ETD Outperforms CID and HCD in the Analysis of the Ubiquitylated Proteome

NASA Astrophysics Data System (ADS)

Porras-Yakushi, Tanya R.; Sweredoski, Michael J.; Hess, Sonja

2015-09-01

Comprehensive analysis of the ubiquitylome is a prerequisite to fully understand the regulatory role of ubiquitylation. However, the impact of key mass spectrometry parameters on ubiquitylome analyses has not been fully explored. In this study, we show that using electron transfer dissociation (ETD) fragmentation, either exclusively or as part of a decision tree method, leads to ca. 2-fold increase in ubiquitylation site identifications in K-ɛ-GG peptide-enriched samples over traditional collisional-induced dissociation (CID) or higher-energy collision dissociation (HCD) methods. Precursor ions were predominantly observed as 3+ charged species or higher and in a mass range 300-1200 m/z. N-ethylmaleimide was used as an alkylating agent to reduce false positive identifications resulting from overalkylation with halo-acetamides. These results demonstrate that the application of ETD fragmentation, in addition to narrowing the mass range and using N-ethylmaleimide yields more high-confidence ubiquitylation site identification than conventional CID and HCD analysis.

Identification of apple cultivars on the basis of simple sequence repeat markers.

PubMed

Liu, G S; Zhang, Y G; Tao, R; Fang, J G; Dai, H Y

2014-09-12

DNA markers are useful tools that play an important role in plant cultivar identification. They are usually based on polymerase chain reaction (PCR) and include simple sequence repeats (SSRs), inter-simple sequence repeats, and random amplified polymorphic DNA. However, DNA markers were not used effectively in the complete identification of plant cultivars because of the lack of known DNA fingerprints. Recently, a novel approach called the cultivar identification diagram (CID) strategy was developed to facilitate the use of DNA markers for separate plant individuals. The CID was designed whereby a polymorphic maker was generated from each PCR that directly allowed for cultivar sample separation at each step. Therefore, it could be used to identify cultivars and varieties easily with fewer primers. In this study, 60 apple cultivars, including a few main cultivars in fields and varieties from descendants (Fuji x Telamon) were examined. Of the 20 pairs of SSR primers screened, 8 pairs gave reproducible, polymorphic DNA amplification patterns. The banding patterns obtained from these 8 primers were used to construct a CID map. Each cultivar or variety in this study was distinguished from the others completely, indicating that this method can be used for efficient cultivar identification. The result contributed to studies on germplasm resources and the seedling industry in fruit trees.

Use of CID/ETD Mass Spectrometry to Analyze Glycopeptides

PubMed Central

Mechref, Yehia

2013-01-01

Collision-induced dissociation (CID) tandem mass spectrometry (MS) does not allow the characterization of glycopeptides because of the fragmentation of their glycan structures and limited fragmentation of peptide backbones. Electron-transfer dissociation (ETD) tandem MS, on the other hand, offers an alternative approach allowing the fragmentation of only peptide backbones of glycopeptides. Characterization of glycopeptides using both CID and ETD is summarized in this unit. While CID provide information related to the composition of glycan moiety attached to a peptide backbone, ETD permits de novo sequencing of peptides, since it prompts only peptide backbone fragmentation while keeping posttranslational modifications intact. Radical anions transfer of electrons to peptide backbone which induces cleavage of the N-Cα bond is observed in ETD. The glycan moiety is retained on the peptide backbone, largely unaffected by the ETD process. Accordingly, ETD allows not only the identification of the amino acid sequence of a glycopeptide, but also the unambiguous assignment of its glycosylation site. When data acquired from both fragmentation techniques are combined, it is possible to characterize comprehensively the entire glycopeptide. This is achieved using an instrument capable of alternating between CID and ETD experiments during an LC-MS/MS analysis. This unit discusses the different fragmentation of glycopeptides observed in CID and ETD. Tables of residue masses associated with oxonium ions observed in CID are provided to help in the interpretation of CID mass spectra. The utility of both CID and ETD for better characterization of glycopeptides are demonstrated for a model glycoprotein. PMID:22470127

Coping-Infused Dialogue through Patient-Preferred Live Music: A Medical Music Therapy Protocol and Randomized Pilot Study for Hospitalized Organ Transplant Patients.

PubMed

Hogan, Tyler James; Silverman, Michael J

2015-01-01

Solid organ transplant patients often experience a variety of psychosocial stressors that can lead to distress and may hinder successful recovery. Using coping-infused dialogue (CID) through patient- preferred live music (PPLM) music therapy sessions may improve mood and decrease pain while also imparting psychoeducational knowledge concerning the identification of local and global problems and coping skills. The purpose of this pilot study was to develop a coping-based medical music therapy protocol that combines coping-infused dialogue (CID) with patient-preferred live music (PPLM) and measure the effects of the resulting CID-PPLM protocol on mood (positive and negative affect) and pain in hospitalized transplant patients. Our study used a pre-/posttest single-session wait-list control design. Participants (N=25) were randomly assigned to experimental (CID-PPLM) or control (usual care) conditions. Participants in the CID-PPLM condition received a single 30-minute session that integrated stressor identification and knowledge of coping skills (CID) with patient-preferred live music (PPLM). Results indicated no between-group differences at pretest and significant correlations between pre- and posttest measures. Concerning posttest ANCOVA analyses, there were significant between-group differences in positive affect, negative affect, and pain, with experimental participants having more favorable posttest scores than control participants. Effect sizes were in the medium-to-large range for positive affect (η2=.198), negative affect (η2=.422), and pain (η2=.303). CID through receptive PPLM may be an effective protocol for improving mood and decreasing pain in organ transplant recipients. MT interventions can be an important tool to develop rapport and enhance outcomes with patients. As greater engagement during interventions may have stronger treatment effects, we recommend future research examining patient engagement as a potential mediator of intervention effects, as well as the number of sessions required to maximize clinical outcomes. © the American Music Therapy Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

Analysis of non-enzymatically glycated peptides: neutral-loss-triggered MS3 versus multi-stage activation tandem mass spectrometry

PubMed Central

Zhang, Qibin; Petyuk, Vladislav A.; Schepmoes, Athena A.; Orton, Daniel J.; Monroe, Matthew E.; Yang, Feng; Smith, Richard D.; Metz, Thomas O.

2009-01-01

Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet widely available and often suffers from significantly lower sensitivity than CID. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss-triggered MS3 and multi-stage activation) during liquid chromatography/multi-stage mass spectrometric (LC/MSn) analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss-triggered MS3 experiments, MS3 scans triggered by neutral losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycated peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss-triggered MS3 approach resulted in much higher specificity. Both techniques are viable alternatives to ETD for identifying glycated peptides. PMID:18763275

Navy Littoral Combat Ship (LCS) Program: Background and Issues for Congress

DTIC Science & Technology

2014-03-05

Earlier Press Reports That DOD Was Considering Truncating Program .......................... 16 February 24, 2014, Press Report About Navy Work on...the Navy’s decision (see “Manning and Deployment” above) to increase the size of the LCS core crew to about 50. A November 18, 2013, press report...2010. For a press article on this issue, see Cid Standifer, “FY-11 LCS Contracts On Hold Because Of Continuing Resolution,” Inside the Navy, March

Sulfonium Ion Derivatization, Isobaric Stable Isotope Labeling and Data Dependent CID- and ETD-MS/MS for Enhanced Phosphopeptide Quantitation, Identification and Phosphorylation Site Characterization

PubMed Central

Lu, Yali; Zhou, Xiao; Stemmer, Paul M.; Reid, Gavin E.

2014-01-01

An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded ‘fixed charge’ sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS3, and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S′-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of ‘light’ (S(CH3)2) and ‘heavy’ (S(CD3)2) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS3 or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency. PMID:21952753

Simple Approach for De Novo Structural Identification of Mannose Trisaccharides

NASA Astrophysics Data System (ADS)

Hsu, Hsu Chen; Liew, Chia Yen; Huang, Shih-Pei; Tsai, Shang-Ting; Ni, Chi-Kung

2018-03-01

Oligosaccharides have diverse functions in biological systems. However, the structural determination of oligosaccharides remains difficult and has created a bottleneck in carbohydrate research. In this study, a new approach for the de novo structural determination of underivatized oligosaccharides is demonstrated. A low-energy collision-induced dissociation (CID) of sodium ion adducts was used to facilitate the cleavage of desired chemical bonds during the dissociation. The selection of fragments for the subsequent CID was guided using a procedure that we built from the understanding of the saccharide dissociation mechanism. The linkages, anomeric configurations, and branch locations of oligosaccharides were determined by comparing the CID spectra of oligosaccharide with the fragmentation patterns based on the dissociation mechanism and our specially prepared disaccharide CID spectrum database. The usefulness of this method was demonstrated to determine the structures of several mannose trisaccharides. This method can also be applied in the structural determination of oligosaccharides larger than trisaccharides and containing hexose other than mannose if authentic standards are available. [Figure not available: see fulltext.

Simple Approach for De Novo Structural Identification of Mannose Trisaccharides

NASA Astrophysics Data System (ADS)

Hsu, Hsu Chen; Liew, Chia Yen; Huang, Shih-Pei; Tsai, Shang-Ting; Ni, Chi-Kung

2017-12-01

Oligosaccharides have diverse functions in biological systems. However, the structural determination of oligosaccharides remains difficult and has created a bottleneck in carbohydrate research. In this study, a new approach for the de novo structural determination of underivatized oligosaccharides is demonstrated. A low-energy collision-induced dissociation (CID) of sodium ion adducts was used to facilitate the cleavage of desired chemical bonds during the dissociation. The selection of fragments for the subsequent CID was guided using a procedure that we built from the understanding of the saccharide dissociation mechanism. The linkages, anomeric configurations, and branch locations of oligosaccharides were determined by comparing the CID spectra of oligosaccharide with the fragmentation patterns based on the dissociation mechanism and our specially prepared disaccharide CID spectrum database. The usefulness of this method was demonstrated to determine the structures of several mannose trisaccharides. This method can also be applied in the structural determination of oligosaccharides larger than trisaccharides and containing hexose other than mannose if authentic standards are available. [Figure not available: see fulltext.

Statistical identification of gene association by CID in application of constructing ER regulatory network

PubMed Central

Liu, Li-Yu D; Chen, Chien-Yu; Chen, Mei-Ju M; Tsai, Ming-Shian; Lee, Cho-Han S; Phang, Tzu L; Chang, Li-Yun; Kuo, Wen-Hung; Hwa, Hsiao-Lin; Lien, Huang-Chun; Jung, Shih-Ming; Lin, Yi-Shing; Chang, King-Jen; Hsieh, Fon-Jou

2009-01-01

Background A variety of high-throughput techniques are now available for constructing comprehensive gene regulatory networks in systems biology. In this study, we report a new statistical approach for facilitating in silico inference of regulatory network structure. The new measure of association, coefficient of intrinsic dependence (CID), is model-free and can be applied to both continuous and categorical distributions. When given two variables X and Y, CID answers whether Y is dependent on X by examining the conditional distribution of Y given X. In this paper, we apply CID to analyze the regulatory relationships between transcription factors (TFs) (X) and their downstream genes (Y) based on clinical data. More specifically, we use estrogen receptor α (ERα) as the variable X, and the analyses are based on 48 clinical breast cancer gene expression arrays (48A). Results The analytical utility of CID was evaluated in comparison with four commonly used statistical methods, Galton-Pearson's correlation coefficient (GPCC), Student's t-test (STT), coefficient of determination (CoD), and mutual information (MI). When being compared to GPCC, CoD, and MI, CID reveals its preferential ability to discover the regulatory association where distribution of the mRNA expression levels on X and Y does not fit linear models. On the other hand, when CID is used to measure the association of a continuous variable (Y) against a discrete variable (X), it shows similar performance as compared to STT, and appears to outperform CoD and MI. In addition, this study established a two-layer transcriptional regulatory network to exemplify the usage of CID, in combination with GPCC, in deciphering gene networks based on gene expression profiles from patient arrays. Conclusion CID is shown to provide useful information for identifying associations between genes and transcription factors of interest in patient arrays. When coupled with the relationships detected by GPCC, the association predicted by CID are applicable to the construction of transcriptional regulatory networks. This study shows how information from different data sources and learning algorithms can be integrated to investigate whether relevant regulatory mechanisms identified in cell models can also be partially re-identified in clinical samples of breast cancers. Availability the implementation of CID in R codes can be freely downloaded from . PMID:19292896

Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information

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

Shen, Yufeng; Tolic, Nikola; Purvine, Samuel O.

2011-11-07

The peptidome (i.e. processed and degraded forms of proteins) of e.g. blood can potentially provide insights into disease processes, as well as a source of candidate biomarkers that are unobtainable using conventional bottom-up proteomics approaches. MS dissociation methods, including CID, HCD, and ETD, can each contribute distinct identifications using conventional peptide identification methods (Shen et al. J. Proteome Res. 2011), but such samples still pose significant analysis and informatics challenges. In this work, we explored a simple approach for better utilization of high accuracy fragment ion mass measurements provided e.g. by FT MS/MS and demonstrate significant improvements relative to conventionalmore » descriptive and probabilistic scores methods. For example, at the same FDR level we identified 20-40% more peptides than SEQUEST and Mascot scoring methods using high accuracy fragment ion information (e.g., <10 mass errors) from CID, HCD, and ETD spectra. Species identified covered >90% of all those identified from SEQUEST, Mascot, and MS-GF scoring methods. Additionally, we found that the merging the different fragment spectra provided >60% more species using the UStags method than achieved previously, and enabled >1000 peptidome components to be identified from a single human blood plasma sample with a 0.6% peptide-level FDR, and providing an improved basis for investigation of potentially disease-related peptidome components.« less

Identification and quantification of cardiac glycosides in blood and urine samples by HPLC/MS/MS.

PubMed

Guan, F; Ishii, A; Seno, H; Watanabe-Suzuki, K; Kumazawa, T; Suzuki, O

1999-09-15

Cardiac glycosides (CG) are of forensic importance because of their toxicity and the fact that very limited methods are available for identification of CG in biological samples. In this study, we have developed an identification and quantification method for digoxin, digitoxin, deslanoside, digoxigenin, and digitoxigenin by high-performance liquid chromatography tandem mass spectrometry (HPLC/MS/MS). CG formed abundant [M + NH4]+ ions and much less abundant [M + H]+ ions as observed with electrospray ionization (ESI) source and ammonium formate buffer. Under mild conditions for collision-induced dissociation (CID), each [M + NH4]+ ion fragmented to produce a dominant daughter ion, which was essential to the sensitive method of selected reaction monitoring (SRM) quantification of CG achieved in this study. SRM was compared with selected ion monitoring (SIM) regarding the effects of sample matrixes on the methodology. SRM produced lower detection limits with biological samples than SIM, while both methods produced equal detection limits with CG standards. On the basis of the HPLC/MS/MS results for CG, we have proposed some generalized points for conducting sensitive SRM measurements, in view of the property of analytes as well as instrumental conditions such as the type of HPLC/MS interface and CID parameters. Analytes of which the molecular ion can produce one abundant daughter ion with high yield under CID conditions may be sensitively measured by SRM. ESI is the most soft ionization source developed so far and can afford formation of the fragile molecular ions that are necessary for sensitive SRM detection. Mild CID conditions such as low collision energy and low pressure of collision gas favor production of an abundant daughter ion that is essential to sensitive SRM detection. This knowledge may provide some guidelines for conducting sensitive SRM measurements of very low concentrations of drugs or toxicants in biological samples.

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

Zhang, Qibin; Petyuk, Vladislav A.; Schepmoes, Athena A.

Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet available in all laboratories. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss triggered MS3 and multi-stage activation) during LC-MSn analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss triggered MS3 experiments, MS3 scans triggered by neutral-losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycatedmore » peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss triggered MS3 approach resulted in much higher specificity. Both techniques offer a viable alternative to ETD for identifying glycated peptides when that method is unavailable.« less

Tandem MS Analysis of Selenamide-Derivatized Peptide Ions

NASA Astrophysics Data System (ADS)

Zhang, Yun; Zhang, Hao; Cui, Weidong; Chen, Hao

2011-09-01

Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen ( m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.

Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

NASA Astrophysics Data System (ADS)

Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y.; Drake, Steven K.; Gucek, Marjan; Suffredini, Anthony F.; Sacks, David B.; Yu, Yi-Kuo

2016-02-01

Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple `fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

Determination of the glycation sites of Bacillus anthracis neoglycoconjugate vaccine by MALDI-TOF/TOF-CID-MS/MS and LC-ESI-QqTOF-tandem mass spectrometry

PubMed Central

Jahouh, Farid; Hou, Shu-jie; Kováč, Pavol; Banoub, Joseph H.

2012-01-01

We present herein an efficient mass spectrometric method for the localization of the glycation sites of a model neoglycoconjugate vaccine formed by a construct of the tetrasaccharide side chain of the Bacillus anthracis exosporium and the protein carrier bovine serum albumin. The glycoconjugate was digested with both trypsin and GluC V8 endoproteinases, and the digests were then analyzed by MALDI-TOF/TOF-CID-MS/MS and nano-LC-ESI-QqTOF-CID-MS/MS. The sequences of the unknown peptides analyzed by MALDI-TOF/TOF-CID-MS/MS, following digestion with the GluC V8 endoproteinase, allowed us to recognize three glycopeptides whose glycation occupancies were, respectively, on Lys 235, Lys 420, and Lys 498. Similarly, the same analysis was performed on the tryptic digests, which permitted us to recognize two glycation sites on Lys 100 and Lys 374. In addition, we have also used LC-ESI-QqTOF-CID-MS/MS analysis for the identification of the tryptic digests. However, this analysis identified a higher number of glycopeptides than would be expected from a glycoconjugate composed of a carbohydrate–protein ratio of 5.4:1, which would have resulted in glycation occupancies of 18 specific sites. This discrepancy was due to the large number of glycoforms formed during the synthetic carbohydrate–spacer–carrier protein conjugation. Likewise, the LC-ESI-QqTOF-MS/MS analysis of the GluC V8 digest also identified 17 different glycation sites on the synthetic glycoconjugate. PMID:22012665

Rapid glucosinolate detection and identification using accurate mass MS-MS

USDA-ARS?s Scientific Manuscript database

Currently, there is a demand for accurate evaluation of brassica plat species for their glucosinolate content. An optimized method has been developed for detecting and identifying glucosinolates in plant extracts using MS-MS fragmentation with ion trap collision induced dissociation (CID) and higher...

Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and orbitrap mass spectrometry.

PubMed

Wang, Hao; Straubinger, Robert M; Aletta, John M; Cao, Jin; Duan, Xiaotao; Yu, Haoying; Qu, Jun

2009-03-01

Protein arginine (Arg) methylation serves an important functional role in eucaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron-transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679-695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z = 2-4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns.

Accurate Localization and Relative Quantification of Arginine Methylation Using Nanoflow Liquid Chromatography Coupled to Electron Transfer Dissociation and Orbitrap Mass Spectrometry

PubMed Central

Wang, Hao; Straubinger, Robert M.; Aletta, John M.; Cao, Jin; Duan, Xiaotao; Yu, Haoying; Qu, Jun

2012-01-01

Protein arginine (Arg) methylation serves an important functional role in eukaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly-charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679-695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z=2-4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns. PMID:19110445

Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall

PubMed Central

Lowe, Daniel M.; O’Boyle, Noel M.; Sayle, Roger A.

2016-01-01

Awareness of the adverse effects of chemicals is important in biomedical research and healthcare. Text mining can allow timely and low-cost extraction of this knowledge from the biomedical literature. We extended our text mining solution, LeadMine, to identify diseases and chemical-induced disease relationships (CIDs). LeadMine is a dictionary/grammar-based entity recognizer and was used to recognize and normalize both chemicals and diseases to Medical Subject Headings (MeSH) IDs. The disease lexicon was obtained from three sources: MeSH, the Disease Ontology and Wikipedia. The Wikipedia dictionary was derived from pages with a disease/symptom box, or those where the page title appeared in the lexicon. Composite entities (e.g. heart and lung disease) were detected and mapped to their composite MeSH IDs. For CIDs, we developed a simple pattern-based system to find relationships within the same sentence. Our system was evaluated in the BioCreative V Chemical–Disease Relation task and achieved very good results for both disease concept ID recognition (F1-score: 86.12%) and CIDs (F1-score: 52.20%) on the test set. As our system was over an order of magnitude faster than other solutions evaluated on the task, we were able to apply the same system to the entirety of MEDLINE allowing us to extract a collection of over 250 000 distinct CIDs. PMID:27060160

Characterization of Long-Chain Fatty Acid as N-(4-Aminomethylphenyl) Pyridinium Derivative by MALDI LIFT-TOF/TOF Mass Spectrometry

NASA Astrophysics Data System (ADS)

Frankfater, Cheryl; Jiang, Xuntian; Hsu, Fong-Fu

2018-05-01

Charge remote fragmentation (CRF) elimination of CnH2n+2 residues along the aliphatic tail of long chain fatty acid is hall mark of keV high-energy CID fragmentation process. It is an important fragmentation pathway leading to structural characterization of biomolecules by CID tandem mass spectrometry. In this report, we describe MALDI LIFT TOF-TOF mass spectrometric approach to study a wide variety of fatty acids (FAs), which were derivatized to N-(4-aminomethylphenyl) pyridinium (AMPP) derivative, and desorbed as M+ ions by laser with or without matrix. The high-energy MALDI LIFT TOF-TOF mass spectra of FA-AMPP contain fragment ions mainly deriving from CRF cleavages of CnH2n+2 residues, as expected. These ions together with ions from specific cleavages of the bond(s) involving the functional group within the molecule provide more complete structural identification than those produced by low-energy CID/HCD using a linear ion-trap instrument. However, this LIFT TOF-TOF mass spectrometric approach inherits low sensitivity, a typical feature of high-energy CID tandem mass spectrometry. Because of the lack of unit mass precursor ion selection with sufficient sensitivity of the current LIFT TOF-TOF technology, product ion spectra from same chain length fatty acids with difference in one or two double bonds in a mixture are not distinguishable.

Test Plan for Cask Identification Detector

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

Rauch, Eric Benton

2016-09-29

This document serves to outline the testing of a Used Fuel Cask Identification Detector (CID) currently being designed under the DOE-NE MPACT Campaign. A bench-scale prototype detector will be constructed and tested using surrogate neutron sources. The testing will serve to inform the design of the full detector that is to be used as a way of fingerprinting used fuel storage casks based on the neutron signature produced by the used fuel inside the cask.

Identification of Crosslinked Peptides after Click-based Enrichment Using Sequential CID and ETD Tandem Mass Spectrometry

PubMed Central

Chowdhury, Saiful M.; Du, Xiuxia; Tolić, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

2010-01-01

Chemical crosslinking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of crosslinked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact crosslinkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under condition where the native complex structure is stable. In this study, we present a novel compact crosslinker that contains two distinct features: 1) an alkyne tag and 2) a small molecule detection tag (NO2-) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the crosslinked peptide after proteolytic cleavage after coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO2- moiety provides a secondary means of detecting crosslinked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this crosslinker, which we termed CLIP (Click-enabled Linker for Interacting Proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for crosslinked ubiquitin in highly complex E. coli cell lysates. Sequential CID-MS/MS and ETD-MS/MS of inter-crosslinked peptides (two peptides connected with a crosslinker) are also demonstrated for improved automated identification of crosslinked peptides. PMID:19496583

Plant seed species identification from chemical fingerprints: a high-throughput application of direct analysis in real time mass spectrometry.

PubMed

Lesiak, Ashton D; Cody, Robert B; Dane, A John; Musah, Rabi A

2015-09-01

Plant species identification based on the morphological features of plant parts is a well-established science in botany. However, species identification from seeds has largely been unexplored, despite the fact that the seeds contain all of the genetic information that distinguishes one plant from another. Using seeds of genus Datura plants, we show here that the mass spectrum-derived chemical fingerprints for seeds of the same species are similar. On the other hand, seeds from different species within the same genus display distinct chemical signatures, even though they may contain similar characteristic biomarkers. The intraspecies chemical signature similarities on the one hand, and interspecies fingerprint differences on the other, can be processed by multivariate statistical analysis methods to enable rapid species-level identification and differentiation. The chemical fingerprints can be acquired rapidly and in a high-throughput manner by direct analysis in real time mass spectrometry (DART-MS) analysis of the seeds in their native form, without use of a solvent extract. Importantly, knowledge of the identity of the detected molecules is not required for species level identification. However, confirmation of the presence within the seeds of various characteristic tropane and other alkaloids, including atropine, scopolamine, scopoline, tropine, tropinone, and tyramine, was accomplished by comparison of the in-source collision-induced dissociation (CID) fragmentation patterns of authentic standards, to the fragmentation patterns observed in the seeds when analyzed under similar in-source CID conditions. The advantages, applications, and implications of the chemometric processing of DART-MS derived seed chemical signatures for species level identification and differentiation are discussed.

Models of Information Aggregation Pertaining to Combat Identification: A Review of the Literature (Modele du Regroupement de L’information Concernant L’identification au Combat: Une Analyse Documentaire)

DTIC Science & Technology

2007-04-01

communication from the gunner who is able to offer enhanced visual information about the entity (e.g., insignia, type of weaponry) or radio contact may...1999 (Fuzzy Logic); Clemen & Winkler, in press (Bayes Theorem); Sentz & Ferson, 2002 (Dempster-Shafer)). Humansystems® Combat Identification...incidents when other units get lost and appear in unexpected locations. The formation radios for additional information from the operations officer

Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall.

PubMed

Lowe, Daniel M; O'Boyle, Noel M; Sayle, Roger A

2016-01-01

Awareness of the adverse effects of chemicals is important in biomedical research and healthcare. Text mining can allow timely and low-cost extraction of this knowledge from the biomedical literature. We extended our text mining solution, LeadMine, to identify diseases and chemical-induced disease relationships (CIDs). LeadMine is a dictionary/grammar-based entity recognizer and was used to recognize and normalize both chemicals and diseases to Medical Subject Headings (MeSH) IDs. The disease lexicon was obtained from three sources: MeSH, the Disease Ontology and Wikipedia. The Wikipedia dictionary was derived from pages with a disease/symptom box, or those where the page title appeared in the lexicon. Composite entities (e.g. heart and lung disease) were detected and mapped to their composite MeSH IDs. For CIDs, we developed a simple pattern-based system to find relationships within the same sentence. Our system was evaluated in the BioCreative V Chemical-Disease Relation task and achieved very good results for both disease concept ID recognition (F1-score: 86.12%) and CIDs (F1-score: 52.20%) on the test set. As our system was over an order of magnitude faster than other solutions evaluated on the task, we were able to apply the same system to the entirety of MEDLINE allowing us to extract a collection of over 250 000 distinct CIDs. © The Author(s) 2016. Published by Oxford University Press.

CID-miRNA: A web server for prediction of novel miRNA precursors in human genome

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

Tyagi, Sonika; Vaz, Candida; Gupta, Vipin

2008-08-08

microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes. In this report we describe a tool and a web server, named CID-miRNA, for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filteringmore » systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form. The web server can be accessed at (http://mirna.jnu.ac.in/cidmirna/)« less

Development and practical application of a library of CID accurate mass spectra of more than 2,500 toxic compounds for systematic toxicological analysis by LC-QTOF-MS with data-dependent acquisition.

PubMed

Broecker, Sebastian; Herre, Sieglinde; Wüst, Bernhard; Zweigenbaum, Jerry; Pragst, Fritz

2011-04-01

A library of collision-induced dissociation (CID) accurate mass spectra has been developed for efficient use of liquid chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) as a tool in systematic toxicological analysis. The mass spectra (Δm < 3 ppm) of more than 2,500 illegal and therapeutic drugs, pesticides, alkaloids, other toxic chemicals and metabolites were measured, by use of an Agilent 6530 instrument, by flow-injection of 1 ng of the pure substances in aqueous ammonium formate-formic acid-methanol, with positive and negative electrospray-ionization (ESI), selection of the protonated or deprotonated molecules [M+H](+) or [M-H](-) by the quadrupole, and collision induced dissociation (CID) with nitrogen as collision gas at CID energies of 10, 20, and 40 eV. The fragment mass spectra were controlled for structural plausibility, corrected by recalculation to the theoretical fragment masses and added to a database of accurate mass data and molecular formulas of more than 7,500 toxicologically relevant substances to form the "database and library of toxic compounds". For practical evaluation, blood and urine samples were spiked with a mixture of 33 drugs at seven concentrations between 0.5 and 500 ng mL(-1), prepared by dichloromethane extraction or protein precipitation, and analyzed by LC-QTOF-MS in data-dependent acquisition mode. Unambiguous identification by library search was possible for typical basic drugs down to 0.5-2 ng mL(-1) and for benzodiazepines down to 2-20 ng mL(-1). The efficiency of the method was also demonstrated by re-analysis of venous blood samples from 50 death cases and comparison with previous results. In conclusion, LC-QTOF-MS in data-dependent acquisition mode combined with an accurate mass database and CID spectra library seemed to be one of the most efficient tools for systematic toxicological analysis.

Sequence Elucidation of an Unknown Cyclic Peptide of High Doping Potential by ETD and CID Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Guan, Fuyu; Uboh, Cornelius E.; Soma, Lawrence R.; Rudy, Jeffrey

2011-04-01

Identification of an unknown substance without any information remains a daunting challenge despite advances in chemistry and mass spectrometry. However, an unknown cyclic peptide in a sample with very limited volume seized at a Pennsylvania racetrack has been successfully identified. The unknown sample was determined by accurate mass measurements to contain a small unknown peptide as the major component. Collision-induced dissociation (CID) of the unknown peptide revealed the presence of Lys (not Gln, by accurate mass), Phe, and Arg residues, and absence of any y-type product ion. The latter, together with the tryptic digestion results of the unusual deamidation and absence of any tryptic cleavage, suggests a cyclic structure for the peptide. Electron-transfer dissociation (ETD) of the unknown peptide indicated the presence of Gln (not Lys, by the unusual deamidation), Phe, and Arg residues and their connectivity. After all the results were pieced together, a cyclic tetrapeptide, cyclo[Arg-Lys-N(C6H9)Gln-Phe], is proposed for the unknown peptide. Observations of different amino acid residues from CID and ETD experiments for the peptide were interpreted by a fragmentation pathway proposed, as was preferential CID loss of a Lys residue from the peptide. ETD was used for the first time in sequencing of a cyclic peptide; product ions resulting from ETD of the peptide identified were categorized into two types and named pseudo-b and pseudo-z ions that are important for sequencing of cyclic peptides. The ETD product ions were interpreted by fragmentation pathways proposed. Additionally, multi-stage CID mass spectrometry cannot provide complete sequence information for cyclic peptides containing adjacent Arg and Lys residues. The identified cyclic peptide has not been documented in the literature, its pharmacological effects are unknown, but it might be a "designer" drug with athletic performance-enhancing effects.

Tandem mass spectrometry of isomeric aniline-labeled N-glycans separated on porous graphitic carbon: Revealing the attachment position of terminal sialic acids and structures of neutral glycans.

PubMed

Michael, Claudia; Rizzi, Andreas M

2015-07-15

Quantitative monitoring of changes in the N-glycome upon disease has gained significance in the context of biomarker discovery. Separation and quantification of isobaric glycan isomers can be attained by using high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS). Collision-induced dissociation (CID)-based fragmentation of separated isobaric glycans is evaluated in respect to its potential of providing fragment ions specific for the linkage positions of terminal sialic acids and the presence of intersecting GlcNAc moieties, respectively. N-Glycans were labeled via reductive amination using (12)C6-aniline and (13)C6-aniline as isotope-coded labeling reagents. The differently labeled glycans were merged and separated into various species using a porous graphitic carbon (PGC) stationary phase. Identification of structural features of separated isobaric isomers was performed by CID-based tandem mass spectrometry (MS/MS) carried out in a quadrupole time-of-flight (QqTOF) or a quadrupole ion-trap (IT) mass spectrometer. Working in the negative ion mode, new diagnostic CID fragment ions could be found that are indicative for the α2,6-type linkage of sialic acids. Other diagnostic ions, identified before as being indicative for the substitution of the 6-antenna, could be confirmed as being of relevance also in the case of aniline labeling. In the positive ion mode, CID fragment ions indicative for the structure of short neutral N-glycans were identified. One new diagnostic ion specific for the linkage position of the terminal sialic acids and one for the presence of bisecting GlcNAc in N-glycans were identified. The aniline label introduced for improved relative quantitation in MS(1) was found not to significantly alter the CID fragmentation patterns that were reported previously by other authors for unlabeled/reduced glycans or for glycans with more polar labels. Copyright © 2015 John Wiley & Sons, Ltd.

Identification of a small molecule yeast TORC1 inhibitor with a multiplex screen based on flow cytometry.

PubMed

Chen, Jun; Young, Susan M; Allen, Chris; Seeber, Andrew; Péli-Gulli, Marie-Pierre; Panchaud, Nicolas; Waller, Anna; Ursu, Oleg; Yao, Tuanli; Golden, Jennifer E; Strouse, J Jacob; Carter, Mark B; Kang, Huining; Bologa, Cristian G; Foutz, Terry D; Edwards, Bruce S; Peterson, Blake R; Aubé, Jeffrey; Werner-Washburne, Margaret; Loewith, Robbie J; De Virgilio, Claudio; Sklar, Larry A

2012-04-20

TOR (target of rapamycin) is a serine/threonine kinase, evolutionarily conserved from yeast to human, which functions as a fundamental controller of cell growth. The moderate clinical benefit of rapamycin in mTOR-based therapy of many cancers favors the development of new TOR inhibitors. Here we report a high-throughput flow cytometry multiplexed screen using five GFP-tagged yeast clones that represent the readouts of four branches of the TORC1 signaling pathway in budding yeast. Each GFP-tagged clone was differentially color-coded, and the GFP signal of each clone was measured simultaneously by flow cytometry, which allows rapid prioritization of compounds that likely act through direct modulation of TORC1 or proximal signaling components. A total of 255 compounds were confirmed in dose-response analysis to alter GFP expression in one or more clones. To validate the concept of the high-throughput screen, we have characterized CID 3528206, a small molecule most likely to act on TORC1 as it alters GFP expression in all five GFP clones in a manner analogous to that of rapamycin. We have shown that CID 3528206 inhibited yeast cell growth and that CID 3528206 inhibited TORC1 activity both in vitro and in vivo with EC(50)'s of 150 nM and 3.9 μM, respectively. The results of microarray analysis and yeast GFP collection screen further support the notion that CID 3528206 and rapamycin modulate similar cellular pathways. Together, these results indicate that the HTS has identified a potentially useful small molecule for further development of TOR inhibitors.

Identification, characterization and distribution of monoterpene indole alkaloids in Rauwolfia species by Orbitrap Velos Pro mass spectrometer.

PubMed

Kumar, Sunil; Singh, Awantika; Bajpai, Vikas; Kumar, Brijesh

2016-01-25

Monoterpene indole alkaloids (MIAs) are medicinally important class of compounds abundant in the roots of Rauwolfia species (Apocynaceae). MIAs such as yohimbine (aphrodisiac agent) and reserpine (antihypertensive, tranquilizer) are the official drugs included in Model List of Essential Drugs of World Health Organization (WHO). Therefore, we have attempt to identify and characterize the MIAs in the crude extracts of six Rauwolfia species using ultrahigh-performance liquid chromatography coupled with Orbitrap Velos Pro hybrid mass spectrometer. The identity of the MIAs were construed using the high resolution tandem mass spectrometry (HRMS/MS) spectra of standard compounds 'yohimbine' and 'reserpine' in higher energy collisional dissociation (HCD) and collision-induced dissociation (CID) modes. The diagnostic fragment ions found in HCD mode was highly affected by variation of normalized collision energy (NCE) and gave few product ions ('C-F') while CID produced intense and more diagnostic product ions ('A-F'). Consequently, CID-MS/MS mode provided significantly more structural information about basic skeleton and therefore the recommended mode for analysis of MIAs. Furthermore, six diagnostic fragmentation pathways were established by multi-stage mass analysis (MS(n) (n=5)) analysis which gave information regarding the substitution. Fragment ions 'A-F' revealed the number and position of substituents on indole and terpene moieties. The proposed diagnostic fragmentation pathways have been successfully applied for identification and characterization of MIAs in crude root extracts of six Rauwolfia species. Ten bioactive reserpine class of MIAs were tentatively identified and characterized on the basis of chromatographic and mass spectrometric features as well as HRMS/MS an MS(n) (n=4) analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

The effect of two fixation methods (TAF and DESS) on morphometric parameters of Aphelenchoides ritzemabosi.

PubMed

Chałańska, Aneta; Bogumił, Aleksandra; Malewski, Tadeusz; Kowalewska, Katarzyna

2016-02-19

Identification of nematode species by using conventional methods requires fixation of the isolated material and a suitable preparation for further analyses. Tentative identification using microscopic methods should also be performed prior to initiating molecular studies. In the literature, various methods are described for the preparation of nematodes from the genus Aphelenchoides for identification and microscopic studies. The most commonly used fixatives are formalin (Timm 1969; Szczygieł & Cid del Prado Vera 1981, Crozzoli et al. 2008, Khan et al. 2008), FAA (Wasilewska 1969; Vovlas et al. 2005, Khan et al. 2007) and TAF (Hooper 1958, Chizhov et al. 2006, Jagdale & Grewal 2006).

An enhanced targeted identification strategy for the selective identification of flavonoid O-glycosides from Carthamus tinctorius by integrating offline two-dimensional liquid chromatography/linear ion-trap-Orbitrap mass spectrometry, high-resolution diagnostic product ions/neutral loss filtering and liquid chromatography-solid phase extraction-nuclear magnetic resonance.

PubMed

Yao, Chang-Liang; Yang, Wen-Zhi; Si, Wei; Shen, Yao; Zhang, Nai-Xia; Chen, Hua-Li; Pan, Hui-Qin; Yang, Min; Wu, Wan-Ying; Guo, De-An

2017-03-31

Targeted identification of potentially bioactive molecules from herbal medicines is often stymied by the insufficient chromatographic separation, ubiquitous matrix interference, and pervasive isomerism. An enhanced targeted identification strategy is presented and validated by the selective identification of flavonoid O-glycosides (FOGs) from Carthamus tinctorius. It consists of four steps: (i) enhanced separation and detection by offline two-dimensional liquid chromatography/LTQ-Orbitrap MS (offline 2D-LC/LTQ-Orbitrap MS) using collision-induced dissociation (CID) and high-energy C-trap dissociation (HCD); (ii) improved identification of the major aglycones by acid hydrolysis and LC-SPE-NMR; (iii) simplified spectral elucidation by high-resolution diagnostic product ions/neutral loss filtering; and (iv) more convincing structural identification by matching an in-house library. An offline 2D-LC system configuring an Acchrom XAmide column and a BEH Shield RP-18 UPLC ® column enabled much better separation of the easily co-eluting components. Combined use of CID and HCD could produce complementary fragmentation information. The intensity ratios of the aglycone ion species ([Y 0 -H] - /Y 0 - and [Y 0 -2H] - /Y 0 - ) in the HCD-MS 2 spectra were found diagnostic for discriminating the aglycone subtypes and characterizing the glycosylation patterns. Five aglycone structures (kaempferol, 6-hydroxykaempferol, 6-methoxykaempferol, carthamidin, and isocarthamidin) were identified based on the 1 H-NMR data recorded by LC-SPE-NMR. Of the 107 characterized flavonoids, 80 FOGs were first reported from C. tinctorius. Unknown aglycones, pentose, and novel acyl substituents were discovered. A new compound thereof was isolated and fully identified, which could partially validate the MS-oriented identification. This integral strategy can improve the potency, efficiency, and accuracy in the detection of new compounds from medicinal herbs and other natural sources. Copyright © 2017 Elsevier B.V. All rights reserved.

Biophenols: Enzymes (β-secretase, Cholinesterases, histone deacetylase and tyrosinase) inhibitors from olive (Olea europaea L.).

PubMed

Omar, Syed Haris; Scott, Christopher J; Hamlin, Adam S; Obied, Hassan K

2018-07-01

The focus of this study was on inhibition of enzymes involved in the pathogenesis Alzheimer's disease (AD) including prime amyloid beta (Aβ) producing enzyme (β-secretase: BACE-1) and disease progression enzymes including acetylcholinesterase (AChE), butyrylcholinesterase (BChE), histone deacetylase (HDAC), and tyrosinase along with the catecholamine L-DOPA, by using olive biophenols. Here we report the strongest inhibition of BACE-1 from rutin (IC 50 : 3.8 nM) followed by verbascoside (IC 50 : 6.3 nM) and olive fruit extract (IC 50 : 18 ng), respectively. Olive biophenol, quercetin exhibited strongest enzyme inhibitory activity against tyrosinase (IC 50 : 10.73 μM), BChE (IC 50 : 19.08 μM), AChE (IC 50 : 55.44 μM), and HDAC (IC 50 : 105.1 μM) enzymes. Furthermore, olive biophenol verbascoside (IC 50 : 188.6 μM), and hydroxytyrosol extreme extract (IC 50 : 66.22 μg) were showed the highest levels of inhibition against the HDAC enzyme. Neuroprotective capacity against levodopa-induced toxicity in neuroblastoma (SH-SY5Y) cells of olive biophenols were assessed, where rutin indicated the highest neuroprotection (74%), followed by caffeic acid (73%), and extract hydroxytyrosol extreme (97%), respectively. To the best of our knowledge, this is the first in vitro report on the enzymes inhibitory activity of olive biophenols. Taken together, our in vitro results data suggest that olive biophenols could be a promising natural inhibitor, which may reduce the enzyme-induced toxicity associated with the oxidative stress involved in the progression of AD. Acetylthiocholine iodide (PubChem CID: 74629); S-Butyrylthiocholine chloride (PubChem CID: 3015121); Caffeic acid (PubChem CID: 689043); Dimethyl sulfoxide (DMSO) (PubChem: 679); L-3,4-Dihydroxyphenylalanine (L-DOPA) (PubChem CID: 6047); 5,5'-Dithiobis (2-nitrobenzoic acid) (DTNB) (PubChem CID: 6254); Epigallocatechin gallate (EGCG) (PubChem CID: 65064); Ethylenediamine tetraacetic acid (EDTA) (PubChem CID: 6049); Galantamine hydrobromide (PubChem CID: 121587); l-Glutamine (PubChem CID: 5961); Hydroxytyrosol (PubChem CID: 82755); Kojic acid (PubChem CID: 3840); Luteolin (PubChem CID: 5280445); Oleuropein (PubChem CID: 5281544); Penicillin-streptomycin (PubChem CID: 131715954); Quercetin (PubChem CID: 5280343); Rutin (PubChem CID: 5280805); Tris-HCl buffer (PubChem: 93573); Trypan blue (PubChem: 9562061). Copyright © 2018 Elsevier B.V. All rights reserved.

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

Metastable Atom-Activated Dissociation Mass Spectrometry of Phosphorylated and Sulfonated Peptides in Negative Ion Mode

NASA Astrophysics Data System (ADS)

Cook, Shannon L.; Jackson, Glen P.

2011-06-01

The dissociation behavior of phosphorylated and sulfonated peptide anions was explored using metastable atom-activated dissociation mass spectrometry (MAD-MS) and collision-induced dissociation (CID). A beam of high kinetic energy helium (He) metastable atoms was exposed to isolated phosphorylated and sulfonated peptides in the 3- and 2- charge states. Unlike CID, where phosphate losses are dominant, the major dissociation channels observed using MAD were Cα - C peptide backbone cleavages and neutral losses of CO2, H2O, and [CO2 + H2O] from the charge reduced (oxidized) product ion, consistent with an electron detachment dissociation (EDD) mechanism such as Penning ionization. Regardless of charge state or modification, MAD provides ample backbone cleavages with little modification loss, which allows for unambiguous PTM site determination. The relative abundance of certain fragment ions in MAD is also demonstrated to be somewhat sensitive to the number and location of deprotonation sites, with backbone cleavage somewhat favored adjacent to deprotonated sites like aspartic acid residues. MAD provides a complementary dissociation technique to CID, ECD, ETD, and EDD for peptide sequencing and modification identification. MAD offers the unique ability to analyze highly acidic peptides that contain few to no basic amino acids in either negative or positive ion mode.

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.

Identification of Isomeric N-Glycan Structures by Mass Spectrometry with 157 nm Laser-Induced Photofragmentation

PubMed Central

Devakumar, Arugadoss; Mechref, Yehia; Kang, Pilsoo; Novotny, Milos V.; Reilly, James P.

2008-01-01

Characterization of structural isomers has become increasingly important and extremely challenging in glycobiology. This communication demonstrates the capability of ion-trap mass spectrometry in conjunction with 157 nm photofragmentation to identify different structural isomers of permethylated N-glycans derived from ovalbumin without chromatographic separation. The results are compared with CID experiments. Photodissociation generates extensive cross-ring fragment ions as well as diagnostic glycosidic product ions that are not usually observed in CID MS/MS experiments. The detection of these product ions aids in characterizing indigenous glycan isomers. The ion-trap facilitates MSn experiments on the diagnostic glycosidic fragments and cross-ring product ions generated through photofragmentation, thus allowing unambiguous assignment of all of the isomeric structures associated with the model glycoprotein utilized in this study. Photofragmentation is demonstrated to be a powerful technique for the structural characterization of glycans. PMID:18487060

Electron transfer dissociation of synthetic and natural peptides containing lanthionine/methyllanthionine bridges.

PubMed

Dolle, Ashwini B; Jagadeesh, Narasimhappagari; Bhaumik, Suman; Prakash, Sunita; Biswal, Himansu S; Gowd, Konkallu Hanumae

2018-06-15

The modes of cleavage of lanthionine/methyllanthionine bridges under electron transfer dissociation (ETD) were investigated using synthetic and natural lantipeptides. Knowledge of the mass spectrometric fragmentation of lanthionine/methyllanthionine bridges may assist in the development of analytical methods for the rapid discovery of new lantibiotics. The present study strengthens the advantage of ETD in the characterization of posttranslational modifications of peptides and proteins. Synthetic and natural lantipeptides were obtained by desulfurization of peptide disulfides and cyanogen bromide digestion of the lantibiotic nisin, respectively. These peptides were subjected to electrospray ionization collision-induced dissociation tandem mass spectrometry (CID-MS/MS) and ETD-MS/MS using an HCT ultra ETDII ion trap mass spectrometer. MS 3 CID was performed on the desired product ions to prove cleavage of the lanthionine/methyllanthionine bridge during ETD-MS/MS. ETD has advantages over CID in the cleavage of the side chain of lanthionine/methyllanthionine bridges. The cleavage of the N-Cα backbone peptide bond followed by C-terminal side chain of the lanthionine bridge results in formation of c •+ and z + ions. Cleavage at the preceding peptide bond to the C-terminal side chain of lanthionine/methyllanthionine bridges yields specific fragments with the cysteine/methylcysteine thiyl radical and dehydroalanine. ETD successfully cleaves the lanthionine/methyllanthionine bridges of synthetic and natural lantipeptides. Diagnostic fragment ions of ETD cleavage of lanthionine/methyllanthionine bridges are the N-terminal cysteine/methylcysteine thiyl radical and C-terminal dehydroalanine. Detection of the cysteine/methylcysteine thiyl radical and dehydroalanine in combined ETD-CID-MS may be used for the rapid identification of lantipeptide natural products. Copyright © 2018 John Wiley & Sons, Ltd.

A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides*

PubMed Central

Giese, Sven H.; Fischer, Lutz; Rappsilber, Juri

2016-01-01

Cross-linking/mass spectrometry resolves protein–protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)-cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique cross-linked peptides in high-resolution MS1 and MS2 from published data and validate the observation by a ninefold larger set from currently unpublished data to explore if detailed understanding of their fragmentation behavior would allow computational delivery of information that otherwise would be obtained via isotope labels or CID cleavage of cross-linkers. Isotope-labeled cross-linkers reveal cross-linked and linear fragments in fragmentation spectra. We show that fragment mass and charge alone provide this information, alleviating the need for isotope-labeling for this purpose. Isotope-labeled cross-linkers also indicate cross-linker-containing, albeit not specifically cross-linked, peptides in MS1. We observed that acquisition can be guided to better than twofold enrich cross-linked peptides with minimal losses based on peptide mass and charge alone. By help of CID-cleavable cross-linkers, individual spectra with only linear fragments can be recorded for each peptide in a cross-link. We show that cross-linked fragments of ordinary cross-linked peptides can be linearized computationally and that a simplified subspectrum can be extracted that is enriched in information on one of the two linked peptides. This allows identifying candidates for this peptide in a simplified database search as we propose in a search strategy here. We conclude that the specific behavior of cross-linked peptides in mass spectrometers can be exploited to relax the requirements on cross-linkers. PMID:26719564

Clinically inactive disease in a cohort of children with new-onset polyarticular juvenile idiopathic arthritis treated with early aggressive therapy: time to achievement, total duration, and predictors.

PubMed

Wallace, Carol A; Giannini, Edward H; Spalding, Steven J; Hashkes, Philip J; O'Neil, Kathleen M; Zeft, Andrew S; Szer, Ilona S; Ringold, Sarah; Brunner, Hermine I; Schanberg, Laura E; Sundel, Robert P; Milojevic, Diana S; Punaro, Marilynn G; Chira, Peter; Gottlieb, Beth S; Higgins, Gloria C; Ilowite, Norman T; Kimura, Yukiko; Johnson, Anne; Huang, Bin; Lovell, Daniel J

2014-06-01

To determine the elapsed time while receiving aggressive therapy to the first observation of clinically inactive disease (CID), total duration of CID and potential predictors of this response in a cohort of children with recent onset of polyarticular juvenile idiopathic arthritis (poly-JIA). Eighty-five children were randomized blindly to methotrexate (MTX), etanercept, and rapidly tapered prednisolone (MEP) or MTX monotherapy and assessed for CID over 1 year of treatment. Patients who failed to achieve intermediary endpoints were switched to open-label MEP treatment. Fifty-eight (68.2%) of the 85 patients achieved CID at 1 or more visits including 18 who received blinded MEP, 11 while receiving MTX monotherapy, and 29 while receiving open-label MEP. Patients starting on MEP achieved CID earlier and had more study days in CID compared to those starting MTX, but the differences were not significantly different. Patients given MEP (more aggressive therapy) earlier in the disease course were statistically more likely to have a higher proportion of followup visits in CID than those with longer disease course at baseline. Those who achieved American College of Rheumatology Pediatric 70 response at 4 months had a significantly greater proportion of followup visits in CID, compared to those who failed to achieve this improvement (p < 0.0001). Of the 32 patients who met criteria for CID and then lost CID status, only 3 fulfilled the definition of disease flare. Shorter disease duration prior to treatment, a robust response at 4 months, and more aggressive therapy result in a higher likelihood and longer duration of CID in patients with poly-JIA. The original trial from which data for this analysis were obtained is registered on www.clinicaltrials.gov NCT 00443430.

Genetic control of water use efficiency and leaf carbon isotope discrimination in sunflower (Helianthus annuus L.) subjected to two drought scenarios.

PubMed

Adiredjo, Afifuddin Latif; Navaud, Olivier; Muños, Stephane; Langlade, Nicolas B; Lamaze, Thierry; Grieu, Philippe

2014-01-01

High water use efficiency (WUE) can be achieved by coordination of biomass accumulation and water consumption. WUE is physiologically and genetically linked to carbon isotope discrimination (CID) in leaves of plants. A population of 148 recombinant inbred lines (RILs) of sunflower derived from a cross between XRQ and PSC8 lines was studied to identify quantitative trait loci (QTL) controlling WUE and CID, and to compare QTL associated with these traits in different drought scenarios. We conducted greenhouse experiments in 2011 and 2012 by using 100 balances which provided a daily measurement of water transpired, and we determined WUE, CID, biomass and cumulative water transpired by plants. Wide phenotypic variability, significant genotypic effects, and significant negative correlations between WUE and CID were observed in both experiments. A total of nine QTL controlling WUE and eight controlling CID were identified across the two experiments. A QTL for phenotypic response controlling WUE and CID was also significantly identified. The QTL for WUE were specific to the drought scenarios, whereas the QTL for CID were independent of the drought scenarios and could be found in all the experiments. Our results showed that the stable genomic regions controlling CID were located on the linkage groups 06 and 13 (LG06 and LG13). Three QTL for CID were co-localized with the QTL for WUE, biomass and cumulative water transpired. We found that CID and WUE are highly correlated and have common genetic control. Interestingly, the genetic control of these traits showed an interaction with the environment (between the two drought scenarios and control conditions). Our results open a way for breeding higher WUE by using CID and marker-assisted approaches and therefore help to maintain the stability of sunflower crop production.

Re-investigation of the fragmentation of protonated carotenoids by electrospray ionization and nanospray tandem mass spectrometry.

