis.

PubMed

English, Clayton; Aloi, Joseph J

2015-04-01

Interferon injectables and glatiramer acetate have served as the primary disease-modifying treatments for multiple sclerosis (MS) since their introduction in the 1990s and are first-line treatments for relapsing-remitting forms of MS (RRMS). Many new drug therapies were launched since early 2010, expanding the drug treatment options considerably in a disease state that once had a limited treatment portfolio. The purpose of this review is to critically evaluate the safety profile and efficacy data of disease-modifying agents for MS approved by the US Food and Drug Administration (FDA) from 2010 to the present and provide cost and available pharmacoeconomic data about each new treatment. Peer-reviewed clinical trials, pharmacoeconomic studies, and relevant pharmacokinetic/pharmacologic studies were identified from MEDLINE (January 2000-December 2014) by using the search terms multiple sclerosis, fingolimod, teriflunomide, alemtuzumab, dimethyl fumarate, pegylated interferon, peginterferon beta-1a, glatiramer 3 times weekly, and pharmacoeconomics. Citations from available articles were also reviewed for additional references. The databases publically available at www.clinicaltrials.gov and www.fda.gov were searched for unpublished studies or studies currently in progress. A total of 5 new agents and 1 new dosage formulation were approved by the FDA for the treatment of RRMS since 2010. Peginterferon beta-1a and high-dose glatiramer acetate represent 2 new effective injectable options for MS that reduce burden of administration seen with traditional interferon and low-dose glatiramer acetate. Fingolimod, teriflunomide, and dimethyl fumarate represent new oral agents available for MS, and their efficacy in reducing annualized relapse rates is 48% to 55%, 22% to 36.3%, and 44% to 53%, respectively, compared with placebo. Alemtuzumab is a biologic given over a 2-year span that reduced annualized relapse rates by 55% in treatment-naive patients and by 49% in patients relapsing on prior disease-modifying agents. Treatment emergent adverse effects were common with all new drug treatments. The cost of treating MS remains high, because MS therapies accounted for the highest spending growth of any specialty drug class in 2013. Most therapies cost, on average, US $6000/mo based on wholesale acquisition cost, and few cost-benefit studies are available for new treatments. With expansion of new treatments, patients and providers now have multiple options and improved flexibility in managing MS. The relative place in therapy of new treatments is unknown, and treatment decisions are largely based on patient preference, efficacy, and risk potential. The cost of treating MS continues to be high, even with more treatment options available. Copyright © 2015 Elsevier HS Journals, Inc. All rights reserved.

NRL Fact Book

DTIC Science & Technology

1989-04-01

house research labora- tory under the command of the Chief of Naval Research (CNR). As the corporate research laboratory of the Navy, NRL is an important...L.S. Herrin Ms. B.J. McDonald Mr. R.C. Spragg Ms. M.E. Barton Ms. J. Hileman Title Head, Office of Management and Administration Deputy Head...Administrative Officer Head, Management Information Staff Head, Directives Staff Head, GLISIP Program Point of contact: Ms. B.J. McDonald , Code 1005.2, 767-3634

High Intensity Interval Training Reduces the Levels of Serum Inflammatory Cytokine on Women with Metabolic Syndrome.

PubMed

Steckling, F M; Farinha, J B; Santos, D L D; Bresciani, G; Mortari, J A; Stefanello, S T; Courtes, A A; Duarte, T; Duarte, M M M F; Moresco, R N; Cardoso, M S; Soares, F A A

2016-11-01

Objectives: This study investigate the effects of a high intensity interval training (HIIT) and 2 weeks of detraining in functional and body composition parameters, lipoproteins, glucose metabolismand inflammation markers in postmenopausal women with metabolic syndrome (MS). Design: 17 untrained women with MS underwent a HIIT program for 12 weeks. Methods: The training was performed in treadmills, 3 days per week, with intensity ranging from 70-90% of the maximum heart rate (HR max ) and 2 weeks untrained (inactive). Functional and body composition parameters were evaluated before and after the training, while maximal oxygen uptake, lipoprotein and inflammation markers were analyzed before, after training and also in detraining. Results: The HITT program resulted in changesparameters as glucose, HbA1cand NOx after training. In addition, a reduction in pro-inflammatory interleukins and an increase in IL-10 after the HIIT program were found. However, an increase in plasma levels of lipoprotein was found and body composition parameters remain unaltered.Besides, only 2 weeks of detraining are able to revert the effects on inflammatory parameters afforded by the HIIT program. Conclusions: The HIIT program used here positively affected inflammatory profile and other parameters, as glucose, HbA1cand NOx, on postmenopausal women with MS. Moreover, 2 weeks of detraining can reverse the beneficial effects of HIIT program. Our results point out the necessity to aply acontinuous HITT program, in order maintain the benefits detected, to post menopausal women with MS. © Georg Thieme Verlag KG Stuttgart · New York.

The High Time Resolution Universe Pulsar Survey - XII. Galactic plane acceleration search and the discovery of 60 pulsars

NASA Astrophysics Data System (ADS)

Ng, C.; Champion, D. J.; Bailes, M.; Barr, E. D.; Bates, S. D.; Bhat, N. D. R.; Burgay, M.; Burke-Spolaor, S.; Flynn, C. M. L.; Jameson, A.; Johnston, S.; Keith, M. J.; Kramer, M.; Levin, L.; Petroff, E.; Possenti, A.; Stappers, B. W.; van Straten, W.; Tiburzi, C.; Eatough, R. P.; Lyne, A. G.

2015-07-01

We present initial results from the low-latitude Galactic plane region of the High Time Resolution Universe pulsar survey conducted at the Parkes 64-m radio telescope. We discuss the computational challenges arising from the processing of the terabyte-sized survey data. Two new radio interference mitigation techniques are introduced, as well as a partially coherent segmented acceleration search algorithm which aims to increase our chances of discovering highly relativistic short-orbit binary systems, covering a parameter space including potential pulsar-black hole binaries. We show that under a constant acceleration approximation, a ratio of data length over orbital period of ≈0.1 results in the highest effectiveness for this search algorithm. From the 50 per cent of data processed thus far, we have redetected 435 previously known pulsars and discovered a further 60 pulsars, two of which are fast-spinning pulsars with periods less than 30 ms. PSR J1101-6424 is a millisecond pulsar whose heavy white dwarf (WD) companion and short spin period of 5.1 ms indicate a rare example of full-recycling via Case A Roche lobe overflow. PSR J1757-27 appears to be an isolated recycled pulsar with a relatively long spin period of 17 ms. In addition, PSR J1244-6359 is a mildly recycled binary system with a heavy WD companion, PSR J1755-25 has a significant orbital eccentricity of 0.09 and PSR J1759-24 is likely to be a long-orbit eclipsing binary with orbital period of the order of tens of years. Comparison of our newly discovered pulsar sample to the known population suggests that they belong to an older population. Furthermore, we demonstrate that our current pulsar detection yield is as expected from population synthesis.

The influence of THC:CBD oromucosal spray on driving ability in patients with multiple sclerosis-related spasticity.

PubMed

Celius, Elisabeth G; Vila, Carlos

2018-05-01

Driving ability is a key function for the majority of patients with multiple sclerosis (MS) to help maintain daily interactions. Both physical and cognitive disability, as well as treatments, may affect the ability to drive. Spasticity is a common symptom associated with MS, and it may affect driving performance either directly or via the medications used to treat it. In this article, we review the evidence relating the antispasticity medicine, Δ 9 -tetrahydrocannabinol:cannabidiol (THC:CBD) oromucosal spray (Sativex ® ), and its potential impact on driving performance. Articles were identified by searching PubMed from 1/1/2000 to 30/6/2017 using a specified list of search terms. The articles identified using these search terms were augmented with relevant references from these papers and other articles known to the authors. The results from THC:CBD oromucosal spray driving studies and real-world registries did not show any evidence of an increase in motor vehicle accidents associated with THC:CBD oromucosal spray. The majority of patients reported an improvement in driving ability after starting THC:CBD oromucosal spray, and it was speculated that this may be related to reduced spasticity and/or better cognitive function. It should be noted that THC blood levels are significantly lower than the levels associated with recreational use of herbal cannabis. THC:CBD oromucosal spray was shown not to impair driving performance. However, periodic assessment of patients with MS driving ability is recommended, especially after relapses and changes in treatment. Blood THC measurements might be above authorized thresholds for some countries following administration of THC:CBD oromucosal spray, thus specific knowledge of each country's driving regulations and a medical certificate are recommended.

40 CFR 123.25 - Requirements for permitting.

Code of Federal Regulations, 2012 CFR

2012-07-01

... subchapter N; (38) For a Great Lakes State or Tribe (as defined in 40 CFR 132.2), 40 CFR part 132 (NPDES... NPDES storm water program?); (41) § 122.32 (As an operator of a small MS4, am I regulated under the NPDES storm water program?); (42) § 122.33 (If I am an operator of a regulated small MS4, how do I apply...

40 CFR 123.25 - Requirements for permitting.

Code of Federal Regulations, 2013 CFR

2013-07-01

... subchapter N; (38) For a Great Lakes State or Tribe (as defined in 40 CFR 132.2), 40 CFR part 132 (NPDES... NPDES storm water program?); (41) § 122.32 (As an operator of a small MS4, am I regulated under the NPDES storm water program?); (42) § 122.33 (If I am an operator of a regulated small MS4, how do I apply...

40 CFR 123.25 - Requirements for permitting.

Code of Federal Regulations, 2014 CFR

2014-07-01

... subchapter N; (38) For a Great Lakes State or Tribe (as defined in 40 CFR 132.2), 40 CFR part 132 (NPDES... NPDES storm water program?); (41) § 122.32 (As an operator of a small MS4, am I regulated under the NPDES storm water program?); (42) § 122.33 (If I am an operator of a regulated small MS4, how do I apply...

40 CFR 123.25 - Requirements for permitting.

Code of Federal Regulations, 2011 CFR

2011-07-01

... subchapter N; (38) For a Great Lakes State or Tribe (as defined in 40 CFR 132.2), 40 CFR part 132 (NPDES... NPDES storm water program?); (41) § 122.32 (As an operator of a small MS4, am I regulated under the NPDES storm water program?); (42) § 122.33 (If I am an operator of a regulated small MS4, how do I apply...

Density functional study on the pressure profile of the inhomogeneous fluid mixture

NASA Astrophysics Data System (ADS)

Kang, Yanshuang; Kang, Yanmei; Sun, Zongli; Li, Yushan; Tan, Shanshan

2017-08-01

Not Available Project supported by the National Natural Science Foundation of China (Grant No. 21503077), the Fundamental Research Fund for the Central Universities of China (Grant Nos. 2016MS156 and 13MS105), the Technology Research and Development Program of Hebei Province, China (Grant No. 13213704), and the Program of Study Abroad for Young Teachers by Agricultural University of Hebei.

Effect of a transactional model education program on coping effectiveness in women with multiple sclerosis.

PubMed

Sanaeinasab, Hormoz; Saffari, Mohsen; Hashempour, Mahrokh; Karimi Zarchi, Ali-Akbar; Alghamdi, Waleed A; Koenig, Harold G

2017-10-01

Multiple sclerosis (MS) is a chronic and progressive disease that causes stress due to its unpredictability and lack of definitive treatments. This study examined the effects of an educational program using a transactional model to help women with MS cope with their disease. In a randomized clinical trial, 80 female patients from the MS Society of Iran were randomized to the intervention ( n  = 40) or a control group ( n  = 40). Outcomes were assessed using Cohen's Perceived Stress Scale (PSS) and the Jalowiec Coping Scale (JCS), which were completed by both groups at baseline, 1 month, and 3 months after the intervention. The intervention consisted of six educational sessions administered over 2 months based on a transactional model. The data were analyzed using repeated measures ANOVA. Average PSS scores decreased significantly over time in the intervention group, while increasing in the control group. Between-group differences were significant at both 1-month and 3-month follow-up ( p  < .001). Both problem-focused and emotion-focused coping styles improved over time in use and effectiveness in the intervention group, whereas little or no change occurred in these coping behaviors in the control group. The transactional model-based education program tested here was successful in reducing stress levels and increasing healthy coping styles in women with MS. If these findings are replicated in future studies, widespread adoption of this program may help women with MS cope more successfully with their disease.

Global and selective detection of organohalogens in environmental samples by comprehensive two-dimensional gas chromatography-tandem mass spectrometry and high-resolution time-of-flight mass spectrometry.