PubMed

Neto, Fausto Carnevale; Guaratini, Thais; Costa-Lotufo, Letícia; Colepicolo, Pio; Gates, Paul J; Lopes, Norberto Peporine

2016-07-15

Carotenoids are polyene isoprenoids with an important role in photosynthesis and photoprotection. Their characterization in biological matrices is a crucial subject for biochemical research. In this work we report the full fragmentation of 16 polyenes (carotenes and xanthophylls) by electrospray ionization tandem mass spectrometry (ESI-CID-MS/MS) and nanospray tandem mass spectrometry (nanoESI-CID-MS/MS). Analyses were carried out on a quadrupole time-of-flight (QTOF) mass spectrometer coupled with a nanoESI source and on a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer with an ESI source. The formulae of the product ions were determined by accurate-mass measurements. It is demonstrated that the fragmentation routes observed for the protonated carotenoids derive essentially from charge-remote fragmentations and pericyclic rearrangements, such as electrocyclic and retro-ene eliminations (assisted or not by a sigmatropic hydrogen shift). All mechanisms are dependent on cis-trans isomerization through the formation of several conjugated polyene carbocation intermediates. Some specific ions for the carotenoid epoxides were justified through formation of cyclic oxonium ions. Complete fragmentation pathways of protonated carotenoids by ESI- and nanoESI-CID-MS/MS provided structural information about functional groups, polyene chain and double bonds, and contribute to identification of carotenoids based on MS/MS fragmentation patterns. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Collision-induced dissociative chemical cross-linking reagents and methodology: Applications to protein structural characterization using tandem mass spectrometry analysis.

PubMed

Soderblom, Erik J; Goshe, Michael B

2006-12-01

Chemical cross-linking combined with mass spectrometry is a viable approach to study the low-resolution structure of protein and protein complexes. However, unambiguous identification of the residues involved in a cross-link remains analytically challenging. To enable a more effective analysis across various MS platforms, we have developed a novel set of collision-induced dissociative cross-linking reagents and methodology for chemical cross-linking experiments using tandem mass spectrometry (CID-CXL-MS/MS). These reagents incorporate a single gas-phase cleavable bond within their linker region that can be selectively fragmented within the in-source region of the mass spectrometer, enabling independent MS/MS analysis for each peptide. Initial design concepts were characterized using a synthesized cross-linked peptide complex. Following verification and subsequent optimization of cross-linked peptide complex dissociation, our reagents were applied to homodimeric glutathione S-transferase and monomeric bovine serum albumin. Cross-linked residues identified by our CID-CXL-MS/MS method were in agreement with published crystal structures and previous cross-linking studies using conventional approaches. Common LC/MS/MS acquisition approaches such as data-dependent acquisition experiments using ion trap mass spectrometers and product ion spectral analysis using SEQUEST were shown to be compatible with our CID-CXL-MS/MS reagents, obviating the requirement for high resolution and high mass accuracy measurements to identify both intra- and interpeptide cross-links.

Transgenerational propagation and quantitative maintenance of paternal centromeres depends on Cid/Cenp-A presence in Drosophila sperm.

PubMed

Raychaudhuri, Nitika; Dubruille, Raphaelle; Orsi, Guillermo A; Bagheri, Homayoun C; Loppin, Benjamin; Lehner, Christian F

2012-01-01

In Drosophila melanogaster, as in many animal and plant species, centromere identity is specified epigenetically. In proliferating cells, a centromere-specific histone H3 variant (CenH3), named Cid in Drosophila and Cenp-A in humans, is a crucial component of the epigenetic centromere mark. Hence, maintenance of the amount and chromosomal location of CenH3 during mitotic proliferation is important. Interestingly, CenH3 may have different roles during meiosis and the onset of embryogenesis. In gametes of Caenorhabditis elegans, and possibly in plants, centromere marking is independent of CenH3. Moreover, male gamete differentiation in animals often includes global nucleosome for protamine exchange that potentially could remove CenH3 nucleosomes. Here we demonstrate that the control of Cid loading during male meiosis is distinct from the regulation observed during the mitotic cycles of early embryogenesis. But Cid is present in mature sperm. After strong Cid depletion in sperm, paternal centromeres fail to integrate into the gonomeric spindle of the first mitosis, resulting in gynogenetic haploid embryos. Furthermore, after moderate depletion, paternal centromeres are unable to re-acquire normal Cid levels in the next generation. We conclude that Cid in sperm is an essential component of the epigenetic centromere mark on paternal chromosomes and it exerts quantitative control over centromeric Cid levels throughout development. Hence, the amount of Cid that is loaded during each cell cycle appears to be determined primarily by the preexisting centromeric Cid, with little flexibility for compensation of accidental losses.

Transgenerational Propagation and Quantitative Maintenance of Paternal Centromeres Depends on Cid/Cenp-A Presence in Drosophila Sperm

PubMed Central

Raychaudhuri, Nitika; Dubruille, Raphaelle; Orsi, Guillermo A.; Bagheri, Homayoun C.; Loppin, Benjamin; Lehner, Christian F.

2012-01-01

In Drosophila melanogaster, as in many animal and plant species, centromere identity is specified epigenetically. In proliferating cells, a centromere-specific histone H3 variant (CenH3), named Cid in Drosophila and Cenp-A in humans, is a crucial component of the epigenetic centromere mark. Hence, maintenance of the amount and chromosomal location of CenH3 during mitotic proliferation is important. Interestingly, CenH3 may have different roles during meiosis and the onset of embryogenesis. In gametes of Caenorhabditis elegans, and possibly in plants, centromere marking is independent of CenH3. Moreover, male gamete differentiation in animals often includes global nucleosome for protamine exchange that potentially could remove CenH3 nucleosomes. Here we demonstrate that the control of Cid loading during male meiosis is distinct from the regulation observed during the mitotic cycles of early embryogenesis. But Cid is present in mature sperm. After strong Cid depletion in sperm, paternal centromeres fail to integrate into the gonomeric spindle of the first mitosis, resulting in gynogenetic haploid embryos. Furthermore, after moderate depletion, paternal centromeres are unable to re-acquire normal Cid levels in the next generation. We conclude that Cid in sperm is an essential component of the epigenetic centromere mark on paternal chromosomes and it exerts quantitative control over centromeric Cid levels throughout development. Hence, the amount of Cid that is loaded during each cell cycle appears to be determined primarily by the preexisting centromeric Cid, with little flexibility for compensation of accidental losses. PMID:23300376

Simultaneous detection and identification of precursors, degradation and co-products of chemical warfare agents in drinking water by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry.

PubMed

Tak, Vijay; Purohit, Ajay; Pardasani, Deepak; Goud, D Raghavender; Jain, Rajeev; Dubey, D K

2014-11-28

Environmental markers of chemical warfare agents (CWAs) comprise millions of chemical structures. The simultaneous detection and identification of these environmental markers poses difficulty due to their diverse chemical properties. In this work, by using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF), a generic analytical method for the detection and identification of wide range of environmental markers of CWAs (including precursors, degradation and co-products of nerve agents and sesqui-mustards) in drinking water, was developed. The chromatographic analysis of 55 environmental markers of CWAs including isomeric and isobaric compounds was accomplished within 20 min, using 1.8 μm particle size column. Subsequent identification of the compounds was achieved by the accurate mass measurement of either protonated molecule [M+H](+) or ammonium adduct [M+NH4](+) and fragment ions. Isomeric and isobaric compounds were distinguished by chromatographic retention time, characteristic fragment ions generated by both in-source collision induced dissociation (CID) and CID in the collision cell by MS/MS experiments. The exact mass measurement errors for all ions were observed less than 3 ppm with internal calibration. The method limits of detection (LODs) and limits of quantification (LOQs) were determined in drinking water and found to be 1-50 ng mL(-1) and 5-125 ng mL(-1), respectively. Applicability of the proposed method was proved by determining the environmental markers of CWAs in aqueous samples provided by Organization for the Prohibition of Chemical Weapons during 34th official proficiency test. Copyright © 2014 Elsevier B.V. All rights reserved.

The Implementation of C-ID, R2D2 Model on Learning Reading Comprehension

ERIC Educational Resources Information Center

Rayanto, Yudi Hari; Rusmawan, Putu Ngurah

2016-01-01

The purposes of this research are to find out, (1) whether C-ID, R2D2 model is effective to be implemented on learning Reading comprehension, (2) college students' activity during the implementation of C-ID, R2D2 model on learning Reading comprehension, and 3) college students' learning achievement during the implementation of C-ID, R2D2 model on…

Cid1, a Fission Yeast Protein Required for S-M Checkpoint Control when DNA Polymerase δ or ɛ Is Inactivated

PubMed Central

Wang, Shao-Win; Toda, Takashi; MacCallum, Robert; Harris, Adrian L.; Norbury, Chris

2000-01-01

The S-M checkpoint is an intracellular signaling pathway that ensures that mitosis is not initiated in cells undergoing DNA replication. We identified cid1, a novel fission yeast gene, through its ability when overexpressed to confer specific resistance to a combination of hydroxyurea, which inhibits DNA replication, and caffeine, which overrides the S-M checkpoint. Cid1 overexpression also partially suppressed the hydroxyurea sensitivity characteristic of DNA polymerase δ mutants and mutants defective in the “checkpoint Rad” pathway. Cid1 is a member of a family of putative nucleotidyltransferases including budding yeast Trf4 and Trf5, and mutation of amino acid residues predicted to be essential for this activity resulted in loss of Cid1 function in vivo. Two additional Cid1-like proteins play similar but nonredundant checkpoint-signaling roles in fission yeast. Cells lacking Cid1 were found to be viable but specifically sensitive to the combination of hydroxyurea and caffeine and to be S-M checkpoint defective in the absence of Cds1. Genetic data suggest that Cid1 acts in association with Crb2/Rhp9 and through the checkpoint-signaling kinase Chk1 to inhibit unscheduled mitosis specifically when DNA polymerase δ or ɛ is inhibited. PMID:10757807

Direct analysis in real time high resolution mass spectrometry as a tool for rapid characterization of mind-altering plant materials and revelation of supplement adulteration--The case of Kanna.

PubMed

Lesiak, Ashton D; Cody, Robert B; Ubukata, Masaaki; Musah, Rabi A

2016-03-01

We demonstrate the utility of direct analysis in real time ionization coupled with high resolution time-of-flight mass spectrometry (DART-HRTOFMS) in revealing the adulteration of commercially available Sceletium tortuosum, a mind-altering plant-based drug commonly known as Kanna. Accurate masses consistent with alkaloids previously isolated from S. tortuosum plant material enabled identification of the products as Kanna, and in-source collision-induced dissociation (CID) confirmed the presence of one of these alkaloids, hordenine, while simultaneously revealing the presence of an adulterant. The stimulant ephedrine, which has been banned in herbal products and supplements, was confirmed to be present in a sample through the use of in-source CID. High-throughput DART-HRTOFMS was shown to be a powerful tool to not only screen plant-based drugs of abuse for psychotropic alkaloids, but also to reveal the presence of scheduled substances and adulterants. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Signal processing applications of massively parallel charge domain computing devices

NASA Technical Reports Server (NTRS)

Fijany, Amir (Inventor); Barhen, Jacob (Inventor); Toomarian, Nikzad (Inventor)

1999-01-01

The present invention is embodied in a charge coupled device (CCD)/charge injection device (CID) architecture capable of performing a Fourier transform by simultaneous matrix vector multiplication (MVM) operations in respective plural CCD/CID arrays in parallel in O(1) steps. For example, in one embodiment, a first CCD/CID array stores charge packets representing a first matrix operator based upon permutations of a Hartley transform and computes the Fourier transform of an incoming vector. A second CCD/CID array stores charge packets representing a second matrix operator based upon different permutations of a Hartley transform and computes the Fourier transform of an incoming vector. The incoming vector is applied to the inputs of the two CCD/CID arrays simultaneously, and the real and imaginary parts of the Fourier transform are produced simultaneously in the time required to perform a single MVM operation in a CCD/CID array.

Raman Spectroscopic Characterisation of Australian Banded Iron Formation and Iron Ore

NASA Astrophysics Data System (ADS)

Wells, M. A.; Ramanaidou, E. R.

2012-04-01

In Australia and world-wide over the past 5-10 years, declining reserves of premium, high-grade (>64% Fe), low-P bearing iron ore, have seen iron ore producers increase their utilisation of lower Fe-grade, higher P/Al/Si ore. In Australia, the channel iron deposits (CID), bedded iron deposits (BID) and, more recently, BIF-derived magnetite iron deposits (MID) have seen increased usage driven mainly by the increased demand from Chinese steel mills (Ramanaidou and Wells, 2011). Efficient exploitation and processing of these lower-grade iron ores requires a detailed understanding of their iron oxide and gangue mineralogy and geochemistry. The common Fe-bearing minerals (e.g., hematite, magnetite, goethite and kenomagnetite) in these deposits, as well as gangue minerals such as quartz and carbonates, are all strongly Raman active (e.g., de Faria et al., 1997). Their distinct Raman spectra enable them to be easily detected and mapped in situ in either unprepared material or samples prepared as polished blocks. In this paper, using representative examples of Australian CID ore, martite-goethite bedded iron deposit (BID) ore and banded iron formation (BIF) examined as polished blocks, we present a range of Raman spectra of the key iron ore minerals, and discuss how Raman spectroscopy can be applied to characterising iron ore mineralogy. Raman imaging micrographs, obtained using a StreamLine Plus Raman imaging system, clearly identified the main Fe-oxide and gangue components in the CID, BID and BIF samples when compared to optical micrographs. Raman analysis enabled the unequivocal identification of diamond in the CID ore as a contaminant from the polishing paste used to prepare the sample, and confirmed the presence of hematite in the BID ore in the form of martite, which can be morphologically similar to magnetite and, thus, difficult to otherwise distinguish. Image analysis of Raman mineral maps could be used to quantify mineral abundance based on the number of 'pixels' identified for each phase normalised to the total number of 'pixels' for each area scanned. Shifts in the main phonon lines of goethite and hematite mapped in the CID samples examined were used to estimate the Al substitution in these phases (e.g., Ramanaidou et al. 1996) which were consistent with electron microprobe data. The Raman data demonstrated the Al-free nature of hematite (0.5 mol% Al) and showed that goethite in the CID cortex was more Al-rich (10 mol%) than goethite in the CID matrix (3 mol% Al). Shifts in the excitation bands of carbonate mapped in the BIF sample were well related to the Mg content of Fe-carbonate, based on the work of Rividi et al. (2010) and confirmed by in situ spot analysis using energy dispersive spectroscopy (EDS) and scanning electron microscopy (SEM). This data confirmed the first world-wide occurrence of a high Mg-bearing siderite (pistomesite) in BIF. Detailed, in situ characterisation of the iron oxide and gangue mineralogy of iron ore deposits as provided by Raman spectroscopy provides a step change to current characterisation methods. Understanding and defining their mineralogy and geochemistry is critical in developing strategies to best manage and process existing BID and CID ores, as well as the newly emerging MID ores.

Effect of water stress on carbon isotope discrimination and its relationship with transpiration efficiency and specific leaf area in Cenchrus species.

PubMed

Dubey, Archana; Chandra, Amaresh

2008-05-01

Carbon isotope discrimination (CID) has been proposed in estimating transpiration efficiency (TE) in plants indirectly To identify variations for TE and specific leaf area (SLA) and their association with CID, a glasshouse experiment was conducted using six prominent species of Cenchrus. A significant increase in TE (3.50 to 3.87 g kg(-1)) and decrease in SLA (219.50 to 207.99 cm2 g(-1)) and CID (13.72 to 13.23% per hundred) was observed from well watered to stress condition. Results indicated a direct relationship of SLA with CID (r = 0.511* and 0.544*) and inverse relationship between TE and CID (r = -0.229 and -0.270) However the relationship of TE with CID was insignificant. A positive and significant relationship was visualized between TE and dry matter production in both control (r = 0.917**) and stress (0.718**) treatments. Relationships of total dry matter with SLA and CID were monitored insignificant and negative in control and positive in stress treatment indicated difference in dry matter production under two treatments. It seems that, in Cenchrus species, CID was influenced more by the photosynthetic capacity than by stomatal conductance, as indicated by its positive relationship with SLAin both control (r = 0.511) and stress (r = 0.544) conditions and negative relationship with root dry matter production under control (r = -0.921**) and stress (r = -0.919***) condition. Results showed good correspondence between CID and SLA, indicating that lines having high TE and biomass production can be exploited for their genetic improvement for drought.

Chemical stability of insulin. 5. Isolation, characterization and identification of insulin transformation products.

PubMed

Brange, J; Hallund, O; Sørensen, E

1992-01-01

During storage of insulin formulated for therapy, minor amounts of various degradation and covalent di- and polymerization products are formed [1-3]. The main chemical transformation products were isolated from aged preparations and characterized chemically and biologically. The most prominent products formed in neutral medium were identified as a mixture of deamidation products hydrolyzed at residue B3, namely isoAsp B3 and Asp B3 derivatives. A hydrolysis product formed only in crystals of insulin zinc suspensions containing a surplus of zinc ions in the supernatant was identified as an A8-A9 cleavage product. The small amounts of covalent insulin dimers (CID) formed in all formulations were shown to be a heterogenous mixture of 5-6 different CIDs with a composition dependent on the pharmaceutical formulation. The chemical characteristics of the CIDs indicate that they are formed through a transamidation reaction mainly between the B-chain N-terminal and one of the four amide side-chains of the A chain. GlnA15, AsnA18 and, in particular, AsnA21 participate in the formation of such isopeptide links between two insulin molecules. The covalent insulin-protamine products (CIPP) formed during storage of NPH preparations presumably originate from a similar reaction between the protamine N-terminal with an amide in insulin. Covalent polymerization products, mainly formed during storage of amorphously suspended insulin at higher temperature, were shown to be due to disulfide interactions. Biological in vivo potencies relative to native insulin were less than 2% for the split-(A8-A9)-product and for the covalent disulfide exchange polymers, 4% for the CIPP, approximately 15% for the CIDs, whereas the B3 derivatives exhibited full potency. Rabbit immunization experiments revealed that none of the insulin transformation products had significantly increased immunogenicity in rabbits.

A Computer Based Educational Aid for the Instruction of Combat Modeling

DTIC Science & Technology

1992-02-27

representation (36:363-370), and, as Knuth put it, "An algorithm must be seen to be believed" (23:4). Graphics not only aid in achieving instructional...consisted primarily of research, identification and use of existing combat model computer algorithms , interviews, and use of operation research...to-air combat models’ operating manuals provided valuable insight into pro- gram structure and algorithms used to represent the combat. From these

Optimization of parameters for coverage of low molecular weight proteins

PubMed Central

Müller, Stephan A.; Kohajda, Tibor; Findeiß, Sven; Stadler, Peter F.; Washietl, Stefan; Kellis, Manolis; von Bergen, Martin

2010-01-01

Proteins with molecular weights of <25 kDa are involved in major biological processes such as ribosome formation, stress adaption (e.g., temperature reduction) and cell cycle control. Despite their importance, the coverage of smaller proteins in standard proteome studies is rather sparse. Here we investigated biochemical and mass spectrometric parameters that influence coverage and validity of identification. The underrepresentation of low molecular weight (LMW) proteins may be attributed to the low numbers of proteolytic peptides formed by tryptic digestion as well as their tendency to be lost in protein separation and concentration/desalting procedures. In a systematic investigation of the LMW proteome of Escherichia coli, a total of 455 LMW proteins (27% of the 1672 listed in the SwissProt protein database) were identified, corresponding to a coverage of 62% of the known cytosolic LMW proteins. Of these proteins, 93 had not yet been functionally classified, and five had not previously been confirmed at the protein level. In this study, the influences of protein extraction (either urea or TFA), proteolytic digestion (solely, and the combined usage of trypsin and AspN as endoproteases) and protein separation (gel- or non-gel-based) were investigated. Compared to the standard procedure based solely on the use of urea lysis buffer, in-gel separation and tryptic digestion, the complementary use of TFA for extraction or endoprotease AspN for proteolysis permits the identification of an extra 72 (32%) and 51 proteins (23%), respectively. Regarding mass spectrometry analysis with an LTQ Orbitrap mass spectrometer, collision-induced fragmentation (CID and HCD) and electron transfer dissociation using the linear ion trap (IT) or the Orbitrap as the analyzer were compared. IT-CID was found to yield the best identification rate, whereas IT-ETD provided almost comparable results in terms of LMW proteome coverage. The high overlap between the proteins identified with IT-CID and IT-ETD allowed the validation of 75% of the identified proteins using this orthogonal fragmentation technique. Furthermore, a new approach to evaluating and improving the completeness of protein databases that utilizes the program RNAcode was introduced and examined. Electronic supplementary material The online version of this article (doi:10.1007/s00216-010-4093-x) contains supplementary material, which is available to authorized users. PMID:20803007

The Cell Cycle Timing of Centromeric Chromatin Assembly in Drosophila Meiosis Is Distinct from Mitosis Yet Requires CAL1 and CENP-C

PubMed Central

Gorgescu, Walter; Tang, Jonathan; Costes, Sylvain V.; Karpen, Gary H.

2012-01-01

CENP-A (CID in flies) is the histone H3 variant essential for centromere specification, kinetochore formation, and chromosome segregation during cell division. Recent studies have elucidated major cell cycle mechanisms and factors critical for CENP-A incorporation in mitosis, predominantly in cultured cells. However, we do not understand the roles, regulation, and cell cycle timing of CENP-A assembly in somatic tissues in multicellular organisms and in meiosis, the specialized cell division cycle that gives rise to haploid gametes. Here we investigate the timing and requirements for CID assembly in mitotic tissues and male and female meiosis in Drosophila melanogaster, using fixed and live imaging combined with genetic approaches. We find that CID assembly initiates at late telophase and continues during G1 phase in somatic tissues in the organism, later than the metaphase assembly observed in cultured cells. Furthermore, CID assembly occurs at two distinct cell cycle phases during male meiosis: prophase of meiosis I and after exit from meiosis II, in spermatids. CID assembly in prophase I is also conserved in female meiosis. Interestingly, we observe a novel decrease in CID levels after the end of meiosis I and before meiosis II, which correlates temporally with changes in kinetochore organization and orientation. We also demonstrate that CID is retained on mature sperm despite the gross chromatin remodeling that occurs during protamine exchange. Finally, we show that the centromere proteins CAL1 and CENP-C are both required for CID assembly in meiosis and normal progression through spermatogenesis. We conclude that the cell cycle timing of CID assembly in meiosis is different from mitosis and that the efficient propagation of CID through meiotic divisions and on sperm is likely to be important for centromere specification in the developing zygote. PMID:23300382

Electrospray ionization mass spectrometry for the hydrolysis complexes of cisplatin: implications for the hydrolysis process of platinum complexes.

PubMed

Feifan, Xie; Pieter, Colin; Jan, Van Bocxlaer

2017-07-01

Non-enzyme-dependent hydrolysis of the drug cisplatin is important for its mode of action and toxicity. However, up until today, the hydrolysis process of cisplatin is still not completely understood. In the present study, the hydrolysis of cisplatin in an aqueous solution was systematically investigated by using electrospray ionization mass spectrometry coupled to liquid chromatography. A variety of previously unreported hydrolysis complexes corresponding to monomeric, dimeric and trimeric species were detected and identified. The characteristics of the Pt-containing complexes were investigated by using collision-induced dissociation (CID). The hydrolysis complexes demonstrate distinctive and correlative CID characteristics, which provides tools for an informative identification. The most frequently observed dissociation mechanism was sequential loss of NH 3 , H 2 O and HCl. Loss of the Pt atom was observed as the final step during the CID process. The formation mechanisms of the observed complexes were explored and experimentally examined. The strongly bound dimeric species, which existed in solution, are assumed to be formed from the clustering of the parent compound and its monohydrated or dihydrated complexes. The role of the electrospray process in the formation of some of the observed ions was also evaluated, and the electrospray ionization-related cold clusters were identified. The previously reported hydrolysis equilibria were tested and subsequently refined via a hydrolysis study resulting in a renewed mechanistic equilibrium system of cisplatin as proposed from our results. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Mass Spectrometry as a Powerful Analytical Technique for the Structural Characterization of Synthesized and Natural Products

NASA Astrophysics Data System (ADS)

Es-Safi, Nour-Eddine; Essassi, El Mokhtar; Massoui, Mohamed; Banoub, Joseph

Mass spectrometry is an important tool for the identification and structural elucidation of natural and synthesized compounds. Its high sensitivity and the possibility of coupling liquid chromatography with mass spectrometry detection make it a technique of choice for the investigation of complex mixtures like raw natural extracts. The mass spectrometer is a universal detector that can achieve very high sensitivity and provide information on the molecular mass. More detailed information can be subsequently obtained by resorting to collision-induced dissociation tandem mass spectrometry (CID-MS/MS). In this review, the application of mass spectrometric techniques for the identification of natural and synthetic compounds is presented. The gas-phase fragmentation patterns of a series of four natural flavonoid glycosides, three synthesized benzodiazepines and two synthesized quinoxalinone derivatives were investigated using electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry techniques. Exact accurate masses were measured using a modorate resolution quadrupole orthogonal time-of-flight QqTOF-MS/MS hybrid mass spectrometer instrument. Confirmation of the molecular masses and the chemical structures of the studied compounds were achieved by exploring the gas-phase breakdown routes of the ionized molecules. This was rationalized by conducting low-energy collision CID-MS/MS analyses (product ion- and precursor ion scans) using a conventional quadrupole hexapole-quadrupole (QhQ) tandem mass spectrometer.

Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry.

PubMed

Maslen, Sarah; Sadowski, Pawel; Adam, Alex; Lilley, Kathryn; Stephens, Elaine

2006-12-15

The detailed characterization of protein N-glycosylation is very demanding given the many different glycoforms and structural isomers that can exist on glycoproteins. Here we report a fast and sensitive method for the extensive structure elucidation of reducing-end labeled N-glycan mixtures using a combination of capillary normal-phase HPLC coupled off-line to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and TOF/TOF-MS/MS. Using this method, isobaric N-glycans released from honey bee phospholipase A2 and Arabidopsis thaliana glycoproteins were separated by normal-phase chromatography and subsequently identified by key fragment ions in the MALDI-TOF/TOF tandem mass spectra. In addition, linkage and branching information were provided by abundant cross-ring and "elimination" fragment ions in the MALDI-CID spectra that gave extensive structural information. Furthermore, the fragmentation characteristics of N-glycans reductively aminated with 2-aminobenzoic acid and 2-aminobenzamide were compared. The identification of N-glycans containing 3-linked core fucose was facilitated by distinctive ions present only in the MALDI-CID spectra of 2-aminobenzoic acid-labeled oligosaccharides. To our knowledge, this is the first MS/MS-based technique that allows confident identification of N-glycans containing 3-linked core fucose, which is a major allergenic determinant on insect and plant glycoproteins.

Clinical, immunologic, and genetic spectrum of 696 patients with combined immunodeficiency.

PubMed

Abolhassani, Hassan; Chou, Janet; Bainter, Wayne; Platt, Craig D; Tavassoli, Mahmood; Momen, Tooba; Tavakol, Marzieh; Eslamian, Mohammad Hossein; Gharagozlou, Mohammad; Movahedi, Masoud; Ghadami, Mohsen; Hamidieh, Amir Ali; Azizi, Gholamreza; Yazdani, Reza; Afarideh, Mohsen; Ghajar, Alireza; Havaei, Arash; Chavoshzadeh, Zahra; Mahdaviani, Seyed Alireza; Cheraghi, Taher; Behniafard, Nasrin; Amin, Reza; Aleyasin, Soheila; Faridhosseini, Reza; Jabbari-Azad, Farahzad; Nabavi, Mohammamd; Bemanian, Mohammad Hassan; Arshi, Saba; Molatefi, Rasol; Sherkat, Roya; Mansouri, Mahboubeh; Mesdaghi, Mehrnaz; Babaie, Delara; Mohammadzadeh, Iraj; Ghaffari, Javad; Shafiei, Alireza; Kalantari, Najmeddin; Ahanchian, Hamid; Khoshkhui, Maryam; Soheili, Habib; Dabbaghzadeh, Abbas; Shirkani, Afshin; Nasiri Kalmarzi, Rasoul; Mortazavi, Seyed Hamidreza; Tafaroji, Javad; Khalili, Abbas; Mohammadi, Javad; Negahdari, Babak; Joghataei, Mohammad-Taghi; Al-Ramadi, Basel K; Picard, Capucine; Parvaneh, Nima; Rezaei, Nima; Chatila, Talal A; Massaad, Michel J; Keles, Sevgi; Hammarström, Lennart; Geha, Raif S; Aghamohammadi, Asghar

2018-04-01

Combined immunodeficiencies (CIDs) are diseases of defective adaptive immunity with diverse clinical phenotypes. Although CIDs are more prevalent in the Middle East than Western countries, the resources for genetic diagnosis are limited. This study aims to characterize the categories of patients with CIDs in Iran clinically and genetically. Clinical and laboratory data were obtained from 696 patients with CIDs. Patients were subdivided into those with syndromic (344 patients) and nonsyndromic (352 patients) CIDs. Targeted DNA sequencing was performed on 243 (34.9%) patients. The overall diagnostic yield of the 243 sequenced patients was 77.8% (189 patients). The clinical diagnosis of hyper-IgE syndrome (P < .001), onset of disease at greater than 5 years (P = .02), and absence of multiple affected family members (P = .04) were significantly more frequent in the patients without a genetic diagnosis. An autosomal recessive disease was found in 62.9% of patients, reflecting the high rate of consanguinity in this cohort. Mutations impairing VDJ recombination and DNA repair were the most common underlying causes of CIDs. However, in patients with syndromic CIDs, autosomal recessive mutations in ataxia-telangiectasia mutated (ATM), autosomal dominant mutations in signal transducer and activator of transcription 3 (STAT3), and microdeletions in 22q11.21 were the most commonly affected genomic loci. Patients with syndromic CIDs had a significantly lower 5-year survival rate rather than those with nonsyndromic CIDs. This study provides proof of principle for the application of targeted next-generation sequencing panels in countries with limited diagnostic resources. The effect of genetic diagnosis on clinical care requires continued improvements in therapeutic resources for these patients. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. All rights reserved.

Is triglyceride/HDL ratio a reliable screening test for assessment of atherosclerotic risk in patients with chronic inflammatory disease?

PubMed

Keles, Nursen; Aksu, Feyza; Aciksari, Gonul; Yilmaz, Yusuf; Demircioglu, Kenan; Kostek, Osman; Cekin, Muhammed Esad; Kalcik, Macit; Caliskan, Mustafa

2016-01-01

The term chronic inflammatory disease (CID) refers to a category of inflammatory diseases that includes Ankylosing spondylitis (AS) and familial Mediterranean fever (FMF). The incidence of adverse cardiovascular events is greater among patients with CID, though they may not have conventional atherosclerotic risk factors. Endothelial dysfunction is one of the underlying fundamental mechanisms that trigger development of atherosclerotic alterations in arteries, and flow-mediated dilatation (FMD) is a noninvasive method to determine endothelial dysfunction. Recent studies have shown a relationship between high triglyceride high-density lipoprotein cholesterol (TG/HDL-C) ratio and coronary atherosclerosis. Many studies have demonstrated that patients with CID have lower FMD values compared to healthy population, indicating endothelial dysfunction. However TG/HDL ratio and its relationship to FMD in patients with CID has not been investigated. The present study investigated whether TG/HDL ratio in CID patients differs from that of healthy population, and its relationship to FMD in patients with CID. A total of 58 patients with CID and a group of 58 healthy volunteer individuals were enrolled in the study. FMD measurements were taken with high resolution ultrasound (US), and TG/HDL ratios were calculated. Patients with CID had significantly higher TG/HDL-C ratio (2.5 [2.2-2.8] vs 2.3 [2.1-2.5]; p=0.03) and lower FMD values (5.2 [4.2-6.3] vs 6.7 [6.3-9.7]; p<0.001), compared to healthy group, and a negative correlation was found between FMD levels and TG/HDL ratio of the study population. Higher TG/HDL ratio and lower FMD values found in CID patients may reflect increased atherosclerotic risk.

Is triglyceride/HDL ratio a reliable screening test for assessment of atherosclerotic risk in patients with chronic inflammatory disease?

PubMed Central

Keles, Nursen; Aksu, Feyza; Aciksari, Gonul; Yilmaz, Yusuf; Demircioglu, Kenan; Kostek, Osman; Cekin, Muhammed Esad; Kalcik, Macit; Caliskan, Mustafa

2016-01-01

OBJECTIVE: The term chronic inflammatory disease (CID) refers to a category of inflammatory diseases that includes Ankylosing spondylitis (AS) and familial Mediterranean fever (FMF). The incidence of adverse cardiovascular events is greater among patients with CID, though they may not have conventional atherosclerotic risk factors. Endothelial dysfunction is one of the underlying fundamental mechanisms that trigger development of atherosclerotic alterations in arteries, and flow-mediated dilatation (FMD) is a noninvasive method to determine endothelial dysfunction. Recent studies have shown a relationship between high triglyceride high-density lipoprotein cholesterol (TG/HDL-C) ratio and coronary atherosclerosis. Many studies have demonstrated that patients with CID have lower FMD values compared to healthy population, indicating endothelial dysfunction. However TG/HDL ratio and its relationship to FMD in patients with CID has not been investigated. The present study investigated whether TG/HDL ratio in CID patients differs from that of healthy population, and its relationship to FMD in patients with CID. METHODS: A total of 58 patients with CID and a group of 58 healthy volunteer individuals were enrolled in the study. FMD measurements were taken with high resolution ultrasound (US), and TG/HDL ratios were calculated. RESULTS: Patients with CID had significantly higher TG/HDL-C ratio (2.5 [2.2–2.8] vs 2.3 [2.1–2.5]; p=0.03) and lower FMD values (5.2 [4.2–6.3] vs 6.7 [6.3–9.7]; p<0.001), compared to healthy group, and a negative correlation was found between FMD levels and TG/HDL ratio of the study population. CONCLUSION: Higher TG/HDL ratio and lower FMD values found in CID patients may reflect increased atherosclerotic risk. PMID:28058384

Antimicrobial Activity of Galangin and Its Effects on Murein Hydrolases of Vancomycin-Intermediate Staphylococcus aureus (VISA) Strain Mu50.

PubMed

Ouyang, Jing; Sun, Fengjun; Feng, Wei; Xie, Yonghong; Ren, Lijuan; Chen, Yongchuan

2018-01-01

Backgroud: Antibiotic treatment for infections caused by vancomycin-intermediate Staphylococcus aureus (VISA) strains is challenging, and only a few effective and curative methods have been developed to combat these strains. This study aimed to investigate the antimicrobial activity of galangin against S. aureus and its effects on the murein hydrolases of VISA strain Mu50. This is the first report on these effects of galangin, and it may help to improve the treatment for VISA infections by demonstrating the effective use of galangin. Firstly, the minimum inhibitory concentration (MIC) and growth curve were used to investigate the antimicrobial activity of galangin against S. aureus. Secondly, transmission electron microscopy (TEM) was used to observe morphological changes of VISA strain Mu50. Thirdly, Triton X-100-induced autolysis and cell wall hydrolysis assays were performed to determine the activities of the murein hydrolases of Mu50. Finally, fluorescence real-time quantitative PCR was used to investigate the expression of the murein hydrolase-related Mu50 genes. The results indicated that the MIC of galangin was 32 μg/mL against ATCC25293, N315, and Mu50, and galangin could significantly suppress the bacterial growth (p < 0.05) with concentrations of 4, 8 and 16 μg/mL, compared with control group (0 μg/mL). To explore the possible reasons of bacteriostatic effects of galangin, we observed morphological changes using TEM which showed that the division of Mu50 daughter cells treated with galangin was obviously inhibited. Considering the vital role of murein hydrolases in cellular division, assays were performed, and galangin markedly decreased Triton X-100-induced autolysis and cell wall hydrolysis. Galangin also significantly inhibited the expression of the murein hydrolase genes (atl, lytM, and lytN) and their regulatory genes (cidR, cidA, and cidB). Our findings indicated that galangin can effectively inhibit murein hydrolase activity as well as the growth of VISA strain Mu50. © 2017 S. Karger AG, Basel.

Implementation of Dipolar Resonant Excitation for Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS

PubMed Central

Webb, Ian K.; Chen, Tsung-Chi; Danielson, William F.; Ibrahim, Yehia M.; Tang, Keqi; Anderson, Gordon A.; Smith, Richard D.

2014-01-01

An ion mobility/time-of-flight mass spectrometer (IMS/TOF MS) platform that allows for resonant excitation collision induced dissociation (CID) is presented. Highly efficient, mass-resolved fragmentation without additional excitation of product ions was accomplished and over-fragmentation common in beam-type CID experiments was alleviated. A quadrupole ion guide was modified to apply a dipolar AC signal across a pair of rods for resonant excitation. The method was characterized with singly protonated methionine enkephalin and triply protonated peptide angiotensin I, yielding maximum CID efficiencies of 44% and 84%, respectively. The Mathieu qx,y parameter was set at 0.707 for these experiments to maximize pseudopotential well depths and CID efficiencies. Resonant excitation CID was compared to beam-type CID for the peptide mixture. The ability to apply resonant waveforms in mobility-resolved windows is demonstrated with a peptide mixture yielding fragmentation over a range of mass-to-charge (m/z) ratios within a single IMS-MS analysis. PMID:24470195

Identification with groups: the role of personality and context.

PubMed

Sagiv, Lilach; Roccas, Sonia; Hazan, Osnat

2012-04-01

Is identification a product of personality or of the context? We examine this question by adopting a multidimensional conceptualization of identification (the CIDS model) that integrates research perspectives on personality and contextual effects. We investigate (Study 1) the relationships of traits to identification with the nation (students, N = 77), the army (soldiers, N = 220), and a business school (students, N = 123). Then we show that the modes of identification vary in their stability across social contexts and in their susceptibility to contextual change. Idealizing groups' symbols ("deference" identification) is especially stable across different foci of identification (Study 2): the military and former high school (soldiers, N = 188), the business school and the nation (students, = 62), and the military and one's ethnic group (soldiers, N = 95). Perceiving the group as a central part of the self ("importance" identification) is the most susceptible to contextual effects of priming values (Study 3; students, N = 80, 60) and the group's status (Study 4; students, N = 68). © 2011 The Authors. Journal of Personality © 2012, Wiley Periodicals, Inc.

32 CFR 633.11 - Access to CID reports.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 4 2013-07-01 2013-07-01 false Access to CID reports. 633.11 Section 633.11 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.11 - Access to CID reports.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 32 National Defense 4 2014-07-01 2013-07-01 true Access to CID reports. 633.11 Section 633.11 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.12 - Amendment to CID reports.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 4 2011-07-01 2011-07-01 false Amendment to CID reports. 633.12 Section 633.12 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.12 - Amendment to CID reports.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 4 2013-07-01 2013-07-01 false Amendment to CID reports. 633.12 Section 633.12 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.11 - Access to CID reports.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 4 2011-07-01 2011-07-01 false Access to CID reports. 633.11 Section 633.11 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.11 - Access to CID reports.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 4 2012-07-01 2011-07-01 true Access to CID reports. 633.11 Section 633.11 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.12 - Amendment to CID reports.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 4 2010-07-01 2010-07-01 true Amendment to CID reports. 633.12 Section 633.12 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.12 - Amendment to CID reports.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 32 National Defense 4 2014-07-01 2013-07-01 true Amendment to CID reports. 633.12 Section 633.12 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.11 - Access to CID reports.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 4 2010-07-01 2010-07-01 true Access to CID reports. 633.11 Section 633.11 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

32 CFR 633.12 - Amendment to CID reports.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 4 2012-07-01 2011-07-01 true Amendment to CID reports. 633.12 Section 633.12 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS INDIVIDUAL REQUESTS FOR ACCESS OR AMENDMENT OF CID REPORTS OF INVESTIGATION § 633...

A pseudo MS3 approach for identification of disulfide-bonded proteins: uncommon product ions and database search.

PubMed

Chen, Jianzhong; Shiyanov, Pavel; Schlager, John J; Green, Kari B

2012-02-01

It has previously been reported that disulfide and backbone bonds of native intact proteins can be concurrently cleaved using electrospray ionization (ESI) and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). However, the cleavages of disulfide bonds result in different cysteine modifications in product ions, making it difficult to identify the disulfide-bonded proteins via database search. To solve this identification problem, we have developed a pseudo MS(3) approach by combining nozzle-skimmer dissociation (NSD) and CID on a quadrupole time-of-flight (Q-TOF) mass spectrometer using chicken lysozyme as a model. Although many of the product ions were similar to those typically seen in MS/MS spectra of enzymatically derived peptides, additional uncommon product ions were detected including c(i-1) ions (the i(th) residue being aspartic acid, arginine, lysine and dehydroalanine) as well as those from a scrambled sequence. The formation of these uncommon types of product ions, likely caused by the lack of mobile protons, were proposed to involve bond rearrangements via a six-membered ring transition state and/or salt bridge(s). A search of 20 pseudo MS(3) spectra against the Gallus gallus (chicken) database using Batch-Tag, a program originally designed for bottom up MS/MS analysis, identified chicken lysozyme as the only hit with the expectation values less than 0.02 for 12 of the spectra. The pseudo MS(3) approach may help to identify disulfide-bonded proteins and determine the associated post-translational modifications (PTMs); the confidence in the identification may be improved by incorporating the fragmentation characteristics into currently available search programs. © American Society for Mass Spectrometry, 2011

30 CFR 550.297 - What information must a CID contain?

Code of Federal Regulations, 2014 CFR

2014-07-01

... drilled before your CID submittal that define the extent of the reservoirs. You must notify BOEM of any well that is drilled to total depth during the CID evaluation period and you may be required to update..., caliper curves) curves in an acceptable digital format; (4) Sidewall core/whole core and pressure-volume...

30 CFR 550.297 - What information must a CID contain?

Code of Federal Regulations, 2013 CFR

2013-07-01

... drilled before your CID submittal that define the extent of the reservoirs. You must notify BOEM of any well that is drilled to total depth during the CID evaluation period and you may be required to update..., caliper curves) curves in an acceptable digital format; (4) Sidewall core/whole core and pressure-volume...

30 CFR 550.297 - What information must a CID contain?

Code of Federal Regulations, 2012 CFR

2012-07-01

... drilled before your CID submittal that define the extent of the reservoirs. You must notify BOEM of any well that is drilled to total depth during the CID evaluation period and you may be required to update..., caliper curves) curves in an acceptable digital format; (4) Sidewall core/whole core and pressure-volume...

Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

PubMed Central

Mahdi, Chanif; Nurdiana, Nurdiana; Kikuchi, Takheshi; Fatchiyah, Fatchiyah

2014-01-01

To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX), the three-dimensional (3D) structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli alcohol isomers. Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking tools by Hex 8.0. Interactions were further visualized by using Discovery Studio Client 3.5 software tool. The binding energy of molecular interaction was calculated by AMBER12 and Virtual Molecular Dynamic 1.9.1 software. The analysis of the alpha-Patchouli alcohol isomer compounds showed that all alpha-Patchouli alcohol isomers were suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) of alpha-Patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117) was suggested as candidate for a selective COX-1 inhibitor and CID521903 as nonselective COX-1/COX-2. PMID:25484897

De novo peptide sequencing using CID and HCD spectra pairs.

PubMed

Yan, Yan; Kusalik, Anthony J; Wu, Fang-Xiang

2016-10-01

In tandem mass spectrometry (MS/MS), there are several different fragmentation techniques possible, including, collision-induced dissociation (CID) higher energy collisional dissociation (HCD), electron-capture dissociation (ECD), and electron transfer dissociation (ETD). When using pairs of spectra for de novo peptide sequencing, the most popular methods are designed for CID (or HCD) and ECD (or ETD) spectra because of the complementarity between them. Less attention has been paid to the use of CID and HCD spectra pairs. In this study, a new de novo peptide sequencing method is proposed for these spectra pairs. This method includes a CID and HCD spectra merging criterion and a parent mass correction step, along with improvements to our previously proposed algorithm for sequencing merged spectra. Three pairs of spectral datasets were used to investigate and compare the performance of the proposed method with other existing methods designed for single spectrum (HCD or CID) sequencing. Experimental results showed that full-length peptide sequencing accuracy was increased significantly by using spectra pairs in the proposed method, with the highest accuracy reaching 81.31%. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A systematic literature review of the economic implications of chemotherapy-induced diarrhea and its impact on quality of life.

PubMed

Tarricone, Rosanna; Abu Koush, Dana; Nyanzi-Wakholi, Barbara; Medina-Lara, Antonieta

2016-03-01

Chemotherapy-induced diarrhea (CID) diminishes physical performance, raises anxiety and depression levels, and increases healthcare resource utilization. To understand the impact that CID has on health-related quality of life (HRQoL) and on healthcare resource utilization. Systematic searches were conducted in MEDLINE, EMBASE, DARE, and the NHS EED databases. A total of 22 articles were retrieved for full review (n=17, HRQoL; n=5 healthcare resource utilization). Only 2 studies had assessed HRQoL in patients experiencing CID, while cost studies demonstrated that CID episodes are unnecessarily expensive and can be avoided if diagnosed and treated early. Better management of CID has the potential to reduce overall economic burden and improve patients' HRQoL. Available evidence also relays the need to conduct larger studies that assess HRQoL and consider cost beyond direct medical costs in order to understand the full impact of CID on HRQoL and healthcare resource utilization. Crown Copyright © 2016. Published by Elsevier Ireland Ltd. All rights reserved.

A practical approach to reduce interference due to in-source collision-induced dissociation of acylglucuronides in LC-MS/MS.

PubMed

Mess, Jean-Nicholas; Bérubé, Eugénie-Raphaelle; Furtado, Milton; Garofolo, Fabio

2011-08-01

In LC-MS/MS, glucuronide conjugated metabolites may convert back to the parent drug due to in-source collision-induced dissociation (CID). During the bioanalysis of naproxen, it was noticed that naproxen acylglucuronide exhibited intense in-source CID to the naproxen [M+H](+) ion under positive ESI. However, no in-source CID of the acylglucuronide to the naproxen [M+NH(4)](+) adduct was observed. Furthermore, absolutely no in-source CID was detected under negative ESI. This phenomenon was not only observed for naproxen acylglucuronide but for eight other acylglucuronides compounds. We have shown that monitoring the parent drug [M-H](-) or [M+NH(4)](+) whenever possible could be an easy approach used by bioanalytical scientists to minimize the impact of in-source CID of acylglucuronides to the parent drug.

The computer integrated documentation project: A merge of hypermedia and AI techniques

NASA Technical Reports Server (NTRS)

Mathe, Nathalie; Boy, Guy

1993-01-01

To generate intelligent indexing that allows context-sensitive information retrieval, a system must be able to acquire knowledge directly through interaction with users. In this paper, we present the architecture for CID (Computer Integrated Documentation). CID is a system that enables integration of various technical documents in a hypertext framework and includes an intelligent browsing system that incorporates indexing in context. CID's knowledge-based indexing mechanism allows case based knowledge acquisition by experimentation. It utilizes on-line user information requirements and suggestions either to reinforce current indexing in case of success or to generate new knowledge in case of failure. This allows CID's intelligent interface system to provide helpful responses, based on previous experience (user feedback). We describe CID's current capabilities and provide an overview of our plans for extending the system.

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

Zhang, Qibin; Tang, Ning; Brock, Jonathan W.

Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was observed that ETD fragmentation mode resultedmore » in a significantly higher number of glycated peptide identifications (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing dual glycation enrichment on both the protein and peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS with ETD as the fragmentation mode is an efficient approach for analyses of glycated proteins and can have broad applications in studies of diabetes mellitus.« less

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.

Enrichment and Analysis of Non-enzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron Transfer Dissociation Mass Spectrometry

PubMed Central

Zhang, Qibin; Tang, Ning; Brock, Jonathan W. C.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John W.; Smith, Richard D.; Metz, Thomas O.

2008-01-01

Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. ETD fragmentation mode permitted identification of a significantly higher number of glycated peptides (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing enrichment on first the protein and then the peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS and using ETD as the fragmentation mode is an efficient approach for analysis of glycated proteins and may have broad application in studies of diabetes mellitus. PMID:17488106

Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry

NASA Astrophysics Data System (ADS)

Chen, Guangming; Zhang, Yixiang; Trinidad, Jonathan C.; Dann, Charles

2018-03-01

Sulfotyrosine and phosphotyrosine are two post-translational modifications present in higher eukaryotes. A simple and direct mass spectrometry method to distinguish between these modifications is crucial to advance our understanding of the sulfoproteome. While sulfation and phosphorylation are nominally isobaric, the accurate mass of the sulfuryl moiety is 9.6 mDa less than the phosphoryl moiety. Based on this difference, we have used an Orbitrap Fusion Lumos mass spectrometer to characterize, resolve, and distinguish between sulfotyrosine and phosphotyrosine modifications using a set of model peptides. Multiple fragmentation techniques, namely HCD, CID, ETD, ETciD, and EThcD, have been used to compare the different fragmentation behaviors between peptides modified with these species. Sulfotyrosine undergoes neutral loss using HCD and CID, but the sulfuryl moiety is largely stable under ETD. In contrast, phosphotyrosine is stable during fragmentation using all these methods. This differential stability provides a mechanism to distinguish sulfopeptides from phosphopeptides. Based on the rigorous characterization presented herein, this work serves as a model for accurate identification of phosphotyrosine and, more challenging, sulfotyrosine, in complex proteomic samples. [Figure not available: see fulltext.

Assigning Peptide Disulfide Linkage Pattern Among Regio-Isomers via Methoxy Addition to Disulfide and Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Durand, Kirt L.; Tan, Lei; Stinson, Craig A.; Love-Nkansah, Chasity B.; Ma, Xiaoxiao; Xia, Yu

2017-06-01

Pinpointing disulfide linkage pattern is critical in the characterization of proteins and peptides consisting of multiple disulfide bonds. Herein, we report a method based on coupling online disulfide modification and tandem mass spectrometry (MS/MS) to distinguish peptide disulfide regio-isomers. Such a method relies on a new disulfide bond cleavage reaction in solution, involving methanol as a reactant and 254 nm ultraviolet (UV) irradiation. This reaction leads to selective cleavage of a disulfide bond and formation of sulfenic methyl ester (-SOCH3) at one cysteine residue and a thiol (-SH) at the other. Under low energy collision-induced dissociation (CID), cysteine sulfenic methyl ester motif produces a signature methanol loss (-32 Da), allowing its identification from other possible isomeric structures such as S-hydroxylmethyl (-SCH2OH) and methyl sulfoxide (-S(O)-CH3). Since disulfide bond can be selectively cleaved and modified upon methoxy addition, subsequent MS2 CID of the methoxy addition product provides enhanced sequence coverage as demonstrated by the analysis of bovine insulin. More importantly, this reaction does not induce disulfide scrambling, likely due to the fact that radical intermediates are not involved in the process. An approach based on methoxy addition followed by MS3 CID has been developed for assigning disulfide linkage patterns in peptide disulfide regio-isomers. This methodology was successfully applied to characterizing peptide systems having two disulfide bonds and three disulfide linkage isomers: side-by-side, overlapped, and looped-within-a-loop configurations. [Figure not available: see fulltext.

Consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114001 reduces the duration of respiratory infections in the elderly in a randomised controlled trial.

PubMed

Guillemard, E; Tondu, F; Lacoin, F; Schrezenmeir, J

2010-01-01

Common infectious diseases (CID) of the airways and the gastrointestinal tract are still a considerable cause of morbidity and mortality in elderly. The present study examined the beneficial effect of a dairy product containing the probiotic strain Lactobacillus casei DN-114 001 (fermented product) on the resistance of free-living elderly to CID. The study was multicentric, double blind and controlled, involving 1072 volunteers (median age = 76.0 years) randomised for consumption of either 200 g/d of fermented (n 537) or control (non-fermented) dairy product (n 535) for 3 months, followed by an additional 1 month's follow-up. The results showed that, when considering all CID, the fermented product significantly reduced the average duration per episode of CID (6.5 v. 8 d in control group; P = 0.008) and the cumulative duration of CID (7 v. 8 d in control group; P = 0.009). Reduction in both episode and cumulative durations was also significant for all upper respiratory tract infections (URTI; P < 0.001) and for rhinopharyngitis (P < 0.001). This was accompanied with an increase of L. casei species in stools throughout the fermented product consumption (2-3.8 x 107 equivalents of colony-forming unit/g of stools, P < 0.001). The cumulative number of CID (primary outcome) was not different between groups nor was the CID severity, fever, pathogens' occurrence, medication, immune blood parameters and quality of life. The fermented product was safe and well tolerated. In conclusion, consumption of a fermented dairy product containing the probiotic strain L. casei DN-114 001 in elderly was associated with a decreased duration of CID in comparison with the control group, especially for URTI such as rhinopharyngitis.

Patients with chronic insomnia disorder have increased serum levels of neurofilaments, neuron-specific enolase and S100B: does organic brain damage exist?

PubMed

Zhang, Ping; Tan, Cheng-Wen; Chen, Gui-Hai; Ge, Yi-Jun; Xu, Jing; Xia, Lan; Wang, Fang; Li, Xue-Yan; Kong, Xiao-Yi

2018-02-13

The aims of this study were to investigate whether serum levels of neurofilaments heavy chain (NfH) and light chain (NfL), neuron-specific enolase (NSE) and S100 calcium binding protein B (S100B): (1) change, (2) alleviate in post-therapy and (3) are associated with sleep quality and cognitive dysfunction, in patients with chronic insomnia disorder (CID). Forty CID outpatients constituted free-therapy group (ft-CID), in which twenty-four patients completed follow-up after six-month treatment to form re-visiting group (rv-CID), and twenty healthy good sleepers constituted control group (HC). All subjects completed questionnaires, polysomnography, Chinese-Beijing Version of Montreal Cognitive Assessment (MoCA-C) and Nine Box Maze Test (NBMT) to assess sleep and neuropsychological function. The serum levels of NfH, NfL, NSE and S100B were detected using enzyme-linked immunosorbent assay. The ft-CID had higher levels of NfH, NfL, NSE and S100B than the HC. Of note, the levels of NfH, NfL and NSE were significantly reduced in the rv-CID compared to the ft-CID, but not the level of S100B. Principal components analysis revealed that in these serum biomarkers, NfL and S100B had a substantial correlation with subjective and objective sleep parameters. The CID patients had elevated serum levels of NfH, NfL, NSE and S100B, indicating existence of damaged brain microstructure, including neurons, astrocytes and neuronal terminals, which were associated with the insomniac severity or/and cognitive dysfunction and could significantly reduce after effective therapy apart from the S100B. Copyright © 2018 Elsevier B.V. All rights reserved.

Differentiation of the Stereochemistry and Anomeric Configuration for 1-3 Linked Disaccharides Via Tandem Mass Spectrometry and 18O-labeling

NASA Astrophysics Data System (ADS)

Konda, Chiharu; Bendiak, Brad; Xia, Yu

2012-02-01

Collision-induced dissociation (CID) of deprotonated hexose-containing disaccharides ( m/z 341) with 1-2, 1-4, and 1-6 linkages yields product ions at m/z 221, which have been identified as glycosyl-glycolaldehyde anions. From disaccharides with these linkages, CID of m/z 221 ions produces distinct fragmentation patterns that enable the stereochemistries and anomeric configurations of the non-reducing sugar units to be determined. However, only trace quantities of m/z 221 ions can be generated for 1-3 linkages in Paul or linear ion traps, preventing further CID analysis. Here we demonstrate that high intensities of m/z 221 ions can be built up in the linear ion trap (Q3) from beam-type CID of a series of 1-3 linked disaccharides conducted on a triple quadrupole/linear ion trap mass spectrometer. 18O-labeling at the carbonyl position of the reducing sugar allowed mass-discrimination of the "sidedness" of dissociation events to either side of the glycosidic linkage. Under relatively low energy beam-type CID and ion trap CID, an m/z 223 product ion containing 18O predominated. It was a structural isomer that fragmented quite differently than the glycosyl-glycolaldehydes and did not provide structural information about the non-reducing sugar. Under higher collision energy beam-type CID conditions, the formation of m/z 221 ions, which have the glycosyl-glycolaldehyde structures, were favored. Characteristic fragmentation patterns were observed for each m/z 221 ion from higher energy beam-type CID of 1-3 linked disaccharides and the stereochemistry of the non-reducing sugar, together with the anomeric configuration, were successfully identified both with and without 18O-labeling of the reducing sugar carbonyl group.

Combat Identification Systems COMO Integrated Air Defense Model Evaluation (CISE) Study

DTIC Science & Technology

1989-02-01

use K or IR , whichever one applies) E-6 CAA-SR-89- 3 Subroutine PDECLR 1/21/88 Before label 1000 Insert: IF (IR.GT.10) IR a 10 These changes were made...Internal Distribution: Unclassified Library 2 F-2 CAA-SR-89- 3 GLOSSARY 1. ABBREVIATIONS, ACRONYMS, AND SHORT TERMS ADM2 Air Defense Models Modification...STUDY REPORT ’ , CAA-Sn-89- 3 i , .- CD o COMBAT IDENTIFICATION SYSTEMS N COMO INTEGRATED AIR DEFENSE MODEL EVALUATION (CISE) STUDY FEBRUARY 1989

U.S. ARMY HUMAN FACTORS RESEARCH AND DEVELOPMENT ANNUAL CONFERENCE, INDIVIDUAL AND SMALL-UNIT TRAINING FOR COMBAT OPERATIONS (12TH, FORT BENNING, GEORGIA, OCTOBER 1966).

ERIC Educational Resources Information Center

JACOBS, T.O.; AND OTHERS

RESEARCH IN THE AREA OF MILITARY TRAINING AND TRAINING METHODS WAS REVIEWED AND ASSESSED FOR (1) ITS RELEVANCE TO MODERN COMBAT OPERATIONS (IDENTIFICATION OF COMBAT TASKS, DEVELOPMENT OF SKILL TRAINING, AND EVALUATION) AND (2) ITS EFFICIENCY (REDUCED COST AND TIME AND INCREASED TRAINEE PROFICIENCY, OR BOTH). CASES OF EFFECTIVE RESEARCH IN USE OF…

Enhanced characterization of singly protonated phosphopeptide ions by femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fs-LID-MS/MS).

PubMed

Smith, Scott A; Kalcic, Christine L; Safran, Kyle A; Stemmer, Paul M; Dantus, Marcos; Reid, Gavin E

2010-12-01

To develop an improved understanding of the regulatory role that post-translational modifications (PTMs) involving phosphorylation play in the maintenance of normal cellular function, tandem mass spectrometry (MS/MS) strategies coupled with ion activation techniques such as collision-induced dissociation (CID) and electron-transfer dissociation (ETD) are typically employed to identify the presence and site-specific locations of the phosphate moieties within a given phosphoprotein of interest. However, the ability of these techniques to obtain sufficient structural information for unambiguous phosphopeptide identification and characterization is highly dependent on the ion activation method employed and the properties of the precursor ion that is subjected to dissociation. Herein, we describe the application of a recently developed alternative ion activation technique for phosphopeptide analysis, termed femtosecond laser-induced ionization/dissociation (fs-LID). In contrast to CID and ETD, fs-LID is shown to be particularly suited to the analysis of singly protonated phosphopeptide ions, yielding a wide range of product ions including a, b, c, x, y, and z sequence ions, as well as ions that are potentially diagnostic of the positions of phosphorylation (e.g., 'a(n)+1-98'). Importantly, the lack of phosphate moiety losses or phosphate group 'scrambling' provides unambiguous information for sequence identification and phosphorylation site characterization. Therefore, fs-LID-MS/MS can serve as a complementary technique to established methodologies for phosphoproteomic analysis. Copyright © 2010. Published by Elsevier Inc.

Psychosocial Adaptation to Disability Within the Context of Positive Psychology: Philosophical Aspects and Historical Roots.

PubMed

Livneh, Hanoch; Martz, Erin

2016-03-01

The purpose of this article is to review the conceptual and clinical similarities that exist between the principles of positive psychology and those underlying rehabilitation counseling and psychology, occupational rehabilitation, and those espoused by the field of psychosocial adaptation to chronic illness and disability (CID). Three themes were selected for review. These included the historical contributions of early scholars in the area of psychosocial adaptation to CID that later were indirectly infused into mainstream positive psychology; state and trait constructs that constitute much of the infrastructure of positive psychology and psychosocial adaptation to CID; and, finally, the philosophical congruencies between positive psychology and psychosocial adaptation to CID. The existing literature indicates that there is a substantial philosophical and conceptual overlap between the fields of positive psychology and psychosocial adaptation to CID. Since theoreticians and researchers, from both fields, often use differing terminology and definitions to describe similar concepts, as well as seek similar research goals, it would behoove both fields to seek a closer partnership in order to establish a meaningful dialogue that focuses on human strengths and virtues in the lives of people with CID.

Rapid mitigation of carrier-induced degradation in commercial silicon solar cells

NASA Astrophysics Data System (ADS)

Hallam, Brett J.; Chan, Catherine E.; Chen, Ran; Wang, Sisi; Ji, Jingjia; Mai, Ly; Abbott, Malcolm D.; Payne, David N. R.; Kim, Moonyong; Chen, Daniel; Chong, CheeMun; Wenham, Stuart R.

2017-08-01

We report on the progress for the understanding of carrier-induced degradation (CID) in p-type mono and multi-crystalline silicon (mc-Si) solar cells, and methods of mitigation. Defect formation is a key aspect to mitigating CID. Illuminated annealing can be used for both mono and mc-Si solar cells to reduce CID. The latest results of an 8-s UNSW advanced hydrogenation process applied to industrial p-type Czochralski PERC solar cells are shown with average efficiency enhancements of 1.1% absolute from eight different solar cell manufacturers. Results from three new industrial CID mitigation tools are presented, reducing CID to 0.8-1.1% relative, compared to 4.2% relative on control cells. Similar advanced hydrogenation processes can also be applied to multi-crystalline silicon passivated emitter with rear local contact (PERC) cells, however to date, the processes take longer and are less effective. Modifications to the firing processes can also suppress CID in multi-crystalline cells during subsequent illumination. The most stable results are achieved with a multi-stage process consisting of a second firing process at a reduced firing temperature, followed by extended illuminated annealing.

Elve Doublets: The Ionospheric Fingerprints of Compact Intracloud Discharges

NASA Astrophysics Data System (ADS)

da Silva, C. L.; Marshall, R. A.; Pasko, V. P.

2015-12-01

Compact intracloud discharges (CIDs) persist to date as one of the most mysterious lightning manifestations. CIDs are known to be the strongest natural sources of radio-frequency radiation on Earth. At VHF frequencies, approximately above 30 MHz, their emitted power is ten times stronger than that of other lightning processes. The well-known strength of CIDs in VHF contrasts with the lack of substantial optical measurements. CID's VLF/LF electric field change waveforms resemble one full cycle of a distorted sine function, with the first half-cycle being (a few times) larger-amplitude and shorter-duration than the second. For this reason CIDs have been dubbed narrow bipolar events (NBEs). NBE waveshapes are strikingly similar to the largest initial breakdown pulses (IBPs) that occur during the earlier stages of a conventional lightning flash, called classic IBPs. The similarity between classic IBP and NBE far-field waveforms, combined with the fact that positive-polarity NBEs frequently appear as the first event in an otherwise regular positive intracloud discharge, may be indicative that the source of these two E-field pulse types share the same physical mechanism inside thunderclouds [da Silva and Pasko, JGR, 120, 4989-5009, 2015]. In this presentation, we introduce a novel way to investigate CIDs. We show evidence that CIDs can produce an unique ionospheric signature, named "elve doublets". These signatures are characterized by a pair of elves separated in time by 80-160 microseconds. Our analysis combines fast photometric elve data, equivalent-transmission-line models to describe the dynamics of CID source currents, and FDTD modeling of electromagnetic wave propagation in the Earth-ionosphere waveguide accounting for its nonlinear interaction with the lower ionosphere [Marshall et al., GRL, 42, 2015, doi:10.1002/2015GL064862]. We show that typical (negative-polarity) CID altitudes, between 14-22 km, explain the time delay observed in elve doublets, where the first elve in the doublet is generated by the direct EMP path and the second is generated by its ground reflection. Furthermore, we show that the relative brightness of the first and second elves is likely related to the CID orientation, and angles of 5°-20° with respect to the vertical are consistent with the observed brightness ratios.

Linkage Determination of Linear Oligosaccharides by MSn (n > 2) Collision-Induced Dissociation of Z1 Ions in the Negative Ion Mode

NASA Astrophysics Data System (ADS)

Konda, Chiharu; Bendiak, Brad; Xia, Yu

2014-02-01

Obtaining unambiguous linkage information between sugars in oligosaccharides is an important step in their detailed structural analysis. An approach is described that provides greater confidence in linkage determination for linear oligosaccharides based on multiple-stage tandem mass spectrometry (MSn, n >2) and collision-induced dissociation (CID) of Z1 ions in the negative ion mode. Under low energy CID conditions, disaccharides 18O-labeled on the reducing carbonyl group gave rise to Z1 product ions (m/z 163) derived from the reducing sugar, which could be mass-discriminated from other possible structural isomers having m/z 161. MS3 CID of these m/z 163 ions showed distinct fragmentation fingerprints corresponding to the linkage types and largely unaffected by sugar unit identities or their anomeric configurations. This unique property allowed standard CID spectra of Z1 ions to be generated from a small set of disaccharide samples that were representative of many other possible isomeric structures. With the use of MSn CID (n = 3 - 5), model linear oligosaccharides were dissociated into overlapping disaccharide structures, which were subsequently fragmented to form their corresponding Z1 ions. CID data of these Z1 ions were collected and compared with the standard database of Z1 ion CID using spectra similarity scores for linkage determination. As the proof-of-principle tests demonstrated, we achieved correct determination of individual linkage types along with their locations within two trisaccharides and a pentasaccharide.

Evidence for Sequence Scrambling and Divergent H/D Exchange Reactions of Doubly-Charged Isobaric b-Type Fragment Ions

NASA Astrophysics Data System (ADS)

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H.; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10 2+ that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10 2+ and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10 2+, suggesting that b10 2+ may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10 2+; over 30 % of the observed SORI-CID fragment ions from substance P b10 2+ had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10 2+, whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10 2+.

Evidence for sequence scrambling and divergent H/D exchange reactions of doubly-charged isobaric b-type fragment ions.

PubMed

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10(2+) that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10(2+) and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10(2+), suggesting that b10(2+) may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10(2+); over 30% of the observed SORI-CID fragment ions from substance P b10(2+) had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10(2+), whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10(2+).

Artichoke (Cynara cardunculus L. var. scolymus) waste as a natural source of carbonyl trapping and antiglycative agents.

PubMed

Maietta, Mariarosa; Colombo, Raffaella; Lavecchia, Roberto; Sorrenti, Milena; Zuorro, Antonio; Papetti, Adele

2017-10-01

The role of polyphenolic compounds extractable from artichoke solid wastes in the formation of advanced glycation end products (AGEs) was studied. Outer bracts and stems were extracted using different water-ethanol mixtures and HPLC-DAD analyses indicated aqueous and hydro-alcoholic 20:80 stem extracts as the richest in polyphenols. The samples were characterized in their phenolic composition (using mass spectrometry) and antioxidant capacity. Antiglycative capacity was evaluated by in vitro BSA-sugars (glucose, fructose, and ribose) and BSA-methylglyoxal (MGO) tests, formation of Amadori products assay, direct glyoxal (GO) and MGO trapping capacity. Results indicated both extracts as effective inhibitors of fructosamine formation and antiglycative agents. In particular, aqueous extract showed the best activity in the systems containing glucose and fructose, differently from ethanolic extract, that was demonstrated able to better inhibit AGEs formation when ribose or MGO act as precursors. Ethanolic extract was also shown to be able to trap MGO and GO, with efficiency increasing after 24hours of incubation time. These activities are partially correlated with the antioxidant effect of the extract, as demonstrated by the scavenger capacity against ABTS cation and DPPH stable radicals; this relationship is evident when the model system, containing protein incubated with ribose or MGO, is considered. The different activities of the tested extracts could probably be ascribed to the different composition in chlorogenic acids (CQAs), being aqueous extract richer in 1-CQA, 3-CQA, and 1,3-di-CQA, and ethanolic extract in 5-CQA, caffeic acid, 1,5-di-CQA. These findings support further investigations to study the stability of the different CQAs in simil-physiological conditions and the feasibility of artichoke waste as antiglycative agents in food or pharmacological preparations. 5-caffeoylquinic acid (PubChem CID 5280633); 3-caffeoylquinic acid (PubChem CID 1794427); 1-caffeoylquinic acid (PubChem CID 10155076); 1,3-di-caffeoylquinic acid (PubChem CID 24720973); 1,5 - di-caffeoylquinic acid (PubChem CID 122685); caffeic acid (PubChem CID 689043); apigenin-7-glucuronide (PubChem CID 5319484); methylglyoxal PubChem CID (880); aminoguanidine hydrochloride (PubChem CID 2734687). Copyright © 2017 Elsevier Ltd. All rights reserved.

Costo-iliac distance: a physical sign of understated importance.

PubMed

Barry, P J; O'Mahony, D

2012-03-01

Osteoporosis is a common condition, especially affecting the older female population. The ability to predict loss of lumbar height using simple anatomical measurements would be a useful tool. Forty subjects were recruited. Mean age was 72 years. Arm span (AS) and the costo-iliac distance (CID) were measured. The CID/AS ratio was calculated. The L(1)-L(4) vertebral height of each patient was obtained from dual-energy X-ray absorptiometry (DEXA). There was a statistically significant correlation between the lumbar height and CID/AS ratio (R (2) = 0.79, p < 0.001). The CID/AS ratio may be a useful bedside test in identifying loss of lumbar vertebral height.

Strategy to improve the quantitative LC-MS analysis of molecular ions resistant to gas-phase collision induced dissociation: application to disulfide-rich cyclic peptides.

PubMed

Ciccimaro, Eugene; Ranasinghe, Asoka; D'Arienzo, Celia; Xu, Carrie; Onorato, Joelle; Drexler, Dieter M; Josephs, Jonathan L; Poss, Michael; Olah, Timothy

2014-12-02

Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here a methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte's surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte's unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma.

Solid State Television Camera (CID)

NASA Technical Reports Server (NTRS)

Steele, D. W.; Green, W. T.

1976-01-01

The design, development and test are described of a charge injection device (CID) camera using a 244x248 element array. A number of video signal processing functions are included which maximize the output video dynamic range while retaining the inherently good resolution response of the CID. Some of the unique features of the camera are: low light level performance, high S/N ratio, antiblooming, geometric distortion, sequential scanning and AGC.

A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure.

PubMed

Munoz-Tello, Paola; Gabus, Caroline; Thore, Stéphane

2014-03-01

The addition of uridine nucleotide by the poly(U) polymerase (PUP) enzymes has a demonstrated impact on various classes of RNAs such as microRNAs (miRNAs), histone-encoding RNAs and messenger RNAs. Cid1 protein is a member of the PUP family. We solved the crystal structure of Cid1 in complex with non-hydrolyzable UMPNPP and a short dinucleotide compound ApU. These structures revealed new residues involved in substrate/product stabilization. In particular, one of the three catalytic aspartate residues explains the RNA dependence of its PUP activity. Moreover, other residues such as residue N165 or the β-trapdoor are shown to be critical for Cid1 activity. We finally suggest that the length and sequence of Cid1 substrate RNA influence the balance between Cid1's processive and distributive activities. We propose that particular processes regulated by PUPs require the enzymes to switch between the two types of activity as shown for the miRNA biogenesis where PUPs can either promote DICER cleavage via short U-tail or trigger miRNA degradation by adding longer poly(U) tail. The enzymatic properties of these enzymes may be critical for determining their particular function in vivo.

A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure

PubMed Central

Munoz-Tello, Paola; Gabus, Caroline; Thore, Stéphane

2014-01-01

The addition of uridine nucleotide by the poly(U) polymerase (PUP) enzymes has a demonstrated impact on various classes of RNAs such as microRNAs (miRNAs), histone-encoding RNAs and messenger RNAs. Cid1 protein is a member of the PUP family. We solved the crystal structure of Cid1 in complex with non-hydrolyzable UMPNPP and a short dinucleotide compound ApU. These structures revealed new residues involved in substrate/product stabilization. In particular, one of the three catalytic aspartate residues explains the RNA dependence of its PUP activity. Moreover, other residues such as residue N165 or the β-trapdoor are shown to be critical for Cid1 activity. We finally suggest that the length and sequence of Cid1 substrate RNA influence the balance between Cid1's processive and distributive activities. We propose that particular processes regulated by PUPs require the enzymes to switch between the two types of activity as shown for the miRNA biogenesis where PUPs can either promote DICER cleavage via short U-tail or trigger miRNA degradation by adding longer poly(U) tail. The enzymatic properties of these enzymes may be critical for determining their particular function in vivo. PMID:24322298

Improved crystallization and diffraction of caffeine-induced death suppressor protein 1 (Cid1)

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

Yates, Luke A., E-mail: luke@strubi.ox.ac.uk; Durrant, Benjamin P.; Barber, Michael

The use of truncation and RNA-binding mutations of caffeine induced death suppressor protein 1 (Cid1) as a means to enhance crystallogenesis leading to an improvement of X-ray diffraction resolution by 1.5 Å is reported. The post-transcriptional addition of uridines to the 3′-end of RNAs is an important regulatory process that is critical for coding and noncoding RNA stability. In fission yeast and metazoans this untemplated 3′-uridylylation is catalysed by a single family of terminal uridylyltransferases (TUTs) whose members are adapted to specific RNA targets. In Schizosaccharomyces pombe the TUT Cid1 is responsible for the uridylylation of polyadenylated mRNAs, targeting themmore » for destruction. In metazoans, the Cid1 orthologues ZCCHC6 and ZCCHC11 uridylate histone mRNAs, targeting them for degradation, but also uridylate microRNAs, altering their maturation. Cid1 has been studied as a model TUT that has provided insights into the larger and more complex metazoan enzyme system. In this paper, two strategies are described that led to improvements both in the crystallogenesis of Cid1 and in the resolution of diffraction by ∼1.5 Å. These advances have allowed high-resolution crystallo@@graphic studies of this TUT system to be initiated.« less

CASTE (Course Assembly System and Tutorial Environment) and CVI: (Combat Vehicle Identification) A First Application of an Intelligent Tutorial System to Combat Vehicle Identification.

DTIC Science & Technology

1984-09-01

based training systems and hence to realize an embedded trainer that is both intelligent and effective . The o(Continued) DO,; FOAM AM 71 1ឹ...Performance Effectiveness and Simulation Approved for public releate; dlitribution unlimited iii &a3laAfc*ia £&&etaL* ■’—’,£-«.■£./■.,’-f...oriented approaches to computer-based training systems and hence realise an embedded trainer that is both intelli- gent and effective . To this end

Developing Human-Machine Interfaces to Support Appropriate Trust and Reliance on Automated Combat Identification Systems (Developpement d’Interfaces Homme-Machine Pour Appuyer la Confiance dans les Systemes Automatises d’Identification au Combat)

DTIC Science & Technology

2008-03-31

on automation; the ‘response bias’ approach. This new approach is based on Signal Detection Theory (SDT) (Macmillan & Creelman , 1991; Wickens...SDT), response bias will vary with the expectation of the target probability, whereas their sensitivity will stay constant (Macmillan & Creelman ...measures, C has the simplest statistical properties (Macmillan & Creelman , 1991, p273), and it was also the measure used in Dzindolet et al.’s study

Stroop Task-Related Brain Activity in Patients With Insomnia: Changes After Cognitive-Behavioral Therapy for Insomnia.

PubMed

Hwang, Jeong Yeon; Kim, Nambeom; Kim, Soohyun; Park, Juhyun; Choi, Jae-Won; Kim, Seog Ju; Kang, Chang-Ki; Lee, Yu Jin

2018-02-16

In the present study, we compared differences in brain activity during the Stroop task between patients with chronic insomnia disorder (CID) and good sleepers (GS). Furthermore, we evaluated changes in Stroop task-related brain activity after cognitive-behavioral therapy for insomnia (CBT-I). The final analysis included 21 patients with CID and 25 GS. All participants underwent functional magnetic resonance imaging (fMRI) while performing the color-word Stroop task. CBT-I, consisting of 5 sessions, was administered to 14 patients with CID in the absence of medication. After CBT-I, fMRI was repeated in the patients with CID while performing the same task. Sleep-related questionnaires and sleep variables from a sleep diary were also obtained before and after CBT-I. No significant differences in behavioral performance in the Stroop task or task-related brain activation were observed between the CID and GS groups. No changes in behavioral performance or brain activity were found after CBT-I. However, clinical improvement in the Insomnia Severity Index (ISI) score was significantly associated with changes in the Stroop task-related regional blood oxygen level-dependent signals in the left supramarginal gyrus. Our findings suggest that cognitive impairment in patients with CID was not detectable by the Stroop task or Stroop task-related brain activation on fMRI. Moreover, there was no altered brain activity during the Stroop task after CBT-I. However, the ISI score reflected changes in the neural correlates of cognitive processes in patients with CID after CBT-I.

The effect of indacaterol/glycopyrronium versus tiotropium or salmeterol/fluticasone on the prevention of clinically important deterioration in COPD.

PubMed

Anzueto, Antonio R; Vogelmeier, Claus F; Kostikas, Konstantinos; Mezzi, Karen; Fucile, Sebastian; Bader, Giovanni; Shen, Steven; Banerji, Donald; Fogel, Robert

2017-01-01

Endpoints that evaluate deterioration rather than improvement of disease may have clinical utility in COPD. In this analysis, we compared the effects of different maintenance treatments on the prevention of clinically important deterioration (CID) in moderate-to-severe COPD patients. Data were analyzed from three 26-week studies comparing indacaterol/glycopyrronium (IND/GLY) with tiotropium (TIO) or salmeterol/fluticasone (SFC). Two definitions of CID were used; each was a composite of three outcome measures typically associated with COPD. Definition 1 (D1) comprised a ≥100 mL decrease in forced expiratory volume in 1 second (FEV 1 ), a ≥4-unit increase in St George's Respiratory Questionnaire, and a moderate-to-severe COPD exacerbation. In Definition 2 (D2), a ≥1-unit decrease in transition dyspnea index replaced FEV 1 . Using D1, IND/GLY significantly reduced the risk of first or sustained CID versus either TIO (hazard ratio 0.72 [0.61, 0.86], P =0.0003 and 0.73 [0.61, 0.89], P =0.001) or SFC (0.67 [0.57, 0.80] and 0.63 [0.52, 0.77], both P <0.0001). With D2, IND/GLY significantly reduced the risk of first, but not sustained, CID versus TIO (0.80 [0.64 to 0.99], P =0.0359 and 0.85 [0.66, 1.10], P =0.2208) and both first and sustained CID versus SFC (0.73 [0.61, 0.88], P =0.001 and 0.72 [0.58, 0.90], P =0.0036). These data confirm the utility of the CID endpoint as a means of monitoring COPD worsening in patients with moderate-to-severe COPD. Using the CID measure, we demonstrated that dual bronchodilation with IND/GLY significantly reduced the risk of CID versus either long-acting muscarinic antagonist or long-acting β 2 -agonist/inhaled corticosteroid treatment, providing further evidence for the benefit of dual bronchodilation in this patient population.

Treatment with sodium nitroprusside improves the endothelial function in aortic rings with endothelial dysfunction.

PubMed

Buzinari, Tereza Cristina; Oishi, Jorge Camargo; De Moraes, Thiago Francisco; Vatanabe, Izabela Pereira; Selistre-de-Araújo, Heloisa Sobreiro; Pestana, Cezar Rangel; Rodrigues, Gerson Jhonatan

2017-07-15

Verify if sodium nitroprusside (SNP) is able to improve endothelial function and if this effect is independent of nitric oxide (NO) release of the compound. Normotensive (2K) and hypertensive (2K-1C) wistar rats were used. Intact endothelium aortas were placed in a myograph and incubated with SNP: 0.1nM; 1nM or 10nM during 30min. Cumulative concentration-effect curves for acetylcholine (Ach) were realized to measure the relaxing capacity. Intracellular NO were measured (by DAF-2DA probe) in HUVEC treated with SNP 0.1nM or DETA/NO 0.1μM. The detection of intracellular superoxide radical (O 2 •- ) was obtained by using DHE probe. Treatment of 2K-1C aortic rings with SNP (0.1; 1.0 and 10nM) improved endothelium dependent relaxation induced by acetylcholine. This improvement induced by SNP was verified at the concentration of 0.1nM, which does not release NO, suggesting that this effect was not induced due to NO release by SNP compound. Besides, we show that the cell treatment with 0.1nM of SNP decreased the fluorescence intensity to DHE in cells stimulated with angiotensin II. These results indicate that SNP decreases the concentration of O 2 •- in HUVEC cells. The SNP at a concentration that does not release NO inside the cells is able to attenuate endothelial dysfunction. Acetylcholine (Ach) (PubChem CID:6060); angiotensin II human (Ang II) (PubChem CID: 16211177); diethylenetriamine/nitric oxide (DETA-NO) (PubChem CID 4518); dihydroethidium (DHE) (PubChem CID: 128682); phenylephrine (Phe) (PubChem CID: 5284443); sodium nitroprusside (SNP) (PubChem CID: 11963579); Thiazolyl Blue Tetrazolium Bromide (MTT) (PubChem CID: 64965); 4,5-diaminofluorescein diacetate (DAF-2DA); 4-hidroxy-Tempo (Tempol) (PubChem CID: 137994), were purchased from Sigma-Aldrich (St. Louis, MO, USA). Copyright © 2017 Elsevier B.V. All rights reserved.

THE ROLE OF GUIDANCE SERVICES IN COMMUNITY ACTION PROGRAMS COMBATING POVERTY.

ERIC Educational Resources Information Center

GUIDANCE OBJECTIVES TO BE INCLUDED IN A COMMUNITY ACTION PROGRAM COMBATING PROVERTY ARE PRESENTED. THE OBJECTIVES INCLUDE EARLY ADJUSTMENT OF STUDENTS, EARLY IDENTIFICATION AND INTERPRETATION OF ABILITIES, EDUCATIONAL AND CAREER PLANS BASED ON ABILITIES AND SKILLS, PARENT UNDERSTANDING OF OPPORTUNITIES, ENCOURAGEMENT OF REALISTIC GOALS IN LINE…

Identification of small-molecule inhibitors of the colorectal cancer oncogene Krüppel-like factor 5 expression by ultrahigh-throughput screening.

PubMed

Bialkowska, Agnieszka B; Crisp, Melissa; Bannister, Thomas; He, Yuanjun; Chowdhury, Sarwat; Schürer, Stephan; Chase, Peter; Spicer, Timothy; Madoux, Franck; Tian, Chenlu; Hodder, Peter; Zaharevitz, Daniel; Yang, Vincent W

2011-11-01

The transcription factor Krüppel-like factor 5 (KLF5) is primarily expressed in the proliferative zone of the mammalian intestinal epithelium, where it regulates cell proliferation. Studies showed that inhibition of KLF5 expression reduces proliferation rates in human colorectal cancer cells and intestinal tumor formation in mice. To identify chemical probes that decrease levels of KLF5, we used cell-based ultrahigh-throughput screening (uHTS) to test compounds in the public domain of NIH, the Molecular Libraries Probe Production Centers Network library. The primary screen involved luciferase assays in the DLD-1/pGL4.18hKLF5p cell line, which stably expressed a luciferase reporter driven by the human KLF5 promoter. A cytotoxicity counterscreen was done in the rat intestinal epithelial cell line, IEC-6. We identified 97 KLF5-selective compounds with EC(50) < 10 μmol/L for KLF5 inhibition and EC(50) > 10 μmol/L for IEC-6 cytotoxicity. The two most potent compounds, CIDs (PubChem Compound IDs) 439501 and 5951923, were further characterized on the basis of computational, Western blot, and cell viability analyses. Both of these compounds, and two newly synthesized structural analogs of CID 5951923, significantly reduced endogenous KLF5 protein levels and decreased viability of several colorectal cancer cell lines without any apparent impact on IEC-6 cells. Finally, when tested in the NCI-60 panel of human cancer cell lines, compound CID 5951923 was selectively active against colon cancer cells. Our results show the feasibility of uHTS in identifying novel compounds that inhibit colorectal cancer cell proliferation by targeting KLF5.

Identification of Small-Molecule Inhibitors of the Colorectal Cancer Oncogene Krüppel-Like Factor 5 Expression by Ultrahigh-Throughput Screening

PubMed Central

Bialkowska, Agnieszka B.; Crisp, Melissa; Bannister, Thomas; He, Yuanjun; Chowdhury, Sarwat; Schürer, Stephan; Chase, Peter; Spicer, Timothy; Madoux, Franck; Tian, Chenlu; Hodder, Peter; Zaharevitz, Daniel; Yang, Vincent W.

2011-01-01

The transcription factor Krüppel-like factor 5 (KLF5) is primarily expressed in the proliferative zone of the mammalian intestinal epithelium where it regulates cell proliferation. Studies showed that inhibition of KLF5 expression reduces proliferation rates in human colorectal cancer cells and intestinal tumor formation in mice. To identify chemical probes that decrease levels of KLF5, we used cell-based ultrahigh-throughput screening (uHTS) to test compounds in the NIH’s public domain, the Molecular Libraries Probe Production Centers Network (MLPCN) library. The primary screen involved luciferase assays in the DLD-1/pGL4.18hKLF5p cell line, which stably expressed a luciferase reporter driven by the human KLF5 promoter. A cytotoxicity counterscreen was performed in the rat intestinal epithelial cell line, IEC-6. We identified 97 KLF5-selective compounds with EC50<10 µM for KLF5 inhibition and EC50>10 µM for IEC-6 cytotoxicity. The two most potent compounds, CIDs (PubChem Compound IDs) 439501 and 5951923, were further characterized based on computational, Western blot, and cell viability analyses. Both of these compounds and two newly-synthesized structural analogs of CID 5951923 significantly reduced endogenous KLF5 protein levels and decreased viability of several colorectal cancer cell lines without any apparent impact on IEC-6 cells. Finally, when tested in the NCI-60 panel of human cancer cell lines, compound CID 5951923 was selectively active against colon cancer cells. Our results demonstrate the feasibility of uHTS in identifying novel compounds that inhibit colorectal cancer cell proliferation by targeting KLF5. PMID:21885866

A Determination of the Benefits Derived by the Air Force from Providing Air Force Officers in the Logistics Field with Graduate Degrees in the Business Area from Civilian Graduate Institutions.

ERIC Educational Resources Information Center

Chamberlin, Brian; Smith, Richard A.

This thesis is concerned with what benefits the Air Force receives from sending logistics officers to civilian graduate institutions (CID). Additionally, the authors wanted to find how CID graduates fare as compared with graduates of the Graduate Logistics Management (GL). Three samples gathered were for CID graduates, the non-degree group…

Gas-phase structural characterization of neuropeptides Y Y1 receptor antagonists using mass spectrometry: Orbitrap vs triple quadrupole.

PubMed

Silva, Eduarda M P; Varandas, Pedro A M M; Melo, Tânia; Barros, Cristina; Alencastre, Inês S; Barreiros, Luísa; Domingues, Pedro; Lamghari, Meriem; Domingues, M Rosário M; Segundo, Marcela A

2018-03-20

Collision induced dissociation of triple quadrupole mass spectrometer (CID-QqQ) and high-energy collision dissociation (HCD) of Orbitrap were compared for four neuropeptides Y Y1 (NPY Y1) receptor antagonists and showed similar qualitative fragmentation and structural information. Orbitrap high resolution and high mass accuracy HCD fragmentation spectra allowed unambiguous identification of product ions in the range 0.04-4.25 ppm. Orbitrap mass spectrometry showed abundant analyte-specific product ions also observed on CID-QqQ. These results show the suitability of these product ions for use in quantitative analysis by MRM mode. In addition, it was found that all compounds could be determined at levels >1 μg L -1 using the QqQ instrument and that the detection limits for this analyzer ranged from 0.02 to 0.6 μg L -1 . Overall, the results obtained from experiments acquired in QqQ show a good agreement with those acquired from the Orbitrap instrument allowing the use of this relatively inexpensive technique (QqQ) for accurate quantification of these compounds in clinical and academic applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Identification of potential leads against 4-hydroxytetrahydrodipicolinate synthase from Mycobacterium tuberculosis

PubMed Central

Rehman, Ajijur; Akhtar, Salman; Siddiqui, Mohd Haris; Sayeed, Usman; Ahmad, Syed Sayeed; Arif, Jamal M.; Khan, M. Kalim A.

2016-01-01

4-hydroxy-tetrahydrodipicolinate synthase (DHDPS) is an important enzyme needed for the biosynthesis of lysine and many more key metabolites in Mycobacterium tuberculosis (Mtb). Inhibition of DHDPS is supposed to a promising therapeutic target due to its specific role in sporulation, cross-linking of the peptidiglycan polymers and biosynthesis of amino acids. In this work, a known inhibitor-based similarity search was carried out against a natural products database (Super Natural II) towards identification of more potent phyto-inhibitors. Molecular interaction studies were accomplished using three different tools to understand and establish the participation of active site residues as the key players in stabilizing the binding mode of ligands and target protein. The best phyto-compound deduced on the basis of binding affinity was further used as a template to make similarity scan across the PubChem Compound database (score > = 80 %) to get more divesred leads. In this search 5098 hits were obtained that further reduced to 262 after drug-likeness filtration. These phytochemicallike compounds were docked at the active site of DHDPS.Then, those hits selected from docking analysis that showing stronger binding and forming maximum H-bonds with the active site residues (Thr54, Thr55, Tyr143, Arg148 and Lys171). Finally, we predicted one phytochemical compound (SN00003544), two PubChem-compounds (CID41032023, CID54025334) akin to phytochemical molecule showing better interactions in comaprison of known inhibitors of target protein.These findings might be further useful to gain the structural insight into the designing of novel leads against DapA family. PMID:28293071

Fast transient analysis and first-stage collision-induced dissociation with the flowing atmospheric-pressure afterglow ionization source to improve analyte detection and identification.

PubMed

Shelley, Jacob T; Hieftje, Gary M

2010-04-01

The recent development of ambient desorption/ionization mass spectrometry (ADI-MS) has enabled fast, simple analysis of many different sample types. The ADI-MS sources have numerous advantages, including little or no required sample pre-treatment, simple mass spectra, and direct analysis of solids and liquids. However, problems of competitive ionization and limited fragmentation require sample-constituent separation, high mass accuracy, and/or tandem mass spectrometry (MS/MS) to detect, identify, and quantify unknown analytes. To maintain the inherent high throughput of ADI-MS, it is essential for the ion source/mass analyzer combination to measure fast transient signals and provide structural information. In the current study, the flowing atmospheric-pressure afterglow (FAPA) ionization source is coupled with a time-of-flight mass spectrometer (TOF-MS) to analyze fast transient signals (<500 ms FWHM). It was found that gas chromatography (GC) coupled with the FAPA source resulted in a reproducible (<5% RSD) and sensitive (detection limits of <6 fmol for a mixture of herbicides) system with analysis times of ca. 5 min. Introducing analytes to the FAPA in a transient was also shown to significantly reduce matrix effects caused by competitive ionization by minimizing the number and amount of constituents introduced into the ionization source. Additionally, MS/MS with FAPA-TOF-MS, enabling analyte identification, was performed via first-stage collision-induced dissociation (CID). Lastly, molecular and structural information was obtained across a fast transient peak by modulating the conditions that caused the first-stage CID.

A hypertext system that learns from user feedback

NASA Technical Reports Server (NTRS)

Mathe, Nathalie

1994-01-01

Retrieving specific information from large amounts of documentation is not an easy task. It could be facilitated if information relevant in the current problem solving context could be automatically supplied to the user. As a first step towards this goal, we have developed an intelligent hypertext system called CID (Computer Integrated Documentation). Besides providing an hypertext interface for browsing large documents, the CID system automatically acquires and reuses the context in which previous searches were appropriate. This mechanism utilizes on-line user information requirements and relevance feedback either to reinforce current indexing in case of success or to generate new knowledge in case of failure. Thus, the user continually augments and refines the intelligence of the retrieval system. This allows the CID system to provide helpful responses, based on previous usage of the documentation, and to improve its performance over time. We successfully tested the CID system with users of the Space Station Freedom requirements documents. We are currently extending CID to other application domains (Space Shuttle operations documents, airplane maintenance manuals, and on-line training). We are also exploring the potential commercialization of this technique.

Collision-Induced Dissociation Study of the Adduct Ions Produced in NO3−-Free Area of Atmospheric Pressure Negative Corona Discharges under Ambient Air Conditions

PubMed Central

Sekimoto, Kanako; Matsuda, Natsuki; Takayama, Mitsuo

2013-01-01

Collision-induced dissociation (CID) experiments of adducts [M+R]− with negative atmospheric ions R− (O2−, HCO3− and COO−(COOH)) produced in NO3−-free discharge area in atmospheric pressure corona discharge ionization (APCDI) method were performed using aliphatic and aromatic compounds M. The [M+R]− adducts for individual R− fragmented to form deprotonated analytes [M−H]− as well as the specific product ions which also occurred in the CID of [M−H]−, independent of analytes with several different functional groups. The results obtained suggested that the specific product ions formed in the CID of [M+R]−, as well as CID of [M−H]−, are generated due to further fragmentation of the product ions [M−H]−. It was concluded, therefore, that CID of [M+R]− formed in NO3−-free discharge area can indirectly lead to the formation of the product ions originating from [M−H]−. PMID:24860710

FORTE Compact Intra-cloud Discharge Detection parameterized by Peak Current

NASA Astrophysics Data System (ADS)

Heavner, M. J.; Suszcynsky, D. M.; Jacobson, A. R.; Heavner, B. D.; Smith, D. A.

2002-12-01

The Los Alamos Sferic Array (EDOT) has recorded over 3.7 million lightning-related fast electric field change data records during April 1 - August 31, 2001 and 2002. The events were detected by three or more stations, allowing for differential-time-of-arrival location determination. The waveforms are characterized with estimated peak currents as well as by event type. Narrow Bipolar Events (NBEs), the VLF/LF signature of Compact Intra-cloud Discharges (CIDs), are generally isolated pulses with identifiable ionospheric reflections, permitting determination of event source altitudes. We briefly review the EDOT characterization of events. The FORTE satellite observes Trans-Ionospheric Pulse Pairs (TIPPs, the VHF satellite signature of CIDs). The subset of coincident EDOT and FORTE CID observations are compared with the total EDOT CID database to characterize the VHF detection efficiency of CIDs. The NBE polarity and altitude are also examined in the context of FORTE TIPP detection. The parameter-dependent detection efficiencies are extrapolated from FORTE orbit to GPS orbit in support of the V-GLASS effort (GPS based global detection of lightning).

Trust Management Considerations For the Cooperative Infrastructure Defense Framework: Trust Relationships, Evidence, and Decisions

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

Maiden, Wendy M.

Cooperative Infrastructure Defense (CID) is a hierarchical, agent-based, adaptive, cyber-security framework designed to collaboratively protect multiple enclaves or organizations participating in a complex infrastructure. CID employs a swarm of lightweight, mobile agents called Sensors designed to roam hosts throughout a security enclave to find indications of anomalies and report them to host-based Sentinels. The Sensors’ findings become pieces of a larger puzzle, which the Sentinel puts together to determine the problem and respond per policy as given by the enclave-level Sergeant agent. Horizontally across multiple enclaves and vertically within each enclave, authentication and access control technologies are necessary but insufficientmore » authorization mechanisms to ensure that CID agents continue to fulfill their roles in a trustworthy manner. Trust management fills the gap, providing mechanisms to detect malicious agents and offering more robust mechanisms for authorization. This paper identifies the trust relationships throughout the CID hierarchy, the types of trust evidence that could be gathered, and the actions that the CID system could take if an entity is determined to be untrustworthy.« less

Computer integrated documentation

NASA Technical Reports Server (NTRS)

Boy, Guy

1991-01-01

The main technical issues of the Computer Integrated Documentation (CID) project are presented. The problem of automation of documents management and maintenance is analyzed both from an artificial intelligence viewpoint and from a human factors viewpoint. Possible technologies for CID are reviewed: conventional approaches to indexing and information retrieval; hypertext; and knowledge based systems. A particular effort was made to provide an appropriate representation for contextual knowledge. This representation is used to generate context on hypertext links. Thus, indexing in CID is context sensitive. The implementation of the current version of CID is described. It includes a hypertext data base, a knowledge based management and maintenance system, and a user interface. A series is also presented of theoretical considerations as navigation in hyperspace, acquisition of indexing knowledge, generation and maintenance of a large documentation, and relation to other work.

Roles of the combined irrigation, drainage, and storage of the canal network in improving water reuse in the irrigation districts along the lower Yellow River, China

NASA Astrophysics Data System (ADS)

Liu, Lei; Luo, Yi; He, Chansheng; Lai, Jianbin; Li, Xiubin

2010-09-01

SummaryThe commonly used irrigation system in the irrigation districts (with a combined irrigation area of 3.334 × 10 6 ha) along the lower Yellow River of China is canal network. It delivers water from the Yellow River to the fields, collects surface runoff and drainage from cropland, and stores both of them for subsequent irrigation uses. This paper developed a new combined irrigation, drainage, and storage (CIDS) module for the SWAT2000 model, simulated the multiple roles of the CIDS canal system, and estimated its performance in improving water reuse in the irrigation districts under different irrigation and water diversion scenarios. The simulation results show that the annual evapotranspiration (ET) of the double-cropping winter wheat and summer maize was the highest under the full irrigation scenario (automatic irrigation), and the lowest under the no irrigation scenario. It varied between these two values when different irrigation schedules were adopted. Precipitation could only meet the water requirement of the double-cropping system by 62-96% on an annual basis; that of the winter wheat by 32-36%, summer maize by 92-123%, and cotton by 87-98% on a seasonal basis. Hence, effective irrigation management for winter wheat is critical to ensure high wheat yield in the study area. Runoff generation was closely related to precipitation and influenced by irrigation. The highest and lowest annual runoff accounted for 19% and 11% of the annual precipitation under the full irrigation and no irrigation scenarios, respectively. Nearly 70% of the annual runoff occurred during months of July and August due to the concentrated precipitation in these 2 months. The CIDS canals play an important role in delivering the diversion water from the Yellow River, intercepting the surface runoff and drainage from cropland (inflow of the CIDS canal) and recharging the shallow aquifer for later use. Roughly 14-26% of the simulated total flow in the CIDS canal system recharged shallow aquifer through canal seepage. The water flowing out of the canal system accounted for approximately 32% of the water in the CIDS canals. The storage capacity of the CIDS canals is negatively correlated to the precipitation. In years with abundant precipitation, the volume of the surface runoff and drainage from the cropland may surpass the storage capacities of the CIDS canals, while in years with less precipitation, partial storage capacity of the CIDS canal may be occupied by the diversion water from the Yellow River. Proper maintenance of the storage capacity of the CIDS has the potential in improving the efficiency of reusing the surface runoff and field drainage for irrigation practices to mitigate the increasing water shortage along the lower Yellow River.

Department of Defense Report on Search for Human Radiation Experiment Records, 1944 - 1994, Volume 1

DTIC Science & Technology

1997-06-01

CID93-027 1993 60MG035 1993 CID92-221 1993 CID92-272 Regional cerebral blood flow and glucose rate in patients with complex partial seizures ...34 illnesses or injuries in the body whose diagnosis previously required exploratory surgery or educated guesses. In industrial uses, x-ray machines...all unnecessary physical and mental suffering and injury . f. -No experiment should be conducted where there is an a priori reason to believe that

Screening and confirmation capabilities of liquid chromatography-time-of-flight mass spectrometry for the determination of 200 multiclass sport drugs in urine.

PubMed

Domínguez-Romero, Juan C; García-Reyes, Juan F; Lara-Ortega, Felipe J; Molina-Díaz, Antonio

2015-03-01

In this article, a screening method for the determination of 200 sport drugs in human urine has been developed using liquid-chromatography electrospray time-of-flight mass spectrometry (LC-TOFMS). The chromatographic separation of the targeted doping agents was carried out by fast liquid chromatography using a C18 column (4.6×50 mm) with 1.8 μm particle size. Accurate mass measurements of the selected ion (typically [M+H](+) and [M-H](-)) along with retention time matching was used for the screening and detection of the targeted species. The proposed methodology comprised also a simple sample treatment stage based on solid-phase extraction (SPE) with polymeric cartridges. The SPE method displayed satisfactory recoveries rates (between 70 and 120%) for the majority of the compounds at both concentration levels tested (2.5 and 25 μg L(-1)). The overall performance of the method was satisfactory with all 200 compounds fulfilling WADA minimum required performance levels (MRPLs), with limits of quantitation lower than 1 μg L(-1) for 80% of the compounds, and showing an appropriate linearity (r(2)>0.99) in most cases. Additionally, the ability of "in-source" collision induced dissociation (CID) for confirmatory purposes was examined using as criterion the presence of two high-resolution ions with relevant abundances for unambiguous confirmation. This stringent criterion was fulfilled for 75% of the species using in-source CID fragmentation. The use of an improved approach based on CID performed on a dedicated collision cell without precursor ion selection (using a Q-TOF) provided at least two ions in all cases with the exception of 2-aminoheptane. Finally, based on the use of diagnostic fragment ions, a workflow for the comprehensive screening and identification of non-targeted compounds (viz. compounds with no primary standards or retention time information available, such as metabolites) has been also examined using rat urine samples. The proposed screening method has proved to be effective for the analysis of targeted compounds, and also for the identification of metabolites, expanding easily the search for doping agents not only limited to specific banned parent compounds but also to derivate compounds with similar structure as well as metabolites. Copyright © 2014 Elsevier B.V. All rights reserved.

The effect of indacaterol/glycopyrronium versus tiotropium or salmeterol/fluticasone on the prevention of clinically important deterioration in COPD

PubMed Central

Anzueto, Antonio R; Vogelmeier, Claus F; Kostikas, Konstantinos; Mezzi, Karen; Fucile, Sebastian; Bader, Giovanni; Shen, Steven; Banerji, Donald; Fogel, Robert

2017-01-01

Background Endpoints that evaluate deterioration rather than improvement of disease may have clinical utility in COPD. In this analysis, we compared the effects of different maintenance treatments on the prevention of clinically important deterioration (CID) in moderate-to-severe COPD patients. Methods Data were analyzed from three 26-week studies comparing indacaterol/glycopyrronium (IND/GLY) with tiotropium (TIO) or salmeterol/fluticasone (SFC). Two definitions of CID were used; each was a composite of three outcome measures typically associated with COPD. Definition 1 (D1) comprised a ≥100 mL decrease in forced expiratory volume in 1 second (FEV1), a ≥4-unit increase in St George’s Respiratory Questionnaire, and a moderate-to-severe COPD exacerbation. In Definition 2 (D2), a ≥1-unit decrease in transition dyspnea index replaced FEV1. Results Using D1, IND/GLY significantly reduced the risk of first or sustained CID versus either TIO (hazard ratio 0.72 [0.61, 0.86], P=0.0003 and 0.73 [0.61, 0.89], P=0.001) or SFC (0.67 [0.57, 0.80] and 0.63 [0.52, 0.77], both P<0.0001). With D2, IND/GLY significantly reduced the risk of first, but not sustained, CID versus TIO (0.80 [0.64 to 0.99], P=0.0359 and 0.85 [0.66, 1.10], P=0.2208) and both first and sustained CID versus SFC (0.73 [0.61, 0.88], P=0.001 and 0.72 [0.58, 0.90], P=0.0036). Conclusion These data confirm the utility of the CID endpoint as a means of monitoring COPD worsening in patients with moderate-to-severe COPD. Using the CID measure, we demonstrated that dual bronchodilation with IND/GLY significantly reduced the risk of CID versus either long-acting muscarinic antagonist or long-acting β2-agonist/inhaled corticosteroid treatment, providing further evidence for the benefit of dual bronchodilation in this patient population. PMID:28496316

Assessing the stroke-specific quality of life for outcome measurement in stroke rehabilitation: minimal detectable change and clinically important difference.

PubMed

Lin, Keh-chung; Fu, Tiffany; Wu, Ching-yi; Hsieh, Ching-ju

2011-01-19

This study was conducted to establish the minimal detectable change (MDC) and clinically important differences (CIDs) of the physical category of the Stroke-Specific Quality of Life Scale in patients with stroke. MDC and CIDs scores were calculated from the data of 74 participants enrolled in randomized controlled trials investigating the effects of two rehabilitation programs in patients with stroke. These participants received treatments for 3 weeks and underwent clinical assessment before and after treatment. To obtain test-retest reliability for calculating MDC, another 25 patients with chronic stroke were recruited. The MDC was calculated from the standard error of measurement (SEM) to indicate a real change with 95% confidence for individual patients (MDC95). Distribution-based and anchor-based methods were adopted to triangulate the ranges of minimal CIDs. The percentage of scale width was calculated by dividing the MDC and CIDs by the total score range of each physical category. The percentage of patients exceeding MDC95 and minimal CIDs was also reported. The MDC95 of the mobility, self-care, and upper extremity (UE) function subscales were 5.9, 4.0, and 5.3 respectively. The minimal CID ranges for these 3 subscales were 1.5 to 2.4, 1.2 to 1.9, and 1.2 to 1.8. The percentage of patients exceeding MDC95 and minimal CIDs of the mobility, self-care, and UE function subscales were 9.5% to 28.4%, 6.8% to 28.4%, and 12.2% to 33.8%, respectively. The change score of an individual patient has to reach 5.9, 4.0, and 5.3 on the 3 subscales to indicate a true change. The mean change scores of a group of patients with stroke on these subscales should reach the lower bound of CID ranges of 1.5 (6.3% scale width), 1.2 (6.0% scale width), and 1.2 (6.0% scale width) to be regarded as clinically important change. This information may facilitate interpretations of patient-reported outcomes after stroke rehabilitation. Future research is warranted to validate these findings.