PubMed

Hashimoto, Shunji; Takazawa, Yoshikatsu; Fushimi, Akihiro; Tanabe, Kiyoshi; Shibata, Yasuyuki; Ieda, Teruyo; Ochiai, Nobuo; Kanda, Hirooki; Ohura, Takeshi; Tao, Qingping; Reichenbach, Stephen E

2011-06-17

We successfully detected halogenated compounds from several kinds of environmental samples by using a comprehensive two-dimensional gas chromatograph coupled with a tandem mass spectrometer (GC×GC-MS/MS). For the global detection of organohalogens, fly ash sample extracts were directly measured without any cleanup process. The global and selective detection of halogenated compounds was achieved by neutral loss scans of chlorine, bromine and/or fluorine using an MS/MS. It was also possible to search for and identify compounds using two-dimensional mass chromatograms and mass profiles obtained from measurements of the same sample with a GC×GC-high resolution time-of-flight mass spectrometer (HRTofMS) under the same conditions as those used for the GC×GC-MS/MS. In this study, novel software tools were also developed to help find target (halogenated) compounds in the data provided by a GC×GC-HRTofMS. As a result, many dioxin and polychlorinated biphenyl congeners and many other halogenated compounds were found in fly ash extract and sediment samples. By extracting the desired information, which concerned organohalogens in this study, from huge quantities of data with the GC×GC-HRTofMS, we reveal the possibility of realizing the total global detection of compounds with one GC measurement of a sample without any pre-treatment. Copyright © 2011 Elsevier B.V. All rights reserved.

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.

PubMed

Crowell, Kevin L; Slysz, Gordon W; Baker, Erin S; LaMarche, Brian L; Monroe, Matthew E; Ibrahim, Yehia M; Payne, Samuel H; Anderson, Gordon A; Smith, Richard D

2013-11-01

The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing. We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension. LC-IMS-MS Feature Finder is available as a command-line tool for download at http://omics.pnl.gov/software/LC-IMS-MS_Feature_Finder.php. The Microsoft.NET Framework 4.0 is required to run the software. All other dependencies are included with the software package. Usage of this software is limited to non-profit research to use (see README). rds@pnnl.gov. Supplementary data are available at Bioinformatics online.

Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale

PubMed Central

Durbin, Kenneth R.; Tran, John C.; Zamdborg, Leonid; Sweet, Steve M. M.; Catherman, Adam D.; Lee, Ji Eun; Li, Mingxi; Kellie, John F.; Kelleher, Neil L.

2011-01-01

Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale. PMID:20848673

Analysis of the reaction products from micro-vial pyrolysis of the mixture glucose/proline and of a tobacco leaf extract:Search for Amadori intermediates.

PubMed

Mitsui, Kazuhisa; David, Frank; Tienpont, Bart; Sandra, Koen; Ochiai, Nobuo; Tamura, Hirotoshi; Sandra, Pat

2015-11-27

Micro-vial pyrolysis (PyroVial) was used to study the production of compounds important for the aroma of heat-treated natural products such as tobacco. Firstly, a mixture of glucose and proline was pyrolyzed as model, as this sugar and amino acid are also abundant in tobacco leaf (Nicotiana tobacum L.). The pyrolysate was analyzed using headspace-GC–MS, liquid injection GC–MS and LC–MS. Next, micro-vial pyrolysis in combination with LC–MS was applied to tobacco leaf extract. Using MS deconvolution, molecular feature extraction and differential analysis it was possible to identify Amadori intermediates of the Maillard reaction in the tobacco leaf extract. The intermediate disappeared as was the case for 1-deoxy-1-prolino-β-d-fructose or the concentration decreased in the pyrolysate compared to the original extract such as for the 1-deoxy-1-[2-(3-pyridyl)-1-pyrrolidinyl]-β-d-fructose isomers indicating that Amadori intermediates are important precursors for aroma compound formation.

Target objects defined by a conjunction of colour and shape can be selected independently and in parallel.

PubMed

Jenkins, Michael; Grubert, Anna; Eimer, Martin

2017-11-01

It is generally assumed that during search for targets defined by a feature conjunction, attention is allocated sequentially to individual objects. We tested this hypothesis by tracking the time course of attentional processing biases with the N2pc component in tasks where observers searched for two targets defined by a colour/shape conjunction. In Experiment 1, two displays presented in rapid succession (100 ms or 10 ms SOA) each contained a target and a colour-matching or shape-matching distractor on opposite sides. Target objects in both displays elicited N2pc components of similar size that overlapped in time when the SOA was 10 ms, suggesting that attention was allocated in parallel to both targets. Analogous results were found in Experiment 2, where targets and partially matching distractors were both accompanied by an object without target-matching features. Colour-matching and shape-matching distractors also elicited N2pc components, and the target N2pc was initially identical to the sum of the two distractor N2pcs, suggesting that the initial phase of attentional object selection was guided independently by feature templates for target colour and shape. Beyond 230 ms after display onset, the target N2pc became superadditive, indicating that attentional selection processes now started to be sensitive to the presence of feature conjunctions. Results show that independent attentional selection processes can be activated in parallel by two target objects in situations where these objects are defined by a feature conjunction.

MALDI-TOF mass spectrometry-based identification of group A Streptococcus isolated from areas of the 2011 scarlet fever outbreak in china.

PubMed

Xiao, Di; You, Yuanhai; Bi, Zhenwang; Wang, Haibin; Zhang, Yongchan; Hu, Bin; Song, Yanyan; Zhang, Huifang; Kou, Zengqiang; Yan, Xiaomei; Zhang, Menghan; Jin, Lianmei; Jiang, Xihong; Su, Peng; Bi, Zhenqiang; Luo, Fengji; Zhang, Jianzhong

2013-03-01

There was a dramatic increase in scarlet fever cases in China from March to July 2011. Group A Streptococcus (GAS) is the only pathogen known to cause scarlet fever. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled to Biotyper system was used for GAS identification in 2011. A local reference database (LRD) was constructed, evaluated and used to identify GAS isolates. The 75 GAS strains used to evaluate the LRD were all identified correctly. Of the 157 suspected β-hemolytic strains isolated from 298 throat swab samples, 127 (100%) and 120 (94.5%) of the isolates were identified as GAS by the MALDI-TOF MS system and the conventional bacitracin sensitivity test method, respectively. All 202 (100%) isolates were identified at the species level by searching the LRD, while 182 (90.1%) were identified by searching the original reference database (ORD). There were statistically significant differences with a high degree of credibility at species level (χ(2)=6.052, P<0.05 between the LRD and ORD). The test turnaround time was shortened 36-48h, and the cost of each sample is one-tenth of the cost of conventional methods. Establishing a domestic database is the most effective way to improve the identification efficiency using a MALDI-TOF MS system. MALDI-TOF MS is a viable alternative to conventional methods and may aid in the diagnosis and surveillance of GAS. Copyright © 2013 Elsevier B.V. All rights reserved.

Patterns of chemical diversity in the marine ascidian Phallusia spp.: anti-tumor activity and metabolic pathway inhibiting steroid biosynthesis.

PubMed

Palanisamy, Satheesh Kumar; Arumugam, Velusamy; Peter, Magesh D; Sundaresan, Umamaheswari

2018-05-01

The complex nature of marine biodiversity is partially responsible for the lack of studies in Indian ascidian species, which often target a small number of novel biomolecules. We performed untargeted metabolomics using gas chromatography-mass spectrometry (GC-MS) in two invasive ascidian species to investigate the inter-specific chemical diversity of Phallusia nigra and P. arabica in search of drug-like properties and metabolic pathways. The chemical profiling of individual ascidian species was obtained using GC-MS, and the metabolites were determined by searching in NIST library and literature data. The principal component analysis of GC-MS mass spectral variables showed a clear discrimination of these two ascidian species based on the chemical composition and taxonomy. The metabolites, lipids, macrolides, and steroids contributed strongly to the discrimination of these two species. Results of this study confirmed that GC-MS-based chemical profiling could be utilized as a tool for chemotaxonomic classification of ascidian species. The extract of P. nigra showed promising anti-tumor activity against HT29 colon cancer 35 µM and MCF7-breast cancer (34.76 µM) cells compared to P. arabica . Of the more than 70 metabolites measured, 18 metabolites that mapped various pathways linked to three metabolic pathways being impacted and altered in steroid biosynthesis, primary bile acid biosynthesis, and steroid hormone biosynthesis were observed to have changed significantly ( p  > 0.004, FDR < 0.01). Also, higher expression of this pathway was associated with more significant cytotoxicity in breast and colon carcinoma cells.

Evaluation of a localization training program for hearing impaired listeners.

PubMed

Kuk, Francis; Keenan, Denise M; Lau, Chi; Crose, Bryan; Schumacher, Jennifer

2014-01-01

To evaluate the effectiveness of a home-based and a laboratory-based localization training program. This study examined the effectiveness of a localization training program on improving the localization ability of 15 participants with a mild-to-moderately severe hearing loss. These participants had worn the study hearing aids in a previous study. The training consisted of laboratory-based training and home-based training. The participants were divided into three groups: a control group, a group that performed the laboratory training first followed by the home training, and a group that completed the home training first followed by the laboratory training. The participants were evaluated before any training (baseline), at 2 weeks, 1 month, 2 months, and 3 months after baseline testing. All training was completed by the second month. The participants only wore the study hearing aids between the second month and the third month. Localization testing and laboratory training were conducted in a sound-treated room with a 360 degree, 12 loudspeaker array. There were three stimuli each randomly presented three times from each loudspeaker (nine test items from each loudspeaker) for a total of 108 items on each test or training trial. The stimuli, including a continuous noise, a telephone ring, and a speech passage "Search for the sound from this speaker" were high-pass filtered above 2000 Hz. The test stimuli had a duration of 300 ms, whereas the training stimuli had five durations (3 s, 2 s, 1 s, 500 ms, and 300 ms) and four back attenuation (-8, -4, -2, and 0 dB re: front presentation) values. All stimuli were presented at 30 dB SL or the most comfortable listening level of the participants. Each participant completed 6 to 8, 2 hr laboratory-based training within a month. The home training required a two-loudspeaker computer system using 30 different sounds of various durations (5) by attenuation (4) combinations. The participants were required to use the home training program for 30 min per day, 5 days per week for 4 weeks. Localization data were evaluated using a 30 degree error criterion. There was a significant difference in localization scores for sounds that originated from the back between baseline and 3 months for the two groups that received training. The performance of the control group remained the same across the 3 month period. Generalization to other stimuli and in the unaided condition was also seen. There were no significant differences in localization performance from other directions between baseline and 3 months. These results indicated that the training program was effective in improving the localization skills of these listeners under the current test set-up. The current study demonstrated that hearing aid wearers can be trained on their front/back localization skills using either laboratory-based or home-based training program. The effectiveness of the training was generalized to other acoustic stimuli and the unaided conditions when the stimulus levels were fixed.

Method development and application of offline two-dimensional liquid chromatography/quadrupole time-of-flight mass spectrometry-fast data directed analysis for comprehensive characterization of the saponins from Xueshuantong Injection.

PubMed

Yang, Wenzhi; Zhang, Jingxian; Yao, Changliang; Qiu, Shi; Chen, Ming; Pan, Huiqin; Shi, Xiaojian; Wu, Wanying; Guo, Dean

2016-09-05

Xueshuantong Injection (XSTI), derived from Notoginseng total saponins, is a popular traditional Chinese medicine injection for the treatment of thrombus-resultant diseases. Current knowledge on its therapeutic basis is limited to five major saponins, whereas those minor ones are rarely investigated. We herein develop an offline two-dimensional liquid chromatography/quadrupole time-of-flight mass spectrometry-fast data directed analysis (offline 2D LC/QTOF-Fast DDA) approach to systematically characterize the saponins contained in XSTI. Key parameters affecting chromatographic separation in 2D LC (including stationary phase, mobile phase, column temperature, and gradient elution program) and the detection by QTOF MS (involving spray voltage, cone voltage, and ramp collision energy) were optimized in sequence. The configured offline 2D LC system showed an orthogonality of 0.84 and a theoretical peak capacity of 8976. Total saponins in XSTI were fractionated into eleven samples by the first-dimensional hydrophilic interaction chromatography, which were further analyzed by reversed-phase UHPLC/QTOF-Fast DDA in negative ion mode. The fragmentation features evidenced from 36 saponin reference standards, high-accuracy MS and Fast-DDA-MS(2) data, elemental composition (C<80, H<120, O<50), double-bond equivalent (DBE 5-15), and searching an in-house library of Panax notoginseng, were simultaneously utilized for structural elucidation. Ultimately, 148 saponins were separated and characterized, and 80 have not been isolated from P. notoginseng. An in-depth depiction of the chemical composition of XSTI was achieved. The results obtained would benefit better understanding of the therapeutic basis and significant promotion on the quality standard of XSTI as well as other homologous products. Copyright © 2016. Published by Elsevier B.V.