Assessing the Stroke-Specific Quality of Life for Outcome Measurement in Stroke Rehabilitation: Minimal Detectable Change and Clinically Important Difference

PubMed Central

2011-01-01

Background This study was conducted to establish the minimal detectable change (MDC) and clinically important differences (CIDs) of the physical category of the Stroke-Specific Quality of Life Scale in patients with stroke. Methods MDC and CIDs scores were calculated from the data of 74 participants enrolled in randomized controlled trials investigating the effects of two rehabilitation programs in patients with stroke. These participants received treatments for 3 weeks and underwent clinical assessment before and after treatment. To obtain test-retest reliability for calculating MDC, another 25 patients with chronic stroke were recruited. The MDC was calculated from the standard error of measurement (SEM) to indicate a real change with 95% confidence for individual patients (MDC95). Distribution-based and anchor-based methods were adopted to triangulate the ranges of minimal CIDs. The percentage of scale width was calculated by dividing the MDC and CIDs by the total score range of each physical category. The percentage of patients exceeding MDC95 and minimal CIDs was also reported. Results The MDC95 of the mobility, self-care, and upper extremity (UE) function subscales were 5.9, 4.0, and 5.3 respectively. The minimal CID ranges for these 3 subscales were 1.5 to 2.4, 1.2 to 1.9, and 1.2 to 1.8. The percentage of patients exceeding MDC95 and minimal CIDs of the mobility, self-care, and UE function subscales were 9.5% to 28.4%, 6.8% to 28.4%, and 12.2% to 33.8%, respectively. Conclusions The change score of an individual patient has to reach 5.9, 4.0, and 5.3 on the 3 subscales to indicate a true change. The mean change scores of a group of patients with stroke on these subscales should reach the lower bound of CID ranges of 1.5 (6.3% scale width), 1.2 (6.0% scale width), and 1.2 (6.0% scale width) to be regarded as clinically important change. This information may facilitate interpretations of patient-reported outcomes after stroke rehabilitation. Future research is warranted to validate these findings. PMID:21247433

Comparison of the impact of six heat-load management strategies on thermal responses and milk production of feed-pad and pasture fed dairy cows in a subtropical environment

NASA Astrophysics Data System (ADS)

Davison, T. M.; Jonsson, N. N.; Mayer, D. G.; Gaughan, J. B.; Ehrlich, W. K.; McGowan, M. R.

2016-12-01

Exposure to hot environments affects milk yield (MY) and milk composition of pasture and feed-pad fed dairy cows in subtropical regions. This study was undertaken during summer to compare MY and physiology of cows exposed to six heat-load management treatments. Seventy-eight Holstein-Friesian cows were blocked by season of calving, parity, milk yield, BW, and milk protein (%) and milk fat (%) measured in 2 weeks prior to the start of the study. Within blocks, cows were randomly allocated to one of the following treatments: open-sided iron roofed day pen adjacent to dairy (CID) + sprinklers (SP); CID only; non-shaded pen adjacent to dairy + SP (NSD + SP); open-sided shade cloth roofed day pen adjacent to dairy (SCD); NSD + sprinkler (sprinkler on for 45 min at 1100 h if mean respiration rate >80 breaths per minute (NSD + WSP) ); open-sided shade cloth roofed structure over feed bunk in paddock + 1 km walk to and from the dairy (SCP + WLK). Sprinklers for CID + SP and NSD + SP cycled 2 min on, 12 min off when ambient temperature >26°C. The highest milk yields were in the CID + SP and CID treatments (23.9 L cow-1 day-1), intermediate for NSD + SP, SCD and SCP + WLK (22.4 L cow-1 day-1), and lowest for NSD + WSP (21.3 L cow-1 day-1) ( P < 0.05). The highest ( P < 0.05) feed intakes occurred in the CID + SP and CID treatments while intake was lowest ( P < 0.05) for NSD + WSP and SCP + WLK. Weather data were collected on site at 10-min intervals, and from these, THI was calculated. Nonlinear regression modelling of MY × THI and heat-load management treatment demonstrated that cows in CID + SP showed no decline in MY out to a THI break point value of 83.2, whereas the pooled MY of the other treatments declined when THI >80.7. A combination of iron roof shade plus water sprinkling throughout the day provided the most effective control of heat load.

The Scaling Law of The Near-Field Coseismic Ionospheric Disturbances

NASA Astrophysics Data System (ADS)

Cahyadi, M.; Heki, K.

2013-12-01

Coseismic ionospheric disturbances (CIDs) appear shortly after relatively large earthquakes as a result of ionospheric irregularity associated with passing atmospheric waves excited by the earthquakes. CIDs appearing approximately 10 minutes after earthquakes are caused by acoustic waves generated by coseismic vertical movements of the crust or the sea surface, and they propagate as fast as ~1 km/second over the distance of hundreds of kilometres. Here we collected past examples of CID detected in Total Electron Content (TEC) by GPS observations for 21 earthquakes 1994-2012 distributed worldwide. Their moment magnitudes (Mw) range from 6.6 to 9.2, and include two normal fault earthquakes that occurred in the outer rise region of the trenches (2007 January central Kuril earthquake, and 2012 December Tohoku-oki earthquake), and two strike-slip earthquakes (the main shock and the largest aftershock of the 2012 North Sumatra earthquakes). The rest are all reverse-fault earthquakes. We tried to select the pair of GPS satellite and station showing the largest CID amplitudes. Due to the directivity, the ionospheric piercing point (IPP) of line-of-sight (LOS) should be on the southern/northern side for earthquakes in the northern/southern hemisphere. We also selected GPS stations lying on the same side of IPP and located farther than IPP, to enable shallow-angle LOS penetration with the CID wavefront. We also selected CIDs with (1) appearance time not later than 15 minutes after earthquakes, and (2) sharp peaks. The first ensures that IPPs are close to the epicentres and geometric decays are insignificant. The second condition is the manifestation of the shallow angle penetration of LOS. The peak amplitudes were derived by (1) finding the peak TEC value, (2) going back in time from the peak by 90 seconds, and (3) calculating the TEC difference at the two epochs. We also obtained background vertical TEC from Global Ionospheric Maps (GIM), and expressed the CID amplitudes as percents relative to the background TEC. When we plot relative CID amplitudes as a function of seismic moment in the double logarithmic plot, data are distributed roughly around a line, suggesting that they obey a certain scaling law. The slope of the line shows that the CID amplitudes increase by two orders of magnitude as Mw increases by three. We speculate that this reflects the scaling law governing the maximum uplift in relatively large shallow-angle reverse faultings. This scaling law and its empirical factor-two uncertainty in CID amplitude imply that we can determine Mw with an uncertainty of ×0.45 by measuring CID amplitudes. This is useful for early warning in a region where tsunamis arrive at the coast later than acoustic waves arrive at the ionospheric F layer, and this is the case for the Pacific coast of NE Japan. There are two earthquakes deviating negatively beyond the factor 2 uncertainty. They are the 2012 North Sumatra earthquake (Mw8.6), the largest strike-slip earthquakes ever recorded, and its largest aftershock (Mw8.1). This negative deviation would possibly reflect the smaller vertical crustal movements in strike-slip earthquakes than dip-slip events.

Application of low-noise CID imagers in scientific instrumentation cameras

NASA Astrophysics Data System (ADS)

Carbone, Joseph; Hutton, J.; Arnold, Frank S.; Zarnowski, Jeffrey J.; Vangorden, Steven; Pilon, Michael J.; Wadsworth, Mark V.

1991-07-01

CIDTEC has developed a PC-based instrumentation camera incorporating a preamplifier per row CID imager and a microprocessor/LCA camera controller. The camera takes advantage of CID X-Y addressability to randomly read individual pixels and potentially overlapping pixel subsets in true nondestructive (NDRO) as well as destructive readout modes. Using an oxy- nitride fabricated CID and the NDRO readout technique, pixel full well and noise levels of approximately 1*10(superscript 6) and 40 electrons, respectively, were measured. Data taken from test structures indicates noise levels (which appear to be 1/f limited) can be reduced by a factor of two by eliminating the nitride under the preamplifier gate. Due to software programmability, versatile readout capabilities, wide dynamic range, and extended UV/IR capability, this camera appears to be ideally suited for use in spectroscopy and other scientific applications.

Hilda Cid: physicist, crystallographer, structural biologist

NASA Astrophysics Data System (ADS)

Gutiérrez, Gonzalo

2016-05-01

A brief review of Dr. Hilda Cid, Chilean scientist who excelled in the field of crystallography, is presented. Dr. Cid was born in 1933 in Talcahuano, where she completed her primary and secondary education, graduating as a Teacher of mathematics and physics from the University of Chile in 1958. She continued graduate studies at MIT, USA, where obtained the PhD in 1964. Upon her return to Chile, she joined the Austral University in Valdivia, where she dedicated to characterize, by X-ray, biological material. During that time, she was actively involved in the social changes taking place in the university and in the country. Thus, following the bloody coup of 1973, she and her family were persecuted and forced to go into exile to Sweden. In the decade of the 1980 she returns to Chile, and settles at University of Concepción, where she teaches, conducts research and organizes a number of latino-american courses and symposiums. Knowing that Hilda Cid formed a real school, where her students -now distinguished professionals and researchers- cast their teachings through Chile and other countries, we ended the article with a reflection about why Hilda Cid, despite its obvious scientific achievements, remains ignored by most of the scientific establishment in Chile.

History of chronic inflammatory disorders increases the risk of Merkel cell carcinoma, but does not correlate with Merkel cell polyomavirus infection.

PubMed

Sahi, Helka; Sihto, Harri; Artama, Miia; Koljonen, Virve; Böhling, Tom; Pukkala, Eero

2017-01-17

We aimed to assess the connection between chronic inflammatory disorders (CIDs) and Merkel cell carcinoma (MCC). Merkel cell carcinoma cases diagnosed in 1978-2009 were extracted from the Finnish Cancer Registry and controls from the Population Registry. Information on reimbursed CIDs was linked to clinicopathological data including Merkel cell polyomavirus (MCV) status by qPCR and immunohistochemistry for the large T antigen of MCV (LTA), Ki-67 and tumour-infiltrating lymphocytes. Chronic inflammatory disorders increased the risk of MCC significantly (odds ratio (OR) 1.39, 95% confidence interval (CI) 1.03-1.88), specifically connective tissue/systemic diseases (OR 1.75, 95% CI 1.09-1.80) and diabetic conditions (OR 1.51, 95% CI 1.03-2.22). Chronic inflammatory disorders associated with larger tumour diameter (P=0.02) and higher Ki-67 expression (P=0.005). The expression of LTA was seen significantly more often in the absence of CIDs (P=0.05). Patients with CID are at significantly higher risk for aggressive MCC. Merkel cell polyomavirus positivity is more common in MCC patients unafflicted by CID.

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.

Effects of consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114 001 on common respiratory and gastrointestinal infections in shift workers in a randomized controlled trial.

PubMed

Guillemard, Eric; Tanguy, Jérôme; Flavigny, Ann'Laure; de la Motte, Stephan; Schrezenmeir, Juergen

2010-10-01

The risk of infection may be increased in people under stress such as shift workers. This study examined the effect of a fermented dairy product containing the probiotic Lactobacillus casei DN-114 001 (verum) on the incidence of respiratory and gastrointestinal common infectious diseases (CIDs) and on immune functions in healthy shift workers. The study was single-center, randomized, double-blind, and controlled. Volunteers received 200 g/day of verum (n = 500) or control product (n = 500) for 3 months; 1-month follow-up was carried out. The cumulated number of CIDs (primary outcome) was not significantly different between groups. Because the Poisson distribution of the primary parameter did not fully fit the observed data, a post hoc categorical analysis was applied and showed a significantly lower cumulated number of CIDs in the verum group during the product consumption phase (odds ratio [OR] = 0.75, 95% confidence interval [CI] 0.59-0.95, p = 0.017). Verum also reduced the proportion of volunteers experiencing at least 1 CID (43% vs. 51%, p = 0.005), increased the time to the first occurrence of CID (p = 0.017) in the whole population, and reduced the cumulated number of CIDs in the subgroup of smokers (p = 0.033). In the course of CID, cumulated duration of fever was lower in the verum group (in the whole study phase) (p = 0.022), and an increase in leukocyte, neutrophil, and natural killer (NK) cell counts and activity (p = 0.047 to p < 0.001) was observed compared with control group. Verum was safe and well tolerated. The results indicate that daily consumption of a fermented dairy product containing Lactobacillus casei DN-114 001 could reduce the risk of common infections in stressed individuals such as shift workers.

Low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) mass spectrometry for structural elucidation of saccharides and clarification of their dissolution mechanism in DMAc/LiCl.

PubMed

Bayat, Parisa; Lesage, Denis; Cole, Richard B

2018-05-29

The dissolution mechanism of oligosaccharides in N,N-dimethylacetamide/lithium chloride (DMAc/LiCl), a solvent used for cellulose dissolution, and the capabilities of low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) for structural analysis of carbohydrates were investigated. Comparing the spectra obtained using three techniques shows that, generally, when working with mono-lithiated sugars, CID spectra provide more structurally informative fragments, and glycosidic bond cleavage is the main pathway. However, when working with di-lithiated sugars, HCD spectra can be more informative providing predominately cross-ring cleavage fragments. This is because HCD is a non-resonant activation technique and it allows a higher amount of energy to be deposited in a short time, giving access to more endothermic decomposition pathways as well as consecutive fragmentations. The difference in preferred dissociation pathways of mono-lithiated and di-lithiated sugars indicates that the presence of the second lithium strongly influences the relative rate constants for cross-ring cleavages (rearrangement) vs. direct glycosidic bond cleavages, and disfavors the latter. Regarding the dissolution mechanism of sugars in DMAc/LiCl, CID and HCD experiments on di-lithiated and tri-lithiated sugars reveal that intensities of product ions containing two Li + or three Li + , respectively, are higher than those bearing only one Li + . In addition, comparing the fragmentation spectra (both HCD and CID) of LiCl adducted lithiated sugar and NaCl adducted sodiated sugar shows that while, in the latter case, loss of NaCl is dominant, in the former case, loss of HCl occurs preferentially. The compiled evidence implies that there is a strong and direct interaction between lithium and the saccharide during the dissolution process in the DMAc/LiCl solvent system. This article is protected by copyright. All rights reserved.

Modelling volumetric growth in a thick walled fibre reinforced artery

NASA Astrophysics Data System (ADS)

Eriksson, T. S. E.; Watton, P. N.; Luo, X. Y.; Ventikos, Y.

2014-12-01

A novel framework for simulating growth and remodelling (G&R) of a fibre-reinforced artery, including volumetric adaption, is proposed. We show how to implement this model into a finite element framework and propose and examine two underlying assumptions for modelling growth, namely constant individual density (CID) or adaptive individual density (AID). Moreover, we formulate a novel approach which utilises a combination of both AID and CID to simulate volumetric G&R for a tissue composed of several different constituents. We consider a special case of the G&R of an artery subjected to prescribed elastin degradation and we theorise on the assumptions and suitability of CID, AID and the mixed approach for modelling arterial biology. For simulating the volumetric changes that occur during aneurysm enlargement, we observe that it is advantageous to describe the growth of collagen using CID whilst it is preferable to model the atrophy of elastin using AID.

Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin

NASA Astrophysics Data System (ADS)

Medzihradszky, Katalin F.; Bohlen, Christopher J.

2012-05-01

A 7 kDa toxin isolated from the venom of the Texas coral snake ( Micrurus tener tener) was subjected to collision-induced dissociation (CID) and electron-transfer dissociation (ETD) analyses both before and after reduction at low pH. Manual and automated approaches to de novo sequencing are compared in detail. Manual de novo sequencing utilizing the combination of high accuracy CID and ETD data and an acid-related cleavage yielded the N-terminal half of the sequence from the reduced species. The intact polypeptide, containing 3 disulfide bridges produced a series of unusual fragments in ion trap CID experiments: abundant internal amino acid losses were detected, and also one of the disulfide-linkage positions could be determined from fragments formed by the cleavage of two bonds. In addition, internal and c-type fragments were also observed.

Forensic timber identification: It's time to integrate disciplines to combat illegal logging

Treesearch

Eleanor E. Dormontt; Markus Boner; Birgit Braun; Gerhard Breulmann; Bernd Degen; Edgard Espinoza; Shelley Gardner; Phil Guillery; John C. Hermanson; Gerald Koch; Soon Leong Lee; Milton Kanashiro; Anto Rimbawanto; Darren Thomas; Alex C. Wiedenhoeft; Yafang Yin; Johannes Zahnen; Andrew J. Lowe

2015-01-01

The prosecution of illegal logging crimes is hampered by a lack of available forensic timber identification tools, both for screening of suspectmaterial and definitive identification of illegally sourcedwood. Reputable timber traders are also struggling to police their own supply chains and comply with the growing requirement for due diligence with respect to timber...

Rational design of protamine nanocapsules as antigen delivery carriers.

PubMed

González-Aramundiz, José Vicente; Presas, Elena; Dalmau-Mena, Inmaculada; Martínez-Pulgarín, Susana; Alonso, Covadonga; Escribano, José M; Alonso, María J; Csaba, Noemi Stefánia

2017-01-10

Current challenges in global immunization indicate the demand for new delivery strategies, which could be applied to the development of new vaccines against emerging diseases, as well as to improve safety and efficacy of currently existing vaccine formulations. Here, we report a novel antigen nanocarrier consisting of an oily core and a protamine shell, further stabilized with pegylated surfactants. These nanocarriers, named protamine nanocapsules, were rationally designed to promote the intracellular delivery of antigens to immunocompetent cells and to trigger an efficient and long-lasting immune response. Protamine nanocapsules have nanometric size, positive zeta potential and high association capacity for H1N1 influenza hemagglutinin, a protein that was used here as a model antigen. The new formulation shows an attractive stability profile both, as an aqueous suspension or a freeze-dried powder formulation. In vitro studies showed that protamine nanocapsules were efficiently internalized by macrophages without eliciting significant toxicity. In vivo studies indicate that antigen-loaded nanocapsules trigger immune responses comparable to those achieved with alum, even when using significantly lower antigen doses, thus indicating their adjuvant properties. These promising in vivo data, alongside with their versatility for the loading of different antigens and oily immunomodulators and their excellent stability profile, make these nanocapsules a promising platform for the delivery of antigens. Protamine sulphate (PubChem SID: 7849283), Sodium Cholate (PubChem CID: 23668194), Miglyol (PubChem CID: 53471835), α tocopherol (PubChem CID: 14985), Tween® 20(PubChem CID: 443314), Tween® 80(PubChem CID: 5281955), TPGS (PubChem CID: 71406). Copyright © 2016 Elsevier B.V. All rights reserved.

Implementation of dipolar direct current (DDC) collision-induced dissociation in storage and transmission modes on a quadrupole/time-of-flight tandem mass spectrometer.

PubMed

Webb, Ian K; Londry, Frank A; McLuckey, Scott A

2011-09-15

Means for effecting dipolar direct current collision-induced dissociation (DDC CID) on a quadrupole/time-of-flight in a mass spectrometer have been implemented for the broadband dissociation of a wide range of analyte ions. The DDC fragmentation method in electrodynamic storage and transmission devices provides a means for inducing fragmentation of ions over a large mass-to-charge range simultaneously. It can be effected within an ion storage step in a quadrupole collision cell that is operated as a linear ion trap or as ions are continuously transmitted through the collision cell. A DDC potential is applied across one pair of rods in the quadrupole collision cell of a QqTOF hybrid mass spectrometer to effect fragmentation. In this study, ions derived from a small drug molecule, a model peptide, a small protein, and an oligonucleotide were subjected to the DDC CID method in either an ion trapping or an ion transmission mode (or both). Several key experimental parameters that affect DDC CID results, such as time, voltage, low mass cutoff, and bath gas pressure, are illustrated with protonated leucine enkephalin. The DDC CID dissociation method gives a readily tunable, broadband tool for probing the primary structures of a wide range of analyte ions. The method provides an alternative to the narrow resonance conditions of conventional ion trap CID and it can access more extensive sequential fragmentation, depending upon conditions. The DDC CID approach constitutes a collision analog to infrared multiphoton dissociation (IRMPD). Copyright © 2011 John Wiley & Sons, Ltd.

Structural Characterization and Absolute Quantification of Microcystin Peptides Using Collision-Induced and Ultraviolet Photo-Dissociation Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Attard, Troy J.; Carter, Melissa D.; Fang, Mengxuan; Johnson, Rudolph C.; Reid, Gavin E.

2018-05-01

Microcystin (MC) peptides produced by cyanobacteria pose a hepatotoxic threat to human health upon ingestion from contaminated drinking water. While rapid MC identification and quantification in contaminated body fluids or tissue samples is important for patient treatment and outcomes, conventional immunoassay-based measurement strategies typically lack the specificity required for unambiguous determination of specific MC variants, whose toxicity can significantly vary depending on their structures. Furthermore, the unambiguous identification and accurate quantitation of MC variants using tandem mass spectrometry (MS/MS)-based methods can be limited due to a current lack of appropriate stable isotope-labeled internal standards. To address these limitations, we have systematically examined here the sequence and charge state dependence to the formation and absolute abundance of both "global" and "variant-specific" product ions from representative MC-LR, MC-YR, MC-RR, and MC-LA peptides, using higher-energy collisional dissociation (HCD)-MS/MS, ion-trap collision-induced dissociation (CID)-MS/MS and CID-MS3, and 193 nm ultraviolet photodissociation (UPVD)-MS/MS. HCD-MS/MS was found to provide the greatest detection sensitivity for both global and variant-specific product ions in each of the MC variants, except for MC-YR where a variant-specific product uniquely formed via UPVD-MS/MS was observed with the greatest absolute abundance. A simple methodology for the preparation and characterization of 18O-stable isotope-labeled MC reference materials for use as internal standards was also developed. Finally, we have demonstrated the applicability of the methods developed herein for absolute quantification of MC-LR present in human urine samples, using capillary scale liquid chromatography coupled with ultra-high resolution / accurate mass spectrometry and HCD-MS/MS.

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

Performance Characteristics of 1977 Ford 300 CID Engine

DOT National Transportation Integrated Search

1980-02-01

Experimental data were obtained in dynamometer tests of a 1977 Ford 300 CID engine to determine fuel consumption and emissions (hydrocarbons, carbon monoxide, and oxides of Nitrogen) at steady-state engine operating modes. The objective of the test w...

Performance Characteristics of 1977 Chrysler 318 CID Engine

DOT National Transportation Integrated Search

1980-02-01

Experimental data were obtained in dynamometer tests of a 1977 Chrysler 318 CID engine to determine fuel consumption and emissions (hydrocarbons, carbon monoxide, and oxides of nitrogen) at steady-state engine operating modes. The objective of the te...

Mass spectral analysis of N-oxides of Chemical Weapons Convention related aminoethanols under electrospray ionization conditions.

PubMed

Sridhar, L; Karthikraj, R; Murty, M R V S; Raju, N Prasada; Vairamani, M; Prabhakar, S

2011-02-28

N,N'-Dialkylaminoethanols are the hydrolyzed products or precursors of chemical warfare agents such as V-agents and nitrogen mustards, and they are prone to undergo oxidation in environmental matrices or during decontamination processes. Consequently, screening of the oxidized products of aminoethanols in aqueous samples is an important task in the verification of chemical weapons convention-related chemicals. Here we report the successful characterization of the N-oxides of N,N'-dialkylaminoethanols, alkyl diethanolamines, and triethanolamine using positive ion electrospray ionization mass spectrometry. The collision-induced dissociation (CID) spectra of the [M+H](+) and [M+Na](+) ions show diagnostic product ions that enable the unambiguous identification of the studied N-oxides, including those of isomeric compounds. The proposed fragmentation pathways are supported by high-resolution mass spectrometry data and product/precursor ion spectra. The CID spectra of [M+H](+) ions included [MH-CH(4)O(2)](+) as the key product ion, in addition to a distinctive alkene loss that allowed us to recognize the alkyl group attached to the nitrogen. The [M+Na](+) ions show characteristic product ions due to the loss of groups (R) attached to nitrogen either as a radical (R) or as a molecule [R+H or (R-H)] after hydrogen migration. Copyright © 2011 John Wiley & Sons, Ltd.

A general analytical strategy for the characterization of phenolic compounds in fruit juices by high-performance liquid chromatography with diode array detection coupled to electrospray ionization and triple quadrupole mass spectrometry.

PubMed

Abad-García, Beatriz; Berrueta, Luis A; Garmón-Lobato, Sergio; Gallo, Blanca; Vicente, Francisca

2009-07-10

In the present study, a methodology based on liquid chromatography with diode array detection (HPLC/DAD) coupled to an electrospray ionization (ESI) interface and a triple quadrupole mass spectrometer for the simultaneous identification of phenolic compounds in fruit juices has been developed. 72 available phenolic compound standards from diverse families present in fruits have been studied in order to analyze their fragmentation pattern. As a result, a general strategy for the characterization of unknown phenolic compounds in fruit juices was designed: (i) taking into account its UV-visible spectrum and elution order, assign the unknown polyphenol to a polyphenol class, (ii) identify the quasi-molecular ion using positive and negative MS spectra, being supported by adducts generated with solvent or sodium and molecular complexes, (iii) determinate the pattern of glycosylation in positive mode using ESI(+)-CID MS/MS product ion scan experiments, selecting the quasi-molecular ion as precursor ion, and finally, (iv) study the identity of the aglycone through ESI(+)-CID MS/MS product ion spectra from the protonated aglycone, [Y(0)](+). This strategy was successfully employed for the characterization of known and unknown phenolic compounds in juices from 17 different fruits.

A chemical and computational approach to comprehensive glycation characterization on antibodies

PubMed Central

Saleem, Ramsey A; Affholter, Brittany R; Deng, Sihong; Campbell, Phil C; Matthies, Kelli; Eakin, Catherine M; Wallace, Alison

2015-01-01

Non-enzymatic glycation is a challenging post-translational modification to characterize due to the structural heterogeneity it generates in proteins. Glycation has become increasingly recognized as an important product quality attribute to monitor, particularly for the biotechnology sector, which produces recombinant proteins under conditions that are amenable to protein glycation. The elucidation of sites of glycation can be problematic using conventional collision-induced dissociation (CID)-based mass spectrometry because of the predominance of neutral loss ions. A method to characterize glycation using an IgG1 monoclonal antibody (mAb) as a model is reported here. The sugars present on this mAb were derivatized using sodium borohydride chemistry to stabilize the linkage and identified using CID-based MS2 mass spectrometry and spectral search engines. Quantification of specific glycation sites was then done using a targeted MS1 based approach, which allowed the identification of a glycation hot spot in the heavy chain complementarity-determining region 3 of the mAb. This targeted approach provided a path forward to developing a structural understanding of the propensity of sites to become glycated on mAbs. Through structural analysis we propose a model in which the number and 3-dimensional distances of carboxylic acid amino acyl residues create a favorable environment for glycation to occur. PMID:26030340

Friction Tests of a Chrysler 1978, 225 CID Engine

DOT National Transportation Integrated Search

1980-09-01

This document reports tests on a 1978 Chrysler, 225 CID, six-cylinder engine to determine the losses due to friction and accessories. The tests were conducted at the Automotive Research laboratory of the Transportation Systems Center with the engine ...

Performance Characteristics of 1977 General Motors 350 CID Engine

DOT National Transportation Integrated Search

1980-02-01

Experimental data were obtained in dynamometer tests of a 1977 GM 350 CID engine to determine fuel consumption and emissions (hydrocarbons, carbon monoxide, and oxides of nitrogen) at steady-state engine operating modes. The objective of the test was...

Performance Characteristics of 1977 American Motors 304 CID Engine

DOT National Transportation Integrated Search

1980-02-01

Experimental data were obtained in dynamometer tests of a 1977 AM 304 CID engine to determine fuel consumption and emissions (hydrocarbons, carbon monoxide, and oxides of nitrogen) at steady-state engine operating modes. The objective of the test was...

30 CFR 250.298 - How long will MMS take to evaluate and make a decision on the CID?

Code of Federal Regulations, 2010 CFR

2010-07-01

... THE INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Plans and... CID request based on your commitment to develop economically producible reservoirs according to sound...

After-Test Engine Inspection of U.S. Army Administrative and Light-Tactical Vehicles Operated on Gasohol and Unleaded Gasoline.

DTIC Science & Technology

1983-02-01

Force 76-84 @ 1.82 (338)-(374)@(46.23) Intake 174.0 71 220.3 215-237 @ 1.39 88 85 81 95-105 @ I 13/16" (774) (316) (980) (956)-(1054)@ (391) (378) (360...Mfg. Specs per Veh. Gasohol Gasoline Station Chrysler V-8, 318 CID 07121303 5 16 31 -- Ft. Belvoir 07090311 6 16 38 -- Ft. Belvoir 03223146 5 16...TABLE 6. CRC RATINGS FOR TEST ENGINES FROM FT. BELVOIR, VA Type Engine Chrysler V-8, 318 CID Jeep, 4 Cylinder, 140 CID Serial Number 07121303 07090311

Missed opportunities for earlier diagnosis of HIV in patients who presented with advanced HIV disease: a retrospective cohort study

PubMed Central

Levy, Itzchak; Maor, Yasmin; Mahroum, Naim; Olmer, Liraz; Wieder, Anat; Litchevski, Vladislav; Mor, Orna; Rahav, Galia

2016-01-01

Objective To quantify and characterise missed opportunities for earlier HIV diagnosis in patients diagnosed with advanced HIV. Design A retrospective observational cohort study. Setting A central tertiary medical centre in Israel. Measures The proportion of patients with advanced HIV, the proportion of missed opportunities to diagnose them earlier, and the rate of clinical indicator diseases (CIDs) in those patients. Results Between 2010 and 2015, 356 patients were diagnosed with HIV, 118 (33.4%) were diagnosed late, 57 (16%) with advanced HIV disease. Old age (OR=1.45 (95% CI 1.16 to 1.74)) and being heterosexual (OR=2.65 (95% CI 1.21 to 5.78)) were significant risk factors for being diagnosed late. All patients with advanced disease had at least one CID that did not lead to an HIV test in the 5 years prior to AIDS diagnosis. The median time between CID and AIDS diagnosis was 24 months (IQR 10–30). 60% of CIDs were missed by a general practitioner and 40% by a specialist. Conclusions Missed opportunities to early diagnosis of HIV occur in primary and secondary care. Lack of national guidelines, lack of knowledge regarding CIDs and communication barriers with patients may contribute to a late diagnosis of HIV. PMID:28186940

Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

NASA Astrophysics Data System (ADS)

Viglino, Emilie; Lai, Cheuk Kuen; Mu, Xiaoyan; Chu, Ivan K.; Tureček, František

2016-09-01

We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H]+● and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS3 dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%-94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in CuII(2,2 ':6 ',2 ″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR]+● that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing Cα-radical positions in peptide cation radical intermediates.

Cultural translation of refugee trauma: Cultural idioms of distress among Somali refugees in displacement.

PubMed

Im, Hyojin; Ferguson, Aidan; Hunter, Margaret

2017-01-01

Westernized approaches to mental health care often place limited emphasis on refugees' own experiences and cultural explanations of symptoms and distress. In order to effectively assess community mental health needs and develop interventions grounded in local needs, mental health programs need to be informed by an understanding of cultural features of mental health, including cultural idioms of distress (CIDs). The current study aims to explore CIDs among Somali refugees displaced in Kenya to understand mental health needs in cultural context and serve the community in a culturally responsive and sensitive manner. This research was conducted as a two-phase qualitative study. First, key informant interviews with Somali mental health stakeholders generated a list of 7 common Somali CIDs: buufis, buqsanaan, welwel, murug, qaracan, jinn, and waali. Typologies of each CID were further explored through four focus group interviews with Somali community members. The findings from a template analysis revealed Somali lay beliefs on how trauma and daily stressors are experienced and discussed in the form of CIDs and how each term is utilized and understood in attributing symptoms to associated causes. This study highlights the need to incorporate colloquial terms in mental health assessment and to adopt a culturally relevant framework to encourage wider utilization of services and religious/spiritual support systems.

A brief review of machine vision in the context of automated wood identification systems

Treesearch

John C. Hermanson; Alex C. Wiedenhoeft

2011-01-01

The need for accurate and rapid field identification of wood to combat illegal logging around the world is outpacing the ability to train personnel to perform this task. Despite increased interest in non-anatomical (DNA, spectroscopic, chemical) methods for wood identification, anatomical characteristics are the least labile data that can be extracted from solid wood...

Chronic inflammatory disease and osteopathy: a systematic review.

PubMed

Cicchitti, Luca; Martelli, Marta; Cerritelli, Francesco

2015-01-01

Chronic inflammatory diseases (CID) are globally highly prevalent and characterized by severe pathological medical conditions. Several trials were conducted aiming at measuring the effects of manipulative therapies on patients affected by CID. The purpose of this review was to explore the extent to which osteopathic manipulative treatment (OMT) can be benefi-cial in medical conditions also classified as CID. This review included any type of experimental study which enrolled sub-jects with CID comparing OMT with any type of control procedure. The search was conducted on eight databases in January 2014 using a pragmatic literature search approach. Two independent re-viewers conducted study selection and data extraction for each study. The risk of bias was evaluated according to the Cochrane methods. Heterogeneity was assessed and meta-analysis performed where possible. 10 studies met the inclusion criteria for this review enrolling 386 subjects. The search identified six RCTs, one laboratory study, one cross-over pilot studies, one observation-al study and one case control pilot study. Results suggest a potential effect of osteopathic medicine on patients with medical pathologies associated with CID (in particular Chronic Obstructive Pul-monary Disease (COPD), Irritable Bowel Syndrome, Asthma and Peripheral Arterial Disease) com-pared to no treatment or sham therapy although data remain elusive. Moreover one study showed possible effects on arthritis rat model. Meta-analysis was performed for COPD studies only show-ing no effect of any type of OMT applied versus control. No major side effects were reported by those receiving OMT. The present systematic review showed inconsistent data on the effect of OMT in the treatment of medical conditions potentially associated with CID, however the OMT appears to be a safe approach. Further more robust trials are needed to determine the direction and magnitude of the effect of OMT and to generalize favorable results.

Lipid prodrug nanocarriers in cancer therapy.

PubMed

Mura, Simona; Bui, Duc Trung; Couvreur, Patrick; Nicolas, Julien

2015-06-28

Application of nanotechnology in the medical field (i.e., nanomedicine) plays an important role in the development of novel drug delivery methods. Nanoscale drug delivery systems can indeed be customized with specific functionalities in order to improve the efficacy of the treatments. However, despite the progresses of the last decades, nanomedicines still face important obstacles related to: (i) the physico-chemical properties of the drug moieties which may reduce the total amount of loaded drug; (ii) the rapid and uncontrolled release (i.e., burst release) of the encapsulated drug after administration and (iii) the instability of the drug in biological media where a fast transformation into inactive metabolites can occur. As an alternative strategy to alleviate these drawbacks, the prodrug approach has found wide application. The covalent modification of a drug molecule into an inactive precursor from which the drug will be freed after administration offers several benefits such as: (i) a sustained drug release (mediated by chemical or enzymatic hydrolysis of the linkage between the drug-moiety and its promoiety); (ii) an increase of the drug chemical stability and solubility and, (iii) a reduced toxicity before the metabolization occurs. Lipids have been widely used as building blocks for the design of various prodrugs. Interestingly enough, these lipid-derivatized drugs can be delivered through a nanoparticulate form due to their ability to self-assemble and/or to be incorporated into lipid/polymer matrices. Among the several prodrugs developed so far, this review will focus on the main achievements in the field of lipid-based prodrug nanocarriers designed to improve the efficacy of anticancer drugs. Gemcitabine (Pubchem CID: 60750); 5-fluorouracil (Pubchem CID: 3385); Doxorubicin (Pubchem CID: 31703); Docetaxel (Pubchem CID: 148124); Methotrexate (Pubchem CID: 126941); Paclitaxel (Pubchem CID: 36314). Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative collision induced mass spectrometry of substituted piperazines - A correlative analysis between theory and experiment

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2017-12-01

The present paper deals with quantitative kinetics and thermodynamics of collision induced dissociation (CID) reactions of piperazines under different experimental conditions together with a systematic description of effect of counter-ions on common MS fragment reactions of piperazines; and intra-molecular effect of quaternary cyclization of substituted piperazines yielding to quaternary salts. There are discussed quantitative model equations of rate constants as well as free Gibbs energies of series of m-independent CID fragment processes in GP, which have been evidenced experimentally. Both kinetic and thermodynamic parameters are also predicted by computational density functional theory (DFT) and ab initio both static and dynamic methods. The paper examines validity of Maxwell-Boltzmann distribution to non-Boltzmann CID processes in quantitatively as well. The experiments conducted within the latter framework yield to an excellent correspondence with theoretical quantum chemical modeling. The important property of presented model equations of reaction kinetics is the applicability in predicting unknown and assigning of known mass spectrometric (MS) patterns. The nature of "GP" continuum of CID-MS coupled scheme of measurements with electrospray ionization (ESI) source is discussed, performing parallel computations in gas-phase (GP) and polar continuum at different temperatures and ionic strengths. The effect of pressure is presented. The study contributes significantly to methodological and phenomenological developments of CID-MS and its analytical implementations for quantitative and structural analyses. It also demonstrates great prospective of a complementary application of experimental CID-MS and computational quantum chemistry studying chemical reactivity, among others. To a considerable extend this work underlies the place of computational quantum chemistry to the field of experimental analytical chemistry in particular highlighting the structural analysis.

Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction.

PubMed

Le, Hoang-Quynh; Tran, Mai-Vu; Dang, Thanh Hai; Ha, Quang-Thuy; Collier, Nigel

2016-07-01

The BioCreative V chemical-disease relation (CDR) track was proposed to accelerate the progress of text mining in facilitating integrative understanding of chemicals, diseases and their relations. In this article, we describe an extension of our system (namely UET-CAM) that participated in the BioCreative V CDR. The original UET-CAM system's performance was ranked fourth among 18 participating systems by the BioCreative CDR track committee. In the Disease Named Entity Recognition and Normalization (DNER) phase, our system employed joint inference (decoding) with a perceptron-based named entity recognizer (NER) and a back-off model with Semantic Supervised Indexing and Skip-gram for named entity normalization. In the chemical-induced disease (CID) relation extraction phase, we proposed a pipeline that includes a coreference resolution module and a Support Vector Machine relation extraction model. The former module utilized a multi-pass sieve to extend entity recall. In this article, the UET-CAM system was improved by adding a 'silver' CID corpus to train the prediction model. This silver standard corpus of more than 50 thousand sentences was automatically built based on the Comparative Toxicogenomics Database (CTD) database. We evaluated our method on the CDR test set. Results showed that our system could reach the state of the art performance with F1 of 82.44 for the DNER task and 58.90 for the CID task. Analysis demonstrated substantial benefits of both the multi-pass sieve coreference resolution method (F1 + 4.13%) and the silver CID corpus (F1 +7.3%).Database URL: SilverCID-The silver-standard corpus for CID relation extraction is freely online available at: https://zenodo.org/record/34530 (doi:10.5281/zenodo.34530). © The Author(s) 2016. Published by Oxford University Press.

Multifaceted metabolomics approaches for characterization of lignocellulosic biomass degradation products formed during ammonia fiber expansion pretreatment

NASA Astrophysics Data System (ADS)

Vismeh, Ramin

Lignocellulosic biomass represents a rather unused resource for production of biofuels, and it offers an alternative to food sources including corn starch. However, structural and compositional impediments limit the digestibility of sugar polymers in biomass cell walls. Thermochemical pretreatments improve accessibility of cellulose and hemicellulose to hydrolytic enzymes. However, most pretreatment methods generate compounds that either inhibit enzymatic hydrolysis or exhibit toxicity to fermentive microorganisms. Characterization and quantification of these products are essential for understanding chemistry of the pretreatment and optimizing the process efficiency to achieve higher ethanol yields. Identification of oligosaccharides released during pretreatment is also critical for choosing hydrolases necessary for cost-effective hydrolysis of cellulose and hemicellulose to fermentable monomeric sugars. Two chapters in this dissertation describe new mass spectrometry-based strategies for characterization and quantification of products that are formed during ammonia fiber expansion (AFEX) pretreatment of corn stover. Comparison of Liquid Chromatography Mass Spectrometry (LC/MS) profiles of AFEX-treated corn stover (AFEXTCS) and untreated corn stover (UTCS) extract shows that ammonolysis of lignin carbohydrate ester linkages generates a suite of nitrogenous compounds that are present only in the AFEXTCS extract and represent a loss of ammonia during processing. Several of these products including acetamide, feruloyl, coumaroyl and diferuloyl amides were characterized and quantified in the AFEXTCS extracts. The total amount of characterized and uncharacterized phenolic amides measured 17.4 mg/g AFEXTCS. Maillard reaction products including pyrazines and imidazoles were also identified and measured in the AFEXTCS extract totaling almost 1 mg/g AFEXTCS. The total of quantified nitrogenous products that are formed during AFEX was 43.4 mg/g AFEXTCS which was equivalent to 45-50 % of ammonia that is lost during the pretreatment. Methodology for identification, detection and quantification of various diferulate cross-linkers in forms of Di-Acids (Di-Ac), Acid-Amide (Ac-Am), and Di-Amides (Di-Am) in AFEX and NaOH treated corn stover using ultrahigh performance liquid chromatography/tandem mass spectrometry (LC/MS/MS) is presented. Characterization of isomeric diferulates was based on the distinguishing fragments formed upon collision induced dissociation (CID) of [M+H]+ ions of each diferulate isomer. LC separations combined with quasi-simultaneous acquisition of mass spectra at multiple collision energies provide fast spectrum acquisition using a time-of-flight (TOF) mass analyzer. This approach, called mux-CID, generates molecular and fragment ion mass information at different collision energies for molecular and adduct ions of oligosaccharides in a single analysis. Non-selective CID facilitated characterization of glucans and arabinoxylans in the AFEXTCS extracts. A LC/MS gradient based on multiplexed-CID detection was developed and applied to profile oligosaccharides in AFEXTCS extract. This method detected glucans with degree of polymerization (DP) from 2 to 22 after solid phase extraction (SPE) enrichment using porous graphitized carbon (PGC), which proved essential for recoveries of specific oligosaccharides. Arabinoxylans were also detected and partially characterized using this strategy after hydrolysis using xylanase. A relative quantification based on peak areas showed removal of almost 85% of the acetate esters of arabinoxylans after AFEX.

Baseline Fuel Economy and Emissions Tests of a Chrysler 1978, 225 CID Engine

DOT National Transportation Integrated Search

1980-09-01

This document reports on baseline engine tests of a Chrysler 1978, 225 CID, six-cylinder engine. The tests were conducted in the Automotive Research Laboratory at the Transportation Systems Center. Test results presented herein are also filed on comp...

Career Information Delivery Systems: A Summary Status Report. NOICC Occasional Paper.

ERIC Educational Resources Information Center

Hopkins, Valorie; Kinnison, Joyce; Morgenthau, Eleanor; Ollis, Harvey

The National Occupational Information Coordinating Committee/State Occupational Information Coordinating Committees (NOICC/SOICC) Network sponsors numerous occupational information programs and systems, including career information delivery systems (CIDS). CIDS provide useful national, state, and local information for people who are exploring,…

MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation.

PubMed

Degroeve, Sven; Maddelein, Davy; Martens, Lennart

2015-07-01

We present an MS(2) peak intensity prediction server that computes MS(2) charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published MS(2)PIP model for Orbitrap-LTQ CID spectra. Predicted MS(2) spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations. In addition, we added prediction models for HCD fragmentation (Q-Exactive Orbitrap) and show that these models compute accurate intensity predictions on par with CID performance. We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method. The MS(2)PIP prediction server is accessible from http://iomics.ugent.be/ms2pip. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mass spectrometry detection and imaging of inorganic and organic explosive device signatures using desorption electro-flow focusing ionization.

PubMed

Forbes, Thomas P; Sisco, Edward

2014-08-05

We demonstrate the coupling of desorption electro-flow focusing ionization (DEFFI) with in-source collision induced dissociation (CID) for the mass spectrometric (MS) detection and imaging of explosive device components, including both inorganic and organic explosives and energetic materials. We utilize in-source CID to enhance ion collisions with atmospheric gas, thereby reducing adducts and minimizing organic contaminants. Optimization of the MS signal response as a function of in-source CID potential demonstrated contrasting trends for the detection of inorganic and organic explosive device components. DEFFI-MS and in-source CID enabled isotopic and molecular speciation of inorganic components, providing further physicochemical information. The developed system facilitated the direct detection and chemical mapping of trace analytes collected with Nomex swabs and spatially resolved distributions within artificial fingerprints from forensic lift tape. The results presented here provide the forensic and security sectors a powerful tool for the detection, chemical imaging, and inorganic speciation of explosives device signatures.

Psychosocial Adaptation to Disability Within the Context of Positive Psychology: Findings from the Literature.

PubMed

Martz, Erin; Livneh, Hanoch

2016-03-01

This purpose of this article is to review of the trends of research that examined positive psychology constructs in the context of adapting to chronic illness and disability (CID). This article examines the empirical findings on the relationships between six selected positive psychology-associated constructs (optimism, hope, resilience, benefit-finding, meaning-making, and post-traumatic growth) and adaptation to disability. Six positive psychology constructs were selected to represent the trends found in recent literature published on CID. The process of choosing these six variables included reviewing chapters on positive psychology and CID, reviewing the top rehabilitation journals that typically publish articles on psychosocial adaptation to CID, using search engines to find relevant journal articles published since the year 2000, and selecting the most important constructs based on the authors’ professional judgment. The available evidence supports the unique benefits of these six positive psychology constructs in predicting successful adaptation to a range of disabling conditions. Based on the available findings, the authors offer four suggestions for occupational rehabilitation researchers.

Functional implications from the Cid1 poly(U) polymerase crystal structure.

PubMed

Munoz-Tello, Paola; Gabus, Caroline; Thore, Stéphane

2012-06-06

In eukaryotes, mRNA degradation begins with poly(A) tail removal, followed by decapping, and the mRNA body is degraded by exonucleases. In recent years, the major influence of 3'-end uridylation as a regulatory step within several RNA degradation pathways has generated significant attention toward the responsible enzymes, which are called poly(U) polymerases (PUPs). We determined the atomic structure of the Cid1 protein, the founding member of the PUP family, in its UTP-bound form, allowing unambiguous positioning of the UTP molecule. Our data also suggest that the RNA substrate accommodation and product translocation by the Cid1 protein rely on local and global movements of the enzyme. Supplemented by point mutations, the atomic model is used to propose a catalytic cycle. Our study underlines the Cid1 RNA binding properties, a feature with critical implications for miRNAs, histone mRNAs, and, more generally, cellular RNA degradation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Axial spatial distribution focusing: improving MALDI-TOF/RTOF mass spectrometric performance for high-energy collision-induced dissociation of biomolecules.

PubMed

Belgacem, O; Pittenauer, E; Openshaw, M E; Hart, P J; Bowdler, A; Allmaier, G

2016-02-15

For the last two decades, curved field reflectron technology has been used in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometers, assisting in the generation of post-source-decay (PSD) or collision-induced dissociation (CID) without decelerating precursor ions, producing true high-energy CID spectra. The result was the generation of product ion mass spectra with product ions typical of high-energy (10 keV and beyond) collision processes. The disadvantage of this approach was the lack of resolution in CID spectra resulting from the excess laser energy deposition used to generate those MS/MS spectra. The work presented in this study overcomes this limitation and includes comprehensive examples of high-energy and high-resolution CID MALDI-MS/MS spectra of biomolecules. The devices used in this study are TOF/RTOF instruments equipped with a high-vacuum MALDI ion source. High-resolution and high-energy CID spectra result from the use of axial spatial distribution focusing (ASDF) in combination with curved field reflectron technology. A CID spectrum of the P14 R1 peptide exhibits product ion resolution in excess of 10,000 (FWHM) but at the same time yields typical high-energy product ions such as w- and [y-2]-type ion series. High-energy CID spectra of lipids, exemplified by a glycerophospholipid and triglyceride, demonstrate C-C backbone fragmentation elucidating the presence of a hydroxyl group in addition to double-bond positioning. A complex high mannose carbohydrate (Man)8 (GlcNAc)2 was also studied at 20 keV collision energy and revealed further high-energy product ions with very high resolution, allowing unambiguous detection and characterization of cross-ring cleavage-related ions. This is the first comprehensive study using a MALDI-TOF/RTOF instrument equipped with a curved field reflectron and an ASDF device prior to the reflectron. © 2015 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd. © 2015 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.

Prognosis and survival analysis of paraquat poisoned patients based on improved HPLC-UV method.

PubMed

Hong, Guangliang; Hu, Lufeng; Tang, Yahui; Zhang, Tao; Kang, Xiaowen; Zhao, Guangju; Lu, Zhongqiu

2016-01-01

Paraquat (PQ) has caused deaths of numerous people around the world. In order to assess the lethal plasma concentration, the patients who acquired acute PQ intoxication were analyzed by plasma concentration monitoring. The plasma PQ concentrations were determined by high performance liquid chromatography (HPLC) which used 5-bromopyrimidine as internal standard and trichloroacetic acid-methanol (1:9) as protein precipitant. The liver, kidney and coagulation function were determined by automatic biochemical analyzer. According to plasma PQ concentration, 90 patients were divided into four groups: trace PQ group (<50ng/mL), low PQ group (<1000ng/mL), medium PQ group (1000-5000ng/mL) and high PQ group (>5000ng/mL). The clinical data from the four groups was statistically analyzed. The results showed the developed HPLC methods exhibited a high degree of accuracy and good linearity within 50-25000ng/mL (R=0.9998). The Spearman's correlation analysis showed PQ concentration had a strong relationship to total bilirubin, direct bilirubin, aspartic transaminase, urea nitrogen, prothrombin time, prothrombin activity, and international normalized ratio (P<0.01). The cured or survival PQ poisoned patients among the trace PQ group, the low PQ group, the medium PQ group, and the high PQ group were 19/19 (100%), 19/21 (90.47%), 11/25 (44.0%), and 0/25 (0%) respectively. The mean hospital days were (10.37±8.04), (18.76±12.06), (16.76±14.44), and (4.04±5.41) days respectively. The Cox regression analysis indicated that plasma PQ concentration was highly related to prognosis (P<0.05). In conclusion, no patient presenting with a PQ concentration over 5000ng/mL survived. The plasma PQ level is related to liver, kidney and coagulation function, which can be used as an important clinical index to judge the prognosis of PQ poisoned patients. Paraquat (PubChem CID: 15938), 5-bromopyrimidine (PubChem CID: 78344), acetonitrile (PubChem CID: 6342), sodium dihydrogen phosphate (PubChem CID: 23672064), sodium heptanesulfonate (PubChem CID: 23672332), methylprednisolone (PubChem CID: 6741), cyclophosphamide (PubChem CID: 2907). Copyright © 2016. Published by Elsevier Inc.

Type-II InAs/GaSb (InAsSb) superlattices for interband cascade midwavelength detectors

NASA Astrophysics Data System (ADS)

Hackiewicz, Klaudia; Martyniuk, Piotr

2018-02-01

Type-II superlattice (T2SL) interband cascade infrared detectors (IB CIDs) proved to be a promising candidate for short response time devices operating in room and higher temperatures. The current status of the higher operating temperature (HOT) T2SLs InAs/GaSb and InAs/InAsSb IB CID is presented. We compare both materials with HgCdTe alloy, which is widely described in literature. The detectivity of midwave infrared (MWIR) T2SLs InAs/GaSb and InAs/InAsSb based IB CID has been demonstrated up to 380 K.

41 CFR 101-29.208 - Commercial item description (CID).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 2 2010-07-01 2010-07-01 true Commercial item... PRODUCT DESCRIPTIONS 29.2-Definitions § 101-29.208 Commercial item description (CID). A commercial item... characteristics of available, acceptable commercial products that will satisfy the Government's needs. These...

Improved close-in detection for the mine hunter/killer system

NASA Astrophysics Data System (ADS)

Bishop, Steven S.; Campana, Stephen B.; Duston, Brian M.; Lang, David A.; Wiggins, Carl M.

2001-10-01

The Close-In Detector (CID) is the vehicle-mounted multi-sensor anti-tank landmine detection technology for the Army CECOM Night Vision Electronic Sensors Directorate (NVESD) Mine Hunter-Killer (MH/K) Program. The CID includes two down-looking sensor arrays: a 20-antenna ground-penetrating radar (GPR) and a 16-coil metal detector (MD). These arrays span 3-meters in front of a high mobility, multipurpose wheeled vehicle (HMMWV). The CID also includes a roof-mounted, forward looking infrared (FLIR) camera that images a trapezoidal area of the road ahead of the vehicle. Signals from each of the three sensors are processed separately to detect and localize objects of interest. Features of candidate objects are integrated in a processor that uses them to discriminates between anti-tank (AT) mines and clutter and produces a list of suspected mine locations which are passed to the neutralization subsystem of MH/K. This paper reviews the current design and performance of the CID based on field test results on dirt and gravel mine test lanes. Improvements in CID performance for probability of detection, false alarm rate, target positional accuracy and system rate of advance over the past year and a half that meet most of the program goals are described. Sensor performances are compared, and the effectiveness of six different sensor fusion approaches are measured and compared.

GPS detection of ionospheric Rayleigh wave and its source following the 2012 Haida Gwaii earthquake

NASA Astrophysics Data System (ADS)

Jin, Shuanggen; Jin, Rui; Li, D.

2017-01-01

The processes and sources of seismo-ionospheric disturbances are still not clear. In this paper, coseismic ionospheric disturbances (CIDs) are investigated by dual-frequency GPS observations following the Mw = 7.8 earthquake as results of the oblique-thrust fault in the Haida Gwaii region, Canada, on 28 October 2012. Results show that the CIDs with an amplitude of up to 0.15 total electron content units (TECU) are found with spreading out at 2.20 km/s, which agree well with the Rayleigh wave propagation speed at 2.22 km/s detected by the bottom pressure records at about 10 min after the onset. The CIDs are a result of the upward propagation acoustic waves trigged by the Rayleigh wave in sequence from near field to far field. The strong correlation is found between the CIDs and the vertical ground motion recorded by seismometers nearby the epicenter. The total electron content (TEC) series from lower-elevation angle GPS observations have higher perturbation amplitudes. Furthermore, the simulated ionospheric disturbance following a vertical Gauss pulse on the ground based on the finite difference time domain method confirms the ionospheric Rayleigh wave signature in the near field and the vertical ground motion dependence theoretically. The vertical ground motion is the dominant source of the ionospheric Rayleigh wave and affects the CID waveform directly.

Numerical simulations of compact intracloud discharges as the Relativistic Runaway Electron Avalanche-Extensive Air Shower process

NASA Astrophysics Data System (ADS)

Arabshahi, S.; Dwyer, J. R.; Nag, A.; Rakov, V. A.; Rassoul, H. K.

2014-01-01

Compact intracloud discharges (CIDs) are sources of the powerful, often isolated radio pulses emitted by thunderstorms. The VLF-LF radio pulses are called narrow bipolar pulses (NBPs). It is still not clear how CIDs are produced, but two categories of theoretical models that have previously been considered are the Transmission Line (TL) model and the Relativistic Runaway Electron Avalanche-Extensive Air Showers (RREA-EAS) model. In this paper, we perform numerical calculations of RREA-EASs for various electric field configurations inside thunderstorms. The results of these calculations are compared to results from the other models and to the experimental data. Our analysis shows that different theoretical models predict different fundamental characteristics for CIDs. Therefore, many previously published properties of CIDs are highly model dependent. This is because of the fact that measurements of the radiation field usually provide information about the current moment of the source, and different physical models with different discharge currents could have the same current moment. We have also found that although the RREA-EAS model could explain the current moments of CIDs, the required electric fields in the thundercloud are rather large and may not be realistic. Furthermore, the production of NBPs from RREA-EAS requires very energetic primary cosmic ray particles, not observed in nature. If such ultrahigh-energy particles were responsible for NBPs, then they should be far less frequent than is actually observed.

Reflections on Doctoral Education in Chemistry. Carnegie Essays on the Doctorate: Chemistry.

ERIC Educational Resources Information Center

Kwiram, Alvin L.

The Carnegie Foundation commissioned a collection of essays as part of the Carnegie Initiative on the Doctorate (CID). Essays and essayists represent six disciplines that are part of the CID: chemistry, education, English, history, mathematics, and neuroscience. Intended to engender conversation about the conceptual foundation of doctoral…

The Ph.D. in Education. Carnegie Essays on the Doctorate: Education.

ERIC Educational Resources Information Center

Richardson, Virginia

The Carnegie Foundation commissioned a collection of essays as part of the Carnegie Initiative on the Doctorate (CID). Essays and essayists represent six disciplines that are part of the CID: chemistry, education, English, history, mathematics, and neuroscience. Intended to engender conversation about the conceptual foundation of doctoral…

The Doctorate in Chemistry. Carnegie Essays on the Doctorate: Chemistry.

ERIC Educational Resources Information Center

Breslow, Ronald

The Carnegie Foundation commissioned a collection of essays as part of the Carnegie Initiative on the Doctorate (CID). Essays and essayists represent six disciplines that are part of the CID: chemistry, education, English, history, mathematics, and neuroscience. Intended to engender conversation about the conceptual foundation of doctoral…

Performance Characteristics of Automotive Engines in the United States : Report No. 10. Chevrolet (1975) 250 CID 1-BBL Engine.

DOT National Transportation Integrated Search

1977-08-01

Experimental data were obtained in dynamometer tests of a 1975 Chevrolet 250-CID, 1-bbl engine to determine fuel consumption and emissions (hydrocarbons, carbon monoxide, and oxides of nitrogen) at steady-state engine operating modes. The objective o...

Performance Characteristics of Automotive Engines in the United States : Report No. 9. Chrysler (1975) 225-CID 1-BBL Engine.

DOT National Transportation Integrated Search

1977-08-01

Experimental data were obtained in dynamometer tests of a 1975 Chrysler 225-CID, 1-bbl engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, and oxides of nitrogen) at steady-state engine operating modes. The objective of ...

IDENTIFYING COMPOUNDS USING SOURCE CID ON AN ORTHOGONAL ACCELERATION TIME-OF-FLIGHT MASS SPECTROMETER

EPA Science Inventory

Exact mass libraries of ESI and APCI mass spectra are not commercially available In-house libraries are dependent on CID parameters and are instrument specific. The ability to identify compounds without reliance on mass spectral libraries is therefore more crucial for liquid sam...

30 CFR 250.297 - What information must a CID contain?

Code of Federal Regulations, 2010 CFR

2010-07-01

... GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Plans and Information Conservation... drilled before your CID submittal, that define the extent of the reservoirs. You must notify MMS of any... provided for each hydrocarbon-bearing reservoir that is penetrated by a well that would meet the...

Performance Characteristics of Automotive Engines in the United States : Third Series - Report No. 14 - 1978 Buick 196 CID (3.2L)

DOT National Transportation Integrated Search

1981-02-01

Experimental data were obtained in dynamometer tests of a 1978 Buick 231 CID turbocharged to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the prog...

Performance Characteristics of Automotive Engines in the United States : Third Series - Report No. 13 - 1977 Chrysler 318 CID (5.2L)

DOT National Transportation Integrated Search

1981-06-01

Experimental data were obtained in dynamometer tests of a 1977 Chrysler 318 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program...

Performance Characteristics of Automotive Engines in the United States, Third Series - Report No. 10, 1978 Honda, 98 CID (1.6 Liters)

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 Honda 98 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program is ...

Performance Characteristics of Automotive Engines in the United States : Second Series - Report No. 4 - 1976 Chevrolet 85 CID (1.4 Liters), IV.

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1976 Chevrolet 85 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the program...

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 20 - 1975 Chevrolet 350 CID (5.7 Liters) ...

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1975 Chevrolet 350 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the progra...

Performance Characteristics of Automotive Engines in the United States : Report No. 11. Chrysler (1975) 318-CID 2-BBL Engine.

DOT National Transportation Integrated Search

1977-08-01

Experimental data were obtained in dynamometer tests of a 1975 Chrysler 318-CID, 2-bbl engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, and oxides of nitrogen) at steady-state engine operating modes. The objective of ...

Comparison of Specialty Medication Use for Common Chronic Inflammatory Diseases Among Health Exchange and Other Commercially Insured Members.

PubMed

Chen, Xiaoxue; Gautam, Santosh; Ruggieri, Alexander; Richards, Thomas; Devries, Andrea; Sylwestrzak, Gosia

2018-01-01

The Affordable Care Act of 2010 allows the purchase of health insurance through special marketplaces called "health exchanges." The majority of individuals enrolling in the exchanges were previously uninsured, older, and sicker than other commercially insured members. Early evidence also suggests that exchange plan members use more costly specialty drugs compared with other commercially insured members. To (a) examine patient characteristics and specialty drug use for common chronic inflammatory diseases (CIDs) among exchange plan members compared with other commercially insured members and (b) explore variations in specialty drug use within exchange plans by metal tiers (bronze, silver, gold, and platinum), as well as across local markets. This analysis included adults aged ≥ 18 years who were enrolled in exchange plans (exchange population) and other commercial health plans (nonexchange population). The primary outcome was the likelihood of using specialty drugs prescribed to treat common CIDs, such as rheumatoid arthritis, ankylosing spondylitis, Crohn's disease, ulcerative colitis, psoriatic arthritis, and psoriasis. The adjusted likelihood of using CID specialty drugs was calculated from logistic regression controlling for prevalence of CIDs and other health risk factors. A total of 931,384 exchange plan members and 2,682,855 nonexchange plan members were included in the analysis. Compared with the nonexchange population, the exchange population was older, more likely to be female, had more comorbid conditions, but filled fewer prescriptions. The 2 groups were similar in terms of CID prevalence. The observed likelihood of CID specialty drug use was 20.0% lower in the exchange versus the nonexchange populations (341 users per 100,000 exchange members vs. 427 users per 100,000 nonexchange members; P < 0.001). Within the exchange population, the observed likelihood of CID specialty drug use was 132 per 100,000 bronze plan members (69.1% lower than nonexchange); 326 per 100,000 silver plan members (23.5% lower than nonexchange); 579 per 100,000 gold plan members (35.6% higher than nonexchange); and 672 per 100,000 platinum plan members (57.5% higher than nonexchange). All differences were statistically significant at P < 0.001. There were also large differences by local market, ranging from 49.1% lower to 75.8% higher CID use in the exchange population than in the nonexchange population. After adjustment, the exchange population was 16.6% less likely to use CID specialty drugs than the nonexchange population (P < 0.001). Large variation in specialty drug use within the exchange plan metal tiers was reduced. After adjustment, the higher use of CID specialty drugs among the exchange population in certain local plans was no longer statistically significant. Members insured through exchange plans were older and sicker than those with nonexchange plans, but they did not use more CID specialty drugs compared with the nonexchange population. Large variations were seen among the exchange plan metal tiers and by local markets, which were often related to the risk profiles of exchange plan enrollees. Funding for this study was provided by Anthem. Anthem had no role in study design, data interpretation, manuscript development, or the decision to publish. Chen, Gautam, DeVries, and Sylwestrzak are employees of HealthCore, a wholly owned subsidiary of Anthem. Richards is an employee of Anthem. Ruggieri is a former employee of Anthem and a current employee of MedImpact Healthcare Systems. Study concept and design were contributed by Ruggieri, Richards, DeVries, and Sylwestrzak. Chen took the lead in data collection, along with Gautam. Data interpretation was performed by Chen, along with the other authors. The manuscript was written by Chen, Gautam, Sylwestrzak, and DeVries and revised by Chen, Gautam, and Sylwestrzak, along with the other authors.

Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

DOE PAGES

Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

2013-03-07

In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

Training and Human Factors Research in Military Systems. A Final Report

DTIC Science & Technology

1989-05-01

Combat vehicle Human factors/ identification (CVI), Operational test and evaluatio (Continued) 19. ABSTRACT (Continue on reverse if necessaty and...prepared on the management of CVI for service schools (1985). * A videotape entitled "Training for Combat" was prepared as an update for the CVI and TAATS...media, and the effects of image motion on CVI training performance. Future Developments The ART -Fort Hood TAATS program was terminated in 1987, and

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 12 - 1975 Perkins Diesel 247 CID (4.0 Liters)

DOT National Transportation Integrated Search

1978-04-01

Experimental data were obtained in dynamometer tests of a 1975 Perkins 247-CID diesel engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the p...

Performance Characteristics of Automotive Engines in the United States : Third Series - Report No. 11 - 1978 Oldsmobile Diesel, 350 CID (5.7 Liters)

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 Oldsmobile Diesel, 350 CID (5.7 Liters) engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The o...

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 14 - 1975 Mazda Rotary 70 CID (1.1 Liters), 4V

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1975 Mazda 70 CID, 4V rotary engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the ...

The Carnegie Initiative on the Doctorate: The Case of Mathematics. Carnegie Essays on the Doctorate: Mathematics.

ERIC Educational Resources Information Center

Bass, Hyman

The Carnegie Foundation commissioned a collection of essays as part of the Carnegie Initiative on the Doctorate (CID). Essays and essayists represent six disciplines that are part of the CID: chemistry, education, English, history, mathematics, and neuroscience. Intended to engender conversation about the conceptual foundation of doctoral…

The Mathematics Doctorate: A Time for Change? Carnegie Essays on the Doctorate: Mathematics.

ERIC Educational Resources Information Center

Chan, Tony F.

The Carnegie Foundation commissioned a collection of essays as part of the Carnegie Initiative on the Doctorate (CID). Essays and essayists represent six disciplines that are part of the CID: chemistry, education, English, history, mathematics, and neuroscience. Intended to engender conversation about the conceptual foundation of doctoral…

Words and Responsibilities: Graduate Education and the Humanities. Carnegie Essays on the Doctorate: Humanities.

ERIC Educational Resources Information Center

Stimpson, Catharine R.

The Carnegie Foundation commissioned a collection of essays as part of the Carnegie Initiative on the Doctorate (CID). Essays and essayists represent six disciplines that are part of the CID: chemistry, education, English, history, mathematics, and neuroscience. Intended to engender conversation about the conceptual foundation of doctoral…

The Ph.D. in English: Towards a New Consensus. Carnegie Essays on the Doctorate: English.

ERIC Educational Resources Information Center

Graff, Gerald

The Carnegie Foundation commissioned a collection of essays as part of the Carnegie Initiative on the Doctorate (CID). Essays and essayists represent six disciplines that are part of the CID: chemistry, education, English, history, mathematics, and neuroscience. Intended to engender conversation about the conceptual foundation of doctoral…

Performance Characteristics of Automotive Engines in the United States, Third Series - Report No. 6, 1978 Volkswagen Diesel, 90 CID (1.5 Liter), F.I.

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 VW 90 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program is to ...

Performance Characteristics of Automotive Engines in the United States, Third Series - Report No. 7, 1978 Ford, 98 CID (1.6 Liters), 2V

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1977 Chrysler 318 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program...

30 CFR 250.297 - What information must a CID contain?

Code of Federal Regulations, 2011 CFR

2011-07-01

..., DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Plans... reservoirs. You must notify MMS of any well that is drilled to total depth during the CID evaluation period... available. Information must be provided for each hydrocarbon-bearing reservoir that is penetrated by a well...

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 13 - 1975 American Motors 258 CID (4.2 Liters)

DOT National Transportation Integrated Search

1978-04-01

Experimental data were obtained in dynamometer tests of a 1975 AMC 258-CID production 1V engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of th...

Performance Characteristics of Automotive Engines in the United States, Third Series - Report No. 2, 1978 Pontiac, 301 CID (4.9 Liters), 2V

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 Pontiac 301 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program ...

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 17 - 1975 Buick 455 CID (7.5 Liters), 4V

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1975 Buick 455 CID, 4V engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the progra...

Performance Characteristics of Automotive Engines in the United States : Second Series - Report No. 2 - 1976 Chevrolet 305 CID (5.0 Liters), 2V

DOT National Transportation Integrated Search

1978-04-01

Experimental data were obtained in dynamometer tests of a 1976 Chevrolet 305-CID V-8 engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the pr...

Performance Characteristics of Automotive Engines in the United States : Third Series - Report No. 12 - 1978 Ford 140 CID (2.3 Liters), 2V

DOT National Transportation Integrated Search

1980-09-01

Experimental data were obtained in dynamometer tests of a 1978 Ford 140 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program is ...

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 16 - 1975 Volvo 121 CID (2.0 Liters), F.I.

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1975 Volvo, 2.0 liter (121 CID) engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of t...

Performance Characteristics of Automotive Engines in the United States : Second Series - Report No. 5 - 1977 Ford 140 CID (2.3 Liters), 2V

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1977 Ford 2.3 liter (140 CID) engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the...

Performance Characteristics of Automotive Engines in the United States : Third Series - Report No. 1 - 1977 Volvo 130 CID (2.1 Liters), F.I.

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1977 Volvo 130 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the program is...

Performance Characteristics of Automotive Engines in the United States : Second Series - Report No. 7 - 1977 Ford 171 CID (2.8 Liters), 2V

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1977 Ford 171 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the program is ...

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 15 - 1975 Dodge Colt 98 CID (1.6 Liters), 2V

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1975 Dodge Colt 1.6 liter (98 CID) engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective o...

Performance Characteristics of Automotive Engines in the United States : Second Series - Report No. 3 - 1977 Chrysler 225 CID (3.7 Liters), 2V

DOT National Transportation Integrated Search

1978-04-01

Experimental data were obtained in dynamometer tests of a 1977 Chrysler 225-CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the program...

Performance Characteristics of Automotive Engines in the United States, Third Series - Report No. 9, 1978 Ford, 300 CID (4.9 Liters), 1V

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 Ford 140 300 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program...

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 18 - 1976 Ford 400 CID (6.6 Liters), 2V

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1976 Ford 400 CID, 2V engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of the program...

Performance Characteristics of Automotive Engines in the United States : First Series - Report No. 19 - 1975 Ford Windsor 351 CID (5.7 Liters), 2V

DOT National Transportation Integrated Search

1978-05-01

Experimental data were obtained in dynamometer tests of a 1975 Ford 351 CID, 2V, Windsor engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine-operating modes. The objective of th...

Performance Characteristics of Automotive Engines in the United States, Third Series - Report No. 5, 1978 Chevrolet, 200 CID (3.3 Liter), 2V

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 Chevrolet 200 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the progra...

Performance Characteristics of Automotive Engines in the United States, Third Series, Report No. 8, 1978 Buick, 231 CID (3.8 Liters), 4V, Turbocharge

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 Buick 231 CID turbocharged to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the prog...

Performance Characteristics of Automotive Engines in the United States, Third Series - Report No. 4, 1978 Pontiac, 151 CID (2.5 Liters), 2V

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 Pontiac 151 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program ...

Performance Characteristics of Automotive Engines in the United States, Third Series, Report No. 3, 1978 AMC, 121 CID (2.0 Liters), 2V

DOT National Transportation Integrated Search

1979-02-01

Experimental data were obtained in dynamometer tests of a 1978 AMC 121 CID engine to determine fuel consumption and emissions (hydrocarbon, carbon monoxide, oxides of nitrogen) at steady-state engine operating modes. The objective of the program is t...

Close-in detection system for the Mine Hunter/Killer program

NASA Astrophysics Data System (ADS)

Bishop, Steven S.; Campana, Stephen B.; Lang, David A.; Wiggins, Carl M.

2000-08-01

The Close-in Detection (CID) System is the vehicle-mounted multisensor landmine detection system for the Army CECOM Night Vision Electronic Sensors Directorate (NVESD) Mine Hunter/Killer (MH/K) Program. The CID System is being developed by BAE Systems in San Diego, CA. TRW Systems and Information Technology Group in Arlington, VA and a team of specialists for ERIM, E-OIR, SNL, and APL/JHU support NVESD in the development, analysis and testing of the CID and associated signal and data processing. The CID System includes tow down-looking sensor arrays: a ground- penetrating radar (GPR) array, and a set of Electro-Magnetic Induction (EMI) coils for metal detection. These arrays span a 3-meter wide swath in front of a high mobility, multipurpose wheeled vehicle. The system also includes a forward looking IR imaging system mounted on the roof of the vehicle and covering a swath of the road ahead of the vehicle. Signals from each sensor are processed separately to detect and localize objects of interest. Features of candidate objects are integrated in a processor that uses them to discriminates between anti-tank miens and clutter. Mine locations are passed to the neutralization subsystem of MH/K. This paper reviews the design of the sensors and signal processing of the CID system and gives examples and analysis of recent test results at the NVESD mine lanes. The strengths and weaknesses of each sensor are discussed, and the application of multisensor fusion is illustrated.

Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides.

PubMed

Lakbub, Jude C; Su, Xiaomeng; Zhu, Zhikai; Patabandige, Milani W; Hua, David; Go, Eden P; Desaire, Heather

2017-08-04

The glycopeptide analysis field is tightly constrained by a lack of effective tools that translate mass spectrometry data into meaningful chemical information, and perhaps the most challenging aspect of building effective glycopeptide analysis software is designing an accurate scoring algorithm for MS/MS data. We provide the glycoproteomics community with two tools to address this challenge. The first tool, a curated set of 100 expert-assigned CID spectra of glycopeptides, contains a diverse set of spectra from a variety of glycan types; the second tool, Glycopeptide Decoy Generator, is a new software application that generates glycopeptide decoys de novo. We developed these tools so that emerging methods of assigning glycopeptides' CID spectra could be rigorously tested. Software developers or those interested in developing skills in expert (manual) analysis can use these tools to facilitate their work. We demonstrate the tools' utility in assessing the quality of one particular glycopeptide software package, GlycoPep Grader, which assigns glycopeptides to CID spectra. We first acquired the set of 100 expert assigned CID spectra; then, we used the Decoy Generator (described herein) to generate 20 decoys per target glycopeptide. The assigned spectra and decoys were used to test the accuracy of GlycoPep Grader's scoring algorithm; new strengths and weaknesses were identified in the algorithm using this approach. Both newly developed tools are freely available. The software can be downloaded at http://glycopro.chem.ku.edu/GPJ.jar.

Chronic Inflammatory Disease and Osteopathy: A Systematic Review

PubMed Central

Cicchitti, Luca; Martelli, Marta; Cerritelli, Francesco

2015-01-01

Background Chronic inflammatory diseases (CID) are globally highly prevalent and characterized by severe pathological medical conditions. Several trials were conducted aiming at measuring the effects of manipulative therapies on patients affected by CID. The purpose of this review was to explore the extent to which osteopathic manipulative treatment (OMT) can be benefi-cial in medical conditions also classified as CID. Methods This review included any type of experimental study which enrolled sub-jects with CID comparing OMT with any type of control procedure. The search was conducted on eight databases in January 2014 using a pragmatic literature search approach. Two independent re-viewers conducted study selection and data extraction for each study. The risk of bias was evaluated according to the Cochrane methods. Heterogeneity was assessed and meta-analysis performed where possible. Results 10 studies met the inclusion criteria for this review enrolling 386 subjects. The search identified six RCTs, one laboratory study, one cross-over pilot studies, one observation-al study and one case control pilot study. Results suggest a potential effect of osteopathic medicine on patients with medical pathologies associated with CID (in particular Chronic Obstructive Pul-monary Disease (COPD), Irritable Bowel Syndrome, Asthma and Peripheral Arterial Disease) com-pared to no treatment or sham therapy although data remain elusive. Moreover one study showed possible effects on arthritis rat model. Meta-analysis was performed for COPD studies only show-ing no effect of any type of OMT applied versus control. No major side effects were reported by those receiving OMT. Conclusion The present systematic review showed inconsistent data on the effect of OMT in the treatment of medical conditions potentially associated with CID, however the OMT appears to be a safe approach. Further more robust trials are needed to determine the direction and magnitude of the effect of OMT and to generalize favorable results. PMID:25781621

Constraints on the Nature of CID-42: Recoil Kick or Supermassive Black Hole Pair?

NASA Technical Reports Server (NTRS)

Blecha, Laura; Civano, Francesca; Elvis, Martin; Loeb, Abraham

2012-01-01

The galaxy CXOC J100043.1+020637, also known as CID-42, is a highly unusual object. An apparent galaxy merger remnant, it displays signatures of both an inspiraling, kiloparsecscale active galactic nucleus (AGN) pair and of a recoiling AGN with a kick velocity approximately greater than 1300 km s(exp -1). Among recoiling AGN candidates, CID-42 alone has both spatial offsets (in optical and X-ray bands) and spectroscopic offsets. In order to constrain the relative likelihood of both scenarios, we develop models using hydrodynamic galaxy merger simulations coupled with radiative transfer calculations. Our gas-rich, major merger models are generally well matched to the galactic morphology and to the inferred stellar mass and star formation rate. We show that a recoiling supermassive black hole (SMBH) in CID-42 should be observable as an AGN at the time of observation. However, in order for the recoiling AGN to produce narrow-line emission, it must be observed shortly after the kick while it still inhabits a dense gaseous region, implying a large total kick velocity (vk approximately greater than 2000 km s(exp -1)). For the dual AGN scenario, an unusually large broad-line offset is required, and the best match to the observed morphology requires a galaxy that is less luminous than CID-42. Further, the lack of X-ray emission from one of the two optical nuclei is not easily attributed to an intrinsically quiescent SMBH or to a Compton-thick galactic environment. While the current data do not allow either the recoiling or the dual AGN scenario for CID-42 to be excluded, our models highlight the most relevant parameters for distinguishing these possibilities with future observations. In particular, high-quality, spatially-resolved spectra that can pinpoint the origin of the broad and narrow line features will be critical for determining the nature of this unique source.

Prevention of clinically important deteriorations in COPD with umeclidinium/vilanterol.

PubMed

Singh, Dave; Maleki-Yazdi, M Reza; Tombs, Lee; Iqbal, Ahmar; Fahy, William A; Naya, Ian

2016-01-01

Minimizing the risk of disease progression and exacerbations is the key goal of COPD management, as these are well-established indicators of poor COPD prognosis. We developed a novel composite end point assessing three important aspects (lung function, health status, and exacerbations) of worsening in COPD. The objective was to determine whether dual bronchodilation with umeclidinium/vilanterol (UMEC/VI) reduces clinically important deteriorations (CIDs) in COPD versus placebo or bronchodilator monotherapy. This study is a post hoc analysis of two 24-week trials comparing UMEC/VI 62.5/25 µg with UMEC 62.5 µg, VI 25 µg, or placebo (Study A; NCT01313650), or UMEC/VI 62.5/25 µg with tiotropium (TIO) 18 µg (Study B; NCT01777334) in patients with symptomatic COPD, without a history of frequent exacerbations. Deterioration was assessed as the time to a first CID, a composite measure defined as a decrease of ≥100 mL in trough forced expiratory volume in 1 second or ≥4-unit increase in St George's Respiratory Questionnaire total score or an on-treatment moderate-to-severe COPD exacerbation. In Study A, fewer patients experienced a first CID with UMEC/VI (44%) versus UMEC (50%), VI (56%), and placebo (75%). The risk of a first CID was reduced with UMEC/VI (hazard ratio [HR]: 0.37 [95% confidence interval, CI: 0.30, 0.45]), UMEC (HR: 0.46 [95% CI: 0.38, 0.56]), and VI (HR: 0.55 [95% CI: 0.45, 0.66]; all P<0.001) versus placebo, and with UMEC/VI versus UMEC (HR: 0.80 [95% CI: 0.65, 0.97]; P<0.05) and versus VI (HR: 0.67 [95% CI: 0.55, 0.81]; P<0.001). In Study B, fewer patients experienced a first CID with UMEC/VI (41%) versus TIO (59%). UMEC/VI reduced the risk of a first composite CID by 43% versus TIO (HR: 0.57 [95% CI: 0.47, 0.69]; P<0.001). This exploratory analysis, using a new assessment of clinical deterioration in COPD, revealed that a majority of symptomatic patients with low exacerbation risk experienced a deterioration during the 24-week study periods. UMEC/VI reduces the risk of a first CID versus placebo or bronchodilator monotherapy.

Prevention of clinically important deteriorations in COPD with umeclidinium/vilanterol

PubMed Central

Singh, Dave; Maleki-Yazdi, M Reza; Tombs, Lee; Iqbal, Ahmar; Fahy, William A; Naya, Ian

2016-01-01

Background Minimizing the risk of disease progression and exacerbations is the key goal of COPD management, as these are well-established indicators of poor COPD prognosis. We developed a novel composite end point assessing three important aspects (lung function, health status, and exacerbations) of worsening in COPD. The objective was to determine whether dual bronchodilation with umeclidinium/vilanterol (UMEC/VI) reduces clinically important deteriorations (CIDs) in COPD versus placebo or bronchodilator monotherapy. Methods This study is a post hoc analysis of two 24-week trials comparing UMEC/VI 62.5/25 µg with UMEC 62.5 µg, VI 25 µg, or placebo (Study A; NCT01313650), or UMEC/VI 62.5/25 µg with tiotropium (TIO) 18 µg (Study B; NCT01777334) in patients with symptomatic COPD, without a history of frequent exacerbations. Deterioration was assessed as the time to a first CID, a composite measure defined as a decrease of ≥100 mL in trough forced expiratory volume in 1 second or ≥4-unit increase in St George’s Respiratory Questionnaire total score or an on-treatment moderate-to-severe COPD exacerbation. Results In Study A, fewer patients experienced a first CID with UMEC/VI (44%) versus UMEC (50%), VI (56%), and placebo (75%). The risk of a first CID was reduced with UMEC/VI (hazard ratio [HR]: 0.37 [95% confidence interval, CI: 0.30, 0.45]), UMEC (HR: 0.46 [95% CI: 0.38, 0.56]), and VI (HR: 0.55 [95% CI: 0.45, 0.66]; all P<0.001) versus placebo, and with UMEC/VI versus UMEC (HR: 0.80 [95% CI: 0.65, 0.97]; P<0.05) and versus VI (HR: 0.67 [95% CI: 0.55, 0.81]; P<0.001). In Study B, fewer patients experienced a first CID with UMEC/VI (41%) versus TIO (59%). UMEC/VI reduced the risk of a first composite CID by 43% versus TIO (HR: 0.57 [95% CI: 0.47, 0.69]; P<0.001). Conclusion This exploratory analysis, using a new assessment of clinical deterioration in COPD, revealed that a majority of symptomatic patients with low exacerbation risk experienced a deterioration during the 24-week study periods. UMEC/VI reduces the risk of a first CID versus placebo or bronchodilator monotherapy. PMID:27445468

The comparative behaviour of two combat boots under impact.

PubMed

Newell, Nicolas; Masouros, Spyros D; Pullen, Andy D; Bull, Anthony M J

2012-04-01

Improvised explosive devices have become the characteristic weapon of conflicts in Iraq and Afghanistan. While little can be done to mitigate against the effects of blast in free-field explosions, scaled blast simulations have shown that the combat boot can attenuate the effects on the vehicle occupants of anti-vehicular mine blasts. Although the combat boot offers some protection to the lower limb, its behaviour at the energies seen in anti-vehicular mine blast has not been documented previously. The sole of eight same-size combat boots from two brands currently used by UK troops deployed to Iraq and Afghanistan were impacted at energies of up to 518 J, using a spring-assisted drop rig. The results showed that the Meindl Desert Fox combat boot consistently experienced a lower peak force at lower impact energies and a longer time-to-peak force at higher impact energies when compared with the Lowa Desert Fox combat boot. This reduction in the peak force and extended rise time, resulting in a lower energy transfer rate, is a potentially positive mitigating effect in terms of the trauma experienced by the lower limb. Currently, combat boots are tested under impact at the energies seen during heel strike in running. Through the identification of significantly different behaviours at high loading, this study has shown that there is rationale in adding the performance of combat boots under impact at energies above those set out in international standards to the list of criteria for the selection of a combat boot.

Rethinking the Ph.D. in English. Carnegie Essays on the Doctorate: English.

ERIC Educational Resources Information Center

Lunsford, Andrea Abernethy

The Carnegie Foundation commissioned a series of essays as part of the Carnegie Initiative on the Doctorate (CID). The essays and essayists represent six disciplines that are part of the CID: chemistry, education, English, history, mathematics, and neuroscience. The essay explores the Ph.D. in English and suggests changes the author would make in…

FELIN: tailored optronics and systems solutions for dismounted combat

NASA Astrophysics Data System (ADS)

Milcent, A. M.

2009-05-01

The FELIN French modernization program for dismounted combat provides the Armies with info-centric systems which dramatically enhance the performances of the soldier and the platoon. Sagem now has available a portfolio of various equipments, providing C4I, data and voice digital communication, and enhanced vision for day and night operations, through compact high performance electro-optics. The FELIN system provides the infantryman with a high-tech integrated and modular system which increases significantly their detection, recognition, identification capabilities, their situation awareness and information sharing, and this in any dismounted close combat situation. Among the key technologies used in this system, infrared and intensified vision provide a significant improvement in capability, observation performance and protection of the ground soldiers. This paper presents in detail the developed equipments, with an emphasis on lessons learned from the technical and operational feedback from dismounted close combat field tests.

Centrifuge-simulated suborbital spaceflight in subjects with cardiac implanted devices.

PubMed

Blue, Rebecca S; Reyes, David P; Castleberry, Tarah L; Vanderploeg, James M

2015-04-01

Future commercial spaceflight participants (SFPs) with conditions requiring personal medical devices represent a unique challenge. The behavior under stress of cardiac implanted devices (CIDs) such as pacemakers is of special concern. No known data currently exist on how such devices may react to the stresses of spaceflight. We examined the responses of two volunteer subjects with CIDs to G forces in a centrifuge to evaluate how similar potential commercial SFPs might tolerate the forces of spaceflight. Two subjects, 75- and 79-yr-old men with histories of atrial fibrillation and implanted dual-lead, rate-responsive pacemakers, underwent seven centrifuge runs over 2 d. Day 1 consisted of two +Gz runs (peak = +3.5 Gz, run 2) and two +Gx runs (peak = +6.0 Gx, run 4). Day 2 consisted of three runs approximating suborbital spaceflight profiles (combined +Gx/+Gz). Data collected included blood pressures, electrocardiograms, pulse oximetry, neurovestibular exams, and postrun questionnaires regarding motion sickness, disorientation, greyout, and other symptoms. Despite both subjects' significant medical histories, neither had abnormal physiological responses. Post-spin analysis demonstrated no lead displacement, damage, or malfunction of either CID. Potential risks to SFPs with CIDs include increased arrhythmogenesis, lead displacement, and device damage. There are no known prior studies of individuals with CIDs exposed to accelerations anticipated during the dynamic phases of suborbital spaceflight. These cases demonstrate that even individuals with significant medical histories and implanted devices can tolerate the acceleration exposures of commercial spaceflight. Further investigation will determine which personal medical devices present significant risks during suborbital flight and beyond.

Trial of Early Aggressive Therapy in Polyarticular Juvenile Idiopathic Arthritis

PubMed Central

Wallace, Carol A.; Giannini, Edward H.; Spalding, Steven J.; Hashkes, Philip J.; O’Neil, Kathleen M.; Zeft, Andrew S.; Szer, Ilona S.; Ringold, Sarah; Brunner, Hermine I.; Schanberg, Laura E.; Sundel, Robert P.; Milojevic, Diana; Punaro, Marilynn G.; Chira, Peter; Gottlieb, Beth S.; Higgins, Gloria C.; Ilowite, Norman T.; Kimura, Yukiko; Hamilton, Stephanie; Johnson, Anne; Huang, Bin; Lovell, Daniel J.

2011-01-01

OBJECTIVES To determine if aggressive treatment initiated early in the course of rheumatoid factor positive or negative polyarticular juvenile idiopathic arthritis (poly-JIA) can induce clinical inactive disease (CID) within 6 months. METHODS Between May 2007 and October 2010 a multi-center, prospective, double blind, randomized, placebo controlled trial of two aggressive treatments was conducted in 85 children aged 2 to 16 years with polyarticular JIA of less than 12 months duration. Patients received either methotrexate 0.5 mg/kg/wk SQ (40 mg max), etanercept 0.8 mg/kg/wk (50 mg max), prednisolone 0.5 mg/kg/d (60 mg max) tapered to 0 by 17 weeks (Arm 1), or methotrexate (same dose as Arm 1), etanercept placebo, and prednisolone placebo (Arm 2). The primary outcome was CID at 6 months. An exploratory phase determined the rate of clinical remission on medication (6 months of continuous CID) at 12 months. RESULTS By 6 months, 17 of 42 (40%) of patients in Arm 1 and 10 of 43 (23%) in Arm 2 had achieved CID (X2 = 2.91; p = 0.088). After 12 months, 9 patients in Arm 1 and 3 in Arm 2 achieved clinical remission on medication (p = 0.0534). There were no significant inter-arm differences in adverse events. CONCLUSIONS Although this study did not meet its primary endpoint, early aggressive therapy in this cohort of children with recent onset polyarticular JIA resulted in substantial proportions of patients in both arms achieving CID by 6 months and clinical remission on medication within 12 months of treatment. PMID:22183975

Finding the Enemy: Using 3-D Laser Radar (LADAR) Imaging for Real Time Combat Identification of Ground Targets in an Obscured Environment

DTIC Science & Technology

2010-04-01

AIR COMMAND AND STAFF COLLEGE AIR UNIVERSITY FINDING THE ENEMY: USING 3-D LASER RADAR (LADAR) IMAGING FOR REAL TIME COMBAT...Faculty In Partial Fulfillment of Graduation Requirements Advisor: Lt Col Terry Bullard Maxwell Air Force Base, Alabama April 2010...position of the US government or the Department of Defense. In accordance with Air Force Instruction 51-303, it is not copyrighted, but is the property of

Postconcussive Symptom Reporting Among US Combat Veterans With Mild Traumatic Brain Injury From Operation Iraqi Freedom

DTIC Science & Technology

2012-01-01

memory problems (OR = 1.86; 95% CI = 1.20-2.88), tinnitus (OR = 1.63; 95% CI = 1.10-2.41), and dizziness (OR = 2.13; 95% CI = 1.06-4.29) compared with...consequences among combat veterans even when accounting for co-occurring psychological morbidity. The identification of postconcussive symptoms related to...Research Center, San Diego, California. This work was supported by the US Navy Bureau of Medicine under the Wounded, Ill and Injured/ Psychological Health

Experimental Investigations on the Distortion of ISAR Images Using Different Radar Waveforms

DTIC Science & Technology

2003-09-01

des cibles fera partie int~grante d’une nouvelle approche pour la gestion des donn~es relatives A l’espace de combat, comme les nouvelles initiatives de ... risque de tir fratricide en conditions de combat. En somme, l’identification des cibles, particuli~rement en mode de non-cooperation, jouera un r~le...Defence, 2003 © Sa majest6 la reine, repr~sent~e par le ministre de la Defense nationale, 2003 Abstract Experimental results have shown that the

Current radar-responsive tag development activities at Sandia National Laboratories

NASA Astrophysics Data System (ADS)

Ormesher, Richard C.; Plummer, Kenneth W.; Wells, Lars M.

2004-08-01

Over the past ten years, Sandia has developed RF radar responsive tag systems and supporting technologies for various government agencies and industry partners. RF tags can function as RF transmitters or radar transponders that enable tagging, tracking, and location determination functions. Expertise in tag architecture, microwave and radar design, signal analysis and processing techniques, digital design, modeling and simulation, and testing have been directly applicable to these tag programs. In general, the radar responsive tag designs have emphasized low power, small package size, and the ability to be detected by the radar at long ranges. Recently, there has been an interest in using radar responsive tags for Blue Force tracking and Combat ID (CID). The main reason for this interest is to allow airborne surveillance radars to easily distinguish U.S. assets from those of opposing forces. A Blue Force tracking capability would add materially to situational awareness. Combat ID is also an issue, as evidenced by the fact that approximately one-quarter of all U.S. casualties in the Gulf War took the form of ground troops killed by friendly fire. Because the evolution of warfare in the intervening decade has made asymmetric warfare the norm rather than the exception, swarming engagements in which U.S. forces will be freely intermixed with opposing forces is a situation that must be anticipated. Increasing utilization of precision munitions can be expected to drive fires progressively closer to engaged allied troops at times when visual de-confliction is not an option. In view of these trends, it becomes increasingly important that U.S. ground forces have a widely proliferated all-weather radar responsive tag that communicates to all-weather surveillance. The purpose of this paper is to provide an overview of the recent, current, and future radar responsive research and development activities at Sandia National Laboratories that support both the Blue Force Tracking and Combat ID application. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company for the United States Departments of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Developing Technical Expertise in Secondary Technical Schools: The Effect of 4C/ID Learning Environments

ERIC Educational Resources Information Center

Sarfo, Frederick K.; Elen, Jan

2007-01-01

In this study, the effectiveness of learning environments, developed in line with the specifications of the four components instructional design model (4C/ID model) and the additional effect of ICT for fostering the development of technical expertise in traditional Ghanaian classrooms, was assessed. The study had a one-by-one-by-two…

30 CFR 250.296 - When and how must I submit a CID or a revision to a CID?

Code of Federal Regulations, 2010 CFR

2010-07-01

... INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Plans and Information... service fee listed in § 250.125. (b) If you decide not to develop a reservoir you committed to develop in... to develop the reservoir and before the reservoir is bypassed. The Regional Supervisor will approve...

30 CFR 250.296 - When and how must I submit a CID or a revision to a CID?

Code of Federal Regulations, 2011 CFR

2011-07-01

..., AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER... accompanied by payment of the service fee listed in § 250.125. (b) If you decide not to develop a reservoir... after making your decision not to develop the reservoir and before the reservoir is bypassed. The...

Even-electron [M-H](+) ions generated by loss of AgH from argentinated peptides with N-terminal imine groups.

PubMed

Plaviak, Alexandra; Osburn, Sandra; Patterson, Khiry; van Stipdonk, Michael J

2016-01-15

Experiments were performed to probe the creation of apparent even-electron, [M-H](+) ions by CID of Ag-cationized peptides with N-terminal imine groups (Schiff bases). Imine-modified peptides were prepared using condensation reactions with aldehydes. Ag(+) -cationized precursors were generated by electrospray ionization (ESI). Tandem mass spectrometry (MS(n) ) and collision-induced dissociation (CID) were performed using a linear ion trap mass spectrometer. Loss of AgH from peptide [M + Ag](+) ions, at the MS/MS stage, creates closed-shell [M-H](+) ions from imine-modified peptides. Isotope labeling unambiguously identifies the imine C-H group as the source of H eliminated in AgH. Subsequent CID of the [M-H](+) ions generated sequence ions that are analogous to those produced from [M + H](+) ions of the imine-modified peptides. Experiments show (a) formation of novel even-electron peptide cations by CID and (b) the extent to which sequence ions (conventional b, a and y ions) are generated from peptides with fixed charge site and thus lacking a conventional mobile proton. Copyright © 2015 John Wiley & Sons, Ltd.

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.

PubMed

Kim, Ji Hun; Titus, Katelyn R; Gong, Wanfeng; Beagan, Jonathan A; Cao, Zhendong; Phillips-Cremins, Jennifer E

2018-05-14

Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher-resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C. Copyright © 2018 Elsevier Inc. All rights reserved.

Preventing Student Disengagement and Keeping Students on the Graduation Path in Urban Middle-Grades Schools: Early Identification and Effective Interventions

ERIC Educational Resources Information Center

Balfanz, Robert; Herzog, Liza; Iver, Douglas J. Mac

2007-01-01

This article considers the practical, conceptual, and empirical foundations of an early identification and intervention system for middle-grades schools to combat student disengagement and increase graduation rates in our nation's cities. Many students in urban schools become disengaged at the start of the middle grades, which greatly reduces the…

Effective Use of Water and Increased Dry Matter Partitioned to Grain Contribute to Yield of Common Bean Improved for Drought Resistance

PubMed Central

Polania, Jose A.; Poschenrieder, Charlotte; Beebe, Stephen; Rao, Idupulapati M.

2016-01-01

Common bean (Phaseolus vulgaris L.) is the most important food legume in the diet of poor people in the tropics. Drought causes severe yield loss in this crop. Identification of traits associated with drought resistance contributes to improving the process of generating bean genotypes adapted to these conditions. Field studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia, to determine the relationship between grain yield and different parameters such as effective use of water (EUW), canopy biomass, and dry partitioning indices (pod partitioning index, harvest index, and pod harvest index) in elite lines selected for drought resistance over the past decade. Carbon isotope discrimination (CID) was used for estimation of water use efficiency (WUE). The main objectives were: (i) to identify specific morpho-physiological traits that contribute to improved resistance to drought in lines developed over several cycles of breeding and that could be useful as selection criteria in breeding; and (ii) to identify genotypes with desirable traits that could serve as parents in the corresponding breeding programs. A set of 36 bean genotypes belonging to the Middle American gene pool were evaluated under field conditions with two levels of water supply (irrigated and drought) over two seasons. Eight bean lines (NCB 280, NCB 226, SEN 56, SCR 2, SCR 16, SMC 141, RCB 593, and BFS 67) were identified as resistant to drought stress. Resistance to terminal drought stress was positively associated with EUW combined with increased dry matter partitioned to pod and seed production and negatively associated with days to flowering and days to physiological maturity. Differences in genotypic response were observed between grain CID and grain yield under irrigated and drought stress. Based on phenotypic differences in CID, leaf stomatal conductance, canopy biomass, and grain yield under drought stress, the lines tested were classified into two groups, water savers and water spenders. Pod harvest index could be a useful selection criterion in breeding programs to select for drought resistance in common bean. PMID:27242861

Recurrent (2;2) and (2;8) Translocations in Rhabdomyosarcoma without the Canonical PAX-FOXO1 fuse PAX3 to Members of the Nuclear Receptor Transcriptional Coactivator (NCOA) Family

PubMed Central

Sumegi, Janos; Streblow, Renae; Frayer, Robert W.; Cin, Paola Dal; Rosenberg, Andrew; Meloni-Ehrig, Aurelia; Bridge, Julia A.

2009-01-01

The fusion oncoproteins PAX3-FOXO1 [t(2;13)(q35;q14)] and PAX7-FOXO1 [t(1;13)(p36;q14)] typify alveolar rhabdomyosarcoma (ARMS); however, 20-30% of cases lack these specific translocations. In this study, cytogenetic and/or molecular characterization to include FISH, RT-PCR and sequencing analyses of five rhabdomyosarcomas [four ARMS and one embryonal rhabdomyosarcoma (ERMS)] with novel, recurrent t(2;2)(p23;q35) or t(2;8)(q35;q13) revealed that these non-canonical translocations fuse PAX3 to NCOA1 or NCOA2 respectively. The PAX3-NCOA1 and PAX3-NCOA2 transcripts encode chimeric proteins composed of the paired-box and homeodomain DNA-binding domains of PAX3, and the CID domain, the Q-rich region and the AD2 domain of NCOA1 or NCOA2. To investigate the biological function of these recurrent variant translocations, the coding regions of PAX3-NCOA1 and PAX3-NCOA2 cDNA constructs were introduced into expression vectors with tetracycline-regulated expression. Both fusion proteins showed transforming activity in the soft agar assay. Deletion of the AD2 portion of the PAX3-NCOA fusion proteins reduced the transforming activity of each chimeric protein. Similarly, but with greater impact, CID domain deletion fully abrogated the transforming activity of the chimeric protein. These studies: (1) expand our knowledge of PAX3 variant translocations in RMS with identification of a novel PAX3-NCOA2 fusion; (2) show that both PAX3-NCOA1 and PAX3-NCOA2 represent recurrent RMS rearrangements; (3) confirm the transforming activity of both translocation events and demonstrate the essentiality of intact AD2 and CID domains for optimal transforming activity; and, (5) provide alternative approaches (FISH and RT-PCR) for detecting PAX-NCOA fusions in nondividing cells of RMS. The latter could potentially be utilized as aids in diagnostically challenging cases. PMID:19953635

Learning Electrical Circuits: The Effects of the 4C-ID Instructional Approach in the Acquisition and Transfer of Knowledge

ERIC Educational Resources Information Center

Melo, Mário; Miranda, Guilhermina Lobato

2015-01-01

This study was designed to investigate the effects of two instructional approaches (4C-ID versus conventional) on learners' knowledge-acquisition and learning transfer of the electrical circuits content in Physics. Participants were 129 9th graders from a secondary school in Lisbon, M = 14.3 years, SD = 0.54. The participants were divided in two…

ToF-SIMS Parallel Imaging MS/MS of Lipid Species in Thin Tissue Sections.

PubMed

Bruinen, Anne Lisa; Fisher, Gregory L; Heeren, Ron M A

2017-01-01

Unambiguous identification of detected species is essential in complex biomedical samples. To date, there are not many mass spectrometry imaging techniques that can provide both high spatial resolution and identification capabilities. A new and patented imaging tandem mass spectrometer, exploiting the unique characteristics of the nanoTOF II (Physical Electronics, USA) TOF-SIMS TRIFT instrument, was developed to address this.Tandem mass spectrometry is based on the selection of precursor ions from the full secondary ion spectrum (MS 1 ), followed by energetic activation and fragmentation, and collection of the fragment ions to obtain a tandem MS spectrum (MS 2 ). The PHI NanoTOF II mass spectrometer is equipped with a high-energy collision induced dissociation (CID) fragmentation cell as well as a second time-of-flight analyzer developed for simultaneous ToF-SIMS and tandem MS imaging experiments.We describe here the results of a ToF-SIMS imaging experiment on a thin tissue section of an infected zebrafish as a model organism for tuberculosis. The focus is on the obtained ion distribution plot of a fatty acid as well as its identification by tandem mass spectrometry.

B2-kinin receptors in the dorsal periaqueductal gray are implicated in the panicolytic-like effect of opiorphin.

PubMed

Sestile, Caio César; Maraschin, Jhonatan Christian; Rangel, Marcel Pereira; Santana, Rosangela Getirana; Zangrossi, Hélio; Graeff, Frederico Guilherme; Audi, Elisabeth Aparecida

2017-10-03

Reported results have shown that the pentapeptide opiorphin inhibits oligopeptidases that degrade brain neuropeptides, and has analgesic and antidepressant effects in experimental animals, without either tolerance or dependency after chronic administration. In a previous study we showed that opiorphin has a panicolytic-like effect in the dorsal periaqueductal gray (dPAG) electrical stimulation test (EST), mediated by the μ-opioid receptor (MOR). This study further analyzes the mechanism of opiorphin panicolytic action, using the EST and drug injection inside the dPAG. The obtained results showed that blockade of the 5-HT 1A receptors with WAY-100635 did not change the escape-impairing effect of opiorphin, and combined injection of sub-effective doses of opiorphin and the 5-HT 1A -agonist 8-OH-DPAT did not have a significant anti-escape effect. In contrast, the anti-escape effect of opiorphin was antagonized by pretreatment with the kinin B2 receptor blocker HOE-140, and association of sub-effective doses of opiorphin and bradykinin caused a significant anti-escape effect. The anti-escape effect of bradykinin was not affected by previous administration of WAY-100635. Therefore, the anti-escape effect of opiorphin in the dPAG seems to be mediated by endogenous bradykinin, acting on kinin B2 receptors, which previous results have shown to interact synergistically with MOR in the dPAG to restrain escape in two animal models of panic. Chemical compounds: Opiorphin (PubChem CID: 25195667); WAY100635 maleate salt (PubChem CID: 11957721); 8-OH-DPAT hydrobromide (PubChem CID: 6917794); Bradykinin (PubChem CID: 439201); HOE-140 (Icatibant) (PubChem CID: 6918173). Copyright © 2017 Elsevier Inc. All rights reserved.

UniNovo: a universal tool for de novo peptide sequencing.

PubMed

Jeong, Kyowon; Kim, Sangtae; Pevzner, Pavel A

2013-08-15

Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but de novo peptide sequencing algorithms to analyze tandem mass (MS/MS) spectra are lagging behind. Although existing de novo sequencing tools perform well on certain types of spectra [e.g. Collision Induced Dissociation (CID) spectra of tryptic peptides], their performance often deteriorates on other types of spectra, such as Electron Transfer Dissociation (ETD), Higher-energy Collisional Dissociation (HCD) spectra or spectra of non-tryptic digests. Thus, rather than developing a new algorithm for each type of spectra, we develop a universal de novo sequencing algorithm called UniNovo that works well for all types of spectra or even for spectral pairs (e.g. CID/ETD spectral pairs). UniNovo uses an improved scoring function that captures the dependences between different ion types, where such dependencies are learned automatically using a modified offset frequency function. The performance of UniNovo is compared with PepNovo+, PEAKS and pNovo using various types of spectra. The results show that the performance of UniNovo is superior to other tools for ETD spectra and superior or comparable with others for CID and HCD spectra. UniNovo also estimates the probability that each reported reconstruction is correct, using simple statistics that are readily obtained from a small training dataset. We demonstrate that the estimation is accurate for all tested types of spectra (including CID, HCD, ETD, CID/ETD and HCD/ETD spectra of trypsin, LysC or AspN digested peptides). UniNovo is implemented in JAVA and tested on Windows, Ubuntu and OS X machines. UniNovo is available at http://proteomics.ucsd.edu/Software/UniNovo.html along with the manual.

Electron Transfer Dissociation and Collision-Induced Dissociation of Underivatized Metallated Oligosaccharides

NASA Astrophysics Data System (ADS)

Schaller-Duke, Ranelle M.; Bogala, Mallikharjuna R.; Cassady, Carolyn J.

2018-02-01

Electron transfer dissociation (ETD) and collision-induced dissociation (CID) were used to investigate underivatized, metal-cationized oligosaccharides formed via electrospray ionization (ESI). Reducing and non-reducing sugars were studied including the tetrasaccharides maltotetraose, 3α,4β,3α-galactotetraose, stachyose, nystose, and a heptasaccharide, maltoheptaose. Univalent alkali, divalent alkaline earth, divalent and trivalent transition metal ions, and a boron group trivalent metal ion were adducted to the non-permethylated oligosaccharides. ESI generated [M + Met]+, [M + 2Met]2+, [M + Met]2+, [M + Met - H]+, and [M + Met - 2H]+ most intensely along with low intensity nitrate adducts, depending on the metal and sugar ionized. The ability of these metal ions to produce oligosaccharide adduct ions by ESI had the general trend: Ca(II) > Mg(II) > Ni(II) > Co(II) > Zn(II) > Cu(II) > Na(I) > K(I) > Al(III) ≈ Fe(III) ≈ Cr(III). Although trivalent metals were utilized, no triply charged ions were formed. Metal cations allowed for high ESI signal intensity without permethylation. ETD and CID on [M + Met]2+ produced various glycosidic and cross-ring cleavages, with ETD producing more cross-ring and internal ions, which are useful for structural analysis. Product ion intensities varied based on glycosidic-bond linkage and identity of monosaccharide sub-unit, and metal adducts. ETD and CID showed high fragmentation efficiency, often with complete precursor dissociation, depending on the identity of the adducted metal ion. Loss of water was occasionally observed, but elimination of small neutral molecules was not prevalent. For both ETD and CID, [M + Co]2+ produced the most uniform structurally informative dissociation with all oligosaccharides studied. The ETD and CID spectra were complementary. [Figure not available: see fulltext.

Patient characteristics associated with response to NSAID monotherapy in children with systemic juvenile idiopathic arthritis.