Using health promotion guidelines for persons with disabilities to develop and evaluate a physical activity program for individuals with multiple sclerosis: A feasibility study.

PubMed

Dixon-Ibarra, Alicia; Nery-Hurwit, Mara; Driver, Simon; MacDonald, Megan

2017-04-01

The Health Education for Persons with Multiple Sclerosis (HEMS) program was developed in response to the need for interventions aimed at increasing physical activity for individuals with Multiple Sclerosis (MS). It was developed and evaluated using Drum and colleagues (2009) guidelines for implementing health promotion programs for individuals with disabilities. The purpose of this feasibility study is to describe the development, implementation, and evaluation of the HEMS program. Thirteen individuals with MS completed the 8-week health education program. A mixed method approach for evaluation was implemented (i.e., survey and focus groups). Process and resource feasibility demonstrated that over half of the participants attended at least 80% of the weekly sessions. Focus group data provided valuable feedback for future iterations of the program including critiques on the delivery, content, and group support provided. Outcome evaluation showed increases in self-efficacy (survey), improvements in theoretical constructs (focus groups), and increased physical activity (focus groups). Results show that health promotion programs for persons with MS can improve physical activity and related constructs. Next steps will be to revise, implement, and reevaluate the HEMS program in a larger randomized control trial. Published by Elsevier Ltd.

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

PubMed

Beisken, Stephan; Earll, Mark; Portwood, David; Seymour, Mark; Steinbeck, Christoph

2014-04-01

Liquid chromatography coupled to mass spectrometry (LC-MS) is commonly applied to investigate the small molecule complement of organisms. Several software tools are typically joined in custom pipelines to semi-automatically process and analyse the resulting data. General workflow environments like the Konstanz Information Miner (KNIME) offer the potential of an all-in-one solution to process LC-MS data by allowing easy integration of different tools and scripts. We describe MassCascade and its workflow plug-in for processing LC-MS data. The Java library integrates frequently used algorithms in a modular fashion, thus enabling it to serve as back-end for graphical front-ends. The functions available in MassCascade have been encapsulated in a plug-in for the workflow environment KNIME, allowing combined use with e.g. statistical workflow nodes from other providers and making the tool intuitive to use without knowledge of programming. The design of the software guarantees a high level of modularity where processing functions can be quickly replaced or concatenated. MassCascade is an open-source library for LC-MS data processing in metabolomics. It embraces the concept of visual programming through its KNIME plug-in, simplifying the process of building complex workflows. The library was validated using open data.

Profiling optimization for big data transfer over dedicated channels

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

Yun, D.; Wu, Qishi; Rao, Nageswara S

The transfer of big data is increasingly supported by dedicated channels in high-performance networks, where transport protocols play an important role in maximizing applicationlevel throughput and link utilization. The performance of transport protocols largely depend on their control parameter settings, but it is prohibitively time consuming to conduct an exhaustive search in a large parameter space to find the best set of parameter values. We propose FastProf, a stochastic approximation-based transport profiler, to quickly determine the optimal operational zone of a given data transfer protocol/method over dedicated channels. We implement and test the proposed method using both emulations based onmore » real-life performance measurements and experiments over physical connections with short (2 ms) and long (380 ms) delays. Both the emulation and experimental results show that FastProf significantly reduces the profiling overhead while achieving a comparable level of end-to-end throughput performance with the exhaustive search-based approach.« less

SEARCH: Study of Environmental Arctic Change--A System-scale, Cross-disciplinary, Long-term Arctic Research Program

NASA Astrophysics Data System (ADS)

Wiggins, H. V.; Schlosser, P.; Loring, A. J.; Warnick, W. K.; Committee, S. S.

2008-12-01

The Study of Environmental Arctic Change (SEARCH) is a multi-agency effort to observe, understand, and guide responses to changes in the arctic system. Interrelated environmental changes in the Arctic are affecting ecosystems and living resources and are impacting local and global communities and economic activities. Under the SEARCH program, guided by the Science Steering Committee (SSC), the Interagency Program Management Committee (IPMC), and the Observing, Understanding, and Responding to Change panels, scientists with a variety of expertise--atmosphere, ocean and sea ice, hydrology and cryosphere, terrestrial ecosystems, human dimensions, and paleoclimatology--work together to achieve goals of the program. Over 150 projects and activities contribute to SEARCH implementation. The Observing Change component is underway through National Science Foundation's (NSF) Arctic Observing Network (AON), NOAA-sponsored atmospheric and sea ice observations, and other relevant national and international efforts, including the EU- sponsored Developing Arctic Modelling and Observing Capabilities for Long-term Environmental Studies (DAMOCLES) Program. The Understanding Change component of SEARCH consists of modeling and analysis efforts, with strong linkages to relevant programs such as NSF's Arctic System Synthesis (ARCSS) Program. The Responding to Change element is driven by stakeholder research and applications addressing social and economic concerns. As a national program under the International Study of Arctic Change (ISAC), SEARCH is also working to expand international connections in an effort to better understand the global arctic system. SEARCH is sponsored by eight (8) U.S. agencies, including: the National Science Foundation (NSF), the National Oceanic and Atmospheric Administration (NOAA), the National Aeronautics and Space Administration (NASA), the Department of Defense (DOD), the Department of Energy (DOE), the Department of the Interior (DOI), the Smithsonian Institution, and the U.S. Department of Agriculture (USDA). The U.S. Arctic Research Commission participates as an IPMC observer. For further information, please visit the website: http://www.arcus.org/search or contact: Helen V. Wiggins: helen@arcus.org, SEARCH Project Office, Arctic Research Consortium of the U.S. (ARCUS); or Peter Schlosser, schlosser@ldeo.columbia.edu, SEARCH SSC Chair.

Factors Affecting Employment Among Informal Caregivers Assisting People with Multiple Sclerosis

PubMed Central

Huang, Chunfeng; Zheng, Zhida

2013-01-01

The objective of this study was to identify characteristics of informal caregivers, caregiving, and the people with multiple sclerosis (MS) receiving assistance that are associated with reduced caregiver employment. Data were collected during telephone interviews with 530 MS caregivers, including 215 employed caregivers, with these survey data analyzed using logistic regression. Poorer cognitive ability by the care recipient to make decisions about daily tasks and more caregiving hours per week predicted reduced caregiver employment. Better physical health domains of caregiver quality of life were associated with significantly lower odds of reduced employment. Health professionals treating informal caregivers, as well as those treating people with MS, need to be aware of respite, support, and intervention programs available to MS caregivers and refer them to these programs, which could reduce the negative impact of caregiving on employment. PMID:24453784

Effects of a 4-month Ananda Yoga program on physical and mental health outcomes for persons with multiple sclerosis.

PubMed

Salgado, Bryan Coleman; Jones, Maitri; Ilgun, Suzanne; McCord, Gyandev; Loper-Powers, Mangala; van Houten, Peter

2013-01-01

Yoga has been found to be effective for addressing problems with strength, flexibility, balance, gait, anxiety, depression, and concentration. Varying degrees of these problems occur in individuals with multiple sclerosis (MS). This study examined the effects of a comprehensive, 4-month yoga program on strength, mobility, balance, respiratory function, and quality of life for individuals with MS. Twenty four individuals with MS participated in an intensive Ananda Yoga training followed by 17 weeks of home practice. Significant improvements in functional strength, balance, and peak expiratory flow and a trend toward improvements in mental health and quality of life outcomes were detected following the intervention. The results of this exploratory study suggest that yoga can have a positive impact on physical functioning and quality of life for persons with mild to moderate MS.

MS PHD'S: A successful model for reaching underrepresented minorities (URM) students through virtual platforms

NASA Astrophysics Data System (ADS)

Scott, O.; Johnson, A.; Williamson, V.; Ricciardi, L.; Jearld, A., Jr.; Guzman, W. I.

2014-12-01

To successfully recruit and retain underrepresented minority (URM) students and early career scientists, many programs supplement traditional curricular activities with multiple online platforms, establishing "virtual communities" that are free and easily accessible. These virtual communities offer readily sustainable opportunities to facilitate communication across a wide range of cultural lines and socioeconomic levels thereby broadening participation and inclusivity in STEM. Established in 2003, the Minorities Striving and Pursuing Higher Degrees of Success (MS PHD'S) in Earth System Science Professional Development Program has successfully used virtual community tools such as a listserv, community forum, social media, and VoIP technologies, to extend the face-to-face activities of the program and support the advancement of URM students and early career scientists in STEM. The use of multiple facets of virtual community by MS PHD'S participants supports and encourages "real life" interactions and mentorship, facilitates networking and professional development, and maintains continuity of shared networks. The program is now in its ninth cohort and supports 213 participants. To date, 54 participants have completed their PhD and another 61 are currently enrolled in doctoral programs.

[Fingolimod compassionate use program: case study on the concept of a therapy option for multiple sclerosis prior to marketing approval].

PubMed

Haas, J; Linker, R A; Hartung, H P; Meergans, M; Ortler, S; Tracik, F

2012-12-01

In order to meet the needs of therapy of multiple sclerosis (MS) new immune therapies with a user-friendly application and better effectiveness together with good tolerability are necessary. With respect to its potential to improve MS therapy, patients with a high medical need were given access to Fingolimod even before marketing approval. Therefore, a compassionate use program unique in the field of MS was initiated. In total 137 centers participated (75 % outpatient neurologists and 25 % hospitals). Within 19 weeks 135 patients were enrolled to receive Fingolimod. The patients in the compassionate use program can be representatively described as showing hardly controllable disease activity and progression with currently available, often poorly tolerated therapy. The compassionate use program for these patients offered better control of the disease with Fingolimod. The adverse events were as expected. The Fingolimod compassionate use program demonstrated the need for this new therapeutic option. Patients who were not yet sufficiently treated were provided with an effective therapy with a good safety profile and a user-friendly administration form.

40 CFR 122.33 - If I am an operator of a regulated small MS4, how do I apply for an NPDES permit and when do I...

Code of Federal Regulations, 2011 CFR

2011-07-01

... information that your NPDES permitting authority requests. A storm sewer map that satisfies the requirement of... area as a medium or large MS4 with an NPDES storm water permit and that other MS4 is willing to have you participate in its storm water program, you and the other MS4 may jointly seek a modification of...

40 CFR 122.33 - If I am an operator of a regulated small MS4, how do I apply for an NPDES permit and when do I...

Code of Federal Regulations, 2014 CFR

2014-07-01

... information that your NPDES permitting authority requests. A storm sewer map that satisfies the requirement of... area as a medium or large MS4 with an NPDES storm water permit and that other MS4 is willing to have you participate in its storm water program, you and the other MS4 may jointly seek a modification of...

40 CFR 122.33 - If I am an operator of a regulated small MS4, how do I apply for an NPDES permit and when do I...

Code of Federal Regulations, 2012 CFR

2012-07-01

... information that your NPDES permitting authority requests. A storm sewer map that satisfies the requirement of... area as a medium or large MS4 with an NPDES storm water permit and that other MS4 is willing to have you participate in its storm water program, you and the other MS4 may jointly seek a modification of...

40 CFR 122.33 - If I am an operator of a regulated small MS4, how do I apply for an NPDES permit and when do I...

Code of Federal Regulations, 2013 CFR

2013-07-01

... information that your NPDES permitting authority requests. A storm sewer map that satisfies the requirement of... area as a medium or large MS4 with an NPDES storm water permit and that other MS4 is willing to have you participate in its storm water program, you and the other MS4 may jointly seek a modification of...

40 CFR 122.33 - If I am an operator of a regulated small MS4, how do I apply for an NPDES permit and when do I...

Code of Federal Regulations, 2010 CFR

2010-07-01

... information that your NPDES permitting authority requests. A storm sewer map that satisfies the requirement of... area as a medium or large MS4 with an NPDES storm water permit and that other MS4 is willing to have you participate in its storm water program, you and the other MS4 may jointly seek a modification of...

An update on MS Nurse PROfessional, an ongoing project of the European Multiple Sclerosis Platform.

PubMed

Winslow, Anne

2016-12-01

Within the multidisciplinary team required to manage people with multiple sclerosis (MS) effectively, the nurse is the central component of coordinated care and support. A 2009 survey led by the European Multiple Sclerosis Platform, an umbrella organization of national MS associations, identified variance and disparity across Europe in the nursing care of MS patients. This led to development of MS Nurse PROfessional, a continuing medical education-accredited modular online learning program endorsed and approved by leading international nursing and professional groups, and people with MS, as a tool to support the evolving role of the European MS nurse. Analysis of participant experience and nurse practice to date has been overwhelmingly positive. Expansion of MS Nurse PRO is underway or planned for future.