PubMed

Sura, Anjali; Failing, Christopher; Sturza, Julie; Stannard, Jasmine; Riebschleger, Meredith

2018-01-05

Systemic juvenile idiopathic arthritis (sJIA) is an auto-inflammatory disease characterized by fever, arthritis, and ≥1 of rash, generalized lymphadenopathy, hepato/splenomegaly, and serositis. Non-steroidal anti-inflammatory drugs (NSAIDs) are among the initial treatments of sJIA, but there is currently no evidence indicating which children should undergo a trial of NSAID monotherapy and which should not. Our objective is to identify presentation characteristics which are associated with response and lack of response to a trial of NSAID monotherapy. This is a retrospective single-center cohort study of children diagnosed with sJIA from 2000 to 2014. Patient demographics and disease characteristics were investigated to identify predictors of response to NSAID monotherapy. Eighty-seven children were newly diagnosed with sJIA 2000-2014. Thirteen of the 51 children who received NSAID monotherapy achieved clinically inactive disease (CID) without other medications. Age at presentation (≤8 years old), initial joint count (≤5), and C-reactive protein (CRP) (≤13 mg/dL) at diagnosis were associated with achievement of CID on NSAIDs alone. Physicians were less likely to trial NSAID monotherapy if the patient had either serositis or macrophage activation syndrome (MAS) at diagnosis. Ultimate achievement of CID and time to CID were not significantly affected by whether the patient received a trial of NSAID monotherapy. While a subset of children with sJIA can achieve CID with NSAID monotherapy, we recommend against a trial in patients who are >8 years old, with >5 joints involved, or with CRP > 13 mg/dL. Patients who undergo a trial of NSAID monotherapy should follow up within 2-4 weeks to evaluate for possible need for drug escalation. Clinical trials are necessary to confirm these findings.

Electron Transfer Dissociation and Collision-Induced Dissociation of Underivatized Metallated Oligosaccharides

NASA Astrophysics Data System (ADS)

Schaller-Duke, Ranelle M.; Bogala, Mallikharjuna R.; Cassady, Carolyn J.

2018-05-01

Electron transfer dissociation (ETD) and collision-induced dissociation (CID) were used to investigate underivatized, metal-cationized oligosaccharides formed via electrospray ionization (ESI). Reducing and non-reducing sugars were studied including the tetrasaccharides maltotetraose, 3α,4β,3α-galactotetraose, stachyose, nystose, and a heptasaccharide, maltoheptaose. Univalent alkali, divalent alkaline earth, divalent and trivalent transition metal ions, and a boron group trivalent metal ion were adducted to the non-permethylated oligosaccharides. ESI generated [M + Met]+, [M + 2Met]2+, [M + Met]2+, [M + Met - H]+, and [M + Met - 2H]+ most intensely along with low intensity nitrate adducts, depending on the metal and sugar ionized. The ability of these metal ions to produce oligosaccharide adduct ions by ESI had the general trend: Ca(II) > Mg(II) > Ni(II) > Co(II) > Zn(II) > Cu(II) > Na(I) > K(I) > Al(III) ≈ Fe(III) ≈ Cr(III). Although trivalent metals were utilized, no triply charged ions were formed. Metal cations allowed for high ESI signal intensity without permethylation. ETD and CID on [M + Met]2+ produced various glycosidic and cross-ring cleavages, with ETD producing more cross-ring and internal ions, which are useful for structural analysis. Product ion intensities varied based on glycosidic-bond linkage and identity of monosaccharide sub-unit, and metal adducts. ETD and CID showed high fragmentation efficiency, often with complete precursor dissociation, depending on the identity of the adducted metal ion. Loss of water was occasionally observed, but elimination of small neutral molecules was not prevalent. For both ETD and CID, [M + Co]2+ produced the most uniform structurally informative dissociation with all oligosaccharides studied. The ETD and CID spectra were complementary. [Figure not available: see fulltext.

Fermented Milk Consumption and Common Infections in Children Attending Day-Care Centers: A Randomized Trial.

PubMed

Prodeus, Andrey; Niborski, Violeta; Schrezenmeir, Juergen; Gorelov, Alexander; Shcherbina, Anna; Rumyantsev, Alexander

2016-11-01

This multicenter, double-blind, randomized, placebo-controlled clinical trial investigated the effect of a fermented milk product containing the Lactobacillus casei National Collection of Microorganisms and Cell Cultures (CNCM) I-1518 strain on respiratory and gastrointestinal common infectious diseases (CIDs) in children attending day-care centers in Russia. Children ages 3 to 6 years received 100 g of a fermented milk product (n = 300) or a control product (n = 299) twice daily for 3 months, followed by a 1-month observation period. The primary outcome was the incidence of CIDs during the product consumption period. There was no significant difference in the incidence of CIDs between the groups (N = 98 with fermented milk product vs N = 93 with control product). The overall number of CIDs (and no severe cases at all) in both study groups and in all 12 centers, however, was unexpectedly low resulting in underpowering of the study. No differences were found between the groups in the duration or severity of disease, duration of sick leave from day-care centers, parental missed working days, or in quality-of-life dimensions on the PedsQL questionnaire (P > 0.05).There was, however, a significantly lower incidence of the most frequently observed CID, rhinopharyngitis, in children consuming the fermented milk product compared with those consuming the control product (N = 81 vs N = 100, relative risk 0.82, 95% confidence interval 0.69-0.96, P = 0.017) when considering the entire study period. Although no other significant differences were shown between the fermented milk and control product groups in this study, lower incidence of rhinopharyngitis may indicate a beneficial effect of this fermented milk product.

Safety and retention rate of off-label uses of TNF antagonists in rheumatic conditions: data from the Spanish registry BIOBADASER 2.0.

PubMed

Carmona, Loreto; Descalzo, Miguel A; Ruiz-Montesinos, Dolores; Manero-Ruiz, Francisco J; Perez-Pampin, Eva; Gomez-Reino, Juan J

2011-01-01

To compare the safety and retention rate of TNF antagonists used in approved indications (AIs) and non-AIs. Analysis of the Spanish registry BIOBADASER 2.0 (February 2000 to October 2009). Patients were classified into AIs and off-label uses (OUs), according to the European Medicines Agency approval. Retention rates, incidence rates (IRs) and IR ratios (IRRs) of adverse events (AEs) with 95% CI were compared between uses, by log-rank test, cause-specific Cox regression models and generalized linear models with Poisson's distribution. First treatment with TNF antagonist was available in 5150 patients, of whom 4594 (89%) were AIs (2854 RA, 882 AS and 858 PsA) and 556 (11%) were OUs [437 chronic arthropathies in the spectrum of SpAs (CA) and 119 chronic immune-mediated diseases (CIDs)]. The IR of AE was largest in CID (649 events per 1000 patient-years) and lowest in PsA (250 events per 1000 patient-years). The occurrence of AEs was significantly associated with OU [IRR of CA vs RA 1.33 (95% CI 1.19, 1.49); IRR of CID vs RA 1.94 (95% CI 1.62, 2.31). The largest hazard ratio for discontinuation was for CID vs RA (1.33; 95% CI 1.02, 1.71) and especially vs AS (2.18; 95% CI 1.63, 2.90). OUs of TNF antagonists need a very close ascertainment of risk/benefit. The safety and retention pattern for CID is similar to that for RA and the pattern for CA resembles that of AS. This study shows an additional value of a national registry.

Homology modeling, molecular dynamics, and virtual screening of NorA efflux pump inhibitors of Staphylococcus aureus

PubMed Central

Bhaskar, Baki Vijaya; Babu, Tirumalasetty Muni Chandra; Reddy, Netala Vasudeva; Rajendra, Wudayagiri

2016-01-01

Emerging drug resistance in clinical isolates of Staphylococcus aureus might be implicated to the overexpression of NorA efflux pump which is capable of extruding numerous structurally diverse compounds. However, NorA efflux pump is considered as a potential drug target for the development of efflux pump inhibitors. In the present study, NorA model was constructed based on the crystal structure of glycerol-3-phosphate transporter (PDBID: 1PW4). Molecular dynamics (MD) simulation was performed using NAMD2.7 for NorA which is embedded in the hydrated lipid bilayer. Structural design of NorA unveils amino (N)- and carboxyl (C)-terminal domains which are connected by long cytoplasmic loop. N and C domains are composed of six transmembrane α-helices (TM) which exhibits pseudo-twofold symmetry and possess voluminous substrate binding cavity between TM helices. Molecular docking of reserpine, totarol, ferruginol, salvin, thioxanthene, phenothiazine, omeprazole, verapamil, nalidixic acid, ciprofloxacin, levofloxacin, and acridine to NorA found that all the molecules were bound at the large hydrophobic cleft and indicated significant interactions with the key residues. In addition, structure-based virtual screening was employed which indicates that 14 potent novel lead molecules such as CID58685302, CID58685367, CID5799283, CID5578487, CID60028372, ZINC12196383, ZINC72140751, ZINC72137843, ZINC39227983, ZINC43742707, ZINC12196375, ZINC66166948, ZINC39228014, and ZINC14616160 have highest binding affinity for NorA. These lead molecules displayed considerable pharmacological properties as evidenced by Lipinski rule of five and prophecy of toxicity risk assessment. Thus, the present study will be helpful in designing and synthesis of a novel class of NorA efflux pump inhibitors that restore the susceptibilities of drug compounds. PMID:27757014

Homology modeling, molecular dynamics, and virtual screening of NorA efflux pump inhibitors of Staphylococcus aureus.

PubMed

Bhaskar, Baki Vijaya; Babu, Tirumalasetty Muni Chandra; Reddy, Netala Vasudeva; Rajendra, Wudayagiri

2016-01-01

Emerging drug resistance in clinical isolates of Staphylococcus aureus might be implicated to the overexpression of NorA efflux pump which is capable of extruding numerous structurally diverse compounds. However, NorA efflux pump is considered as a potential drug target for the development of efflux pump inhibitors. In the present study, NorA model was constructed based on the crystal structure of glycerol-3-phosphate transporter (PDBID: 1PW4). Molecular dynamics (MD) simulation was performed using NAMD2.7 for NorA which is embedded in the hydrated lipid bilayer. Structural design of NorA unveils amino (N)- and carboxyl (C)-terminal domains which are connected by long cytoplasmic loop. N and C domains are composed of six transmembrane α-helices (TM) which exhibits pseudo-twofold symmetry and possess voluminous substrate binding cavity between TM helices. Molecular docking of reserpine, totarol, ferruginol, salvin, thioxanthene, phenothiazine, omeprazole, verapamil, nalidixic acid, ciprofloxacin, levofloxacin, and acridine to NorA found that all the molecules were bound at the large hydrophobic cleft and indicated significant interactions with the key residues. In addition, structure-based virtual screening was employed which indicates that 14 potent novel lead molecules such as CID58685302, CID58685367, CID5799283, CID5578487, CID60028372, ZINC12196383, ZINC72140751, ZINC72137843, ZINC39227983, ZINC43742707, ZINC12196375, ZINC66166948, ZINC39228014, and ZINC14616160 have highest binding affinity for NorA. These lead molecules displayed considerable pharmacological properties as evidenced by Lipinski rule of five and prophecy of toxicity risk assessment. Thus, the present study will be helpful in designing and synthesis of a novel class of NorA efflux pump inhibitors that restore the susceptibilities of drug compounds.

Patients with chronic insomnia have selective impairments in memory that are modulated by cortisol.

PubMed

Chen, Gui-Hai; Xia, Lan; Wang, Fang; Li, Xue-Wei; Jiao, Chuan-An

2016-10-01

Memory impairment is a frequent complaint in insomniacs; however, it is not consistently demonstrated. It is unknown whether memory impairment in insomniacs involves neuroendocrine dysfunction. The participants in this study were selected from the clinical setting and included 21 patients with chronic insomnia disorder (CID), 25 patients with insomnia and comorbid depressive disorder (CDD), and 20 control participants without insomnia. We evaluated spatial working and reference memory, object working and reference memory, and object recognition memory using the Nine Box Maze Test. We also evaluated serum neuroendocrine hormone levels. Compared to the controls, the CID patients made significantly more errors in spatial working and object recognition memory (p < .05), whereas the CDD patients performed poorly in all the assessed memory types (p < .05). In addition, the CID patients had higher levels (mean difference [95% CI]) of corticotrophin-releasing hormone, cortisol (31.98 [23.97, 39.98] μg/l), total triiodothyronine (667.58 [505.71, 829.45] μg/l), and total thyroxine (41.49 [33.23, 49.74] μg/l) (p < .05), and lower levels of thyrotropin-releasing hormone (-35.93 [-38.83, -33.02] ng/l), gonadotropin-releasing hormone (-4.50 [-5.02, -3.98] ng/l) (p < .05), and adrenocorticotropic hormone compared to the CDD patients. After controlling for confounding variables, the partial correlation analysis revealed that the levels of cortisol positively correlated with the errors in object working memory (r = .534, p = .033) and negatively correlated with the errors in object recognition memory (r = -.659, p = .006) in the CID patients. The results suggest that the CID patients had selective memory impairment, which may be mediated by increased cortisol levels. © 2016 Society for Psychophysiological Research.

Analysis of oversulfation in biglycan chondroitin/dermatan sulfate oligosaccharides by chip-based nanoelectrospray ionization multistage mass spectrometry.

PubMed

Flangea, Corina; Sisu, Eugen; Seidler, Daniela G; Zamfir, Alina D

2012-01-15

Biglycan (BGN) is a small proteoglycan that consists of a protein core containing leucine-rich repeat regions and two glycosaminoglycan (GAG) chains of either chondroitin sulfate (CS) or dermatan sulfate (DS) type. The development of novel, highly efficient analytical methods for structural identification of BGN-derived CS/DS motifs, possibly implicated in biological events, is currently the focus of research. In this work, an improved analytical method based on fully automated chip-nanoelectrospray ionization (nanoESI) in conjunction with high-capacity ion trap (HCT) multistage mass spectrometry (MS) by collision-induced dissociation (CID) was for the first time applied to BGN CS/DS oligosaccharide analysis. The CS/DS chains were released from transfected 293 BGN by β-elimination. The chain was digested with AC I lyase, and the resulting mixture was purified and subsequently separated by size exclusion chromatography (SEC). Di- and tetrasaccharide fractions were pooled and characterized in detail using the developed chip-nanoESI protocol. The chip-nanoESI MS profile in the negative ion mode revealed the presence of under-, regularly, and oversulfated species in both di- and tetrasaccharide fractions. CID MS(2)-MS(3) yielded sequence patterns consistent with unusual oversulfated 4,5-Δ-GlcA(2S)-GalNAc(4S) and 4,5-Δ-GlcA(2S)-GalNAc(6S)-IdoA(2S)-GalNAc(6S) motifs. Copyright © 2011 Elsevier Inc. All rights reserved.

Structural Analysis of Unsaturated Glycosphingolipids Using Shotgun Ozone-Induced Dissociation Mass Spectrometry

NASA Astrophysics Data System (ADS)

Barrientos, Rodell C.; Vu, Ngoc; Zhang, Qibin

2017-08-01

Glycosphingolipids are essential biomolecules widely distributed across biological kingdoms yet remain relatively underexplored owing to both compositional and structural complexity. While the glycan head group has been the subject of most studies, there is paucity of reports on the lipid moiety, particularly the location of unsaturation. In this paper, ozone-induced dissociation mass spectrometry (OzID-MS) implemented in a traveling wave-based quadrupole time-of-flight (Q-ToF) mass spectrometer was applied to study unsaturated glycosphingolipids using shotgun approach. Resulting high resolution mass spectra facilitated the unambiguous identification of diagnostic OzID product ions. Using [M+Na]+ adducts of authentic standards, we observed that the long chain base and fatty acyl unsaturation had distinct reactivity with ozone. The reactivity of unsaturation in the fatty acyl chain was about 8-fold higher than that in the long chain base, which enables their straightforward differentiation. Influence of the head group, fatty acyl hydroxylation, and length of fatty acyl chain on the oxidative cleavage of double bonds was also observed. Application of this technique to bovine brain galactocerebrosides revealed co-isolated isobaric and regioisomeric species, which otherwise would be incompletely identified using contemporary collision-induced dissociation (CID) alone. These results highlight the potential of OzID-MS in glycosphingolipids research, which not only provides complementary structural information to existing CID technique but also facilitates de novo structural determination of these complex biomolecules. [Figure not available: see fulltext.

Management of Cardiovascular Risk in Patients with Chronic Inflammatory Diseases: Current Evidence and Future Perspectives.

PubMed

Lindhardsen, Jesper; Kristensen, Søren Lund; Ahlehoff, Ole

2016-02-01

An increased risk of cardiovascular disease (CVD) has been observed in a range of chronic inflammatory diseases (CID), including rheumatoid arthritis (RA), psoriasis, inflammatory bowel diseases (IBD), and systemic lupus erythematosus (SLE). The increased risk of CVDs and reduced life expectancy in these conditions has stimulated considerable research and started an ongoing discussion on the need for a multidisciplinary approach and dedicated guidelines on CVD prevention in these patients. In addition, the possibility of inhibiting inflammation as a means to preventing CVD in these patients has gained considerable interest in recent years. We briefly summarize the current level of evidence of the association between CIDs and CVD and cardiovascular risk management recommendations. Perspectives of ongoing and planned trials are discussed in consideration of potential ways to improve primary and secondary CVD prevention in patients with CID.

Facilitating access to information in large documents with an intelligent hypertext system

NASA Technical Reports Server (NTRS)

Mathe, Nathalie

1993-01-01

Retrieving specific information from large amounts of documentation is not an easy task. It could be facilitated if information relevant in the current problem solving context could be automatically supplied to the user. As a first step towards this goal, we have developed an intelligent hypertext system called CID (Computer Integrated Documentation) and tested it on the Space Station Freedom requirement documents. The CID system enables integration of various technical documents in a hypertext framework and includes an intelligent context-sensitive indexing and retrieval mechanism. This mechanism utilizes on-line user information requirements and relevance feedback either to reinforce current indexing in case of success or to generate new knowledge in case of failure. This allows the CID system to provide helpful responses, based on previous usage of the documentation, and to improve its performance over time.

From student to steward: the Interdisciplinary Program in Neuroscience at Georgetown University as a case study in professional development during doctoral training.

PubMed

Ullrich, Lauren; Dumanis, Sonya B; Evans, Tanya M; Jeannotte, Alexis M; Leonard, Carrie; Rozzi, Summer J; Taylor, Caitlin M; Gale, Karen; Kanwal, Jagmeet S; Maguire-Zeiss, Kathleen A; Wolfe, Barry B; Forcelli, Patrick A

2014-01-01

A key facet of professional development is the formation of professional identity. At its most basic level, professional identity for a scientist centers on mastery of a discipline and the development of research skills during doctoral training. To develop a broader understanding of professional identity in the context of doctoral training, the Carnegie Initiative on the Doctorate (CID) ran a multi-institutional study from 2001 to 2005. A key outcome of the CID was the development of the concept of 'stewards of the discipline'. The Interdisciplinary Program in Neuroscience (IPN) at Georgetown University participated in CID from 2003 to 2005. Here, we describe the IPN and highlight the programmatic developments resulting from participation in the CID. In particular, we emphasize programmatic activities that are designed to promote professional skills in parallel with scientific development. We describe activities in the domains of leadership, communication, teaching, public outreach, ethics, collaboration, and mentorship. Finally, we provide data that demonstrate that traditional metrics of academic success are not adversely affected by the inclusion of professional development activities in the curricula. By incorporating these seven 'professional development' activities into the required coursework and dissertation research experience, the IPN motivates students to become stewards of the discipline.

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y.; Drake, Steven K.; Gucek, Marjan; Sacks, David B.; Yu, Yi-Kuo

2018-06-01

Rapid and accurate identification and classification of microorganisms is of paramount importance to public health and safety. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is complicating correct microbial identification even in a simple sample due to the large number of candidates present. To properly untwine candidate microbes in samples containing one or more microbes, one needs to go beyond apparent morphology or simple "fingerprinting"; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptide-centric representations of microbes to better separate them and by augmenting our earlier analysis method that yields accurate statistical significance. Here, we present an updated analysis workflow that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using 226 MS/MS publicly available data files (each containing from 2500 to nearly 100,000 MS/MS spectra) and 4000 additional MS/MS data files, that the updated workflow can correctly identify multiple microbes at the genus and often the species level for samples containing more than one microbe. We have also shown that the proposed workflow computes accurate statistical significances, i.e., E values for identified peptides and unified E values for identified microbes. Our updated analysis workflow MiCId, a freely available software for Microorganism Classification and Identification, is available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry.

PubMed

Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y; Drake, Steven K; Gucek, Marjan; Sacks, David B; Yu, Yi-Kuo

2018-06-05

Rapid and accurate identification and classification of microorganisms is of paramount importance to public health and safety. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is complicating correct microbial identification even in a simple sample due to the large number of candidates present. To properly untwine candidate microbes in samples containing one or more microbes, one needs to go beyond apparent morphology or simple "fingerprinting"; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptide-centric representations of microbes to better separate them and by augmenting our earlier analysis method that yields accurate statistical significance. Here, we present an updated analysis workflow that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using 226 MS/MS publicly available data files (each containing from 2500 to nearly 100,000 MS/MS spectra) and 4000 additional MS/MS data files, that the updated workflow can correctly identify multiple microbes at the genus and often the species level for samples containing more than one microbe. We have also shown that the proposed workflow computes accurate statistical significances, i.e., E values for identified peptides and unified E values for identified microbes. Our updated analysis workflow MiCId, a freely available software for Microorganism Classification and Identification, is available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html . Graphical Abstract ᅟ.

Equipment Location Plan, partial basement plan. (Includes identification of each ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Equipment Location Plan, partial basement plan. (Includes identification of each separate CPU, tape drive, hard drive, printer, keyboard, etc., within the data processing center in the southeast part of the basement.) March Air Force Base, Riverside, California, Combat Operations Center, 465-L DPC. By International Electric Corporation, Paramus, New Jersey (3/5/62); for Moffatt and Nichol, Engineers, 122 West Fifth Street, Long Beach, California; for the Corps of Engineers, U.S. Army, Office of the District Engineer, Los Angeles, California. Drawing no. AW-60-02-03, sheet no. 100, approved March, 1962; specifications no. OCI-62-66; D.O. series AW 1596/100, Rev. "A"; file drawer 1290. Last revised 3 October 1966. Scale one-quarter inch to one foot. 28.75x40.5 inches. ink on linen - March Air Force Base, Strategic Air Command, Combat Operations Center, 5220 Riverside Drive, Moreno Valley, Riverside County, CA

Equipment Location Plan, partial first floor plan. (Includes identification of ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Equipment Location Plan, partial first floor plan. (Includes identification of each separate CPU, tape drive, hard drive, printer, keyboard, etc., within the data processing center in the southwest part of the first floor.) March Air Force Base, Riverside, California, Combat Operations Center, 465-L EDTCC/EDLCC. By International Electric Corporation, Paramus, New Jersey (3/5/62); for Moffatt and Nichol, Engineers, 122 West Fifth Street, Long Beach, California; for the Corps of Engineers, U.S. Army, Office of the District Engineer, Los Angeles, California. Drawing no. AW-60-02-03, sheet no. 85, approved March, 1962; specifications no. OCI-62-66; D.O. series AW 1596/85, Rev. "A"; file drawer 1290. Last revised 3 October 1966. Scale one-quarter inch to one foot. 28.75x40.5 inches. ink on linen - March Air Force Base, Strategic Air Command, Combat Operations Center, 5220 Riverside Drive, Moreno Valley, Riverside County, CA

Visible and thermal spectrum synthetic image generation with DIRSIG and MuSES for ground vehicle identification training

NASA Astrophysics Data System (ADS)

May, Christopher M.; Maurer, Tana O.; Sanders, Jeffrey S.

2017-05-01

There is a ubiquitous and never ending need in the US armed forces for training materials that provide the warfighter with the skills needed to differentiate between friendly and enemy forces on the battlefield. The current state of the art in battlefield identification training is the Recognition of Combat Vehicles (ROCV) tool created and maintained by the Communications - Electronics Research, Development and Engineering Center Night Vision and Electronic Sensors Directorate (CERDEC NVESD). The ROC-V training package utilizes measured visual and thermal imagery to train soldiers about the critical visual and thermal cues needed to accurately identify modern military vehicles and combatants. This paper presents an approach that has been developed to augment the existing ROC-V imagery database with synthetically generated multi-spectral imagery that will allow NVESD to provide improved training imagery at significantly lower costs.

Infrared charge-injection-device array performance at low background

NASA Technical Reports Server (NTRS)

Mccreight, C. R.; Goebel, J. H.

1981-01-01

Low-background tests of a 1 x 32 Si:Bi charge-injection-device (CID) IR detector are carried out to evaluate its feasibility for space-based astronomical observations. Optimum performance is obtained at a temperature of 11 K. The sensitivity is found to compare well with that of discrete extrinsic silicon photoconductors. The measured sensitivity and the apparent absence of anomalous effects make extrinsic silicon CID arrays very promising for astronomical applications.

CID overview

NASA Technical Reports Server (NTRS)

Hayduk, R. J.

1986-01-01

On December 1, 1984, NASA and the Federal Aviation Administration (FAA) conducted the first remotely piloted air-to-ground crash test of a transport category aircraft. The Full-Scale Transport Controlled Impact Demonstration (CID) was the culmination of 4 years of effort by the two agencies. NASA and the FAA had many objectives during the joint planning and execution of the Controlled Impact Demonstration. The structural loads experiment was very successful. Ninety-seven percent of the channels were active at impact. The data is still being assessed. Only a portion of the data is presented here; approximately 80 channels of data are available. Analysis of the remaining data is in progress. Interior photography was also very successful. One hundred percent of the cameras functioned. The film contains unique information on the development of fire and smoke in the interior of the aircraft. From a human tolerance point of view, the CID was simulation of a survivable crash.

Fragmentation of alpha-Radical Cations of Arginine-Containing Peptides

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

Laskin, Julia; Yang, Zhibo; Ng, Dominic C.

2010-04-01

Fragmentation pathways of peptide radical cations, M+, with well-defined initial location of the radical site were explored using collision-induced dissociation (CID) experiments. Peptide radical cations were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes [salen = N,N´-ethylenebis (salicylideneaminato)]. Subsequent hydrogen abstraction from the -carbon of the side chain followed by Ca-C bond cleavage results in the loss of a neutral side chain and formation of an a-radical cation with the radical site localized on the a-carbon of the backbone. Similar CID spectra dominated by radical-driven dissociation products were obtained for a number of a-radicals when the basic arginine side chain wasmore » present in the sequence. In contrast, proton-driven fragmentation dominates CID spectra of a-radicals produced via the loss of the arginine side chain. Our results suggest that in most cases radical migration precedes fragmentation of large peptide radical cations.« less

Combat-related blast-induced neurotrauma: a public health problem?

PubMed

Jett, Shirley

2010-01-01

The purpose of this article is to raise nurses' awareness of the significance and potential public health impact of combat-related blast-induced neurotrauma (BINT) in U.S. troops returning from Afghanistan and Iraq. A comprehensive review of the current literature on BINT was completed by the author, based primarily on combat-related blast exposure in the military population. She found that it is necessary to theorize about potential etiologies for mild traumatic brain injury in the military population since the literature suggests that neurological and psychological trauma resulting from military duty may be linked to exposure to blasts. Identification of potential risk factors for BINT in the military population provides direction for scientific inquiry into this emerging phenomenon. Gaps in current knowledge and its health implications for future scientific study in nursing are presented. © 2010 Wiley Periodicals, Inc.

Prevention of IcaA regulated poly N-acetyl glucosamine formation in Staphylococcus aureus biofilm through new-drug like inhibitors: In silico approach and MD simulation study.

PubMed

Gupta, Ayushi; Mishra, Swechha; Singh, Sangeeta; Mishra, Sonali

2017-09-01

The effectiveness of various ligands against the protein structure of IcaA of the IcaABCD gene locus of Staphylococcus aureus were examined using the approach of structure based drug designing in reference with the protein's efficiency to form biofilms. Four compounds CID42738592, CID90468752, CID24277882, and CID6435208 were secluded from a database of 31,242 inhibitory ligands on the justification of the evaluated values falling under the four - tier structure based virtual screening. Under this principle value of least binding energy, human oral absorption and ADME properties were taken into consideration. Using the Glide module of Schrödinger, the above mentioned ligands showed an effective action against the protein IcaA which showed reduced activity as a glucosaminyl transferase. The complex of protein and ligand with best docking score was chosen for simulation studies. Structure based drug designing for the protein IcaA has given us potential leads as anti - biofilm agents. These screened out ligands might enable the development of new therapeutic strategies aimed at disrupting Staphylococcus aureus biofilms. The complex was showing stability towards the end of time for which it has been put for simulation. Thus molecule could be considered for making of biofilms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Intelligent Processing Equipment Projects at DLA

NASA Technical Reports Server (NTRS)

Obrien, Donald F.

1992-01-01

The Defense Logistics Agency is successfully incorporating Intelligent Processing Equipment (IPE) into each of its Manufacturing Technology thrust areas. Several IPE applications are addressed in the manufacturing of two 'soldier support' items: combat rations and military apparel. In combat rations, in-line sensors for food processing are being developed or modified from other industries. In addition, many process controls are being automated to achieve better quality and to gain higher use (soldier) acceptance. IPE applications in military apparel include: in-process quality controls for identification of sewing defects, use of robots in the manufacture of shirt collars, and automated handling of garments for pressing.

Intelligent processing equipment projects at DLA

NASA Astrophysics Data System (ADS)

Obrien, Donald F.

1992-04-01

The Defense Logistics Agency is successfully incorporating Intelligent Processing Equipment (IPE) into each of its Manufacturing Technology thrust areas. Several IPE applications are addressed in the manufacturing of two 'soldier support' items: combat rations and military apparel. In combat rations, in-line sensors for food processing are being developed or modified from other industries. In addition, many process controls are being automated to achieve better quality and to gain higher use (soldier) acceptance. IPE applications in military apparel include: in-process quality controls for identification of sewing defects, use of robots in the manufacture of shirt collars, and automated handling of garments for pressing.

Miocene weathering environments in Western Australia-Inferences from the abundance and 13C/12C of Fe(CO3)OH in CID goethite

NASA Astrophysics Data System (ADS)

Fritz, Tyler O.; Yapp, Crayton J.

2018-04-01

The channel iron deposits (CID) of the Hamersley Province in Western Australia are dominated by pedogenic goethite/hematite-rich ooids and pisoids that were transported to, and deposited in, the meandering channels of Miocene rivers. Information about the Miocene weathering environments that produced the Fe(III) oxides is archived in the mole fraction (X) and δ13C of the Fe(CO3)OH component in solid solution in oolitic CID goethite (α-FeOOH). Values of X and δ13C were measured for 12 oolitic goethite samples from different depths in two cores drilled in CID of the Robe Formation of Mesa J. The weighted-average plateau values of X ranged from 0.0098 to 0.0334, which suggest ambient CO2 concentrations that ranged from ∼50,000 ppm V to perhaps as much as ∼200,000 ppm V at the time of goethite crystallization. In a vadose zone characterized by in situ production of CO2 with steady-state Fickian diffusive transport of the gas, such concentrations would correspond to modeled soil respiration rates (Q) ranging from about 10 to 30 mmol/m2/h. Values for Q of about 10 mmol/m2/h are reported for soils in modern tropical forests with MAP ≥ ∼2000 mm. However, model-derived values of Q that exceed 15 mmol/m2/h are larger than observed in modern systems. This could indicate that some of the CID goethites crystallized in conditions that were phreatic or near phreatic rather than vadose. The δ13C values of the Fe(CO3)OH component in these 12 CID samples ranged from -24.0‰ to -22.3‰, which are among the most negative measured to date. If they reflect steady-state diffusive transport of CO2 in vadose environments, the soil CO2 would have been derived from a source with δ13C values that ranged from ∼-31‰ to -29‰. If, on the other hand, the goethites crystallized in a nearly phreatic environment that was moderately acidic, the inferred δ13C of the ancient CO2 source would have been about -27.6‰ to -25.8‰. In either case, the δ13C values point to in situ oxidation of C3 organic matter as the predominant source of the ambient CO2. The Fe(III) oxides in the CID ooids suggest crystallization in aerobic environments. However, even in aerobic environments, many microbial species can reduce the Fe3+ in oxides to relatively soluble Fe2+ and may have facilitated progressive Fe enrichment during multiple cycles of Fe(III) oxide dissolution and recrystallization. At the same time, microbially mediated oxidation of organic matter could have produced the high concentrations of soil CO2 with the very negative δ13C values recorded in the Fe(CO3)OH component in oolitic goethite. More frequent summer storms in the Miocene, may have been a significant factor in forming and eroding these soil systems and in concentrating large volumes of oolitic Fe(III) oxides in the local river systems to form channel iron deposits. However, published (U-Th)/He ages indicate that the oolitic CID goethites of Mesa J became closed systems after ∼7 Ma, which suggests a change in local climate and/or conditions of burial at about that time in the Miocene.

Role of the C-terminal and chitin insertion domains on enzymatic activity of endochitinase ChiA74 of Bacillus thuringiensis.

PubMed

Juárez-Hernández, Estefania O; Casados-Vázquez, Luz E; Bideshi, Dennis K; Salcedo-Hernández, R; Barboza-Corona, José E

2017-09-01

ChiA74 has modular structure that includes a secretion signal peptide (sp) sequence, and catalytic (CD), chitin insertion (CID), fibronectin type-III (FnIII) and chitin binding (CBD) domains. We described for the first time the existence of a putative CID in ChiA74. Mature ChiA74 lacking its sp sequence (rChiA74Δsp, ∼70kDa) and two truncated versions, rChiA74Δsp-60, rChiA74Δsp-50 lacking, respectively, CBD and CDB-FnIII were produced. rChiA74Δsp and rChiA74Δsp-60 are unstable and were processed to generate stable proteins of ∼50kDa. With colloidal chitin, rChiA74Δsp and rChiA74Δsp-50 had higher activity than rChiA74Δsp-60. rChiA74Δsp showed similar ability to bind chitin than rChiA74Δsp-50. The catalytic efficiencies (kcat/Km) of rChiA74Δsp and rChiA74Δsp-50 were higher, ∼ 21-fold than rChiA74Δsp-60, using chitin as the substrate. Optimal activity was detected at pH 7 and 40°C. Data suggest that the CBD in ChiA74 is important for binding to chitin, but not necessary as the presence of a CID together with the CD in a stable truncated version (i.e. ChiA74Δsp-50) has similar affinity and hydrolytic activity as the mature enzyme. The CID of ChiA74 showed identities of ∼ 55% with CIDs of other chitinases such as those from B. circulans and B. licheniformis, respectively, and conserved residues important for interacting with chitin. Copyright © 2017 Elsevier B.V. All rights reserved.

Gas chromatography/chemical ionization triple quadrupole mass spectrometry analysis of anabolic steroids: ionization and collision-induced dissociation behavior.

PubMed

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

2016-02-28

The detection of new anabolic steroid metabolites and new designer steroids is a challenging task in doping analysis. Switching from electron ionization gas chromatography triple quadrupole mass spectrometry (GC/EI-MS/MS) to chemical ionization (CI) has proven to be an efficient way to increase the sensitivity of GC/MS/MS analyses and facilitate the detection of anabolic steroids. CI also extends the possibilities of GC/MS/MS analyses as the molecular ion is retained in its protonated form due to the softer ionization. In EI it can be difficult to find previously unknown but expected metabolites due to the low abundance or absence of the molecular ion and the extensive (and to a large extent unpredictable) fragmentation. The main aim of this work was to study the CI and collision-induced dissociation (CID) behavior of a large number of anabolic androgenic steroids (AAS) as their trimethylsilyl derivatives in order to determine correlations between structures and CID fragmentation. Clarification of these correlations is needed for the elucidation of structures of unknown steroids and new metabolites. The ionization and CID behavior of 65 AAS have been studied using GC/CI-MS/MS with ammonia as the reagent gas. Glucuronidated AAS reference standards were first hydrolyzed to obtain their free forms. Afterwards, all the standards were derivatized to their trimethylsilyl forms. Full scan and product ion scan analyses were used to examine the ionization and CID behavior. Full scan and product ion scan analyses revealed clear correlations between AAS structure and the obtained mass spectra. These correlations were confirmed by analysis of multiple hydroxylated, methylated, chlorinated and deuterated analogs. AAS have been divided into three groups according to their ionization behavior and into seven groups according to their CID behavior. Correlations between fragmentation and structure were revealed and fragmentation pathways were postulated. Copyright © 2016 John Wiley & Sons, Ltd.

Characterization of Lipopeptide Biosurfactants Produced by Bacillus licheniformis MB01 from Marine Sediments

PubMed Central

Chen, Yulin; Liu, Shiliang A.; Mou, Haijin; Ma, Yunxiao; Li, Meng; Hu, Xiaoke

2017-01-01

Antibiotic resistance has become one of the world’s most severe problems because of the overuse of antibiotics. Antibiotic-resistant bacteria are more difficult to kill and more expensive to treat. Researchers have been studied on antibiotic alternatives such as antimicrobial peptides and lipopeptides. A functional bacteria MB01 producing lipopeptides which can be used as bacteriostat was isolated from the Bohai Sea sediments, which had been identified as Bacillus licheniformis by the morphological, physiological, and biochemical identification and 16s rDNA sequence. The lipopeptides produced by MB01 were determined to be cyclic surfactin homologs by LC-ESI-MS structural identification after crude extraction and LH-20 chromatography. [M+H]+ m/z 994, 1008, 1022, and 1036 were all the characteristic molecular weight of surfactin homologs. CID analysis revealed that the molecular structure of the lipopeptides was Rn-Glu1-Leu/Ile2-Leu3-Val4-Asp5-Leu6-Leu/Ile7. The lipopeptides showed well resistance to UV light and the change of pH and temperature. PMID:28559889

Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS)

NASA Astrophysics Data System (ADS)

Jora, Manasses; Burns, Andrew P.; Ross, Robert L.; Lobue, Peter A.; Zhao, Ruoxia; Palumbo, Cody M.; Beal, Peter A.; Addepalli, Balasubrahmanyam; Limbach, Patrick A.

2018-06-01

The analytical identification of positional isomers (e.g., 3-, N 4-, 5-methylcytidine) within the > 160 different post-transcriptional modifications found in RNA can be challenging. Conventional liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) approaches rely on chromatographic separation for accurate identification because the collision-induced dissociation (CID) mass spectra of these isomers nearly exclusively yield identical nucleobase ions (BH2 +) from the same molecular ion (MH+). Here, we have explored higher-energy collisional dissociation (HCD) as an alternative fragmentation technique to generate more informative product ions that can be used to differentiate positional isomers. LC-MS/MS of modified nucleosides characterized using HCD led to the creation of structure- and HCD energy-specific fragmentation patterns that generated unique fingerprints, which can be used to identify individual positional isomers even when they cannot be separated chromatographically. While particularly useful for identifying positional isomers, the fingerprinting capabilities enabled by HCD also offer the potential to generate HPLC-independent spectral libraries for the rapid analysis of modified ribonucleosides. [Figure not available: see fulltext.

Injury during U.S. Army basic combat training: a systematic review of risk factor studies.

PubMed

Bulzacchelli, Maria T; Sulsky, Sandra I; Rodriguez-Monguio, Rosa; Karlsson, Lee H; Hill, Maj Owen T

2014-12-01

Approximately one quarter of men and half of women in U.S. Army basic combat training experience an injury. Preventing basic combat training-related injuries would reduce associated human and economic costs and discharges from the Army. Identification of risk factors for such injuries is a crucial step toward their prevention. Although some research has begun to address this need, prior studies of risk factors for training-related injury have not been reviewed systematically. This study systematically reviews the literature on risk factors for injury during U.S. Army basic combat training. Original studies of risk factors for injury during U.S. Army basic combat training published since 1990 in peer-reviewed journals were identified using PubMed and manual searches of reference lists. This search was last performed in May 2013. Nineteen studies met the inclusion criteria. Methodologic quality and potential for bias were assessed. The findings of 11 studies deemed to be of high or medium quality were synthesized to determine the level of evidence supporting the association between each risk factor studied and risk of injury during basic combat training. Quality assessment and evidence synthesis were performed from June to September 2013. There is strong or moderate evidence supporting association of older age, history of smoking, and self-rated low physical activity level prior to basic combat training with increased risk of training-related injury among male trainees. There is limited, mixed, or insufficient evidence to identify risk factors for injury among female trainees. Copyright © 2014 American Journal of Preventive Medicine. All rights reserved.

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics

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

Shen, Yufeng; Tolic, Nikola; Piehowski, Paul D.

We report development of an approach providing high-resolution RPLC of proteins and its utility for mass spectrometry-based top-down proteomics. A chromatographic peak capacity of ~450 was achieved for proteins and large polypeptides having MWs up to 43 kDa in the context of proteomics applications. RPLC column lengths from 20 to 200 cm, particle sizes from 1.5 to 5 m, bonding alkyl chains from C1 to C2, C4, C8, and C18, and particle surface structures that spanned porous, superficially porous (porous shell, core-shell), and nonporous were investigated at pressures up to14K psi. Column length was found as the most important factormore » for >20 kDa proteins in gradient RPLC, and shortening column length degraded RPLC resolution and sensitivity regardless of the size and surface structure of the packing particles used. The alkyl chains bonded to the silica particle surface significantly affected the RPLC recovery and efficiency, and short alkyl C1-C4 phases provided higher sensitivity and resolution than C8 and C18 phases. Long gradient separations (e.g., >10 hours) with long columns (e.g., 100 cm) were particularly effective in conjunction with use of high accuracy mass spectrometers (e.g., the Orbitrap Elite) for top-down proteomics with improved proteoform coverage by allowing multiple HCD, CID, and ETD dissociation modes. It was also found that HCD produced small fragments useful for proteoform identification, while low energy CID and ETD often complemented HCD by providing large fragments.« less

Top-down mass spectrometry imaging of intact proteins by laser ablation ESI FT-ICR MS.

PubMed

Kiss, András; Smith, Donald F; Reschke, Brent R; Powell, Matthew J; Heeren, Ron M A

2014-05-01

Laser ablation ESI (LAESI) is a recent development in MS imaging. It has been shown that lipids and small metabolites can be imaged in various samples such as plant material, tissue sections or bacterial colonies without any sample pretreatment. Further, LAESI has been shown to produce multiply charged protein ions from liquids or solid surfaces. This presents a means to address one of the biggest challenges in MS imaging; the identification of proteins directly from biological tissue surfaces. Such identification is hindered by the lack of multiply charged proteins in common MALDI ion sources and the difficulty of performing tandem MS on such large, singly charged ions. We present here top-down identification of intact proteins from tissue with a LAESI ion source combined with a hybrid ion-trap FT-ICR mass spectrometer. The performance of the system was first tested with a standard protein with electron capture dissociation and infrared multiphoton dissociation fragmentation to prove the viability of LAESI FT-ICR for top-down proteomics. Finally, the imaging of a tissue section was performed, where a number of intact proteins were measured and the hemoglobin α chain was identified directly from tissue using CID and infrared multiphoton dissociation fragmentation. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Emergence and evolution of an interaction between intrinsically disordered proteins

PubMed Central

Hultqvist, Greta; Åberg, Emma; Camilloni, Carlo; Sundell, Gustav N; Andersson, Eva; Dogan, Jakob; Chi, Celestine N; Vendruscolo, Michele; Jemth, Per

2017-01-01

Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. However, it is not clear how such interactions emerge and evolve on a molecular level. We performed phylogenetic reconstruction, resurrection and biophysical characterization of two interacting disordered protein domains, CID and NCBD. CID appeared after the divergence of protostomes and deuterostomes 450–600 million years ago, while NCBD was present in the protostome/deuterostome ancestor. The most ancient CID/NCBD formed a relatively weak complex (Kd∼5 µM). At the time of the first vertebrate-specific whole genome duplication, the affinity had increased (Kd∼200 nM) and was maintained in further speciation. Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. DOI: http://dx.doi.org/10.7554/eLife.16059.001 PMID:28398197

The fate of b-ions in the two worlds of collision-induced dissociation.

PubMed

Waldera-Lupa, Daniel M; Stefanski, Anja; Meyer, Helmut E; Stühler, Kai

2013-12-01

Fragment analysis of proteins and peptides by mass spectrometry using collision-induced dissociation (CID) revealed that the pairwise generated N-terminal b- and C-terminal y-ions have different stabilities resulting in underrepresentation of b-ions. Detailed analyses of large-scale spectra databases and synthetic peptides underlined these observations and additionally showed that the fragmentation pattern depends on utilized CID regime. To investigate this underrepresentation further we systematically compared resonant excitation energy and beam-type CID facilitated on different mass spectrometer platforms: (i) quadrupole time-of-flight, (ii) linear ion trap and (iii) three-dimensional ion trap. Detailed analysis of MS/MS data from a standard tryptic protein digest revealed that b-ions are significantly underrepresented on all investigated mass spectrometers. By N-terminal acetylation of tryptic peptides we show for the first time that b-ion cyclization reaction significantly contributes to b-ion underrepresentation even on ion trap instruments and accounts for at most 16% of b-ion loss. © 2013.

Chemical stability of insulin. 2. Formation of higher molecular weight transformation products during storage of pharmaceutical preparations.

PubMed

Brange, J; Havelund, S; Hougaard, P

1992-06-01

Formation of covalent, higher molecular weight transformation (HMWT) products during storage of insulin preparations at 4-45 degrees C was studied by size exclusion chromatography. The main products are covalent insulin dimers (CID), but in protamine-containing preparations the concurrent formation of covalent insulin-protamine (CIP) products takes place. At temperatures greater than or equal to 25 degrees C parallel or consecutive formation of covalent oligo- and polymers can also be observed. Rate of HMWT is only slightly influenced by species of insulin but varies with composition and formulation, and for isophane (NPH) preparations, also with the strength of preparation. Temperature has a pronounced effect on CID, CIP, and, especially, covalent oligo- and polymer formation. The CIDs are apparently formed between molecules within the hexameric unit common for all types of preparations and rate of formation is generally faster in glycerol-containing preparations. Compared with insulin hydrolysis reactions (see the preceding paper), HMWT is one order of magnitude slower, except for NPH preparations.

A selective antagonist reveals a potential role of G protein-coupled receptor 55 in platelet and endothelial cell function.

PubMed

Kargl, Julia; Brown, Andrew J; Andersen, Liisa; Dorn, Georg; Schicho, Rudolf; Waldhoer, Maria; Heinemann, Akos

2013-07-01

The G protein-coupled receptor 55 (GPR55) is a lysophosphatidylinositol (LPI) receptor that is also responsive to certain cannabinoids. Although GPR55 has been implicated in several (patho)physiologic functions, its role remains enigmatic owing mainly to the lack of selective GPR55 antagonists. Here we show that the compound CID16020046 ((4-[4-(3-hydroxyphenyl)-3-(4-methylphenyl)-6-oxo-1H,4H,5H,6H-pyrrolo[3,4-c]pyrazol-5-yl] benzoic acid) is a selective GPR55 antagonist. In yeast cells expressing human GPR55, CID16020046 antagonized agonist-induced receptor activation. In human embryonic kidney (HEK293) cells stably expressing human GPR55, the compound behaved as an antagonist on LPI-mediated Ca²⁺ release and extracellular signal-regulated kinases activation, but not in HEK293 cells expressing cannabinoid receptor 1 or 2 (CB₁ or CB₂). CID16020046 concentration dependently inhibited LPI-induced activation of nuclear factor of activated T-cells (NFAT), nuclear factor κ of activated B cells (NF-κB) and serum response element, translocation of NFAT and NF-κB, and GPR55 internalization. It reduced LPI-induced wound healing in primary human lung microvascular endothelial cells and reversed LPI-inhibited platelet aggregation, suggesting a novel role for GPR55 in platelet and endothelial cell function. CID16020046 is therefore a valuable tool to study GPR55-mediated mechanisms in primary cells and tissues.

Evaluation of coal-related model compounds using a tandem mass spectrometry.

PubMed

Li, Guo-Sheng; Dong, Xueming; Fan, Xing; You, Chun-Yan; Wu, Ge; Zhao, Yun-Peng; Lu, Yao; Wei, Xian-Yong; Ma, Feng-Yun

2018-05-08

Gas chromotography/mass spectrometry (GC/MS) is a routine and basic instrumental method for the analysis of complex coal conversion products in chemical industry. To further enhance practical potentials of GC/MS in chemical industry, a tandem MS method for the selection of ion pair applied in monitoring coal conversions was established by using GC/quadrupole time-of-flight MS (GC/Q-TOF MS). The corresponding fragmentation pathways were explored and suitable ion pairs were screened. Fourteen coal-related model compounds (CRMCs) were analyzed using a GC/Q-TOF MS with different collision induced dissociation (CID) energies (5-20 eV). The fragmentation pathways can offer a better understanding of chemical bond breaking, hydrogen transfer, rearrangement reactions and elimination of neutral fragments for CRMCs during the CID process. The precursor ions of aromatic hydrocarbons without alkyl chain were hard to fragment with a CID energy of 20 eV. But aromatic hydrocarbons with branched chains were prone to fragment via the loss of alkyl chains and further fragmented through ring-open reactions. Compared to C alk -C ar bond, C ar -C ar bond was hard to fragment duo to its high bond dissociation energy. The existence of heteroatoms facilitated fragmentation that was conducive to screening ion pair. The CID technique of GC/Q-TOF MS will contribute to the studies on the organic composition of coals and building monitoring methods for coal conversions via fragmentation and ion pair selection. This article is protected by copyright. All rights reserved.

Rethinking Combat Identification. Joint Center for Lessons Learned Quarterly Bulletin. Volume 4, Issue 3, June 2002

DTIC Science & Technology

2002-06-01

Countermeasures Unit Chief Special Events Management Unit Chief Domestic Terrorism/ Counterterrorism Section Chief International Terrorism Section...Asstistant Director Counter- Terrorism Division Figure 3 Division/Section/Unit Hierarchies The LNO also supports the Special Events Management Unit (SEMU

Identification and feasibility test of specialized rural pedestrian safety training. Volume 1, Program development and evaluation

DOT National Transportation Integrated Search

1981-03-01

This report describes the development and evaluation of a K-12 pedestrian safety curriculum for suburban and rural schools. The three program curriculum, called PEDSAFE, was developed to combat pedestrian accidents which victimize suburban/rural chil...

Assessing the Impact of a Focused Deterrence Strategy to Combat Intimate Partner Domestic Violence.

PubMed

Sechrist, Stacy M; Weil, John D

2018-03-01

The Offender Focused Domestic Violence Initiative (OFDVI) represents for the first time anywhere the application of the evidence-based focused deterrence policing approach to combat intimate partner domestic violence (IPDV). Through holding offenders accountable, the strategy has resulted in 20% reductions each in IPDV-related calls for police service and arrests. Victim injuries have been significantly reduced and the 1-year IPDV offender recidivism rate is about 16-17%. The backbone of the OFDVI strategy is the multidisciplinary collaboration of law enforcement and community partners which has resulted in identification and resolving system issues which have historically allowed offenders to repeat IPDV without consequence.

Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques

DOE PAGES

Ford, Kristina L.; Zeng, Wei; Heazlewood, Joshua L.; ...

2015-08-28

The analysis of post-translational modifications (PTMs) by proteomics is regarded as a technically challenging undertaking. While in recent years approaches to examine and quantify protein phosphorylation have greatly improved, the analysis of many protein modifications, such as glycosylation, are still regarded as problematic. Limitations in the standard proteomics workflow, such as use of suboptimal peptide fragmentation methods, can significantly prevent the identification of glycopeptides. The current generation of tandem mass spectrometers has made available a variety of fragmentation options, many of which are becoming standard features on these instruments. Lastly, we have used three common fragmentation techniques, namely CID, HCD,more » and ETD, to analyze a glycopeptide and highlight how an integrated fragmentation approach can be used to identify the modified residue and characterize the N-glycan on a peptide.« less

Read-noise characterization of focal plane array detectors via mean-variance analysis.

PubMed

Sperline, R P; Knight, A K; Gresham, C A; Koppenaal, D W; Hieftje, G M; Denton, M B

2005-11-01

Mean-variance analysis is described as a method for characterization of the read-noise and gain of focal plane array (FPA) detectors, including charge-coupled devices (CCDs), charge-injection devices (CIDs), and complementary metal-oxide-semiconductor (CMOS) multiplexers (infrared arrays). Practical FPA detector characterization is outlined. The nondestructive readout capability available in some CIDs and FPA devices is discussed as a means for signal-to-noise ratio improvement. Derivations of the equations are fully presented to unify understanding of this method by the spectroscopic community.

Mass Spectral Studies of 1-(2-Chloroethoxy)-2-[(2-chloroethyl)thio] Ethane and Related Compounds Using Gas ChromatographyMass Spectrometry and Gas ChromatographyTriple-Quadrupole Mass Spectrometry

DTIC Science & Technology

2016-02-01

NOTES 14. ABSTRACT: The electron impact and collision-induced- dissociation mass spectra of 1-(2-chloroethoxy)-2-[(2-chloroethyl)thio] ethane and 10...Collision-ion dissociation (CID) Triple-quadrupole mass spectrometry (QQQ) 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT...ratio, 10:1), and a 1.0 µL volume of sample was placed on the column. Nitrogen was used as the collision gas for the collision-induced dissociation (CID

An Analysis of Item Identification for Additive Manufacturing (3-D Printing) Within the Naval Supply Chain

DTIC Science & Technology

2014-12-01

manufacturing BPA blanket purchase agreement BMW Bavarian Motor Works CAD computer-aided design CASREP casualty report CDSA Combat Direction...agreements ( BPA ), and through existing indefinite delivery and indefinite quantity (IDIQ) contracts. These types of procurement methods have less visibility

Gas-phase synthesis of singly and multiply charged polyoxovanadate anions employing electrospray ionization and collision induced dissociation.

PubMed

Al Hasan, Naila M; Johnson, Grant E; Laskin, Julia

2013-09-01

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy(n-) and VxOyCl(n-) ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N(+), tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCl(n-) and VxOyCl(L)((n-1)-) clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl((1-2)-) and VxOy ((1-2)-) anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.

Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

2013-09-01

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy n- and VxOyCln- ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N+, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCln- and VxOyCl(L)(n-1)- clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl(1-2)- and VxOy (1-2)- anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.

Technologies to Combat Aedes Mosquitoes: A Model Based on Smart City.

PubMed

de Souza Silva, Geovanna Cristine; Peltonen, Laura-Maria; Pruinelli, Lisiane; Yoshikazu Shishido, Henrique; Jacklin Eler, Gabrielle

2018-01-01

Aedes aegypti and Aedes albopictus mosquitoes are responsible for the transmission of diseases such as dengue fever, yellow fever, chikungunya fever, zika virus fever, some of which can cause irreversible central nervous system problems and death. This study investigates what technologies are being used for combatting and monitoring the Aedes mosquitoes and to propose joining these technologies into a single and complete solution using the Smart Cities concept. A search for newscasts on Google and mobile apps in app stores were performed to identify technological solutions for combat to Aedes mosquitoes. Also, a model for joint technology was proposed. Results identified the following technologies: 170 software, two sensors, two drones, one electronic device, ten mosquito traps/lures, seven biological tools, six biotechnologies, and eight chemical formulations. Technological resources and adoption of preventive measures by the population could be a useful method for the mosquito control. Examples include a georeferenced model for identification and examination of larvae, application of chemical/biological products, real-time mapping, sending of educational materials via email or social media for the population, and alerts to health professionals in the zones of combat/risk. In combination, these technologies may indicate a better solution to the current problem.

Ion mobility mass spectrometry for ion recovery and clean-up of MS and MS/MS spectra obtained from low abundance viral samples

PubMed Central

Harvey, David J.; Crispin, Max; Bonomelli, Camille; Scrivens, Jim H.

2016-01-01

Graphical abstract Many samples of complex mixtures of N-glycans released from small amounts of material, such as glycoproteins from viruses, present problems for mass spectrometric analysis because of the presence of contaminating material that is difficult to remove by conventional methods without involving sample loss. This paper describes the use of ion mobility for extraction of glycan profiles from such samples and for obtaining clean CID spectra when targeted m/z values capture additional ions from those of the target compound. N-Glycans were released enzymatically from within SDS-PAGE gels, from the representative glycoprotein, gp120 of the human immunodeficiency virus, and examined by direct infusion electrospray in negative mode followed by ion mobility with a Waters Synapt G2 mass spectrometer. Clean profiles of singly, doubly and triply charged N-glycans were obtained from samples in cases where the raw electrospray spectra displayed only a few glycan ions as the result of low sample concentration or the presence of contamination. Ion mobility also enabled uncontaminated CID spectra to be obtained from glycans when their molecular ions displayed coincidence with ions from fragments or multiply charged ions with similar m/z values. This technique proved to be invaluable for removing extraneous ions from many CID spectra. The presence of such ions often produces spectra that are difficult to interpret. Most CID spectra, even those from abundant glycan constituents, benefited from such clean-up showing that the extra dimension provided by ion mobility was invaluable for studies of this type. PMID:26204966

Assignment of the Stereochemistry and Anomeric Configuration of Sugars within Oligosaccharides Via Overlapping Disaccharide Ladders Using MSn

NASA Astrophysics Data System (ADS)

Konda, Chiharu; Londry, Frank A.; Bendiak, Brad; Xia, Yu

2014-08-01

A systematic approach is described that can pinpoint the stereo-structures (sugar identity, anomeric configuration, and location) of individual sugar units within linear oligosaccharides. Using a highly modified mass spectrometer, dissociation of linear oligosaccharides in the gas phase was optimized along multiple-stage tandem dissociation pathways (MSn, n = 4 or 5). The instrument was a hybrid triple quadrupole/linear ion trap mass spectrometer capable of high-efficiency bidirectional ion transfer between quadrupole arrays. Different types of collision-induced dissociation (CID), either on-resonance ion trap or beam-type CID could be utilized at any given stage of dissociation, enabling either glycosidic bond cleavages or cross-ring cleavages to be maximized when wanted. The approach first involves optimizing the isolation of disaccharide units as an ordered set of overlapping substructures via glycosidic bond cleavages during early stages of MSn, with explicit intent to minimize cross-ring cleavages. Subsequently, cross-ring cleavages were optimized for individual disaccharides to yield key diagnostic product ions ( m/ z 221). Finally, fingerprint patterns that establish stereochemistry and anomeric configuration were obtained from the diagnostic ions via CID. Model linear oligosaccharides were derivatized at the reducing end, allowing overlapping ladders of disaccharides to be isolated from MSn. High confidence stereo-structural determination was achieved by matching MSn CID of the diagnostic ions to synthetic standards via a spectral matching algorithm. Using this MSn ( n = 4 or 5) approach, the stereo-structures, anomeric configurations, and locations of three individual sugar units within two pentasaccharides were successfully determined.

Extreme Contrast Ratio Imaging of Sirius with a Charge Injection Device

NASA Astrophysics Data System (ADS)

Batcheldor, D.; Foadi, R.; Bahr, C.; Jenne, J.; Ninkov, Z.; Bhaskaran, S.; Chapman, T.

2016-02-01

The next fundamental steps forward in understanding our place in the universe could be a result of advances in extreme contrast ratio (ECR) imaging and point-spread function (PSF) suppression. For example, blinded by quasar light we have yet to fully understand the processes of galaxy and star formation and evolution, and there is an ongoing race to obtain a direct image of an exo-Earth lost in the glare of its host star. To fully explore the features of these systems, we must perform observations in which contrast ratios (CRs) of at least one billion can be regularly achieved with sub 0.″1 inner working angles. Here, we present the details of a latest-generation 32-bit charge injection device (CID) that could conceivably achieve CRs on the order of one billion. We also demonstrate some of its ECR imaging abilities for astronomical imaging. At a separation of two arcminutes, we report a direct CR of {{Δ }}{m}v=18.3,{log}({CR})=7.3, or 1 part in 20 million, from observations of the Sirius field. The atmospheric conditions present during the collection of this data prevented less modest results, and we expect to be able to achieve higher CRs, with improved inner working angles, simply by operating a CID at a world-class observing site. However, CIDs do not directly provide any PSF suppression. Therefore, combining CID imaging with a simple PSF suppression technique like angular differential imaging could provide a cheap and easy alternative to the complex ECR techniques currently being employed.

Places where preschoolers are (in)active: An observational study on Latino preschoolers and their parents using objective measures

USDA-ARS?s Scientific Manuscript database

To combat the disproportionately higher risk of childhood obesity in Latino preschool-aged children, multilevel interventions targeting physical (in)activity are needed. These require the identification of environmental and psychosocial determinants of physical (in)activity for this ethnic group. Th...

Defending the Homeland: The Case for Integrating National Guard Intelligence Personnel into the State Fusion Centers

DTIC Science & Technology

2011-02-15

already robust lineup of 57 National Guard Combat Support Teams (CSTs) and 17 CBRNE Enhanced Response Force Packages (CERFPs) to increase the existing...analysis of disparate data sources, identification of intelligence gaps, and proactive collection of intelligence against those gaps which could

Regional Collaboration To Combat Substance Abuse: A Local Success Story.

ERIC Educational Resources Information Center

Upperman, James E.

This paper provides information on a substance abuse prevention effort called the Commonwealth Alliance for Drug Rehabilitation and Education (CADRE). After a discussion of the origins of CADRE, five steps taken by CADRE in its substance abuse prevention efforts are described, beginning with organizational establishment. The identification and…

Identification of a new supraclavicular brown fat depot in mice

USDA-ARS?s Scientific Manuscript database

The rediscovery of brown adipose tissue (BAT) in healthy adult humans raises the possibility of utilizing BAT to combat obesity and its related metabolic disorders. Adult humans possess limited amounts of BAT with the most thermoactive depot located in the supraclavicular area of the neck. Understan...

Combat Identification Modeling Using Neural Networks Techniques

DTIC Science & Technology

2009-03-01

Ybarvector SSpe ANOVA Xhatp; clear Yhatp U Z xi xerror yerror Tcrit BoxCoxusedlamda BoxCoxusedlog; clear leveragepoints Cooks DFFITS Cooksinfluence...counter lofFo e; clear lofFpvalue SSlof SSpe StdErr To Tstat Tpvalue Bhat Rstud I VIF; clear invR Tcrit X LofFit ALLREG BOXCOX GRAPHS globalp Warnng

Combat Identification Modeling Using Robust Optimization Techniques

DTIC Science & Technology

2008-03-01

ePRESS Si2 Rstud t nvector groupnum Ybarvector SSpe ANOVA Xhatp; clear Yhatp U Z xi xerror yerror Tcrit BoxCoxusedlamda BoxCoxusedlog; clear...dfsslof; clear nvector ttlvector Ybarvector m j N groupnum counter lofFo e; clear lofFpvalue SSlof SSpe StdErr To Tstat Tpvalue Bhat Rstud I VIF

Female United States Air Force (USAF) pilots: themes, challenges, and possible solutions.

PubMed

McGlohn, S E; King, R E; Butler, J W; Retzlaff, P D

1997-02-01

Identification of stresses of mixed-gender squadrons, attention to the psychological concerns of pilots in combat, and recognition of the difficulties of balancing a career and family are important in today's United States Air Force (USAF). What qualities are desirable in male and female pilots in combat situations, how do men and women view their career and family goals, and how do men and women work together in day-to-day squadron activities versus deployment and combat situations? A semi-structured clinical interview sought in formation about personal/family health, squadron relationships, and career/deployment stresses. The interview covered the effect of grounding for more than 30 d, motivation to fly, health decrements due to aircraft design, teamwork difficulties and blocks to success, career demands, combat and prisoner of war (POW) concerns, stress and coping styles, flying goals, and family/health concerns. There were 114 (64 male and 50 female) pilots who participated in the study. The majority of male pilots interviewed asserted that they would be more protective of a woman in combat than a man and were concerned about their reaction to a female POW. Many women were concerned about being used to exploit men in a POW camp. The majority of pilots believed women were well integrated into their squadrons. Those interviewed reported that the squadron members with the most difficulty dealing with women were older males, including enlisted crew and some commanders. The information gained from this study will assist the USAF in understanding and coping with the psychological stresses associated with combat, deployment, and mixed-gender squadrons.

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.

Identification of Patients with RAG Mutations Previously Diagnosed with Common Variable Immunodeficiency Disorders

PubMed Central

Buchbinder, David; Baker, Rebecca; Lee, Yu Nee; Ravell, Juan; Zhang, Yu; McElwee, Joshua; Nugent, Diane; Coonrod, Emily M.; Durtschi, Jacob D.; Augustine, Nancy H.; Voelkerding, Karl V.; Csomos, Krisztian; Rosen, Lindsey; Browne, Sarah; Walter, Jolan E.; Notarangelo, Luigi D.; Hill, Harry R.; Kumánovics, Attila

2015-01-01

Purpose Combined immunodeficiency (CID) presents a unique challenge to clinicians. Two patients presented with the prior clinical diagnosis of common variable immunodeficiency (CVID) disorder marked by an early age of presentation, opportunistic infections, and persistent lymphopenia. Due to the presence of atypical clinical features, next generation sequencing was applied documenting RAG deficiency in both patients. Methods Two different genetic analysis techniques were applied in these patients including whole exome sequencing in one patient and the use of a gene panel designed to target genes known to cause primary immunodeficiency disorders (PIDD) in a second patient. Sanger dideoxy sequencing was used to confirm RAG1 mutations in both patients. Results Two young adults with a history of recurrent bacterial sinopulmonary infections, viral infections, and autoimmune disease as well as progressive hypogammaglobulinemia, abnormal antibody responses, lymphopenia and a prior diagnosis of CVID disorder were evaluated. Compound heterozygous mutations in RAG1 (1) c256_257delAA, p86VfsX32 and (2) c1835A>G, pH612R were documented in one patient. Compound heterozygous mutations in RAG1 (1) c.1566G>T, p.W522C and (2) c.2689C>T, p. R897X) were documented in a second patient post-mortem following a fatal opportunistic infection. Conclusion Astute clinical judgment in the evaluation of patients with PIDD is necessary. Atypical clinical findings such as early onset, granulomatous disease, or opportunistic infections should support the consideration of atypical forms of late onset CID secondary to RAG deficiency. Next generation sequencing approaches provide powerful tools in the investigation of these patients and may expedite definitive treatments. PMID:25516070

Mechanism of Formation of the Major Estradiol Product Ions Following Collisional Activation of the Molecular Anion in a Tandem Quadrupole Mass Spectrometer

NASA Astrophysics Data System (ADS)

Wooding, Kerry M.; Barkley, Robert M.; Hankin, Joseph A.; Johnson, Christopher A.; Bradford, Andrew P.; Santoro, Nanette; Murphy, Robert C.

2013-10-01

The importance of the mass spectral product ion structure is highlighted in quantitative assays, which typically use multiple reaction monitoring (MRM), and in the discovery of novel metabolites. Estradiol is an important sex steroid whose quantitation and metabolite identification using tandem mass spectrometry has been widely employed in numerous clinical studies. Negative electrospray ionization tandem mass spectrometry of estradiol (E2) results in several product ions, including the abundant m/z 183 and 169. Although m/z 183 is one of the most abundant product ions used in many quantitative assays, the structure of m/z 183 has not been rigorously examined. We suggest a structure for m/z 183 and a mechanism of formation consistent with collision induced dissociation (CID) of E2 and several stable isotopes ([D4]-E2, [13C6]-E2, and [D1]-E2). An additional product ion from E2, namely m/z 169, has also been examined. MS3 experiments indicated that both m/z 183 and m/z 169 originate from only E2 [M - H]- m/z 271. These ions, m/z 183 and m/z 169, were also present in the collision induced decomposition mass spectra of other prominent estrogens, estrone (E1) and estriol (E3), indicating that these two product ions could be used to elucidate the estrogenic origin of novel metabolites. We propose two fragmentation schemes to explain the CID data and suggest a structure of m/z 183 and m/z 169 consistent with several isotopic variants and high resolution mass spectrometric measurements.

Study of Highly Selective and Efficient Thiol Derivatization using Selenium Reagents by Mass Spectrometry

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

Xu, Kehua; Zhang, Yun W.; Tang, Bo

2010-08-15

Biological thiols are critical physiological components and their detection often involves derivatization. This paper reports a systemic mass spectrometry (MS) investigation of the cleavage of Se-N bond by thiol to form a new Se-S bond, the new selenium chemistry for thiol labeling. Our data shows that the reaction is highly selective, rapid, reversible and efficient. For instance, among twenty amino acids, only cysteine was found to be reactive with Se-N containing reagents and the reaction takes place in seconds. By adding dithiothreitol (DTT), the newly formed Se-S bond of peptides/proteins can be reduced back to free thiol. The high selectivitymore » and excellent reversibility of the reaction provide potential of using this chemistry for selective identification of thiol compounds or enriching and purifying thiol peptides/proteins. In addition, the derivatized thiol peptides have interesting dissociation behavior, which is tunable using different selenium reagents. For example, by introducing an adjacent nucleophilic group into the selenium reagent in the case of using ebselen, the reaction product of ebselen with glutathione (GSH) is easy to lose the selenium tag upon collision-induced dissociation (CID), which is useful to "fish out" those peptides containing free cysteine residues by precursor ion scan. By contrast, the selenium tag of N-(phenylseleno) phthalimide reagent can be stable and survive in CID process, which would be of value in pinpointing thiol location using a top-down proteomic approach. Also, the high conversion yield of the reaction allows the counting of total number of thiol in proteins. We believe that ebselen or N-(phenylseleno) phthalimide as tagging thiol-protein reagents will have important applications in both qualitative and quantitative analysis of different thiol-proteins derived from living cells by MS method.« less

Collision-induced dissociation analysis of negative atmospheric ion adducts in atmospheric pressure corona discharge ionization mass spectrometry.

PubMed

Sekimoto, Kanako; Takayama, Mitsuo

2013-05-01

Collision-induced dissociation (CID) experiments were performed on atmospheric ion adducts [M + R](-) formed between various types of organic compounds M and atmospheric negative ions R(-) [such as O2(-), HCO3(-), COO(-)(COOH), NO2(-), NO3(-), and NO3(-)(HNO3)] in negative-ion mode atmospheric pressure corona discharge ionization (APCDI) mass spectrometry. All of the [M + R](-) adducts were fragmented to form deprotonated analytes [M - H](-) and/or atmospheric ions R(-), whose intensities in the CID spectra were dependent on the proton affinities of the [M - H](-) and R(-) fragments. Precursor ions [M + R](-) for which R(-) have higher proton affinities than [M - H](-) formed [M - H](-) as the dominant product. Furthermore, the CID of the adducts with HCO3(-) and NO3(-)(HNO3) led to other product ions such as [M + HO](-) and NO3(-), respectively. The fragmentation behavior of [M + R](-) for each R(-) observed was independent of analyte type (e.g., whether the analyte was aliphatic or aromatic, or possessed certain functional groups).

Discrimination Between Peptide O-Sulfo- and O-Phosphotyrosine Residues by Negative Ion Mode Electrospray Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Edelson-Averbukh, Marina; Shevchenko, Andrej; Pipkorn, Rüdiger; Lehmann, Wolf D.

2011-12-01

Unambiguous differentiation between isobaric sulfated and phosphorylated tyrosine residues (sTyr and pTyr) of proteins by mass spectrometry is challenging, even using high resolution mass spectrometers. Here we show that upon negative ion mode collision-induced dissociation (CID), pTyr- and sTyr-containing peptides exhibit entirely different modification-specific fragmentation patterns leading to a rapid discrimination between the isobaric covalent modifications using the tandem mass spectral data. This study reveals that the ratio between the relative abundances of [M-H-80]- and [M-H-98]- fragment ions in ion-trap CID and higher energy collision dissociation (HCD) spectra of singly deprotonated +80 Da Tyr-peptides can be used as a reliable indication of the Tyr modification group nature. For multiply deprotonated +80 Da Tyr-peptides, CID spectra of sTyr- and pTyr-containing sequences can be readily distinguished based on the presence/absence of the [M-nH-79](n-1)- and [M-nH-79-NL]( n-1)- ( n = 2, 3) fragment ions (NL = neutral loss).

Multiplex real-time PCR for identification of canine parvovirus antigenic types.

PubMed

Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P N; Narang, Deepti

2016-07-01

Canine parvovirus (CPV) is an important disease causing gastroenteritis and/or haemorrhagic gastroenteritis in dogs. There are four antigenic types of CPV reported worldwide viz. CPV 2, CPV 2a, CPV 2b and CPV 2c. The diagnosis of CPV with the identification of the antigen type responsible remains problematic. In the present study, identification as well as antigenic typing of CPV was done using a de novo multiplex real time PCR to combat the problem of antigenic type identification. From the study it could be concluded that the here developed multiplex real time PCR assay could be used for rapid detection of CPV as well as typing of its three antigenic types. Copyright © 2016 Elsevier B.V. All rights reserved.

A Novel Proteomics Approach to Identify SUMOylated Proteins and Their Modification Sites in Human Cells*

PubMed Central

Galisson, Frederic; Mahrouche, Louiza; Courcelles, Mathieu; Bonneil, Eric; Meloche, Sylvain; Chelbi-Alix, Mounira K.; Thibault, Pierre

2011-01-01

The small ubiquitin-related modifier (SUMO) is a small group of proteins that are reversibly attached to protein substrates to modify their functions. The large scale identification of protein SUMOylation and their modification sites in mammalian cells represents a significant challenge because of the relatively small number of in vivo substrates and the dynamic nature of this modification. We report here a novel proteomics approach to selectively enrich and identify SUMO conjugates from human cells. We stably expressed different SUMO paralogs in HEK293 cells, each containing a His6 tag and a strategically located tryptic cleavage site at the C terminus to facilitate the recovery and identification of SUMOylated peptides by affinity enrichment and mass spectrometry. Tryptic peptides with short SUMO remnants offer significant advantages in large scale SUMOylome experiments including the generation of paralog-specific fragment ions following CID and ETD activation, and the identification of modified peptides using conventional database search engines such as Mascot. We identified 205 unique protein substrates together with 17 precise SUMOylation sites present in 12 SUMO protein conjugates including three new sites (Lys-380, Lys-400, and Lys-497) on the protein promyelocytic leukemia. Label-free quantitative proteomics analyses on purified nuclear extracts from untreated and arsenic trioxide-treated cells revealed that all identified SUMOylated sites of promyelocytic leukemia were differentially SUMOylated upon stimulation. PMID:21098080

Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.

PubMed

Cheng, Chia-Ying; Tsai, Chia-Feng; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian

2013-05-03

As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to construct decoy spectral libraries. Most of them construct decoy peptide sequences and then generate theoretical spectra accordingly. In this paper, we propose a method, called precursor-swap, which directly constructs decoy spectral libraries directly at the "spectrum level" without generating decoy peptide sequences by swapping the precursors of two spectra selected according to a very simple rule. Our spectrum-based method does not require additional efforts to deal with ion types (e.g., a, b or c ions), fragment mechanism (e.g., CID, or ETD), or unannotated peaks, but preserves many spectral properties. The precursor-swap method is evaluated on different spectral libraries and the results of obtained decoy ratios show that it is comparable to other methods. Notably, it is efficient in time and memory usage for constructing decoy libraries. A software tool called Precursor-Swap-Decoy-Generation (PSDG) is publicly available for download at http://ms.iis.sinica.edu.tw/PSDG/.

The identification and analytical characterization of 2,2'-difluorofentanyl.

PubMed

Liu, Cuimei; Li, Tao; Han, Yu; Hua, Zhendong; Jia, Wei; Qian, Zhenhua

2018-04-01

New psychoactive substances (NPS) have expanded their distribution and become widely available in the global market in recent years. The illicit use of fentanyl and its analogs has become an important worldwide concern linked to their high potency and risk of fatal overdose. This study describes the analytical characterization of a new fentanyl derivative N-(1-(2-fluorophenethyl)-4-piperidinyl)-N-(2-fluorophenyl)propionamide (2,2'-difluorofentanyl). Identification was based on ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UHPLC-QTOF-MS), gas chromatography-mass spectrometry (GC-MS), Fourier transform infrared (FTIR) spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy. To our knowledge, this study is the first to report on analytical data for this compound. The most abundant fragment ion in the electrospray ionization (ESI) mass spectrum under collision-induced dissociation (CID) mode was formed by the cleavage between the piperidine ring and the N-phenyl-amide moiety of the protonated molecule. Two diagnostic ions in the electron ionization (EI) mass spectrum were formed by the loss of a tropylium ion (M-91), and by the degradation of the piperidine ring and dissociate of the COC 2 H 5 moiety altogether, respectively. Copyright © 2017 John Wiley & Sons, Ltd.

Metabolism studies of benzbromarone in rats by high performance liquid chromatography-quadrupole time of flight mass spectrometry.

PubMed

Wu, Haiqing; Peng, Ying; Wang, Shaojie; Wang, Kai; Zhao, Xunchen; Jiang, Fan

2012-12-12

A high performance liquid chromatography-quadrupole time of flight mass spectrometry (HPLC-QTOF-MS) method was employed in investigation of benzbromarone metabolites in rat plasma, urine, feces and bile samples. Meanwhile, the metabolic pathways of benzbromarone in rats were discussed. The identification was achieved on a reversed-phase C(18) column with mobile phase gradient method. The QTOF-MS was operated under full scan of MS or MS/MS in negative mode. The fragments were acquired by raising collision induced dissociation (CID) energy for speculating the structures of parent ions. According to the information from the chromatograms and mass spectra, 17 metabolites were obtained. Among them, the deoxidized phase I metabolites and an array of phase II metabolites-sulfate conjugates detected in the biological samples made the work more significant. Copyright © 2012 Elsevier B.V. All rights reserved.

Activation of Reactive MALDI Adduct Ions Enables Differentiation of Dihydroxylated Vitamin D Isomers

NASA Astrophysics Data System (ADS)

Qi, Yulin; Müller, Miriam J.; Volmer, Dietrich A.

2017-12-01

Vitamin D compounds are secosteroids, which are best known for their role in bone health. More recent studies have shown that vitamin D metabolites and catabolites such as dihydroxylated species (e.g., 1,25- and 24,25-dihydroxyvitamin D3) play key roles in the pathologies of various diseases. Identification of these isomers by mass spectrometry is challenging and currently relies on liquid chromatography, as the isomers exhibit virtually identical product ion spectra under collision induced dissociation conditions. Here, we developed a simple MALDI-CID method that utilizes ion activation of reactive analyte/matrix adducts to distinguish isomeric dihydroxyvitamin D3 species, without the need for chromatography separation or chemical derivatization techniques. Specifically, reactive 1,5-diaminonaphthalene adducts of dihydroxyvitamin D3 compounds formed during MADI were activated and specific cleavages in the secosteroid's backbone structure were achieved that produced isomer-diagnostic fragment ions. [Figure not available: see fulltext.

Identification and molecular mapping of two soybean aphid resistance genes in soybean PI 587732

USDA-ARS?s Scientific Manuscript database

Soybean [Glycine max (L.) Merr.] continues to be plagued by the soybean aphid (Aphis glycines Matsumura: SA) in North America. New soybean resistance sources are needed to combat the four identified SA biotypes. The objectives of this study were to determine the inheritance of SA resistance in PI 58...

The clinical importance of changes in the 0 to 10 numeric rating scale for worst, least, and average pain intensity: analyses of data from clinical trials of duloxetine in pain disorders.

PubMed

Farrar, John T; Pritchett, Yili L; Robinson, Michael; Prakash, Apurva; Chappell, Amy

2010-02-01

Data on 1,700 patients pooled from 5 randomized, placebo-controlled duloxetine studies (3 in diabetic peripheral neuropathic pain and 2 in fibromyalgia) were analyzed to determine clinically important differences (CIDs) in the 0 to 10 Numeric Rating Scale-Pain Intensity (NRS-PI) for patient-reported "worst" and "least" pain intensity while validating the previously published level for "average" pain. The correspondence between the baseline-to-endpoint raw and percentage change in the NRS-PI for the worst, least, and average pain were compared to patients' perceived improvements at endpoint as measured by the 7-point Patient Global Impression of Improvement (PGI-I) scales. Stratification by baseline pain separated the raw but not the percent change scores. The PGI-I category of "much better" or above was our a priori definition of a CID. Cutoff points for the NRS-PI change scores were determined using a receiver operator curve analysis. A consistent relationship between the worst and average NRS-PI percent change and the PGI-I was demonstrated regardless of the study, pain type, age, sex, or treatment group with a reduction of approximately 34%. The least pain item CID was slightly higher at 41%. Raw change CID cutoff points were approximately -2, -2.5 and -3 for least, average, and worst pain respectively. We determined an anchor-based value for the change in the worst, least, and average pain intensity items of the Brief Pain Inventory that best represents a clinically important difference. Our findings support a standard definition of a clinically important difference in clinical trials of chronic-pain therapies. Copyright 2010 American Pain Society. Published by Elsevier Inc. All rights reserved.

GPR55 promotes migration and adhesion of colon cancer cells indicating a role in metastasis

PubMed Central

Andersen, L; Hasenöhrl, C; Feuersinger, D; Stančić, A; Fauland, A; Magnes, C; El‐Heliebi, A; Lax, S; Uranitsch, S; Haybaeck, J; Heinemann, A

2015-01-01

Background and Purpose Tumour cell migration and adhesion constitute essential features of metastasis. G‐protein coupled receptor 55 (GPR55), a lysophospholipid receptor, has been shown to play an important role in carcinogenesis. Here, we investigated the involvement of GPR55 in migration and metastasis of colon cancer cells. Experimental Approach Adhesion and migration assays using the highly metastatic colon cancer cell line HCT116 and an in vivo assay of liver metastasis were performed. The GPR55 antagonist CID16020046, cannabidiol, a putative GPR55 antagonist and GPR55 siRNA were used to block GPR55 activity in HCT116 colon cancer cells. Key Results HCT116 cells showed a significant decrease in adhesion to endothelial cells and in migration after blockade with CID16020046 or cannabidiol. The inhibitory effects of CID16020046 or cannabidiol were averted by GPR55 siRNA knock down in cancer cells. The integrity of endothelial cell monolayers was increased after pretreatment of HCT116 cells with the antagonists or after GPR55 siRNA knockdown while pretreatment with lysophosphatidylinositol (LPI), the endogenous ligand of GPR55, decreased integrity of the monolayers. LPI also induced migration in GPR55 overexpressing HCT116 cells that was blocked by GPR55 antagonists. In a mouse model of metastasis, the arrest of HCT116 cancer cells in the liver was reduced after treatment with CID16020046 or cannabidiol. Increased levels of LPI (18:0) were found in colon cancer patients when compared with healthy individuals. Conclusions and Implications GPR55 is involved in the migratory behaviour of colon carcinoma cells and may serve as a pharmacological target for the prevention of metastasis. © 2015 The British Pharmacological Society PMID:26436760

Comparison of the South African Spondaic and CID W-1 wordlists for measuring speech recognition threshold

PubMed Central

Soer, Maggi; Pottas, Lidia

2015-01-01

Background The home language of most audiologists in South Africa is either English or Afrikaans, whereas most South Africans speak an African language as their home language. The use of an English wordlist, the South African Spondaic (SAS) wordlist, which is familiar to the English Second Language (ESL) population, was developed by the author for testing the speech recognition threshold (SRT) of ESL speakers. Objectives The aim of this study was to compare the pure-tone average (PTA)/SRT correlation results of ESL participants when using the SAS wordlist (list A) and the CID W-1 spondaic wordlist (list B – less familiar; list C – more familiar CID W-1 words). Method A mixed-group correlational, quantitative design was adopted. PTA and SRT measurements were compared for lists A, B and C for 101 (197 ears) ESL participants with normal hearing or a minimal hearing loss (<26 dBHL; mean age 33.3). Results The Pearson correlation analysis revealed a strong PTA/SRT correlation when using list A (right 0.65; left 0.58) and list C (right 0.63; left 0.56). The use of list B revealed weak correlations (right 0.30; left 0.32). Paired sample t-tests indicated a statistically significantly stronger PTA/SRT correlation when list A was used, rather than list B or list C, at a 95% level of confidence. Conclusions The use of the SAS wordlist yielded a stronger PTA/SRT correlation than the use of the CID W-1 wordlist, when performing SRT testing on South African ESL speakers with normal hearing, or minimal hearing loss (<26 dBHL). PMID:26304218

Combined photoelectron, collision-induced dissociation, and computational studies of parent and fragment anions of N-paranitrophenylsulfonylalanine and N-paranitrophenylalanine

NASA Astrophysics Data System (ADS)

Lambert, Jason; Chen, Jing; Buonaugurio, Angela; Bowen, Kit H.; Do-Thanh, Chi-Linh; Wang, Yilin; Best, Michael D.; Compton, R. N.; Sommerfeld, Thomas

2013-12-01

After synthesizing the compounds N-paranitrophenylsulfonylalanine (NPNPSA) and N-paranitrophenylalanine (NPNPA), the photoelectron spectrum of the valence anion of N-paranitrophenylsulfonylalanine (NPNPSA)-, was measured and the collision-induced dissociation (CID) pathways of deprotonated N-paranitrophenylsulfonylalanine (NPNPSA-H)- and deprotonated N-paranitrophenylalanine (NPNPA-H)- were determined. Pertinent calculations were conducted to analyze both sets of experimental data. From the valence anion photoelectron spectrum of (NPNPSA)-, the adiabatic electron affinity (AEA) of NPNPSA was determined to be 1.7 ± 0.1 eV, while the vertical detachment energy (VDE) of (NPNPSA)- was found to be 2.3 ± 0.1 eV. Calculations for four low lying conformers of (NPNPSA)- gave AEA values in the range of 1.6-2.1 eV and VDE values in the range of 2.0-2.4 eV. These calculations are in very good agreement with the experimental values. While the NPNPA anion (NPNPSA)- was not observed experimentally it was studied computationally. The six low lying (NPNPSA)- conformers were identified and calculated to have AEA values in the range of 0.7-1.2 eV and VDE values in the range of 0.9-1.6 eV. CID was used to study the fragmentation patterns of deprotonated NPNPA and deprotonated NPNPSA. Based on the CID data and calculations, the excess charge was located on the delocalized π-orbitals of the nitrobenzene moiety. This is made evident by the fact that the dominant fragments all contained the nitrobenzene moiety even though the parent anions used for the CID study were formed via deprotonation of the carboxylic acid. The dipole-bound anions of both molecules are studied theoretically using the results of previous studies on nitrobenzene as a reference.

Combined photoelectron, collision-induced dissociation, and computational studies of parent and fragment anions of N-paranitrophenylsulfonylalanine and N-paranitrophenylalanine.

PubMed

Lambert, Jason; Chen, Jing; Buonaugurio, Angela; Bowen, Kit H; Do-Thanh, Chi-Linh; Wang, Yilin; Best, Michael D; Compton, R N; Sommerfeld, Thomas

2013-12-14

After synthesizing the compounds N-paranitrophenylsulfonylalanine (NPNPSA) and N-paranitrophenylalanine (NPNPA), the photoelectron spectrum of the valence anion of N-paranitrophenylsulfonylalanine (NPNPSA)(-), was measured and the collision-induced dissociation (CID) pathways of deprotonated N-paranitrophenylsulfonylalanine (NPNPSA-H)(-) and deprotonated N-paranitrophenylalanine (NPNPA-H)(-) were determined. Pertinent calculations were conducted to analyze both sets of experimental data. From the valence anion photoelectron spectrum of (NPNPSA)(-), the adiabatic electron affinity (AEA) of NPNPSA was determined to be 1.7 ± 0.1 eV, while the vertical detachment energy (VDE) of (NPNPSA)(-) was found to be 2.3 ± 0.1 eV. Calculations for four low lying conformers of (NPNPSA)(-) gave AEA values in the range of 1.6-2.1 eV and VDE values in the range of 2.0-2.4 eV. These calculations are in very good agreement with the experimental values. While the NPNPA anion (NPNPSA)(-) was not observed experimentally it was studied computationally. The six low lying (NPNPSA)(-) conformers were identified and calculated to have AEA values in the range of 0.7-1.2 eV and VDE values in the range of 0.9-1.6 eV. CID was used to study the fragmentation patterns of deprotonated NPNPA and deprotonated NPNPSA. Based on the CID data and calculations, the excess charge was located on the delocalized π-orbitals of the nitrobenzene moiety. This is made evident by the fact that the dominant fragments all contained the nitrobenzene moiety even though the parent anions used for the CID study were formed via deprotonation of the carboxylic acid. The dipole-bound anions of both molecules are studied theoretically using the results of previous studies on nitrobenzene as a reference.

Structure and reactivity of the distonic and aromatic radical cations of tryptophan.

PubMed

Piatkivskyi, Andrii; Osburn, Sandra; Jaderberg, Kendall; Grzetic, Josipa; Steill, Jeffrey D; Oomens, Jos; Zhao, Junfang; Lau, Justin Kai-Chi; Verkerk, Udo H; Hopkinson, Alan C; Siu, K W Michael; Ryzhov, Victor

2013-04-01

In this work, we regiospecifically generate and compare the gas-phase properties of two isomeric forms of tryptophan radical cations-a distonic indolyl N-radical (H3N(+) - TrpN(•)) and a canonical aromatic π (Trp(•+)) radical cation. The distonic radical cation was generated by nitrosylating the indole nitrogen of tryptophan in solution followed by collision-induced dissociation (CID) of the resulting protonated N-nitroso tryptophan. The π-radical cation was produced via CID of the ternary [Cu(II)(terpy)(Trp)](•2+) complex. CID spectra of the two isomeric species were found to be very different, suggesting no interconversion between the isomers. In gas-phase ion-molecule reactions, the distonic radical cation was unreactive towards n-propylsulfide, whereas the π radical cation reacted by hydrogen atom abstraction. DFT calculations revealed that the distonic indolyl radical cation is about 82 kJ/mol higher in energy than the π radical cation of tryptophan. The low reactivity of the distonic nitrogen radical cation was explained by spin delocalization of the radical over the aromatic ring and the remote, localized charge (at the amino nitrogen). The lack of interconversion between the isomers under both trapping and CID conditions was explained by the high rearrangement barrier of ca.137 kJ/mol. Finally, the two isomers were characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy in the ~1000-1800 cm(-1) region. It was found that some of the main experimental IR features overlap between the two species, making their distinction by IRMPD spectroscopy in this region problematic. In addition, DFT theoretical calculations showed that the IR spectra are strongly conformation-dependent.

Rapid identification of Yersinia pestis and Brucella melitensis by chip-based continuous flow PCR

NASA Astrophysics Data System (ADS)

Dietzsch, Michael; Hlawatsch, Nadine; Melzer, Falk; Tomaso, Herbert; Gärtner, Claudia; Neubauer, Heinrich

2012-06-01

To combat the threat of biological agents like Yersinia pestis and Brucella melitensis in bioterroristic scenarios requires fast, easy-to-use and safe identification systems. In this study we describe a system for rapid amplification of specific genetic markers for the identification of Yersinia pestis and Brucella melitensis. Using chip based PCR and continuous flow technology we were able to amplify the targets simultaneously with a 2-step reaction profile within 20 minutes. The subsequent analysis of amplified fragments by standard gel electrophoresis requires another 45 minutes. We were able to detect both pathogens within 75 minutes being much faster than most other nucleic acid amplification technologies.

Scintillator-fiber charged particle track-imaging detector

NASA Technical Reports Server (NTRS)

Binns, W. R.; Israel, M. H.; Klarmann, J.

1983-01-01

A scintillator-fiber charged-particle track-imaging detector was developed using a bundle of square cross section plastic scintillator fiber optics, proximity focused onto an image intensified charge injection device (CID) camera. The tracks of charged particle penetrating into the scintillator fiber bundle are projected onto the CID camera and the imaging information is read out in video format. The detector was exposed to beams of 15 MeV protons and relativistic Neon, Manganese, and Gold nuclei and images of their tracks were obtained. Details of the detector technique, properties of the tracks obtained, and preliminary range measurements of 15 MeV protons stopping in the fiber bundle are presented.

Crash response data system for the controlled impact demonstration (CID) of a full scale transport aircraft

NASA Astrophysics Data System (ADS)

Calloway, Raymond S.; Knight, Vernie H., Jr.

NASA Langley's Crash Response Data System (CRDS) which is designed to acquire aircraft structural and anthropomorphic dummy responses during the full-scale transport CID test is described. Included in the discussion are the system design approach, details on key instrumentation subsystems and operations, overall instrumentation crash performance, and data recovery results. Two autonomous high-environment digital flight instrumentation systems, DAS 1 and DAS 2, were employed to obtain research data from various strain gage, accelerometer, and tensiometric sensors installed in the B-720 test aircraft. The CRDS successfully acquired 343 out of 352 measurements of dynamic crash data.

Planetary investigation utilizing an imaging spectrometer system based upon charge injection technology

NASA Technical Reports Server (NTRS)

Wattson, R. B.; Harvey, P.; Swift, R.

1975-01-01

An intrinsic silicon charge injection device (CID) television sensor array has been used in conjunction with a CaMoO4 colinear tunable acousto optic filter, a 61 inch reflector, a sophisticated computer system, and a digital color TV scan converter/computer to produce near IR images of Saturn and Jupiter with 10A spectral resolution and approximately 3 inch spatial resolution. The CID camera has successfully obtained digitized 100 x 100 array images with 5 minutes of exposure time, and slow-scanned readout to a computer. Details of the equipment setup, innovations, problems, experience, data and final equipment performance limits are given.

The Protonation Site of para-Dimethylaminobenzoic Acid Using Atmospheric Pressure Ionization Methods

NASA Astrophysics Data System (ADS)

Chai, Yunfeng; Weng, Guofeng; Shen, Shanshan; Sun, Cuirong; Pan, Yuanjiang

2015-04-01

The protonation site of para-dimethylaminobenzoic acid ( p-DMABA) was investigated using atmospheric pressure ionization methods (ESI and APCI) coupled with collision-induced dissociation (CID), nuclear magnetic resonance (NMR), and computational chemistry. Theoretical calculations and NMR experiments indicate that the dimethyl amino group is the preferred site of protonation both in the gas phase and aqueous solution. Protonation of p-DMABA occurs at the nitrogen atom by ESI independent of the solvents and other operation conditions under typical thermodynamic control. However, APCI produces a mixture of the nitrogen- and carbonyl oxygen-protonated p-DMABA when aprotic organic solvents (acetonitrile, acetone, and tetrahydrofuran) are used, exhibiting evident kinetic characteristics of protonation. But using protic organic solvents (methanol, ethanol, and isopropanol) in APCI still leads to the formation of thermodynamically stable N-protonated p-DMABA. These structural assignments were based on the different CID behavior of the N- and O-protonated p-DMABA. The losses of methyl radical and water are the diagnostic fragmentations of the N- and O-protonated p-DMABA, respectively. In addition, the N-protonated p-DMABA is more stable than the O-protonated p-DMABA in CID revealed by energy resolved experiments and theoretical calculations.

Chemometric Data Analysis for Deconvolution of Overlapped Ion Mobility Profiles

NASA Astrophysics Data System (ADS)

Zekavat, Behrooz; Solouki, Touradj

2012-11-01

We present the details of a data analysis approach for deconvolution of the ion mobility (IM) overlapped or unresolved species. This approach takes advantage of the ion fragmentation variations as a function of the IM arrival time. The data analysis involves the use of an in-house developed data preprocessing platform for the conversion of the original post-IM/collision-induced dissociation mass spectrometry (post-IM/CID MS) data to a Matlab compatible format for chemometric analysis. We show that principle component analysis (PCA) can be used to examine the post-IM/CID MS profiles for the presence of mobility-overlapped species. Subsequently, using an interactive self-modeling mixture analysis technique, we show how to calculate the total IM spectrum (TIMS) and CID mass spectrum for each component of the IM overlapped mixtures. Moreover, we show that PCA and IM deconvolution techniques provide complementary results to evaluate the validity of the calculated TIMS profiles. We use two binary mixtures with overlapping IM profiles, including (1) a mixture of two non-isobaric peptides (neurotensin (RRPYIL) and a hexapeptide (WHWLQL)), and (2) an isobaric sugar isomer mixture of raffinose and maltotriose, to demonstrate the applicability of the IM deconvolution.

Characterization of Tyrosine Nitration and Cysteine Nitrosylation Modifications by Metastable Atom-Activation Dissociation Mass Spectrometry

NASA Astrophysics Data System (ADS)

Cook, Shannon L.; Jackson, Glen P.

2011-02-01

The fragmentation behavior of nitrated and S-nitrosylated peptides were studied using collision induced dissociation (CID) and metastable atom-activated dissociation mass spectrometry (MAD-MS). Various charge states, such as 1+, 2+, 3+, 2-, of modified and unmodified peptides were exposed to a beam of high kinetic energy helium (He) metastable atoms resulting in extensive backbone fragmentation with significant retention of the post-translation modifications (PTMs). Whereas the high electron affinity of the nitrotyrosine moiety quenches radical chemistry and fragmentation in electron capture dissociation (ECD) and electron transfer dissociation (ETD), MAD does produce numerous backbone cleavages in the vicinity of the modification. Fragment ions of nitrosylated cysteine modifications typically exhibit more abundant neutral losses than nitrated tyrosine modifications because of the extremely labile nature of the nitrosylated cysteine residues. However, compared with CID, MAD produced between 66% and 86% more fragment ions, which preserved the labile -NO modification. MAD was also able to differentiate I/L residues in the modified peptides. MAD is able to induce radical ion chemistry even in the presence of strong radical traps and therefore offers unique advantages to ECD, ETD, and CID for determination of PTMs such as nitrated and S-nitrosylated peptides.

Holistic life-span health outcomes among elite intercollegiate student-athletes.

PubMed

Sorenson, Shawn C; Romano, Russell; Scholefield, Robin M; Martin, Brandon E; Gordon, James E; Azen, Stanley P; Schroeder, E Todd; Salem, George J

2014-01-01

Competitive sports are recognized as having unique health benefits and risks, and the effect of sports on life-span health among elite athletes has received increasing attention. However, supporting scientific data are sparse and do not represent modern athletes. To assess holistic life-span health and health-related quality-of-life (HRQL) among current and former National Collegiate Athletic Association student-athletes (SAs). Cross-sectional study. A large Division I university. Population-based sample of 496 university students and alumni (age 17-84 years), including SAs and an age-matched and sex-matched nonathlete (NA) control group. Participants completed anonymous, self-report questionnaires. We measured the Short-Form 12 (SF-12) physical and mental component HRQL scores and cumulative lifetime experience and relative risk of treatment for joint, cardiopulmonary, and psychosocial health concerns. Older alumni (age 43+ years) SAs reported greater joint health concerns than NAs (larger joint summary scores; P = .04; Cohen d = 0.69; probability of clinically important difference [pCID] = 77%; treatment odds ratio [OR] = 14.0, 95% confidence interval [CI] = 1.6, 126). Joint health for current and younger alumni SAs was similar to that for NAs. Older alumni reported greater cardiopulmonary health concerns than younger alumni (summary score P < .001; d = 1.05; pCID = 85%; OR = 5.8, 95% CI = 2.0, 16) and current students (P < .001; d = 2.25; pCID >99.5%; OR = 7.1, 95% CI = 3.3, 15), but the risk was similar for SAs and NAs. Current SAs demonstrated evidence of better psychosocial health (summary score P = .006; d = -0.52; pCID = 40%) and mental component HRQL (P = .008; d = 0.50; pCID = 48%) versus NAs but similar psychosocial treatment odds (OR = 0.87, 95% CI = 0.39, 1.9). Psychosocial health and mental component HRQL were similar between alumni SAs and NAs. No differences were observed between SAs and NAs in physical component HRQL. The SAs demonstrated significant, clinically meaningful evidence of greater joint health concerns later in life, comparable cardiopulmonary health, and differences in life-span psychosocial health and HRQL profiles compared with NAs. These data provide timely evidence regarding a compelling public issue and highlight the need for further study of life-span health among modern athletes.

Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

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

Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

2013-07-02

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including V xO y n– and V xO yCl n– ions (x = 1–14, y = 2–36, n = 1–3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V 14O 36Cl(L) 5 (L = Et 4N +, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged V xO yCl n– and V xOmore » yCl(L) (n–1)– clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller V xO yCl (1–2)– and V xO y (1–2)– anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged V xO yCl and V xO y species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of V xO yCl and V xO y anions through low-energy CID. Finally and furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.« less

Holistic Life-Span Health Outcomes Among Elite Intercollegiate Student–Athletes

PubMed Central

Sorenson, Shawn C.; Romano, Russell; Scholefield, Robin M.; Martin, Brandon E.; Gordon, James E.; Azen, Stanley P.; Schroeder, E. Todd; Salem, George J.

2014-01-01

Context: Competitive sports are recognized as having unique health benefits and risks, and the effect of sports on life-span health among elite athletes has received increasing attention. However, supporting scientific data are sparse and do not represent modern athletes. Objective: To assess holistic life-span health and health-related quality-of-life (HRQL) among current and former National Collegiate Athletic Association student–athletes (SAs). Design: Cross-sectional study. Setting: A large Division I university. Patients or Other Participants: Population-based sample of 496 university students and alumni (age 17–84 years), including SAs and an age-matched and sex-matched nonathlete (NA) control group. Main Outcome Measure(s): Participants completed anonymous, self-report questionnaires. We measured the Short-Form 12 (SF-12) physical and mental component HRQL scores and cumulative lifetime experience and relative risk of treatment for joint, cardiopulmonary, and psychosocial health concerns. Results: Older alumni (age 43+ years) SAs reported greater joint health concerns than NAs (larger joint summary scores; P = .04; Cohen d = 0.69; probability of clinically important difference [pCID] = 77%; treatment odds ratio [OR] = 14.0, 95% confidence interval [CI] = 1.6, 126). Joint health for current and younger alumni SAs was similar to that for NAs. Older alumni reported greater cardiopulmonary health concerns than younger alumni (summary score P < .001; d = 1.05; pCID = 85%; OR = 5.8, 95% CI = 2.0, 16) and current students (P < .001; d = 2.25; pCID >99.5%; OR = 7.1, 95% CI = 3.3, 15), but the risk was similar for SAs and NAs. Current SAs demonstrated evidence of better psychosocial health (summary score P = .006; d = −0.52; pCID = 40%) and mental component HRQL (P = .008; d = 0.50; pCID = 48%) versus NAs but similar psychosocial treatment odds (OR = 0.87, 95% CI = 0.39, 1.9). Psychosocial health and mental component HRQL were similar between alumni SAs and NAs. No differences were observed between SAs and NAs in physical component HRQL. Conclusions: The SAs demonstrated significant, clinically meaningful evidence of greater joint health concerns later in life, comparable cardiopulmonary health, and differences in life-span psychosocial health and HRQL profiles compared with NAs. These data provide timely evidence regarding a compelling public issue and highlight the need for further study of life-span health among modern athletes. PMID:25117874

Finite element simulation of Reference Point Indentation on bone.

PubMed

Idkaidek, Ashraf; Agarwal, Vineet; Jasiuk, Iwona

2017-01-01

Reference Point Indentation (RPI) is a novel technique aimed to assess bone quality. Measurements are recorded by the BioDent instrument that applies multiple indents to the same location of cortical bone. Ten RPI parameters are obtained from the resulting force-displacement curves. Using the commercial finite element analysis software Abaqus, we assess the significance of the RPI parameters. We create an axisymmetric model and employ an isotropic viscoelastic-plastic constitutive relation with damage to simulate indentations on a human cortical bone. Fracture of bone tissue is not simulated for simplicity. The RPI outputs are computed for different simulated test cases and then compared with experimental results, measured using the BioDent, found in literature. The number of cycles, maximum indentation load, indenter tip radius, and the mechanical properties of bone: Young׳s modulus, compressive yield stress, and viscosity and damage constants, are varied. The trends in the RPI parameters are then investigated. We find that the RPI parameters are sensitive to the mechanical properties of bone. An increase in Young׳s modulus of bone causes the force-displacement loading and unloading slopes to increase and the total indentation distance (TID) to decrease. The compressive yield stress is inversely proportional to a creep indentation distance (CID1) and the TID. The viscosity constant is proportional to the CID1 and an average of the energy dissipated (AvED). The maximum indentation load is proportional to the TID, CID1, loading and unloading slopes, and AvED. The damage parameter is proportional to the TID, but it is inversely proportional to both the loading and unloading slopes and the AvED. The value of an indenter tip radius is proportional to the CID1 and inversely proportional to the TID. The number of load cycles is inversely proportional to an average of a creep indentation depth (AvCID) and the AvED. The indentation distance increase (IDI) is strongly inversely proportional to the compressive yield stress, and strongly proportional to the viscosity constant and maximum applied load, but has weak relation with the damage parameter, indenter tip radius, and elastic modulus. This computational study advances our understanding of the RPI outputs and provides a starting point for more comprehensive computational studies of the RPI technique. Copyright © 2016 Elsevier Ltd. All rights reserved.

SEABEE Combat Handbook. Revision

DTIC Science & Technology

1989-02-01

early stages of any biological disease, the general symptoms are fever , malaise, and * Warning, reporting, detection, and inflammation, identification...be thoroughly scrubbed . Contaminated clothing i ilgclwraeee cus fyusolu scontract a disease from biological warfare in spite must be washed in hot...protective masks, skin decontamination caused by thermal radiation and injuries caused kits, and atropine. 19-16 Chapter 19-CHEMICAL, BIOLOGICAL , AND

Exploiting graph kernels for high performance biomedical relation extraction.

PubMed

Panyam, Nagesh C; Verspoor, Karin; Cohn, Trevor; Ramamohanarao, Kotagiri

2018-01-30

Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineering methods, when classifying highly ordered structures such as trees and graphs obtained from syntactic parsing of a sentence. Tree kernels such as the Subset Tree Kernel and Partial Tree Kernel have been shown to be effective for classifying constituency parse trees and basic dependency parse graphs of a sentence. Graph kernels such as the All Path Graph kernel (APG) and Approximate Subgraph Matching (ASM) kernel have been shown to be suitable for classifying general graphs with cycles, such as the enhanced dependency parse graph of a sentence. In this work, we present a high performance Chemical-Induced Disease (CID) relation extraction system. We present a comparative study of kernel methods for the CID task and also extend our study to the Protein-Protein Interaction (PPI) extraction task, an important biomedical relation extraction task. We discuss novel modifications to the ASM kernel to boost its performance and a method to apply graph kernels for extracting relations expressed in multiple sentences. Our system for CID relation extraction attains an F-score of 60%, without using external knowledge sources or task specific heuristic or rules. In comparison, the state of the art Chemical-Disease Relation Extraction system achieves an F-score of 56% using an ensemble of multiple machine learning methods, which is then boosted to 61% with a rule based system employing task specific post processing rules. For the CID task, graph kernels outperform tree kernels substantially, and the best performance is obtained with APG kernel that attains an F-score of 60%, followed by the ASM kernel at 57%. The performance difference between the ASM and APG kernels for CID sentence level relation extraction is not significant. In our evaluation of ASM for the PPI task, ASM performed better than APG kernel for the BioInfer dataset, in the Area Under Curve (AUC) measure (74% vs 69%). However, for all the other PPI datasets, namely AIMed, HPRD50, IEPA and LLL, ASM is substantially outperformed by the APG kernel in F-score and AUC measures. We demonstrate a high performance Chemical Induced Disease relation extraction, without employing external knowledge sources or task specific heuristics. Our work shows that graph kernels are effective in extracting relations that are expressed in multiple sentences. We also show that the graph kernels, namely the ASM and APG kernels, substantially outperform the tree kernels. Among the graph kernels, we showed the ASM kernel as effective for biomedical relation extraction, with comparable performance to the APG kernel for datasets such as the CID-sentence level relation extraction and BioInfer in PPI. Overall, the APG kernel is shown to be significantly more accurate than the ASM kernel, achieving better performance on most datasets.