Evaluation of a teleconference-delivered energy conservation education program for people with multiple sclerosis.

PubMed

Finlayson, Marcia; Holberg, Christa

2007-10-04

Little is known about the strengths and limitations of teleconference delivery for energy conservation education for people with multiple sclerosis (MS). This study evaluated such a program to address this gap. Data were collected from 28 individuals with MS who participated in a teleconference-delivered energy conservation education program. Participants shared their perspectives on the course and its delivery format. Session notes from the three occupational therapists who delivered the program were also reviewed. Participants found the format to be convenient and relaxed, and the content to be relevant to their everyday lives. Technical issues, lack of time for sharing, and lack of time to practice strategies were limitations. Although the format challenged the occupational therapists' group leadership skills, they were surprised at the extent of group cohesion that developed using this format. Feedback from both people with MS and occupational therapists suggests that providing energy conservation education by teleconference is acceptable, practical, and worth pursuing in the future.

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines.

PubMed

Jones, Andrew R; Siepen, Jennifer A; Hubbard, Simon J; Paton, Norman W

2009-03-01

LC-MS experiments can generate large quantities of data, for which a variety of database search engines are available to make peptide and protein identifications. Decoy databases are becoming widely used to place statistical confidence in result sets, allowing the false discovery rate (FDR) to be estimated. Different search engines produce different identification sets so employing more than one search engine could result in an increased number of peptides (and proteins) being identified, if an appropriate mechanism for combining data can be defined. We have developed a search engine independent score, based on FDR, which allows peptide identifications from different search engines to be combined, called the FDR Score. The results demonstrate that the observed FDR is significantly different when analysing the set of identifications made by all three search engines, by each pair of search engines or by a single search engine. Our algorithm assigns identifications to groups according to the set of search engines that have made the identification, and re-assigns the score (combined FDR Score). The combined FDR Score can differentiate between correct and incorrect peptide identifications with high accuracy, allowing on average 35% more peptide identifications to be made at a fixed FDR than using a single search engine.

Accurate recognition and feature qualify for flavonoid extracts from Liang-wai Gan Cao by liquid chromatography-high resolution-mass spectrometry and computational MS/MS fragmentation.

PubMed

He, Min; Wu, Hai; Nie, Juan; Yan, Pan; Yang, Tian-Biao; Yang, Zhi-Yu; Pei, Rui

2017-11-30

In this study, Liquid Chromatography (LC) separation combined with quadrupole-Time-Of-Flight Mass Spectrometry (qTOF-MS) detection was used to analyze the characteristic ions of the flavonoids from Liang-wai Gan Cao (Radix Glycyrrhizae uralensis). First, accurate mass measurement and isotope curve optimization could provide reliable molecular prediction after noise deduction, baseline calibration and "ghost peak recognition". Thus, some spectral features in the LC-MS data could be clearly explained. Secondly, the chemical structure of flavonoids was deduced by MS/MS fragment ions, and the in-silico spectra by MS-FINDER program provided strong support for overcoming the bottleneck of phytochemical identification. For a predicted formula and experimental MS/MS spectrum, the MS-FINDER program could sort the candidate compounds in the public database based on a comprehensive weighted score, and we took the first 20 reliable compounds to seek the target compound in an in-house database. Certainly, those fragmentation pathways could also be deduced and described as Retro-Diels-Alder (RDA) fragmentation reaction, losses of C 4 H 8 , C 5 H 8 , CH 3 , CO, CO 2 and others. Accordingly, 63 flavonoids were identified, and their in-silico bioactivity were clearly disclosed by some bioinformatics tools. In this experiment, the flavonoids obtained by the four extraction processes were tested by LC-qTOF-MS. We looked for possible Q-markers from these data matrices and then quantified them; their similarities/differences were also described. The results also indicated that the Macroporous Adsorption Resins (MARs) purification is a low cost, environmentally friendly and effective approach. Copyright © 2017 Elsevier B.V. All rights reserved.

Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation.

PubMed

Schilling, Birgit; Rardin, Matthew J; MacLean, Brendan X; Zawadzka, Anna M; Frewen, Barbara E; Cusack, Michael P; Sorensen, Dylan J; Bereman, Michael S; Jing, Enxuan; Wu, Christine C; Verdin, Eric; Kahn, C Ronald; Maccoss, Michael J; Gibson, Bradford W

2012-05-01

Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need for improved label-free approaches. This need is particularly pressing for workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as isobaric tags for relative and absolute quantitation and tandem mass tags may prove problematic or where stable isotope labeling with amino acids in cell culture labeling cannot be readily applied. Skyline is a freely available, open source software tool for quantitative data processing and proteomic analysis. We expanded the capabilities of Skyline to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments. Moreover, unlike existing programs, Skyline MS1 filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. The new quantitative and graphical tools now available in Skyline specifically support interrogation of multiple acquisitions for MS1 filtering, including visual inspection of peak picking and both automated and manual integration, key features often lacking in existing software. In addition, Skyline MS1 filtering displays retention time indicators from underlying MS/MS data contained within the spectral library to ensure proper peak selection. The modular structure of Skyline also provides well defined, customizable data reports and thus allows users to directly connect to existing statistical programs for post hoc data analysis. To demonstrate the utility of the MS1 filtering approach, we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important post-translational modifications: acetylation and phosphorylation, in peptide-centric affinity workflows of increasing complexity using mouse and human models.

Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline

PubMed Central

Schilling, Birgit; Rardin, Matthew J.; MacLean, Brendan X.; Zawadzka, Anna M.; Frewen, Barbara E.; Cusack, Michael P.; Sorensen, Dylan J.; Bereman, Michael S.; Jing, Enxuan; Wu, Christine C.; Verdin, Eric; Kahn, C. Ronald; MacCoss, Michael J.; Gibson, Bradford W.

2012-01-01

Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need for improved label-free approaches. This need is particularly pressing for workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as isobaric tags for relative and absolute quantitation and tandem mass tags may prove problematic or where stable isotope labeling with amino acids in cell culture labeling cannot be readily applied. Skyline is a freely available, open source software tool for quantitative data processing and proteomic analysis. We expanded the capabilities of Skyline to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments. Moreover, unlike existing programs, Skyline MS1 filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. The new quantitative and graphical tools now available in Skyline specifically support interrogation of multiple acquisitions for MS1 filtering, including visual inspection of peak picking and both automated and manual integration, key features often lacking in existing software. In addition, Skyline MS1 filtering displays retention time indicators from underlying MS/MS data contained within the spectral library to ensure proper peak selection. The modular structure of Skyline also provides well defined, customizable data reports and thus allows users to directly connect to existing statistical programs for post hoc data analysis. To demonstrate the utility of the MS1 filtering approach, we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important post-translational modifications: acetylation and phosphorylation, in peptide-centric affinity workflows of increasing complexity using mouse and human models. PMID:22454539

Magnetic resonance imaging in multiple sclerosis--patients' experiences, information interests and responses to an education programme.

PubMed

Brand, Judith; Köpke, Sascha; Kasper, Jürgen; Rahn, Anne; Backhus, Imke; Poettgen, Jana; Stellmann, Jan-Patrick; Siemonsen, Susanne; Heesen, Christoph

2014-01-01

Magnetic resonance imaging (MRI) is a key diagnostic and monitoring tool in multiple sclerosis (MS) management. However, many scientific uncertainties, especially concerning correlates to impairment and prognosis remain. Little is known about MS patients' experiences, knowledge, attitudes, and unmet information needs concerning MRI. We performed qualitative interviews (n = 5) and a survey (n = 104) with MS patients regarding MRI patient information, and basic MRI knowledge. Based on these findings an interactive training program of 2 hours was developed and piloted in n = 26 patients. Interview analyses showed that patients often feel lost in the MRI scanner and left alone with MRI results and images while 90% of patients in the survey expressed a high interest in MRI education. Knowledge on MRI issues was fair with some important knowledge gaps. Major information interests were relevance of lesions as well as the prognostic and diagnostic value of MRI results. The education program was highly appreciated and resulted in a substantial knowledge increase. Patients reported that, based on the program, they felt more competent to engage in encounters with their physicians. This work strongly supports the further development of an evidence-based MRI education program for MS patients to enhance participation in health-care.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

Search for gluon saturation at Bjorken-x of 10-6-10-5 with the LHCb detector

NASA Astrophysics Data System (ADS)

da Silva, Cesar; LHCb Collaboration

2017-09-01

Gluon saturation at small Byorken- x has been in the minds of particle and nuclear physicists for decades. This state can explain several recent observations such as 1) particle collectivity observed in p+p, p+A and A+A collisions at RHIC and LHC; and 2) depleted yield of particles coming from soft gluons. Previous results from DIS experiments at HERA show a fast increase of gluons as their fractional momentum x decreases. The LHCb experiment is a forward spectrometer with vertexing, tracking, p, K, pi , e, μ identification and calorimetry in the rapidity region 1.6 < η < 4.9. LHCb is the only experiment in the world which can probe x 10-6 -10-5 , up to two orders of magnitude smaller than HERA. A direct probe of gluons at small-x and small Q2 can be performed with γ+jet correlation measurements. The current detector acceptance is not optimized for soft particles coming from Q2 < 10 [GeV/c]2 processes, where gluon saturation is expected. R&D is underway for a new tracking detector to be placed inside the LHCb magnet, the Magnet Station (MS), which will enable measurements of these soft particles. This talk is going to report the status of the analysis efforts aimed at finding the gluon saturation scale at LHCb, and details of the MS. Los Alamos National Lab LDRD program.

Recommendations for the detection and therapeutic management of cognitive impairment in multiple sclerosis.

PubMed

Bensa, C; Bodiguel, E; Brassat, D; Laplaud, D; Magy, L; Ouallet, J-C; Zephir, H; De Seze, J; Blanc, F

2012-11-01

The aim of the Multiple Sclerosis Think Tank (Groupe de réflexion sur la sclérose en plaques [GRESEP]) is to prescribe recommendations following a systematic literature search and using a Rand Corporation and California University (RAND/UCLA) appropriateness derived method, in response to practical questions that are raised in the management of patients with multiple sclerosis (MS). The topics of this working program were chosen because they were not addressed in the French recommendations and because of the few data in the literature that enabled practices to be based on validated data. Following the theme on useful serum testing with suspected multiple sclerosis, the subjects of the present work concern the detection and management of cognitive impairment in the beginning stages of the disease course. Two clinical questions were asked: which complementary exams (besides physical examination and neuropsychological tests) would help in the screening of cognitive impairment at the beginning of the disease? What care management should the person with MS and cognitive impairment be offered (treatments and neurocognitive rehabilitation)? The recommendations are the result of a consensus amongst a working group, a rating group and a reading group comprised of hospital neurologists involved in the management of patients with multiple sclerosis. Each recommendation is presented with the degree of consensus that it was accorded. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Effects of an 1-day education program on physical functioning, activity and quality of life in community living persons with multiple sclerosis.

PubMed

Feys, Peter; Tytgat, Katrien; Gijbels, Domien; De Groote, Luc; Baert, Ilse; Van Asch, Paul

2013-01-01

Persons with MS (pwMS) in the community show reduced physical activity while studies demonstrated beneficial effects of exercise therapy in supervised settings. This study investigated, in pwMS living in the community, the effects of a 1-day education program about exercises and sports, on physical activity behavior and related outcome measures as self-efficacy, perceived walking ability, fatigue, perceived impact of MS and quality of life. PwMS attended an education day with theoretical and practical sessions that was organized by the Flemish MS Society and professional exercise experts. Forty-two participants immediately completed questionnaires as well as after three and six months. Overall disability and physical activity level were measured using PDSS (patient determined disease steps) and PASIPD (Physical Activity Scale for Individuals with Physical Disabilities) respectively. Other outcomes were the ESES, MSWS-12, MFIS, MSIS-29 and SF-36. Analyses of variance were performed in groups distinguished by self-reported disability level (PDDS ≤1; n = 24 and PDSS >1; n = 18). Groups differed significantly for perceived walking ability (PDDS,MSWS-12) and physical related-domains of MSIS-29 and SF-36, but not PASIPD. A trend towards significant group*time interaction effect was found for the PASIPD indicating, at 3 and 6 months, increased physical activity in the subgroup PDDS ≤1. For the MSIS-29, a significant time effect was found with reduced impact being largest for the more disabled group at 6 months. No changes were found in other outcome measures. An one-day education program had, depending on perceived disability level, some long-standing effects on physical activity and perceived impact of MS.

SEARCH: Study of Environmental Arctic Change--A System-scale, Cross-disciplinary, Long-term Arctic Research Program

NASA Astrophysics Data System (ADS)

Wiggins, H. V.; Schlosser, P.; Fox, S. E.

2009-12-01

The Study of Environmental Arctic Change (SEARCH) is a multi-agency effort to observe, understand, and guide responses to changes in the changing arctic system. Under the SEARCH program, guided by the Science Steering Committee (SSC), the Observing, Understanding, and Responding to Change panels, and the Interagency Program Management Committee (IPMC), scientists with a variety of expertise work together to achieve goals of the program. Over 150 projects and activities contribute to SEARCH implementation. The Observing Change component is underway through the NSF’s Arctic Observing Network (AON), NOAA-sponsored atmospheric and sea ice observations, and other relevant national and international efforts, including the EU-sponsored Developing Arctic Modeling and Observing Capabilities for Long-term Environmental Studies (DAMOCLES) Program. The Understanding Change component of SEARCH consists of modeling and analysis efforts, including the Sea Ice Outlook project, an international effort to provide a community-wide summary of the expected September arctic sea ice minimum. The Understanding Change component also has strong linkages to programs such as the NSF Arctic System Science (ARCSS) Program. The Responding to Change element will be launched through stakeholder-focused research and applications addressing social and economic concerns. As a national program under the International Study of Arctic Change (ISAC), SEARCH is working to expand international connections. The State of the Arctic Conference (soa.arcus.org), to be held 16-19 March 2010 in Miami, will be a milestone activity of SEARCH and will provide an international forum for discussion of future research directions aimed toward a better understanding of the arctic system and its trajectory. SEARCH is sponsored by eight U.S. agencies that comprise the IPMC, including: the National Science Foundation (NSF), the National Oceanic and Atmospheric Administration (NOAA), the National Aeronautics and Space Administration (NASA), the Department of Defense (DOD), the Department of Energy (DOE), the Department of the Interior (DOI), the Smithsonian Institution, and the U.S. Department of Agriculture (USDA). The U.S. Arctic Research Commission (USARC) participates as an IPMC observer. For more information, visit the website at: http://www.arcus.org/search or contact: Helen V. Wiggins: helen@arcus.org, SEARCH Project Office, ARCUS; or Peter Schlosser, schlosser@ldeo.columbia.edu, SEARCH SSC Chair.

STS-56 MS1 Foale, in LES/LEH, floats during bailout exercises in JSC WETF

NASA Technical Reports Server (NTRS)

1993-01-01

STS-56 Discovery, Orbiter Vehicle (OV) 103, Mission Specialist 1 (MS1) Michael Foale, wearing launch and entry suit (LES) and launch and entry helmet (LEH), floats in a single person life raft during launch emergency egress (bailout) exercises in JSC's Weightless Environment Training Facility (WETF) Bldg 29 pool. Foale's body is covered with the life raft tarp. His head and the space shuttle search and rescue satellite aided tracking (SARSAT) antenna protrude above the tarp. This simulation prepares the astronauts for the event of an emergency egress and subsequent water landing during launch.

STS-55 MS2 Precourt in life raft during egress exercises at JSC's WETF

NASA Technical Reports Server (NTRS)

1992-01-01

Using a small single person life raft, STS-55 Mission Specialist 2 (MS2) Charles J. Precourt floats in the pool located in JSC's Weightless Environment Training Facility (WETF) Bldg 29. Precourt, wearing a launch and entry suit (LES) and launch and entry helmet (LEH), operates the Space Shuttle Search and Rescue Satellite Aided Tracking (SARSAT) portable locating beacon (PLC) as SCUBA-equipped diver looks on. Precourt, along with other crewmembers, practiced launch emergency egress (bailout). STS-55 with the Spacelab Deutsche 2 (SL-D2) payload will fly aboard Columbia, Orbiter Vehicle (OV) 102, in 1993.

Efficacy of aquatic therapy for multiple sclerosis: a systematic review.

PubMed

Corvillo, Iluminada; Varela, Enrique; Armijo, Francisco; Alvarez-Badillo, Antonio; Armijo, Onica; Maraver, Francisco

2017-12-01

Multiple sclerosis (MS) is a chronic, inflammatory, progressive, disabling autoimmune disease affecting the central nervous system. Symptoms and signs of MS vary widely and patients may lose their ability to walk. To date the benefits of aquatic therapy often used for rehabilitation in MS patients have not been reviewed. The aim of this study was to systematically review the current state of aquatic treatment for persons with MS (hydrotherapy, aquatic therapy, aquatic exercises, spa therapy) and to evaluate the scientific evidence supporting the benefits of this therapeutic option. The databases PubMed, Scopus, WoS and PEDro were searched to identify relevant reports published from January 1, 2011 to April 30, 2016. Of 306 articles identified, only 10 fulfilled the inclusion criteria: 5 randomized controlled, 2 simple randomized quasi-experimental, 1 semi-experimental, 1 blind controlled pilot and 1 pilot. Evidence that aquatic treatment improves quality of life in affected patients was very good in two studies, good in four, fair in two and weak in two.

Exploring Short Linear Motifs Using the ELM Database and Tools.

PubMed

Gouw, Marc; Sámano-Sánchez, Hugo; Van Roey, Kim; Diella, Francesca; Gibson, Toby J; Dinkel, Holger

2017-06-27

The Eukaryotic Linear Motif (ELM) resource is dedicated to the characterization and prediction of short linear motifs (SLiMs). SLiMs are compact, degenerate peptide segments found in many proteins and essential to almost all cellular processes. However, despite their abundance, SLiMs remain largely uncharacterized. The ELM database is a collection of manually annotated SLiM instances curated from experimental literature. In this article we illustrate how to browse and search the database for curated SLiM data, and cover the different types of data integrated in the resource. We also cover how to use this resource in order to predict SLiMs in known as well as novel proteins, and how to interpret the results generated by the ELM prediction pipeline. The ELM database is a very rich resource, and in the following protocols we give helpful examples to demonstrate how this knowledge can be used to improve your own research. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Meditation as an Adjunct to the Management of Multiple Sclerosis

PubMed Central

Levin, Adam B.; Hadgkiss, Emily J.; Weiland, Tracey J.; Jelinek, George A.

2014-01-01

Background. Multiple sclerosis (MS) disease course is known to be adversely affected by several factors including stress. A proposed mechanism for decreasing stress and therefore decreasing MS morbidity and improving quality of life is meditation. This review aims to critically analyse the current literature regarding meditation and MS. Methods. Four major databases were used to search for English language papers published before March 2014 with the terms MS, multiple sclerosis, meditation, and mindfulness. Results. 12 pieces of primary literature fitting the selection criteria were selected: two were randomised controlled studies, four were cohort studies, and six were surveys. The current literature varies in quality; however common positive effects of meditation include improved quality of life (QOL) and improved coping skills. Conclusion. All studies suggest possible benefit to the use of meditation as an adjunct to the management of multiple sclerosis. Additional rigorous clinical trials are required to validate the existing findings and determine if meditation has an impact on disease course over time. PMID:25105026

A Selective Impairment in Attentional Disengagement from Erotica in Obsessive-Compulsive Disorder

PubMed Central

Olatunji, Bunmi O.; Ciesielski, Bethany G.; Zald, David H.

2011-01-01

Although an attentional bias for threat has been implicated in obsessive-compulsive disorder (OCD), evidence supporting such a bias has been inconsistent. Furthermore, few studies have made distinctions between attentional capture vs. attentional disengagement and the extent to which different emotional content modulates attention in OCD also remains unclear. To address these issues, we examined patients with OCD (n = 30) and controls (n = 30) during an emotional attentional blink paradigm in which participants searched for a target embedded within a series of rapidly presented images. Critically, an erotic, fear, disgust, or neutral distracter image appeared 200 ms or 800 ms before the target. Impaired target detection was observed among OCD patients relative to controls following erotic distracters, but only when presented 800 ms, and not 200 ms, prior to the target, indicating difficulty with attentional disengagement. Difficulty disengaging from erotic images was significantly correlated with OCD symptoms in the full sample but not with symptoms of trait anxiety. These data delineate a specific information processing abnormality in OCD. PMID:21801779

High intensity interval training for people with multiple sclerosis: A systematic review.

PubMed

Campbell, Evan; Coulter, Elaine H; Paul, Lorna

2018-06-13

Aerobic high intensity interval training (HIIT) is safe in the general population and more efficient in improving fitness than continuous moderate intensity training. The body of literature examining HIIT in multiple sclerosis (MS) is expanding but to date a systematic review has not been conducted. The aim of this review was to investigate the efficacy and safety of HIIT in people with MS. A systematic search was carried out in September 2017 in EMBASE, MEDline, PEDro, CENTRAL and Web of Science Core collections using appropriate keywords and MeSH descriptors. Reference lists of relevant articles were also searched. Articles were eligible for inclusion if they were published in English, used HIIT, and included participants with MS. Quality was assessed using the PEDro scale. The following data were extracted using a standardised form: study design and characteristics, outcome measures, significant results, drop-outs, and adverse events. Seven studies (described by 11 articles) were identified: four randomised controlled trials, one randomised cross-over trial and two cohort studies. PEDro scores ranged from 3 to 8. Included participants (n = 249) were predominantly mildly disabled; one study included only people with progressive MS. Six studies used cycle ergometry and one used arm ergometry to deliver HIIT. One study reported six adverse events, four which could be attributed to the intervention. The other six reported that there were no adverse events. Six studies reported improvements in at least one outcome measure, however there were 60 different outcome measures in the seven studies. The most commonly measured domain was fitness, which improved in five of the six studies measuring aspects of fitness. The only trial not to report positive results included people with progressive and a more severe level of disability (Extended Disability Status Scale 6.0-8.0). HIIT appears to be safe and effective in increasing fitness in people with MS and low levels of disability. Further research is required to explore the effectiveness of HIIT in people with progressive MS and in those with higher levels of disability. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

Inflammation: an important parameter in the search of prostate cancer biomarkers

PubMed Central

2014-01-01

Background A more specific and early diagnostics for prostate cancer (PCa) is highly desirable. In this study, being inflammation the focus of our effort, serum protein profiles were analyzed in order to investigate if this parameter could interfere with the search of discriminating proteins between PCa and benign prostatic hyperplasia (BPH). Methods Patients with clinical suspect of PCa and candidates for trans-rectal ultrasound guided prostate biopsy (TRUS) were enrolled. Histological specimens were examined in order to grade and classify the tumor, identify BPH and detect inflammation. Surface Enhanced Laser Desorption/Ionization-Time of Flight-Mass Spectrometry (SELDI-ToF-MS) and two-dimensional gel electrophoresis (2-DE) coupled with Liquid Chromatography-MS/MS (LC-MS/MS) were used to analyze immuno-depleted serum samples from patients with PCa and BPH. Results The comparison between PCa (with and without inflammation) and BPH (with and without inflammation) serum samples by SELDI-ToF-MS analysis did not show differences in protein expression, while changes were only observed when the concomitant presence of inflammation was taken into consideration. In fact, when samples with histological sign of inflammation were excluded, 20 significantly different protein peaks were detected. Subsequent comparisons (PCa with inflammation vs PCa without inflammation, and BPH with inflammation vs BPH without inflammation) showed that 16 proteins appeared to be modified in the presence of inflammation, while 4 protein peaks were not modified. With 2-DE analysis, comparing PCa without inflammation vs PCa with inflammation, and BPH without inflammation vs the same condition in the presence of inflammation, were identified 29 and 25 differentially expressed protein spots, respectively. Excluding samples with inflammation the comparison between PCa vs BPH showed 9 unique PCa proteins, 4 of which overlapped with those previously identified in the presence of inflammation, while other 2 were new proteins, not identified in our previous comparisons. Conclusions The present study indicates that inflammation might be a confounding parameter during the proteomic research of candidate biomarkers of PCa. These results indicate that some possible biomarker-candidate proteins are strongly influenced by the presence of inflammation, hence only a well-selected protein pattern should be considered for potential marker of PCa. PMID:24944525

Locating Direction Finders in a Generalized Search and Rescue Network

DTIC Science & Technology

1991-03-01

David A . Drake and Alfred B. Marsb. Conv-ersation at NationalI Security Agenc, 29 September 1990. 7. Daskin , Mark S. " A M-admum Fpeced Co-:efing...91 7 19 134 .flT/GORjEnSj9I-M LOCATING DIRECTION FIND’RS IN A GENERALIZED SEARCH AND RESCUE NETWORK THESIS Jean M. Steppe Captain, USAF AFIT/GOR/EN S...91-Mk-7 APPROVED FOR PUBLIC RELI ASE: DISTRIBUTION UNLIMITED. 1191-05734 .. 91.. .7 19 134 i i . nMIGOR4M.S/91-MI LOCATING DIRECTION FINDERS IW A

Finding Protein and Nucleotide Similarities with FASTA

PubMed Central

Pearson, William R.

2016-01-01

The FASTA programs provide a comprehensive set of rapid similarity searching tools ( fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local and global similarity searches ( ssearch36, ggsearch36) and for searching with short peptides and oligonucleotides ( fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity (Unit 3.5). The FASTA programs can produce “BLAST-like” alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases (Unit 9.4). The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. PMID:27010337

Finding Protein and Nucleotide Similarities with FASTA.

PubMed

Pearson, William R

2016-03-24

The FASTA programs provide a comprehensive set of rapid similarity searching tools (fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local, and global similarity searches (ssearch36, ggsearch36), and for searching with short peptides and oligonucleotides (fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity. The FASTA programs can produce "BLAST-like" alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases. The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. Copyright © 2016 John Wiley & Sons, Inc.

Molecular mapping of three nuclear male sterility mutant genes in cultivated sunflower (Helianthus annuus L.)

USDA-ARS?s Scientific Manuscript database

The nuclear male sterility (NMS) trait is a useful tool for sunflower (Helianthus annuus L.) breeding and genetic programs. Previously, we induced NMS mutants in cultivated line HA 89. The mutants possessed single recessive genes, ms6, ms7, and ms8, respectively, in NMS HA 89-872, NMS HA 89-552, and...

MS PHD'S: Effective Pathways to Mentoring for Increasing Diversity in the Geoscience Workforce - What have we done? What can we still do?

NASA Astrophysics Data System (ADS)

Ricciardi, L.; Johnson, A.; Williamson Whitney, V.; Ithier-Guzman, W.; Johnson, A.; Braxton, L.

2011-12-01

In 2003 a young, African-American geoscientist and professor discovered significant gaps in the recruitment and retention of minority students within the post-secondary educational community and a subsequent correlation of underrepresentation within the geosciences workforce. From this research, a unique concept was born: The Minorities Striving and Pursuing Higher Degrees of Success in Earth System Science Professional Development Program (MS PHD'S PDP). This program was founded upon a vision that minorities can and should play a role in facilitating a network to attract, retain and increase minority representation in the geosciences workforce. In 2003, the pilot MS PHD'S program focused on a simple grass roots concept of effective mentoring and professional development administered by and for minorities through professional development activities. Today the program has grown to an impressive number of alumni who, in addition to establishing careers in the ESS professional workforce, also return to mentor the next generation of upcoming minority geoscientists. Alumni, mentors and current participants not only experience what has grown into a three-phase program but also enjoy enhanced benefits of ongoing interaction through social media, list-servs and webinars. While keeping its feet firmly planted in its grass-roots philosophy of effective mentoring and professional development by and for minorities, the MS PHD'S program looks to the future, by asking the question, "What can we do next to ensure the future of maintaining and growing diverse representation in the geosciences workforce?" Looking ahead, future goals for the program include increasing its pilot representation motto of "by and for minorities", exploring new technologies and digital tools, and expanding its supportive network of distinguished academicians, scientific organizations, industry partners, alumni, peers, and representatives of non-science disciplines.

45th Annual Targets, UAVs and Range Operations Symposium and Exhibition - Tools and Technologies for the Warfighter. Volume 2. Wednesday

DTIC Science & Technology

2007-10-31

ENGINEER Ms. Jo-An Williams FINANCE Ms. Leanne Green CONTRACTING Mr. Ken Hislop QF-16 Ms. Lee Neugin QF-4 Mr. Jim Cornwell AFSAT Ms. Audrea Feist DEPUTY...Target Program Manager: Mr. Ken Hislop Description Fullscale Target for Threat-Representative Weapon System Evaluation Meets USAF, Army, Navy, Allied Test...1940 1950 1960 1970 1980 1990 2000 2010 Approved for Public Release: Control No. UMS-2007-927, October 2007 6 A Solid Future for Unmanned Missions

Realistic Fireteam Movement in Urban Environments

DTIC Science & Technology

2010-10-01

00-2010 4 . TITLE AND SUBTITLE Realistic Fireteam Movement in Urban Environments 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...is largely consumed by the data transfer from the GPU to the CPU of the color and stencil buffers. Since this operation would only need to be...cost is given in table 4 . Waypoints Mean Std Dev 1112 1.25ms 0.09ms 3785 4.07ms 0.20ms Table 4 : Threat Probability Model update cost (Intel Q6600

A New Algorithm Using Cross-Assignment for Label-Free Quantitation with LC/LTQ-FT MS

PubMed Central

Andreev, Victor P.; Li, Lingyun; Cao, Lei; Gu, Ye; Rejtar, Tomas; Wu, Shiaw-Lin; Karger, Barry L.

2008-01-01

A new algorithm is described for label-free quantitation of relative protein abundances across multiple complex proteomic samples. Q-MEND is based on the denoising and peak picking algorithm, MEND, previously developed in our laboratory. Q-MEND takes advantage of the high resolution and mass accuracy of the hybrid LTQFT MS mass spectrometer (or other high resolution mass spectrometers, such as a Q-TOF MS). The strategy, termed “cross-assignment”, is introduced to increase substantially the number of quantitated proteins. In this approach, all MS/MS identifications for the set of analyzed samples are combined into a master ID list, and then each LC/MS run is searched for the features that can be assigned to a specific identification from that master list. The reliability of quantitation is enhanced by quantitating separately all peptide charge states, along with a scoring procedure to filter out less reliable peptide abundance measurements. The effectiveness of Q-MEND is illustrated in the relative quantitative analysis of E.coli samples spiked with known amounts of non-E.coli protein digests. A mean quantitation accuracy of 7% and mean precision of 15% is demonstrated. Q-MEND can perform relative quantitation of a set of LC/MS datasets without manual intervention and can generate files compatible with the Guidelines for Proteomic Data Publication. PMID:17441747

A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS.

PubMed

Andreev, Victor P; Li, Lingyun; Cao, Lei; Gu, Ye; Rejtar, Tomas; Wu, Shiaw-Lin; Karger, Barry L

2007-06-01

A new algorithm is described for label-free quantitation of relative protein abundances across multiple complex proteomic samples. Q-MEND is based on the denoising and peak picking algorithm, MEND, previously developed in our laboratory. Q-MEND takes advantage of the high resolution and mass accuracy of the hybrid LTQ-FT MS mass spectrometer (or other high-resolution mass spectrometers, such as a Q-TOF MS). The strategy, termed "cross-assignment", is introduced to increase substantially the number of quantitated proteins. In this approach, all MS/MS identifications for the set of analyzed samples are combined into a master ID list, and then each LC-MS run is searched for the features that can be assigned to a specific identification from that master list. The reliability of quantitation is enhanced by quantitating separately all peptide charge states, along with a scoring procedure to filter out less reliable peptide abundance measurements. The effectiveness of Q-MEND is illustrated in the relative quantitative analysis of Escherichia coli samples spiked with known amounts of non-E. coli protein digests. A mean quantitation accuracy of 7% and mean precision of 15% is demonstrated. Q-MEND can perform relative quantitation of a set of LC-MS data sets without manual intervention and can generate files compatible with the Guidelines for Proteomic Data Publication.

Increased plasma/serum levels of prolactin in multiple sclerosis: a meta-analysis.

PubMed

Wei, Wei; Liu, Lei; Cheng, Zhong-Le; Hu, Bo

2017-08-01

Prolactin (PRL) is a polypeptide hormone that is known to stimulate humoral and cell mediated immune responses. PRL levels have been investigated in several autoimmune diseases including multiple sclerosis (MS); however, these have yielded different and inconsistent results. This study aims to perform a more precise evaluation on the plasma/serum PRL levels in MS patients, and to explore the available influential factors. Research related to plasma/serum PRL levels in MS patients and healthy controls were gathered using PubMed, EMBASE and The Cochrane Library database (until Mar 31 2016). Pooled standard mean difference (SMD) with 95% confidence interval (CI) was calculated by fixed-effects or random-effect model analysis. Heterogeneity test was performed by the Q statistic and quantified using I 2 , and publication bias was evaluated using a funnel plot and Egger's linear regression test. 516 articles were obtained after searching databases, and 8 studies with 426 MS patients and 296 controls were finally included. Meta-analysis revealed that, compared with the control group, the MS group had significantly higher plasma/serum PRL levels, with the SMD of 0.55 and 95%CI (0.39, 0.72). Subgroup analyses showed that region, age and disease duration were associated with PRL level in MS patients. In summary, our meta-analysis revealed a significantly higher PRL level in MS patients than healthy controls, and it is influenced by region, age and disease duration.

Islamic fasting and multiple sclerosis

PubMed Central

2014-01-01

Background Month-long daytime Ramadan fasting pose s major challenges to multiple sclerosis (MS) patients in Muslim countries. Physicians should have practical knowledge on the implications of fasting on MS. We present a summary of database searches (Cochrane Database of Systematic Reviews, PubMed) and a mini-symposium on Ramadan fasting and MS. In this symposium, we aimed to review the effect of fasting on MS and suggest practical guidelines on management. Discussion In general, fasting is possible for most stable patients. Appropriate amendment of drug regimens, careful monitoring of symptoms, as well as providing patients with available evidence on fasting and MS are important parts of management. Evidence from experimental studies suggests that calorie restriction before disease induction reduces inflammation and subsequent demyelination and attenuates disease severity. Fasting does not appear to have unfavorable effects on disease course in patients with mild disability (Expanded Disability Status Scale (EDSS) score ≤3). Most experts believed that during fasting (especially in summer), some MS symptoms (fatigue, fatigue perception, dizziness, spasticity, cognitive problems, weakness, vision, balance, gait) might worsen but return to normal levels during feasting. There was a general consensus that fasting is not safe for patients: on high doses of anti-convulsants, anti-spastics, and corticosteroids; with coagulopathy or active disease; during attacks; with EDSS score ≥7. Summary These data suggest that MS patients should have tailored care. Fasting in MS patients is a challenge that is directly associated with the spiritual belief of the patient. PMID:24655543

Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

NASA Astrophysics Data System (ADS)

Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

2015-01-01

CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

Islamic fasting and multiple sclerosis.

PubMed

Jahromi, Soodeh Razeghi; Sahraian, Mohammad Ali; Ashtari, Fereshteh; Ayromlou, Hormoz; Etemadifar, Massoud; Ghaffarpour, Majid; Mohammadianinejad, Ehsan; Nafissi, Shahriar; Nickseresht, Alireza; Shaygannejad, Vahid; Togha, Mansoreh; Torabi, Hamid Reza; Ziaie, Shadi

2014-03-22

Month-long daytime Ramadan fasting pose s major challenges to multiple sclerosis (MS) patients in Muslim countries. Physicians should have practical knowledge on the implications of fasting on MS. We present a summary of database searches (Cochrane Database of Systematic Reviews, PubMed) and a mini-symposium on Ramadan fasting and MS. In this symposium, we aimed to review the effect of fasting on MS and suggest practical guidelines on management. In general, fasting is possible for most stable patients. Appropriate amendment of drug regimens, careful monitoring of symptoms, as well as providing patients with available evidence on fasting and MS are important parts of management. Evidence from experimental studies suggests that calorie restriction before disease induction reduces inflammation and subsequent demyelination and attenuates disease severity. Fasting does not appear to have unfavorable effects on disease course in patients with mild disability (Expanded Disability Status Scale (EDSS) score ≤3). Most experts believed that during fasting (especially in summer), some MS symptoms (fatigue, fatigue perception, dizziness, spasticity, cognitive problems, weakness, vision, balance, gait) might worsen but return to normal levels during feasting. There was a general consensus that fasting is not safe for patients: on high doses of anti-convulsants, anti-spastics, and corticosteroids; with coagulopathy or active disease; during attacks; with EDSS score ≥7. These data suggest that MS patients should have tailored care. Fasting in MS patients is a challenge that is directly associated with the spiritual belief of the patient.

Discovery and Identification of Dimethylsilanediol as a Contaminant in ISS Potable Water

NASA Technical Reports Server (NTRS)

Rutz, Jeffrey A.; Schultz, John R.; Kuo, C. Mike; Cole, Hraold E.; Manuel, Sam; Curtis, Matthew; Jones, Patrick R.; Sparkman, O. David; McCoy, J. Torin

2010-01-01

In September of 2010, analysis of ISS potable water samples was undertaken to determine the contaminant responsible for a rise in total organic carbon (TOC). As analysis of the routine target list of organic compounds did not reveal the contaminant, efforts to look for unknown compounds was initiated, resulting in an unknown peak being discovered in the gas chromatography/mass spectrometry (GC/MS) analysis for glycols. A mass spectrum of the contaminant was then generated by concentrating one of the samples by evaporation and analyzing by GC/MS in full-scan mode. Although a computer match of the compound s identity could not be obtained with the instrument s database, a search with a more up to date mass spectral library yielded a good match with dimethylsilanediol (DMSD). Inductively Coupled Plasma/Mass Spectrometry (ICP/MS) analyses showed abnormally high silicon levels in the samples, confirming that the unknown contained silicon. DMSD was then synthesized to confirm the identification and provide a standard to develop a calibration curve. Further confirmation was provided by external Direct Analysis in Real Time (DART) GC/MS analysis. A preliminary GC/MS method was then developed and archived samples from various locations on ISS were analyzed to determine the extent of the contamination and provide data for troubleshooting. This paper describes these events in more detail as well as problems encountered in routine GC/MS analyses and the subsequent development of high performance liquid chromatography and LC/MS/MS methods for quantitation of DMSD.

BMI levels with MS Bone mineral density levels in adults with multiple sclerosis: a meta-analysis.

PubMed

Huang, Zhongming; Qi, Yiying; Du, Shaohua; Chen, Guangnan; Yan, Weiqi

2015-01-01

Multiple sclerosis (MS) and osteoporosis (OP) affect a substantial proportion of the population. Accumulating evidence suggests that MS patients are at high risk for OP. We performed a meta-analysis to identify risk factors for lowered bone mineral density (BMD) in MS patients. We searched for articles within the Medline, Embase and Cochrane Library databases, published up to March 2014, pertaining to associations between MS and BMD. A total of 11 studies was included in the meta-analysis. The analysis indicated that MS patients have reduced lumbar spine, femur neck, and hip BMD compared with healthy controls (lumbar spine, standardized mean difference (SMD) = -0.76, 95% CI: -1.07, -0.45; femur neck, SMD = -0.56, 95% CI: -0.84, -0.29; and hip, SMD = -0.62, 95% CI: -0.96, -0.29). Further subgroup analysis revealed that a disease duration of >7 years, total steroid dose during the disease of >15 g, and an Expanded Disability Status Scale (EDSS) score of > 3, increased the risk of reduced BMD in the lumbar spine and femoral neck, but not in the hip. Meta-regression analysis did not explain the heterogeneity in the clinical characteristics or outcome definitions. Our meta-analysis suggests that MS patients have reduced overall BMD compared with healthy controls. Furthermore, disease duration (>7 years), total steroid dose (>15 g), and EDSS score (>3) are risk factors for reduced BMD in MS patients.

Association between circulating leptin levels and multiple sclerosis: a systematic review and meta-analysis.

PubMed

Xie, Xue-Feng; Huang, Xiao-Hui; Shen, Ai-Zong; Li, Jun; Sun, Ye-Huan

2018-05-01

Leptin, synthesised by adipocytes, has been identified as a hormone that can influence inflammatory activity. Several studies have investigated leptin levels in patients with multiple sclerosis (MS), but the results are not consistent. This study aims to derive a more precise evaluation on the relationship between circulating leptin levels and MS. A comprehensive literature searched up to July 2017 was conducted to evaluate the association of circulating leptin levels and MS. The random-effect model was applied to calculate pooled standardised mean difference (SMD) and its 95% CI. Circulating leptin levels of patients with MS and healthy controls. Of 2155 studies identified, 33 met eligibility criteria and 9 studies with 645 patients with MS and 586 controls were finally included in the meta-analysis. Meta-analysis revealed that, compared with the healthy control group, the MS group had significantly higher plasma/serum leptin levels, with the SMD of 0.70% and 95% CI (0.24 to 1.15). Subgroup analyses suggested that the leptin levels of patients with MS were associated with region, age, study sample size, measurement type, gender and blood sample type. Overall, our study suggests that patients with MS have a significantly higher leptin level than in healthy controls. Further mechanism studies and longitudinal large cohort studies are still needed to further reveal the role of leptin in the pathogenesis of MS. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

A Study of Patient Satisfaction in the Pediatrics Clinic at Water Reed Army Medical Center

DTIC Science & Technology

1992-08-01

Coordinated Care Program set forth by the Assistant Secretary of Defense for Health Affairs, Dr. Mendez , (January, 1992): "The Coordinated Care Program...William Walker, MC, Chief, Pediatric Clinic; CPT Kurt Allebach, MS, Administrator, Department of Pediatrics; Ms Carol Tross, Nursing Supervisor...of Defense moves to Coordinated Care with mandatory enrollment ( Mendez , 1992). The impact on this research may be an overestimation of the true level

COSMIC: Software catalog 1991 edition diskette format

NASA Technical Reports Server (NTRS)

1991-01-01

The PC edition of the annual COSMIC Software contains descriptions of the over 1,200 computer programs available for use within the United States as of January 1, 1991. By using the PC version of the catalog, it is possible to conduct extensive searches of the software inventory for programs that meet specific criteria. Elements such as program keywords, hardware specifications, source code languages, and title acronyms can be used for the basis of such searches. After isolating those programs that might be of best interest to the user, it is then possible to either view at the monitor, or generate a hardcopy listing of all information on those packages. In addition to the program elements that the user can search on, information such as total program size, distribution media, and program price, as well as extensive abstracts on the program, are also available to the user at this time. Another useful feature of the catalog allows for the retention of programs that meet certain search criteria between individual sessions of using the catalog. This allows users to save the information on those programs that are of interest to them in different areas of application. They can then recall a specific collection of programs for information retrieval or further search reduction if desired. In addition, this version of the catalog is adaptable to a network/shared resource environment, allowing multiple users access to a single copy of the catalog database simultaneously.

An Overview of NASA's Program of Future M&S VV&A Outreach and Training Activities

NASA Technical Reports Server (NTRS)

Caine, Lisa; Hale, Joseph P.

2006-01-01

NASA's Exploration Systems Mission Directorate (ESMD) is implementing a management approach for modeling and simulation (M&S) that will provide decision-makers information on the model s fidelity, credibility, and quality. The Integrated Modeling & Simulation Verification, Validation and Accreditation (IM&S W&A) process will allow the decision-maker to understand the risks involved in using a model s results for mission-critical decisions. The W&A Technical Working Group (W&A TWG) has been identified to communicate this process throughout the agency. As the W&A experts, the W&A NVG will be the central resource for support of W&A policy, procedures, training and templates for documentation. This presentation will discuss the W&A Technical Working Group s outreach approach aimed at educating M&S program managers, developers, users and proponents on the W&A process, beginning at MSFC with the CLV program.

ISS Expedition E53-54 Soyuz MS-06 Rollout to the Launch Pad

NASA Image and Video Library

2017-09-10

At the Baikonur Cosmodrome in Kazakhstan, the Soyuz MS-06 spacecraft and its Soyuz booster were transported from the Integration Facility to the launch pad on a railcar Sept. 10 for final preparations before launch Sept. 13 to the International Space Station. The Soyuz MS-06 will carry Expedition 53-54 Soyuz Commander Alexander Misurkin of Roscosmos and flight engineers Mark Vande Hei and Joe Acaba of NASA to the orbital complex for a five-and-a-half month mission. Also included are interviews at the launch pad with Joe Montalbano, Deputy ISS Program Manager and Sean Fuller, Director of Human Spaceflight Programs in Russia following the rocket's rollout.

Identification of Unknown Contaminants in Water Samples from ISS Employing Liquid Chromatography/Mass Spectrometry/Mass Spectrometry

NASA Technical Reports Server (NTRS)

Rutz, Jeffrey A.; Schultz, John R.

2008-01-01

Mass Spectrometry/Mass Spectrometry (MS/MS) is a powerful technique for identifying unknown organic compounds. For non-volatile or thermally unstable unknowns dissolved in liquids, liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS) is often the variety of MS/MS used for the identification. One type of LC/MS/MS that is rapidly becoming popular is time-of-flight (TOF) mass spectrometry. This technique is now in use at the Johnson Space Center for identification of unknown nonvolatile organics in water samples from the space program. An example of the successful identification of one unknown is reviewed in detail in this paper. The advantages of time-of-flight instrumentation are demonstrated through this example as well as the strategy employed in using time-of-flight data to identify unknowns.

Marfan syndrome patient experiences as ascertained through postings on social media sites.

PubMed

Kelleher, Erin; Giampietro, Philip F; Moreno, Megan A

2015-11-01

Marfan syndrome (MS) is a connective tissue disorder that affects thousands of adolescents [Population Reference Bureau, 2013]. Some adolescent patients with MS may use social media to express their experiences and emotions, but little is known about what patients choose to share online. To investigate social media content related to Marfan syndrome we used search terms "Marfan syndrome" and "Marfans" on six different social media sites. The top five recent and popular posts for each site were collected and coded weekly for five weeks. Posts were excluded if they were reshared content or not in English. A codebook was developed using an iterative process to categorize posts and comments. Out of 300 posts collected 147 posts (49.0%) were included for evaluation. Categories of displayed content included personal pictures, memes and pictures featuring symptoms of MS (41.5%) and personal MS experiences (27.1% of posts). One quarter of the posts specifically mentioned a positive experience or how thankful the profile owner was for their life. A unique category of posts (13.7%) referenced Austin Carlile, a celebrity singer with MS, as a role model. Physicians and healthcare providers may consider using social media to understand common MS concerns and to place future health education materials. © 2015 Wiley Periodicals, Inc.

First results from the LIFE project: discovery of two magnetic hot evolved stars

NASA Astrophysics Data System (ADS)

Martin, A. J.; Neiner, C.; Oksala, M. E.; Wade, G. A.; Keszthelyi, Z.; Fossati, L.; Marcolino, W.; Mathis, S.; Georgy, C.

2018-04-01

We present the initial results of the Large Impact of magnetic Fields on the Evolution of hot stars (LIFE) project. The focus of this project is the search for magnetic fields in evolved OBA giants and supergiants with visual magnitudes between 4 and 8, with the aim to investigate how the magnetic fields observed in upper main-sequence (MS) stars evolve from the MS until the late post-MS stages. In this paper, we present spectropolarimetric observations of 15 stars observed using the ESPaDOnS instrument of the Canada-France-Hawaii Telescope. For each star, we have determined the fundamental parameters and have used stellar evolution models to calculate their mass, age, and radius. Using the least-squared deconvolution technique, we have produced averaged line profiles for each star. From these profiles, we have measured the longitudinal magnetic field strength and have calculated the detection probability. We report the detection of magnetic fields in two stars of our sample: a weak field of Bl = 1.0 ± 0.2 G is detected in the post-MS A5 star 19 Aur and a stronger field of Bl = -230 ± 10 G is detected in the MS/post-MS B8/9 star HR 3042.

Simulating a Direction-Finder Search for an ELT

NASA Technical Reports Server (NTRS)

Bream, Bruce

2005-01-01

A computer program simulates the operation of direction-finding equipment engaged in a search for an emergency locator transmitter (ELT) aboard an aircraft that has crashed. The simulated equipment is patterned after the equipment used by the Civil Air Patrol to search for missing aircraft. The program is designed to be used for training in radio direction-finding and/or searching for missing aircraft without incurring the expense and risk of using real aircraft and ground search resources. The program places a hidden ELT on a map and enables the user to search for the location of the ELT by moving a 14 NASA Tech Briefs, March 2005 small aircraft image around the map while observing signal-strength and direction readings on a simulated direction- finding locator instrument. As the simulated aircraft is turned and moved on the map, the program updates the readings on the direction-finding instrument to reflect the current position and heading of the aircraft relative to the location of the ELT. The software is distributed in a zip file that contains an installation program. The software runs on the Microsoft Windows 9x, NT, and XP operating systems.

Blade frequency program for nonuniform helicopter rotors, with automated frequency search

NASA Technical Reports Server (NTRS)

Sadler, S. G.

1972-01-01

A computer program for determining the natural frequencies and normal modes of a lumped parameter model of a rotating, twisted beam, with nonuniform mass and elastic properties was developed. The program is used to solve the conditions existing in a helicopter rotor where the outboard end of the rotor has zero forces and moments. Three frequency search methods have been implemented. Including an automatic search technique, which allows the program to find up to the fifteen lowest natural frequencies without the necessity for input estimates of these frequencies.

Social Cognitive Correlates of Physical Activity in Inactive Adults with Multiple Sclerosis

ERIC Educational Resources Information Center

Dlugonski, Deirdre; Wojcicki, Thomas R.; McAuley, Edward; Motl, Robert W.

2011-01-01

Persons with multiple sclerosis (MS) are often physically inactive. This observation has prompted the search for modifiable constructs derived from established theories that act as correlates of physical activity. This study investigated self efficacy, outcome expectations, impediments, and goal setting as correlates of physical activity in…

Developing a Systematic Patent Search Training Program

ERIC Educational Resources Information Center

Zhang, Li

2009-01-01

This study aims to develop a systematic patent training program using patent analysis and citation analysis techniques applied to patents held by the University of Saskatchewan. The results indicate that the target audience will be researchers in life sciences, and aggregated patent database searching and advanced search techniques should be…

Citation Searching: Search Smarter & Find More

ERIC Educational Resources Information Center

Hammond, Chelsea C.; Brown, Stephanie Willen

2008-01-01

The staff at University of Connecticut are participating in Elsevier's Student Ambassador Program (SAmP) in which graduate students train their peers on "citation searching" research using Scopus and Web of Science, two tremendous citation databases. They are in the fourth semester of these training programs, and they are wildly successful: They…

Welcome to CALFED Bay-Delta Program

Science.gov Websites

Skip to: Content | Footer | Accessibility Search: Search CALFED Search CA.GOV | CALFED Bay-Delta California Delta Delta Home About the Delta CALFED Science About the Program Independent Science Board , CALFED Director photo of blue heron Bay-Delta Public Advisory Committee CALFED Agencies Calendar

Effect of exercise interventions on perceived fatigue in people with multiple sclerosis: synthesis of meta-analytic reviews.

PubMed

Safari, Reza; Van der Linden, Marietta L; Mercer, Tom H

2017-06-01

Although exercise training has been advocated as a nonpharmacological treatment for multiple sclerosis (MS) related fatigue, no consensus exists regarding its effectiveness. To address this, we collated meta-analytic reviews that explored the effectiveness of exercise training for the treatment of MS-related fatigue. We searched five online databases for relevant reviews, published since 2005, and identified 172 records. Five reviews were retained for systematic extraction of information and evidence quality analysis. Although our review synthesis indicated that exercise training interventions have a moderate effect on fatigue reduction in people with MS, no clear insight was obtained regarding the relative effectiveness of specific types or modes of exercise intervention. Moreover, Grading of Recommendation Assessment, Development and Evaluation revealed that the overall quality of evidence emanating from these five reviews was 'very low'.

Infectious mononucleosis and multiple sclerosis - Updated review on associated risk.

PubMed

Sheik-Ali, Sharaf

2017-05-01

There has been substantial evidence accumulating on the role of infectious mononucleosis (IM) and the subsequent risk of obtaining Multiple Sclerosis (MS). Up to date studies not previously explored were reviewed by the author to further clarify the association. Medline and Web of Science were searched with no time constraints for articles exploring an association between Multiple Sclerosis and Infectious Mononucleosis. 24 articles were found, totalling 1063 cases and 13,227 cohort/controls. 23/24 (96%) articles reported a significant association of Infectious Mononucleosis on the risk of subsequent multiple sclerosis. Overall, new literature on IM and risk of MS categorically supports the association. Future work should focus on other risk factors such as age and gender on IM and subsequent risk of MS. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

PubMed Central

Droit, Arnaud; Hunter, Joanna M; Rouleau, Michèle; Ethier, Chantal; Picard-Cloutier, Aude; Bourgais, David; Poirier, Guy G

2007-01-01

Background In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools. Description We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified. Conclusion Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5. PMID:18093328

Recommendations and Extraction of Clinical Variables of Pediatric Multiple Sclerosis Using Common Data Elements.

PubMed

Newland, Pamela; Newland, John M; Hendricks-Ferguson, Verna L; Smith, Judith M; Oliver, Brant J

2018-06-01

The purpose of this article was to demonstrate the feasibility of using common data elements (CDEs) to search for information on the pediatric patient with multiple sclerosis (MS) and provide recommendations for future quality improvement and research in the use of CDEs for pediatric MS symptom management strategies Methods: The St. Louis Children's Hospital (SLCH), Washington University (WU) pediatrics data network was evaluated for use of CDEs identified from a database to identify variables in pediatric MS, including the key clinical features from the disease course of MS. The algorithms used were based on International Classification of Diseases, Ninth/Tenth Revision, codes and text keywords to identify pediatric patients with MS from a de-identified database. Data from a coordinating center of SLCH/WU pediatrics data network, which houses inpatient and outpatient records consisting of patients (N = 498 000), were identified, and detailed information regarding the clinical course of MS were located from the text of the medical records, including medications, presence of oligoclonal bands, year of diagnosis, and diagnosis code. There were 466 pediatric patients with MS, with a few also having the comorbid diagnosis of anxiety and depression. St. Louis Children's Hospital/WU pediatrics data network is one of the largest databases in the United States of detailed data, with the ability to query and validate clinical data for research on MS. Nurses and other healthcare professionals working with pediatric MS patients will benefit from having common disease identifiers for quality improvement, research, and practice. The increased knowledge of big data from SLCH/WU pediatrics data network has the potential to provide information for intervention and decision-making that can be personalized to the pediatric MS patient.

Writing across the Curriculum: The Program at Third College, University of California, San Diego.

ERIC Educational Resources Information Center

Kirsch, Gesa

1988-01-01

Describes a writing across the curriculum program at the University of California, San Diego. Reports on the program's design and administration, summarizes how students assess the program, and discusses administrative issues particular to the program. (MS)

Factors influencing moisture analysis in the 3013 destructive examination surveillance program

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

Scogin, J. H.

Thermogravimetric analysis of a solid sample with mass spectrometry (TGA-MS) of the evolved gas is used in the destructive examination (DE) portion of the Integrated Surveillance Program to quantify the moisture content of the material stored in a 3013 container. As with any measurement determined from a small sample, the collection, storage, transportation, and handling of the sample can affect its ability to represent the properties of the bulk material. During the course of the DE program, questions have periodically arisen concerning the ability of the moisture sample to reflect reliably the actual moisture content of the entire material storedmore » in the 3013 container. Most concerns are related to the ability to collect a representative sample and to preserve the moisture content of the sample between collection and analysis. Recent delays in analysis caused by maintenance issues with the TGA-MS instrument presented a unique opportunity to document and quantify the effects various factors have on the TGA-MS moisture measurement. This report will use recent data to document the effects that current sample collection and handling practices have on the TGA-MS moisture measurement. Some suggestions will be made which could improve the current sample collection and handling practices for the TGA-MS moisture measurement so that the analytical results more accurately reflect the moisture content of the material stored in the 3013 container.« less

Effectiveness of cognitive behavioral therapy for the treatment of fatigue in patients with multiple sclerosis: A systematic review and meta-analysis.

PubMed

van den Akker, Lizanne Eva; Beckerman, Heleen; Collette, Emma Hubertine; Eijssen, Isaline Catharine Josephine Maria; Dekker, Joost; de Groot, Vincent

2016-11-01

Fatigue is a frequently occurring symptom of multiple sclerosis (MS) that limits social participation. To systematically determine the short and long-term effects of cognitive behavioral therapy (CBT) for the treatment of MS-related fatigue. Pubmed, Cochrane, EMBASE, Psychology and Behavioral Sciences Collection, ERIC, PsychINFO, Cinahl, PsycARTICLES, and relevant trial registers were searched up to February 2016. In addition, references from retrieved articles were examined. Studies were included if participants had MS, fatigue was a primary outcome measure, the intervention was CBT, and the design was a randomized controlled trial. The search was performed by two independent reviewers, three CBT experts determined whether interventions were CBT. Data on patient and study characteristics and fatigue were systematically extracted using a standardized data extraction form. Two independent reviewers assessed risk of bias using the Cochrane Collaboration risk of bias tool. In the event of disagreement, a third reviewer was consulted. Of the 994 identified studies, 4 studies were included in the meta-analysis, comprising 193 CBT-treated patients and 210 patients who underwent a control treatment. Meta-analyses of these studies showed that CBT treatment had a positive short-term effect on fatigue (standardized mean difference [SMD]=-0.47; 95% confidence interval [CI]=-0.88; -0.06; I 2 =73%). In addition, three studies showed a long-term positive effect of CBT (SMD=-0.30; CI -0.51; -0.08; I 2 =0%). This review found that the use of CBT for the treatment of fatigue in patients with MS has a moderately positive short-term effect. However, this effect decreases with cessation of treatment. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of a novel allergenic protein from the octocoral Scleronephthya gracillima (Kuekenthal) that corresponds to a new GFP-like family named Akane.

PubMed

Kato, Yuko; Jimbo, Mitsuru; Sakakibara, Youichi; Onizuka, Reiko; Takahashi, Tatsuya; Matsuhashi, Sachiko; Mita, Hajime; Amada, Kei; Imahara, Yukimitsu; Tanabe, Kimiko; Toda, Akihisa; Kamiya, Hisao

2017-09-01

Certain marine organisms have been known to cause allergic reactions among occupational fishermen. We have previously reported that bronchial asthma among the workers engaged in spiny lobster fishing in Japan was caused by octocorals such as Dendronephthya sp. and Scleronephthya gracillima (previously named Alcyonium gracillimum). Now we have found another octocoral, Scleronephthya gracillima (Kuekenthal), which causes the allergic disease in fishermen. The octocoral was characterized as a new green fluorescent protein (GFP)-like family. The new allergen has a molecular mass of 27 kDa in 1D and 2D SDS-PAGE under reduced conditions. The 27 kDa component was determined to be an allergen by western blotting, ECL immune staining method and absorption of patient sera with the antigen. Furthermore, the combination of analysis with LC-ESI-MS/MS and MASCOT search in the NCBInr database concluded the 27 kDa component had the sequence YPADI/LPDYFK, and that the 22 kDa component had the sequence QSFPEGFSWER, which both matched a GFP-like protein in Acropora aculeus and in Montastraea annularis. Further analysis by MALDI-TOF/MS/MS and MASCOT search in the NCBInr database of all 27 kDa eight spot components from 2D SDS-PAGE indicated that the sequence QSFPEGFSWER also matched as GFP-like protein in Lobophyllia hemprichii and Scleractinia sp. To our knowledge, this is the first report of the new allergenic protein that corresponds to a new GFP-like protein named Akane, and which has fluorescent emissions in the red and green part of the spectra at 628 nm and 508 nm, respectively. Copyright © 2017 John Wiley & Sons, Ltd.

Standard for Models and Simulations

NASA Technical Reports Server (NTRS)

Steele, Martin J.

2016-01-01

This NASA Technical Standard establishes uniform practices in modeling and simulation to ensure essential requirements are applied to the design, development, and use of models and simulations (MS), while ensuring acceptance criteria are defined by the program project and approved by the responsible Technical Authority. It also provides an approved set of requirements, recommendations, and criteria with which MS may be developed, accepted, and used in support of NASA activities. As the MS disciplines employed and application areas involved are broad, the common aspects of MS across all NASA activities are addressed. The discipline-specific details of a given MS should be obtained from relevant recommended practices. The primary purpose is to reduce the risks associated with MS-influenced decisions by ensuring the complete communication of the credibility of MS results.

GPR data processing computer software for the PC

USGS Publications Warehouse

Lucius, Jeffrey E.; Powers, Michael H.

2002-01-01

The computer software described in this report is designed for processing ground penetrating radar (GPR) data on Intel-compatible personal computers running the MS-DOS operating system or MS Windows 3.x/95/98/ME/2000. The earliest versions of these programs were written starting in 1990. At that time, commercially available GPR software did not meet the processing and display requirements of the USGS. Over the years, the programs were refined and new features and programs were added. The collection of computer programs presented here can perform all basic processing of GPR data, including velocity analysis and generation of CMP stacked sections and data volumes, as well as create publication quality data images.

Beyond Job Search or Basic Education: Rethinking the Role of Skills in Welfare Reform.

ERIC Educational Resources Information Center

Strawn, Julie

Most welfare-to-work programs may be classified as quick employment programs emphasizing individual or group job searches or skill-building programs emphasizing basic education. Although both types of programs offer benefits, they also suffer from significant limitations. To be more effective than their predecessors, current-generation…