Breast cancer and protein biomarkers

PubMed Central

Gam, Lay-Harn

2012-01-01

Breast cancer is a healthcare concern of women worldwide. Despite procedures being available for diagnosis, prognosis and treatment of breast cancer, researchers are working intensively on the disease in order to improve the life quality of breast cancer patients. At present, there is no single treatment known to bring a definite cure for breast cancer. One of the possible solutions for combating breast cancer is through identification of reliable protein biomarkers that can be effectively used for early detection, prognosis and treatments of the cancer. Therefore, the task of identification of biomarkers for breast cancer has become the focus of many researchers worldwide. PMID:24520539

Distinctive and Complementary MS2 Fragmentation Characteristics for Identification of Sulfated Sialylated N-Glycopeptides by nanoLC-MS/MS Workflow

NASA Astrophysics Data System (ADS)

Kuo, Chu-Wei; Guu, Shih-Yun; Khoo, Kay-Hooi

2018-04-01

High sensitivity identification of sulfated glycans carried on specific sites of glycoproteins is an important requisite for investigation of molecular recognition events involved in diverse biological processes. However, aiming for resolving site-specific glycosylation of sulfated glycopeptides by direct LC-MS2 sequencing is technically most challenging. Other than the usual limiting factors such as lower abundance and ionization efficiency compared to analysis of non-glycosylated peptides, confident identification of sulfated glycopeptides among the more abundant non-sulfated glycopeptides requires additional considerations in the selective enrichment and detection strategies. Metal oxide has been applied to enrich phosphopeptides and sialylated glycopeptides, but its use to capture sulfated glycopeptides has not been investigated. Likewise, various complementary MS2 fragmentation modes have yet to be tested against sialylated and non-sialylated sulfoglycopeptides due to limited appropriate sample availability. In this study, we have investigated the feasibility of sequencing tryptic sulfated N-glycopeptide and its MS2 fragmentation characteristics by first optimizing the enrichment methods to allow efficient LC-MS detection and MS2 analysis by a combination of CID, HCD, ETD, and EThcD on hybrid and tribrid Orbitrap instruments. Characteristic sulfated glyco-oxonium ions and direct loss of sulfite from precursors were detected as evidences of sulfate modification. It is anticipated that the technical advances demonstrated in this study would allow a feasible extension of our sulfoglycomic analysis to sulfoglycoproteomics. [Figure not available: see fulltext.

Identification of pesticide transformation products in food by liquid chromatography/time-of-flight mass spectrometry via "fragmentation-degradation" relationships.

PubMed

García-Reyes, Juan F; Molina-Díaz, Antonio; Fernandez-Alba, Amadeo R

2007-01-01

The identification of transformation products of pesticides in foodstuffs is a crucial task difficult to tackle, due to the lack of standards and scarce information available. In this work, we describe a methodology for the identification and structural elucidation of pesticide transformation products in food. The proposed strategy is based on the use of liquid chromatography electrospray time-of-flight mass spectrometry (LC/TOFMS): accurate mass measurements of (molecule and fragment) ions of interest are used in order to establish relationships between fragmentation of the parent pesticides in the instrument (in-source CID fragmentation) and possible degradation products of these pesticides in food. Examples of this strategy showing the potential of LC/TOFMS to determine unknown pesticides in food are described in two different real samples, suggesting that pesticides often are transformed into degradation products in the same fashion that they are fragmented in the instrument. Using the proposed approach and without using standards a priori, based solely on accurate mass measurements of ions and "fragmentation-degradation" relationships, we have identified two parent pesticides (amitraz and malathion) along with six degradation products, m/z 253 (N,N'-bisdimethylphenylformamidine), 163 (N-2,4-dimethylphenyl-N-methyl formamidine), 150 (2,4-dimethylformamidine), and 122 (2,4-dimethylaniline) from amitraz, and m/z 317 and 303, due to ether hydrolysis of methyl and ethyl groups from malathion. Structures for these species were proposed, and the potential of the proposed approach was critically discussed.

Versatile lipid profiling by liquid chromatography-high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer.

PubMed

Gallart-Ayala, H; Courant, F; Severe, S; Antignac, J-P; Morio, F; Abadie, J; Le Bizec, B

2013-09-24

Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC-HRMS or LC-MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and "all ion fragmentation" (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale. Copyright © 2013 Elsevier B.V. All rights reserved.

Towards a Research Agenda for Cyber Friendly Fire

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

Greitzer, Frank L.; Clements, Samuel L.; Carroll, Thomas E.

Historical assessments of combat fratricide reveal principal contributing factors in the effects of stress, degradation of skills due to continuous operations or sleep deprivation, poor situation awareness, and lack of training and discipline in offensive/defense response selection. While these problems are typically addressed in R&D focusing on traditional ground-based combat, there is also an emerging need for improving situation awareness and decision making on defensive/offensive response options in the cyber defense arena, where a mistaken response to an actual or perceived cyber attack could lead to destruction or compromise of friendly cyber assets. The purpose of this report is tomore » examine cognitive factors that may affect cyber situation awareness and describe possible research needs to reduce the likelihood and effects of "friendly cyber fire" on cyber defenses, information infrastructures, and data. The approach is to examine concepts and methods that have been described in research applied to the more traditional problem of mitigating the occurrence of combat identification and fratricide. Application domains of interest include cyber security defense against external or internal (insider) threats.« less

Sovereignty and Collaboration: Affordable Strategies in Times of Austerity

DTIC Science & Technology

2016-10-01

provide precision-guided bombs and a land-support SOVEREIGNTY—ANALYSIS 26 vehicle were delivered for more than 20 percent below the expenditure ini...weapon Precision-guided bomb Support vehicle Panther command & control vehicle Successor Identification Friend or Foe (IFF) Joint combat aircraft...GLMRS) Multi-role armoured vehicle (MRAV) Next-generation light anti-armoured weapon Precision-guided bomb Support vehicle Panther command & control

Case report highlighting how wound path identification on CT can help identify organ damage in abdominal blast injuries.

PubMed

Fischer, Tatjana V; Folio, Les R; Backus, Christopher E; Bunger, Rolf

2012-01-01

Penetrating trauma is frequently encountered in forward deployed military combat hospitals. Abdominal blast injuries represent nearly 11% of combat injuries, and multiplanar computed tomography imaging is optimal for injury assessment and surgical planning. We describe a multiplanar approach to assessment of blast and ballistic injuries, which allows for more expeditious detection of missile tracts and damage caused along the path. Precise delineation of the trajectory path and localization of retained fragments enables time-saving and detailed evaluation of associated tissue and vascular injury. For consistent and reproducible documentation of fragment locations in the body, we propose a localization scheme based on Cartesian coordinates to report 3-dimensional locations of fragments and demonstrating the application in three cases of abdominal blast injury.

U.S. Army physical demands study: Identification and validation of the physically demanding tasks of combat arms occupations.

PubMed

Sharp, Marilyn A; Cohen, Bruce S; Boye, Michael W; Foulis, Stephen A; Redmond, Jan E; Larcom, Kathleen; Hydren, Jay R; Gebhardt, Deborah L; Canino, Maria C; Warr, Bradley J; Zambraski, Edward J

2017-11-01

In 2013, the U.S. Army began developing physical tests to predict a recruit's ability to perform the critical, physically demanding tasks (CPDTs) of combat arms jobs previously not open to women. The purpose of this paper is to describe the methodology and results of analyses of the accuracy and inclusiveness of the critical physically demanding task list. While the job analysis included seven combat arms jobs, only data from the 19D Cavalry Scout occupation are presented as the process was similar for all seven jobs. Job analysis METHODS: As the foundation, senior subject matter experts from each job reviewed materials and reached consensus on the CPDTs and performance standards for each job. The list was reviewed by Army leadership and provided to the researchers. The job analysis consisted of reviewing job and task related documents and field manuals, observing >900 soldiers performing the 32 CPDTs, conducting two focus groups for each job, and analyzing responses to widely distributed job analysis questionnaires. Of the 32 CPDTs identified for seven combat jobs, nine were relevant to 19D soldiers. Focus group discussions and job analysis questionnaire results supported the tasks and standards identified by subject matter experts while also identifying additional tasks. The tasks identified by subject matter experts were representative of the physically demanding aspects of the 19D occupation. Published by Elsevier Ltd.

Hypomorphic Rag1 mutations alter the pre-immune repertoire at early stages of lymphoid development.

PubMed

Ott de Bruin, Lisa M; Bosticardo, Marita; Barbieri, Alessandro; Lin, Sherry G; Rowe, Jared H; Poliani, Pietro L; Ching, Kimberly; Eriksson, Daniel; Landegren, Nils; Kämpe, Olle; Manis, John P; Notarangelo, Luigi D

2018-05-09

Hypomorphic RAG1 mutations allowing residual T and B cell development have been found in patients presenting with delayed-onset combined immune deficiency with granulomas and/or autoimmunity (CID-G/AI) and abnormalities of the peripheral T and B cell repertoire. To examine how hypomorphic Rag1 mutations affect the earliest stages of lymphocyte development, we used CRISPR/Cas9 to generate mouse models with equivalent mutations found in patients with CID-G/AI. Immunological characterization showed partial development of T and B lymphocytes, with persistence of naïve cells, preserved serum immunoglobulin, but impaired antibody responses and presence of autoantibodies, thereby recapitulating the phenotype seen in patients with CID-G/AI. By using high throughput sequencing, we identified marked skewing of Igh V and Trb V gene usage in early progenitors, with a bias for productive Igh and Trb rearrangements after selection occurred and increased apoptosis of B cell progenitors. Rearrangement at the Igk locus was impaired, and polyreactive IgM antibodies were detected. This study provides novel insights in how hypomorphic Rag1 mutations alter the primary repertoire of T and B cells, setting the stage for immune dysregulation frequently seen in patients. Copyright © 2018 American Society of Hematology.

Ion Trap Collisional Activation of c and z• Ions Formed via Gas-Phase Ion/Ion Electron Transfer Dissociation

PubMed Central

Han, Hongling; Xia, Yu; McLuckey, Scott A.

2008-01-01

A series of c- and z•-type product ions formed via gas-phase electron transfer ion/ion reactions between protonated polypeptides with azobenzene radical anions are subjected to ion trap collision activation in a linear ion trap. Fragment ions including a-, b-, y-type and ammonia-loss ions are typically observed in collision induced dissociation (CID) of c ions, showing almost identical CID patterns as those of the C-terminal amidated peptides consisting of the same sequences. Collisional activation of z• species mainly gives rise to side-chain losses and peptide backbone cleavages resulting in a-, b-, c-, x-, y-and z-type ions. Most of the fragmentation pathways of z• species upon ion trap CID can be accounted for by radical driven processes. The side-chain losses from z• species are different from the small losses observed from the charge-reduced peptide molecular species in electron transfer dissociation (ETD), which indicates rearrangement of the radical species. Characteristic side-chain losses are observed for several amino acid residues, which are useful to predict their presence in peptide/protein ions. Furthermore, the unique side-chain losses from leucine and isoleucine residues allow facile distinction of these two isomeric residues. PMID:17608403

Gas-Phase Interaction of Anions with Polyisobutylenes: Collision-Induced Dissociation Study and Quantum Chemical Modeling.

PubMed

Nagy, Lajos; Kuki, Ákos; Deák, György; Purgel, Mihály; Vékony, Ádám; Zsuga, Miklós; Kéki, Sándor

2016-09-01

The gas-phase interaction of anions including fluoride, chloride, bromide, iodide, ethyl sulfate, chlorate, and nitrate with polyisobutylene (PIB) derivatives was studied using collision-induced dissociation (CID). The gas-phase adducts of anions with PIBs ([PIB + anion](-)) were generated from the electrosprayed solution of PIBs in the presence of the corresponding anions. The so-formed adducts subjected to CID showed a loss of anion at different characteristic collision energies, thus allowing the study of the strength of interaction between the anions and nonpolar PIBs having different end-groups. The values of characteristic collision energies (the energy needed to obtain 50% fragmentation) obtained by CID experiments correlated linearly with the binding enthalpies between the anion and PIB, as determined by density functional theory calculations. In the case of halide ions, the critical energies for dissociation, that is, the binding enthalpies for [PIB + anion](-) adducts, increased in the order of I(-) < Br(-) < Cl(-) < F(-). Furthermore, it was found that the binding enthalpies for the adducts formed with halide ions decreased approximately with the square radius of the halide ion, suggesting that the strength of interaction is mainly determined by the "surface" charge density of the halide ion. In addition, the characteristic collision energy versus the number of isobutylene units revealed a linear dependence.

An ab initio chemical reaction model for the direct simulation Monte Carlo study of non-equilibrium nitrogen flows.

PubMed

Mankodi, T K; Bhandarkar, U V; Puranik, B P

2017-08-28

A new ab initio based chemical model for a Direct Simulation Monte Carlo (DSMC) study suitable for simulating rarefied flows with a high degree of non-equilibrium is presented. To this end, Collision Induced Dissociation (CID) cross sections for N 2 +N 2 →N 2 +2N are calculated and published using a global complete active space self-consistent field-complete active space second order perturbation theory N 4 potential energy surface and quasi-classical trajectory algorithm for high energy collisions (up to 30 eV). CID cross sections are calculated for only a selected set of ro-vibrational combinations of the two nitrogen molecules, and a fitting scheme based on spectroscopic weights is presented to interpolate the CID cross section for all possible ro-vibrational combinations. The new chemical model is validated by calculating equilibrium reaction rate coefficients that can be compared well with existing shock tube and computational results. High-enthalpy hypersonic nitrogen flows around a cylinder in the transition flow regime are simulated using DSMC to compare the predictions of the current ab initio based chemical model with the prevailing phenomenological model (the total collision energy model). The differences in the predictions are discussed.

Sensitivity to disinfection of bacterial indicator organisms for monitoring the Salmonella Enteritidis status of layer farms after cleaning and disinfection.

PubMed

Dewaele, I; Ducatelle, R; Herman, L; Heyndrickx, M; De Reu, K

2011-06-01

The present study evaluated Escherichia coli, Enterococcus faecalis, and Enterococcus hirae as potential indicator organisms for the possible Salmonella Enteritidis (SE) presence in layer farms after cleaning and disinfection by comparing their susceptibility to disinfection. A quantitative suspension disinfection test according to European Standard EN1656 was performed using disinfection products CID20 and Virocid (both from CID Lines, Ieper, Belgium). In a preliminary test, the sensitivity to both disinfection products was compared between ATCC strains of SE, E. coli, En. faecalis, and En. hirae. The sensitivity of SE to disinfection was most comparable to that of E. coli. A second disinfection test compared the elimination of E. coli to SE ATCC strains as well as field strains. Results showed no significant effect regarding the strain (P > 0.05 for CID20 and Virocid), meaning that no difference was detected in sensitivity toward disinfection. When comparing the sensitivity in general at species level for all concentrations of disinfectant used, no significant difference was found between E. coli and SE in sensitivity to Virocid (P > 0.05). In conclusion, because of its similar response to disinfection in a suspension disinfection test, E. coli could be used as an indicator for possible Salmonella presence after cleaning and disinfection.

Direct observation of 0.57 eV trap-related RF output power reduction in AlGaN/GaN high electron mobility transistors

NASA Astrophysics Data System (ADS)

Arehart, A. R.; Sasikumar, A.; Rajan, S.; Via, G. D.; Poling, B.; Winningham, B.; Heller, E. R.; Brown, D.; Pei, Y.; Recht, F.; Mishra, U. K.; Ringel, S. A.

2013-02-01

This paper reports direct evidence for trap-related RF output power loss in GaN high electron mobility transistors (HEMTs) grown by metal organic chemical vapor deposition (MOCVD) through increased concentration of a specific electron trap at EC-0.57 eV that is located in the drain access region, as a function of accelerated life testing (ALT). The trap is detected by constant drain current deep level transient spectroscopy (CID-DLTS) and the CID-DLTS thermal emission time constant precisely matches the measured drain lag. Both drain lag and CID-DLTS measurements show this state to already exist in pre-stressed devices, which coupled with its strong increase in concentration as a function of stress in the absence of significant increases in concentrations of other detected traps, imply its role in causing degradation, in particular knee walkout. This study reveals EC-0.57 eV trap concentration tracks degradation induced by ALT for MOCVD-grown HEMTs supplied by several commercial and university sources. The results suggest this defect has a common source and may be a key degradation pathway in AlGaN/GaN HEMTs and/or an indicator to predict device lifetime.

Flavonoid Constituents of Phlomis (Lamiaceae) Species Using Liquid Chromatography Mass Spectrometry.

PubMed

Aghakhani, Fatemeh; Kharazian, Navaz; Lori Gooini, Zahra

2018-03-01

Phlomis is one of the medicinal genera of Lamiaceae. This genus has unique medicinal properties. Consequently, appropriate methods need to be described for the identification of the chemical compounds. A liquid chromatography tandem mass spectrometry (LC-MS/MS) technique on a triple quadrupole mass spectrometer (TQMS) was used for separation and identification of leaf flavonoid compounds for seven Phlomis species including Phlomis kurdia, Ph. aucheri, Ph. olivieri, Ph. bruguieri, Ph. persica, Ph. anisodonta and Ph. elliptica. The flavonoid solution of air-dried leaves (10.5 g) was extracted using 85% methanol. The chromatogram was treated with three systems: methanol-water, chloroform-methanol and acetic acid. The extracts were analysed using LC-MS/MS. The MS 2 detection was performed under negative mode electrospray ionisation (ESI). The identification of constituents was based on authentic references used in the identification process. A total of 35 chemical compounds were detected from which 32 were identified as flavonoids through comparison with published literature and reference standards. These compounds were distributed in four flavonoid classes. Flavones (12), flavonols (11), flavanones (8) and flavane (1) were the main groups appearing in almost all of the studied samples. The flavonoids such as naringenin, chrysoeriol, eriodictyol, dimethoxyflavanone, apigenin, luteolin, kaempferol and rhamnetin were in high proportions. Moreover, 22 flavonoid compounds were first reported in this study for Phlomis species. The fragmentation patterns of the compounds during collision induced dissociation (CID) clarified information of the compounds analysed. The detailed flavonoid compositions of Phlomis species provide the appropriate context from phytochemical and phytotherapeutics points of view. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Top-Down and Bottom-Up Identification of Proteins by Liquid Extraction Surface Analysis Mass Spectrometry of Healthy and Diseased Human Liver Tissue

NASA Astrophysics Data System (ADS)

Sarsby, Joscelyn; Martin, Nicholas J.; Lalor, Patricia F.; Bunch, Josephine; Cooper, Helen J.

2014-09-01

Liquid extraction surface analysis mass spectrometry (LESA MS) has the potential to become a useful tool in the spatially-resolved profiling of proteins in substrates. Here, the approach has been applied to the analysis of thin tissue sections from human liver. The aim was to determine whether LESA MS was a suitable approach for the detection of protein biomarkers of nonalcoholic liver disease (nonalcoholic steatohepatitis, NASH), with a view to the eventual development of LESA MS for imaging NASH pathology. Two approaches were considered. In the first, endogenous proteins were extracted from liver tissue sections by LESA, subjected to automated trypsin digestion, and the resulting peptide mixture was analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) (bottom-up approach). In the second (top-down approach), endogenous proteins were extracted by LESA, and analyzed intact. Selected protein ions were subjected to collision-induced dissociation (CID) and/or electron transfer dissociation (ETD) mass spectrometry. The bottom-up approach resulted in the identification of over 500 proteins; however identification of key protein biomarkers, liver fatty acid binding protein (FABP1), and its variant (Thr→Ala, position 94), was unreliable and irreproducible. Top-down LESA MS analysis of healthy and diseased liver tissue revealed peaks corresponding to multiple (~15-25) proteins. MS/MS of four of these proteins identified them as FABP1, its variant, α-hemoglobin, and 10 kDa heat shock protein. The reliable identification of FABP1 and its variant by top-down LESA MS suggests that the approach may be suitable for imaging NASH pathology in sections from liver biopsies.

Top-down and bottom-up identification of proteins by liquid extraction surface analysis mass spectrometry of healthy and diseased human liver tissue.

PubMed

Sarsby, Joscelyn; Martin, Nicholas J; Lalor, Patricia F; Bunch, Josephine; Cooper, Helen J

2014-11-01

Liquid extraction surface analysis mass spectrometry (LESA MS) has the potential to become a useful tool in the spatially-resolved profiling of proteins in substrates. Here, the approach has been applied to the analysis of thin tissue sections from human liver. The aim was to determine whether LESA MS was a suitable approach for the detection of protein biomarkers of nonalcoholic liver disease (nonalcoholic steatohepatitis, NASH), with a view to the eventual development of LESA MS for imaging NASH pathology. Two approaches were considered. In the first, endogenous proteins were extracted from liver tissue sections by LESA, subjected to automated trypsin digestion, and the resulting peptide mixture was analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) (bottom-up approach). In the second (top-down approach), endogenous proteins were extracted by LESA, and analyzed intact. Selected protein ions were subjected to collision-induced dissociation (CID) and/or electron transfer dissociation (ETD) mass spectrometry. The bottom-up approach resulted in the identification of over 500 proteins; however identification of key protein biomarkers, liver fatty acid binding protein (FABP1), and its variant (Thr→Ala, position 94), was unreliable and irreproducible. Top-down LESA MS analysis of healthy and diseased liver tissue revealed peaks corresponding to multiple (~15-25) proteins. MS/MS of four of these proteins identified them as FABP1, its variant, α-hemoglobin, and 10 kDa heat shock protein. The reliable identification of FABP1 and its variant by top-down LESA MS suggests that the approach may be suitable for imaging NASH pathology in sections from liver biopsies.

Studies in search of selective detection of isomeric biogenic hexen-1-ols and hexanal by flowing afterglow tandem mass spectrometry using [H3O]+ and [NO]+ reagent ions.

PubMed

Dhooghe, Frederik; Vansintjan, Robbe; Schoon, Niels; Amelynck, Crist

2012-08-30

Plants emit a blend of oxygenated volatile C(6) compounds, known as green leaf volatiles (GLVs), in response to leaf tissue damage related to stress conditions. On-line chemical ionization mass spectrometry (CI-MS) techniques have often been used to study the dynamics of these emissions but they fail to selectively detect some important GLV compounds. A flowing afterglow tandem mass spectrometer (FA-TMS) was used to investigate the feasibility of selective on-line detection of isomeric hexen-1-ols and hexanal. Product ions at m/z 101 and 83 from chemical ionization (CI) of these compounds by [H(3)O](+), and product ions at m/z 100, 99, 83, 82 and 72 from CI by [NO](+), have been subjected to collision-induced dissociation (CID) in the collision cell of the TMS at center-of-mass energies ranging between 0 and 9 eV. CID of product ions at m/z 101 and 83 from CI of GLVs with [H(3)O](+) and of product ions at m/z 83, 82 and 72 from CI of GLVs with [NO](+) resulted in identical fragmentation patterns for all measured compounds, ruling out any selectivity. However, CID of product ions at m/z 100 and 99 from CI by [NO](+) led to CID product ions with abundances differing largely between the compounds, allowing the fast selective detection of 2-hexen-1-ols, 3-hexen-1-ols and hexanal with a chosen accuracy within a well-defined range of relative concentrations. This research illustrates that, in contrast to common CI-MS techniques, FA-TMS allows the selective detection of hexanal in a mixture of hexanal and hexen-1-ols with a chosen accuracy for a well-defined range of relative concentrations and represents a step forward in the search for selective detection of GLVs in CI-TMS. Copyright © 2012 John Wiley & Sons, Ltd.

Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

PubMed

Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

2016-06-16

Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration, and proton affinity causes surprising compensation effects among the various energy terms. It appears that this work provides the most detailed account to date of the mechanism whereby noncovalent protein complexes disassemble during CID.

Structural analysis of N-glycans by the glycan-labeling method using 3-aminoquinoline-based liquid matrix in negative-ion MALDI-MS.

PubMed

Nishikaze, Takashi; Kaneshiro, Kaoru; Kawabata, Shin-ichirou; Tanaka, Koichi

2012-11-06

Negative-ion fragmentation of underivatized N-glycans has been proven to be more informative than positive-ion fragmentation. Fluorescent labeling via reductive amination is often employed for glycan analysis, but little is known about the influence of the labeling group on negative-ion fragmentation. We previously demonstrated that the on-target glycan-labeling method using 3-aminoquinoline/α-cyano-4-hydroxycinnamic acid (3AQ/CHCA) liquid matrix enables highly sensitive, rapid, and quantitative N-glycan profiling analysis. The current study investigates the suitability of 3AQ-labeled N-glycans for structural analysis based on negative-ion collision-induced dissociation (CID) spectra. 3AQ-labeled N-glycans exhibited simple and informative CID spectra similar to those of underivatized N-glycans, with product ions due to cross-ring cleavages of the chitobiose core and ions specific to two antennae (D and E ions). The interpretation of diagnostic fragment ions suggested for underivatized N-glycans could be directly applied to the 3AQ-labeled N-glycans. However, fluorescently labeled N-glycans by conventional reductive amination, such as 2-aminobenzamide (2AB)- and 2-pyrydilamine (2PA)-labeled N-glycans, exhibited complicated CID spectra consisting of numerous signals formed by dehydration and multiple cleavages. The complicated spectra of 2AB- and 2PA-labeled N-glycans was found to be due to their open reducing-terminal N-acetylglucosamine (GlcNAc) ring, rather than structural differences in the labeling group in the N-glycan derivative. Finally, as an example, the on-target 3AQ labeling method followed by negative-ion CID was applied to structurally analyze neutral N-glycans released from human epidermal growth factor receptor type 2 (HER2) protein. The glycan-labeling method using 3AQ-based liquid matrix should facilitate highly sensitive quantitative and qualitative analyses of glycans.

Classification of CITES-listed and other neotropical Meliaceae wood images using convolutional neural networks.

PubMed

Ravindran, Prabu; Costa, Adriana; Soares, Richard; Wiedenhoeft, Alex C

2018-01-01

The current state-of-the-art for field wood identification to combat illegal logging relies on experienced practitioners using hand lenses, specialized identification keys, atlases of woods, and field manuals. Accumulation of this expertise is time-consuming and access to training is relatively rare compared to the international demand for field wood identification. A reliable, consistent and cost effective field screening method is necessary for effective global scale enforcement of international treaties such as the Convention on the International Trade in Endagered Species (CITES) or national laws (e.g. the US Lacey Act) governing timber trade and imports. We present highly effective computer vision classification models, based on deep convolutional neural networks, trained via transfer learning, to identify the woods of 10 neotropical species in the family Meliaceae, including CITES-listed Swietenia macrophylla , Swietenia mahagoni , Cedrela fissilis , and Cedrela odorata . We build and evaluate models to classify the 10 woods at the species and genus levels, with image-level model accuracy ranging from 87.4 to 97.5%, with the strongest performance by the genus-level model. Misclassified images are attributed to classes consistent with traditional wood anatomical results, and our species-level accuracy greatly exceeds the resolution of traditional wood identification. The end-to-end trained image classifiers that we present discriminate the woods based on digital images of the transverse surface of solid wood blocks, which are surfaces and images that can be prepared and captured in the field. Hence this work represents a strong proof-of-concept for using computer vision and convolutional neural networks to develop practical models for field screening timber and wood products to combat illegal logging.

Dual-mechanism gastroretentive drug delivery system loaded with an amorphous solid dispersion prepared by hot-melt extrusion.

PubMed

Vo, Anh Q; Feng, Xin; Pimparade, Manjeet; Ye, Xinyou; Kim, Dong Wuk; Martin, Scott T; Repka, Michael A

2017-05-01

In the present study, we aimed to prepare a gastroretentive drug delivery system that would be both highly resistant to gastric emptying via multiple mechanisms and would also potentially induce in situ supersaturation. The bioadhesive floating pellets, loaded with an amorphous solid dispersion, were prepared in a single step of hot-melt extrusion technology. Hydroxypropyl cellulose (Klucel™ MF) and hypromellose (Benecel™ K15M) were used as matrix-forming polymers, and felodipine was used as the model drug. The foam pellets were fabricated based on the expansion of CO 2 , which was generated from sodium bicarbonate during the melt-extrusion process. A 2 n full factorial experimental design was utilized to investigate the effects of formulation compositions to the pellet properties. The melt-extrusion process transformed the crystalline felodipine into an amorphous state that was dispersed and "frozen" in the polymer matrix. All formulations showed high porosity and were able to float immediately, without lag time, on top of gastric fluid, and maintained their buoyancy over 12h. The pellet-specific floating force, which could be as high as 4800μN/g, increased significantly during the first hour, and was relatively stable until 9h. The sodium bicarbonate percentage was found to be most significantly effect to the floating force. The ex vivo bioadhesion force of the pellets to porcine stomach mucosa was approximately 5mN/pellet, which was more than five times higher than the gravitation force of the pellet saturated with water. Drug release was well controlled up to 12h in the sink condition of 0.5% sodium lauryl sulphate in 0.1N HCl. The dissolution at 1, 3, 5, and 8h were 5-12%, 25-45%, 55-80%, and ≥75% respectively for all 11 formulations. In biorelevant dissolution medium, a supersaturated solution was formed, and the concentration was maintained at around 2μg/mL, approximately 10-folds higher than that of the pure felodipine. All input factors significantly affected dissolution in the first 3h, but afterwards, only drug load and hypromellose (HPMC) content had significant effects. The prepared drug delivery system has great potential in overcoming low and fluctuating bioavailability of poorly soluble drugs. Felodipine (PubChem CID: 3333); hypromellose (PubChem CID: 57503849), hydroxypropyl cellulose (PubChem CID: 71306830), sodium bicarbonate (PubChem CID: 516892); sodium carbonate (PubChem CID: 10340). Copyright © 2017 Elsevier B.V. All rights reserved.

Distinguishing aspartic and isoaspartic acids in peptides by several mass spectrometric fragmentation methods

PubMed Central

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

2016-01-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post source decay (PSD), MALDI 157 nm photodissociation, TMPP charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. PMID:27613306

Full-scale Transport Controlled Impact Demonstration Program

NASA Technical Reports Server (NTRS)

1987-01-01

The Federal Aviation Administration (FAA) and NASA conducted a full-scale air-to-surface impact-survivable impact demonstration with a remotely piloted transport aircraft on 1 December 1984, at Edwards Air Force Base, California. The test article consisted of experiments, special equipment, and supporting systems, such as antimisting kerosene (AMK), crashworthiness structural/restraint, analytical modeling, cabin fire safety, flight data recorders, post-impact investigation, instrumentation/data acquisition systems, remotely piloted vehicle/flight control systems, range and flight safety provisions, etc. This report describes the aircraft, experiments, systems, activities, and events which lead up to the Controlled Impact Demonstration (CID). An overview of the final unmanned remote control flight and sequence of impact events are delineated. Preliminary post CID observations are presented.

Toward an Efficient Icing CFD Process Using an Interactive Software Toolkit: Smagglce 2D

NASA Technical Reports Server (NTRS)

Vickerman, Mary B.; Choo, Yung K.; Schilling, Herbert W.; Baez, Marivell; Braun, Donald C.; Cotton, Barbara J.

2001-01-01

Two-dimensional CID analysis for iced airfoils can be a labor-intensive task. The software toolkit SmaggIce 2D is being developed to help streamline the CID process and provide the unique features needed for icing. When complete, it will include a combination of partially automated and fully interactive tools for all aspects of the tasks leading up to the flow analysis: geometry preparation, domain decomposition. block boundary demoralization. gridding, and linking with a flow solver. It also includes tools to perform ice shape characterization, an important aid in determining the relationship between ice characteristics and their effects on aerodynamic performance. Completed tools, work-in-progress, and planned features of the software toolkit are presented here.

Towards a Determination of the Physiological Characteristics Distinguishing Successful Mixed Martial Arts Athletes: A Systematic Review of Combat Sport Literature.

PubMed

James, Lachlan P; Haff, G Gregory; Kelly, Vincent G; Beckman, Emma M

2016-10-01

Mixed martial arts (MMA) is a combat sport underpinned by techniques from other combat disciplines, in addition to strategies unique to the sport itself. These sports can be divided into two distinct categories (grappling or striking) based on differing technical demands. Uniquely, MMA combines both methods of combat and therefore appears to be physiologically complex requiring a spectrum of mechanical and metabolic qualities to drive performance. However, little is known about the physiological characteristics that distinguish higher- from lower-level MMA athletes. Such information provides guidance for training interventions, performance testing and talent identification. Furthermore, while MMA incorporates techniques from both grappling and striking sports, it is unknown precisely how these disciplines differ physiologically. Understanding the relationship between higher-level competitors in grappling and striking combat sports can provide further insight into the development of the optimal performance profile of a higher-level MMA athlete. This article aims to analyse the scientific literature on MMA and the primary combat sports underpinning it to determine the physiological adaptations that distinguish superior competitors, with a view to defining the optimal physiological profile for higher-level MMA performance. Furthermore, this article will explore the differences in these capabilities between grappling- and striking-based combat sports in the context of MMA. A literature search was undertaken via PubMed, Web of Science, SportDiscus and Google Scholar. The following sports were included for systematic review based on their relevance to MMA: mixed martial arts, boxing, Brazilian jiu-jitsu, judo, karate, kickboxing, Muay Thai and wrestling. The inclusion criteria allowed studies that compared athletes of differing competition levels in the same sport using a physiological performance measure. Only male, adult (aged 17-40 years), able-bodied competitors were included. The search history spanned from the earliest record until September 2015. Of the eight combat sports searched for, five were represented across 23 studies. Sixteen investigations described maximal strength or neuromuscular power variables, while 19 articles reported anaerobic or aerobic measures. The results indicate that a number of strength, neuromuscular power and anaerobic variables distinguished higher- from lower-level combat sport athletes. However, these differences were less clear when groups were stratified within, rather than between competition grades. Greater aerobic power was generally not present amongst superior combat sport competitors. There appear to be differing physiological profiles between more successful grappling and striking combat sport athletes. This is represented by high-force demands of grappling sports causing an upwards shift of the entire force-velocity relationship driven by an increase in maximal strength. In comparison, smaller increases in maximal force production with more notable enhancements in lighter load, higher velocity actions may better identify superior performance in striking sports. Anaerobic capabilities largely distinguished higher- from lower-level combat sport athletes. In particular, longer-term anaerobic efforts seem to define successful grappling-based athletes, while superior competitors in striking sports tend to show dominance in shorter-term measures when compared with their lower-level counterparts. Given the demand for both forms of combat in MMA, a spectrum of physiological markers may characterize higher-level competitors. Furthermore, the performance profile of successful MMA athletes may differ based on combat sport history or competition strategy.

Biotechnology: Opportunities to Enhance Army Capabilities

DTIC Science & Technology

1989-12-01

without gene vectors Hand pollination Physical methods for DNA or RNA introduction Artificial insemination Cross-species cell fusion and embryo rescue...antibodies and DNA probes to test blood and anaylyze body fluids for more accurate identification of both suspects and victims. 3 I 6 l Artificial blood for...the Army include: *combat casualty care - wound repair, organ regeneration, nerve cell repair, and artificial blood eprophylaxis - protection from

Forest-Site Planning and Prescription for Control of Annosus Root Disease in Ponderosa Pine and Mixed Conifer Stands

Treesearch

John Nesbitt

1989-01-01

In order to successfully combat pathogens such as annosus root rot, the land manager and pathologist must have periodic dialogue about the pest, its identification, effects, impacts, and cures. The author presents four important topics to structure this dialogue. These are (1) training from the pathologist to the silviculturist or other land manager, (2) site specific...

F-22 Operational Squadron and T-38 Detachment Beddown at Tyndall Air Force Base, Florida

DTIC Science & Technology

2011-08-01

tactics, radar employment, identification, weapons employment, defensive response, electronic countermeasures, and electronic counter...use, and electronic countermeasures. Warning Area, MOA, and ATCAA 2,000 AGL to 60,000 MSL 0.75 to 1.5 hour (Dissimilar) Air Combat...night), air refueling, and strike-force rendezvous, conducting air-to-ground strikes, strike force defense and escort, air intercepts, electronic

Ion Mobility Spectrometry-Mass Spectrometry Coupled with Gas-Phase Hydrogen/Deuterium Exchange for Metabolomics Analyses

NASA Astrophysics Data System (ADS)

Maleki, Hossein; Karanji, Ahmad K.; Majuta, Sandra; Maurer, Megan M.; Valentine, Stephen J.

2018-02-01

Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas. The relative HDX reactivity of a wide variety of molecules is discussed in light of the various molecular structures. Additionally, hydrogen accessibility scoring (HAS) and HDX kinetics modeling of candidate ( in silico) ion structures is utilized to estimate the relative ion conformer populations giving rise to specific HDX behavior. These data interpretation methods are discussed with a focus on developing predictive tools for HDX behavior. Finally, an example is provided in which ion mobility information is supplemented with HDX reactivity data to aid identification efforts of compounds in a metabolite extract.

UV Photofragmentation Dynamics of Protonated Cystine: Disulfide Bond Rupture.

PubMed

Soorkia, Satchin; Dehon, Christophe; Kumar, S Sunil; Pedrazzani, Mélanie; Frantzen, Emilie; Lucas, Bruno; Barat, Michel; Fayeton, Jacqueline A; Jouvet, Christophe

2014-04-03

Disulfide bonds (S-S) play a central role in stabilizing the native structure of proteins against denaturation. Experimentally, identification of these linkages in peptide and protein structure characterization remains challenging. UV photodissociation (UVPD) can be a valuable tool in identifying disulfide linkages. Here, the S-S bond acts as a UV chromophore and absorption of one UV photon corresponds to a σ-σ* transition. We have investigated the photodissociation dynamics of protonated cystine, which is a dimer of two cysteines linked by a disulfide bridge, at 263 nm (4.7 eV) using a multicoincidence technique in which fragments coming from the same fragmentation event are detected. Two types of bond cleavages are observed corresponding to the disulfide (S-S) and adjacent C-S bond ruptures. We show that the S-S cleavage leads to three different fragment ions via three different fragmentation mechanisms. The UVPD results are compared to collision-induced dissociation (CID) and electron-induced dissociation (EID) studies.

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

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

Li, Zhou; Adams, Rachel M; Chourey, Karuna

2012-01-01

A variety of quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling using iTRAQ or TMT. Here, these methods were compared in terms of the depth of proteome coverage, quantification accuracy, precision, and reproducibility using a high-performance hybrid mass spectrometer, LTQ Orbitrap Velos. Our results show that (1) the spectral counting method provides the deepest proteome coverage for identification, but its quantification performance is worse than labeling-based approaches, especially the quantification reproducibility; (2) metabolic labeling and isobaric chemical labeling are capable of accurate, precise, and reproducible quantification and provide deep proteome coverage for quantification. Isobaricmore » chemical labeling surpasses metabolic labeling in terms of quantification precision and reproducibility; (3) iTRAQ and TMT perform similarly in all aspects compared in the current study using a CID-HCD dual scan configuration. Based on the unique advantages of each method, we provide guidance for selection of the appropriate method for a quantitative proteomics study.« less

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments.

PubMed

Harvey, David J; Seabright, Gemma E; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man 8 GlcNAc 2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. Graphical Abstract ᅟ.

Extensive characterization of peptides from Panax ginseng C. A. Meyer using mass spectrometric approach.

PubMed

Ye, Xueting; Zhao, Nan; Yu, Xi; Han, Xiaoli; Gao, Huiyuan; Zhang, Xiaozhe

2016-11-01

Panax ginseng is an important herb that has clear effects on the treatment of diverse diseases. Until now, the natural peptide constitution of this herb remains unclear. Here, we conduct an extensive characterization of Ginseng peptidome using MS-based data mining and sequencing. The screen on the charge states of precursor ions indicated that Ginseng is a peptide-rich herb in comparison of a number of commonly used herbs. The Ginseng peptides were then extracted and submitted to nano-LC-MS/MS analysis using different fragmentation modes, including CID, high-energy collisional dissociation, and electron transfer dissociation. Further database search and de novo sequencing allowed the identification of total 308 peptides, some of which might have important biological activities. This study illustrates the abundance and sequences of endogenous Ginseng peptides, thus providing the information of more candidates for the screening of active compounds for future biological research and drug discovery studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Infection in conflict wounded

PubMed Central

Eardley, W. G. P.; Brown, K. V.; Bonner, T. J.; Green, A. D.; Clasper, J. C.

2011-01-01

Although mechanisms of modern military wounding may be distinct from those of ancient conflicts, the infectious sequelae of ballistic trauma and the evolving microbial flora of war wounds remain a considerable burden on both the injured combatant and their deployed medical systems. Battlefield surgeons of ancient times favoured suppuration in war wounding and as such Galenic encouragement of pus formation would hinder progress in wound care for centuries. Napoleonic surgeons eventually abandoned this mantra, embracing radical surgical intervention, primarily by amputation, to prevent infection. Later, microscopy enabled identification of microorganisms and characterization of wound flora. Concurrent advances in sanitation and evacuation enabled improved outcomes and establishment of modern military medical systems. Advances in medical doctrine and technology afford those injured in current conflicts with increasing survivability through rapid evacuation, sophisticated resuscitation and timely surgical intervention. Infectious complications in those that do survive, however, are a major concern. Addressing antibiotic use, nosocomial transmission and infectious sequelae are a current clinical management and research priority and will remain so in an era characterized by a massive burden of combat extremity injury. This paper provides a review of infection in combat wounding from a historical setting through to the modern evidence base. PMID:21149356

Use of a fermented dairy probiotic drink containing Lactobacillus casei (DN-114 001) to decrease the rate of illness in kids: the DRINK study. A patient-oriented, double-blind, cluster-randomized, placebo-controlled, clinical trial.

PubMed

Merenstein, D; Murphy, M; Fokar, A; Hernandez, R K; Park, H; Nsouli, H; Sanders, M E; Davis, B A; Niborski, V; Tondu, F; Shara, N M

2010-07-01

To evaluate whether a fermented dairy drink containing the probiotic strain Lactobacillus casei DN-114 001 could reduce the incidence of common infectious diseases (CIDs) and the change of behavior because of illness in children. We conducted a double-blinded, randomized, placebo-controlled allocation concealment clinical trial in the Washington, DC metropolitan area. Participants were 638 children 3-6 years old in daycare/schools. The intervention was a fermented dairy drink containing a specific probiotic strain or matching placebo with no live cultures for 90 consecutive days. Two primary outcomes were assessed: incidence of CIDs and change of behavior because of illness (both assessed by parental report). The rate of change of behavior because of illness was similar among active and control groups. However, the incidence rate for CIDs in the active group (0.0782) is 19% lower than that of the control group (0.0986) (incidence rate ratio=0.81, 95% CI: 0.65, 099) P=0.046. Daily intake of a fermented dairy drink containing the probiotic strain L. casei DN-114 001 showed some promise in reducing overall incidence of illness, but was primarily driven by gastrointestinal infections and there were no differences in change of behavior.

Feature co-localization landscape of the human genome

PubMed Central

Ng, Siu-Kin; Hu, Taobo; Long, Xi; Chan, Cheuk-Hin; Tsang, Shui-Ying; Xue, Hong

2016-01-01

Although feature co-localizations could serve as useful guide-posts to genome architecture, a comprehensive and quantitative feature co-localization map of the human genome has been lacking. Herein we show that, in contrast to the conventional bipartite division of genomic sequences into genic and inter-genic regions, pairwise co-localizations of forty-two genomic features in the twenty-two autosomes based on 50-kb to 2,000-kb sequence windows indicate a tripartite zonal architecture comprising Genic zones enriched with gene-related features and Alu-elements; Proximal zones enriched with MIR- and L2-elements, transcription-factor-binding-sites (TFBSs), and conserved-indels (CIDs); and Distal zones enriched with L1-elements. Co-localizations between single-nucleotide-polymorphisms (SNPs) and copy-number-variations (CNVs) reveal a fraction of sequence windows displaying steeply enhanced levels of SNPs, CNVs and recombination rates that point to active adaptive evolution in such pathways as immune response, sensory perceptions, and cognition. The strongest positive co-localization observed between TFBSs and CIDs suggests a regulatory role of CIDs in cooperation with TFBSs. The positive co-localizations of cancer somatic CNVs (CNVT) with all Proximal zone and most Genic zone features, in contrast to the distinctly more restricted co-localizations exhibited by germline CNVs (CNVG), reveal disparate distributions of CNVTs and CNVGs indicative of dissimilarity in their underlying mechanisms. PMID:26854351

Mesalamine inhibits epithelial beta-catenin activation in chronic ulcerative colitis.

PubMed

Brown, Jeffrey B; Lee, Goo; Managlia, Elizabeth; Grimm, Gery R; Dirisina, Ramanarao; Goretsky, Tatiana; Cheresh, Paul; Blatner, Nichole R; Khazaie, Khashayarsha; Yang, Guang-Yu; Li, Linheng; Barrett, Terrence A

2010-02-01

Mesalamine is a mainstay therapeutic agent in chronic ulcerative colitis (CUC) in which condition it reverses crypt architectural changes and reduces colitis-associated cancer (CAC). The present study addressed the possibility that mesalamine reduces beta-catenin-associated progenitor cell activation, Akt-phosphorylated beta-catenin(Ser552) (P-beta-catenin), and colitis-induced dysplasia (CID). Effects of mesalamine on P-beta-catenin staining and function were assessed by immunohistochemistry and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) in biopsy specimens of CUC in mild or "refractory" severe mucosal inflammation. Effects of mesalamine on epithelial proliferation and activation of Akt and beta-catenin were assessed in interleukin (IL)-10(-/-) colitis and CID by immunohistochemistry and Western blotting. Dysplasia was assessed by counting the number and lengths of lesions per colon. Data from IL-10(-/-) and human colitis samples show that mesalamine reduced Akt activation and P-beta-catenin levels in the middle and upper crypt. Reductions in P-beta-catenin in CUC biopsy specimens with severe inflammation suggested that mesalamine reduced P-beta-catenin levels in tissue refractory to mesalamine's anti-inflammatory effects. In IL-10(-/-) mice, mesalamine reduced CID concordant with inhibition of crypt Akt and beta-catenin signaling. The results are consistent with the model that mesalamine contributes to chemoprevention in CAC by reducing beta-catenin signaling within intestinal progenitors.

Electrospray ionization tandem mass spectrometry of ammonium cationized polyethers.

PubMed

Nasioudis, Andreas; Heeren, Ron M A; van Doormalen, Irene; de Wijs-Rot, Nicolette; van den Brink, Oscar F

2011-05-01

Quaternary ammonium salts (Quats) and amines are known to facilitate the MS analysis of high molar mass polyethers by forming low charge state adduct ions. The formation, stability, and behavior upon collision-induced dissociation (CID) of adduct ions of polyethers with a variety of Quats and amines were studied by electrospray ionization quadrupole time-of-flight, quadrupole ion trap, and linear ion trap tandem mass spectrometry (MS/MS). The linear ion trap instrument was part of an Orbitrap hybrid mass spectrometer that allowed accurate mass MS/MS measurements. The Quats and amines studied were of different degree of substitution, structure, and size. The stability of the adduct ions was related to the structure of the cation, especially the amine's degree of substitution. CID of singly/doubly charged primary and tertiary ammonium cationized polymers resulted in the neutral loss of the amine followed by fragmentation of the protonated product ions. The latter reveals information about the monomer unit, polymer sequence, and endgroup structure. In addition, the detection of product ions retaining the ammonium ion was observed. The predominant process in the CID of singly charged quaternary ammonium cationized polymers was cation detachment, whereas their doubly charged adduct ions provided the same information as the primary and tertiary ammonium cationized adduct ions. This study shows the potential of specific amines as tools for the structural elucidation of high molar mass polyethers. © American Society for Mass Spectrometry, 2011

Proton affinity determinations and proton-bound dimer structure indications in C2 to C15, (alpha),(omega)-alkyldiamines

NASA Technical Reports Server (NTRS)

Karpas, Z.; Harden, C. S.; Smith, P. B. W.

1995-01-01

The 'kinetic method' was used to determine the proton affinity (PA) of a,coalkyldiamines from collision induced dissociation (CID) studies of protonated heterodimers. These PA values were consistently lower than those reported in the proton affinity scale. The apparent discrepancy was rationalized in terms of differences in the conformation of the protonated diamine monomers. The minimum energy species, formed by equilibrium proton transfer processes, have a cyclic conformation and the ion charge is shared by both amino-groups which are bridged by the proton. On the other hand, the species formed through dissociation of protonated dimers have a linear structure and the charge is localized on one of the amino-groups. Thus, the difference in the PA values obtained by both methods is a measure of the additional stability acquired by the protonated diamines through cyclization and charge delocalization. The major collision dissociation pathway of the protonated diamine monomers involved elimination of an ammonia moiety. Other reactions observed included loss of the second amino-group and several other bond cleavages. CID of the protonated dimers involved primarily formation of a protonated monomer through cleavage of the weaker hydrogen bond and subsequently loss of ammonia at higher collision energies. As observed from the CID studies, doubly charged ions were also formed from the diamines under conditions of the electrospray ionization.

Formation and Fragmentation Chemistry of Tripositive Ln(TMGA)33+ Complexes in the Gas Phase.

PubMed

Chen, Xiuting; Li, Qingnuan; Gong, Yu

2017-08-01

Electrospray ionization (ESI) of LnCl 3 (Ln = La-Lu except Pm) and TMGA (tetramethyl glutaramide) mixtures resulted in the formation of gas-phase Ln(TMGA) 3 3+ complexes, where tripositive lanthanide cation was coordinated by three neutral TMGA ligands. Collision induced dissociation (CID) was employed to investigate the fragmentation chemistry of these tripositive complexes. Ln(TMGA) 2 (TMGA- 45) 3+ resulting from C carbonyl -N bond cleavage of TMGA and hydrogen transfer is the major CID product for all Ln(TMGA) 3 3+ except Eu(TMGA) 3 3+ which predominantly forms divalent Eu II (TMGA) 2 2+ complex via loss of TMGA + . Analogous Yb II (TMGA) 2 2+ and Sm II (TMGA) 2 2+ complexes arising from charge reduction were also observed, in competition with the formation of charge conserving Yb III (TMGA)(TMGA-H) 2+ and Sm III (TMGA)(TMGA-H) 2+ products. The yield of these charge reducing products follows their reduction potentials in condensed phase. In addition to Ln(TMGA) 3 3+ , tripositive ions such as Ln(TMGA) 4 3+ and Ln(TMGA) 2 3+ were experimentally identified as well. While the former was observed along with Ln(TMGA) 3 3+ during ESI, the latter was observed upon CID of Ln(TMGA) 3 3+ , suggesting two TMGA molecules can stabilize Ln 3+ in the gas phase. Graphical Abstract ᅟ.

Coordination Structure and Fragmentation Chemistry of the Tripositive Lanthanide-Thio-Diglycolamide Complexes.

PubMed

Chen, Xiuting; Li, Qingnuan; Gong, Yu

2017-12-14

Tripositive Ln(TMTDA) 3 3+ complexes (Ln = La-Lu except Pm, TMTDA = tetramethyl 3-thio-diglycolamide) were observed in the gas phase by electrospray ionization of LnCl 3 and TMTDA mixtures. Collision-induced dissociation (CID) was employed to investigate their fragmentation chemistry, which revealed the influence of metal center as well as ligand on the ligated complexes. Ln(TMTDA) 2 (TMTDA-45) 3+ resulting from C carbonyl -N bond cleavage of TMTDA and hydrogen transfer was the major CID product for all Ln(TMTDA) 3 3+ except Eu(TMTDA) 3 3+ , which predominantly formed charge-reducing product Eu II (TMTDA) 2 2+ via electron transfer from TMTDA to Eu 3+ . Density functional theory calculations on the structure of La(TMTDA) 3 3+ and Lu(TMTDA) 3 3+ revealed that Ln 3+ was coordinated by six O carbonyl atoms from three neutral TMTDA ligands, and both complexes possessed C 3h symmetry. The S ether atom deviating from the ligand plane was not coordinated to the metal center. On the basis of the CID results of Ln(TMTDA) 3 3+ , Ln(TMGA) 3 3+ , and Ln(TMOGA) 3 3+ , the fragmentation chemistry associated with the ligand depends on the coordination mode, while the redox chemistry of these tripositive ions is related to the nature of both metal centers and diamide ligands.

Evaluation of the sensitivity of the 'Wiley registry of tandem mass spectral data, MSforID' with MS/MS data of the 'NIST/NIH/EPA mass spectral library'.

PubMed

Oberacher, Herbert; Whitley, Graeme; Berger, Bernd

2013-04-01

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the 'Wiley Registry of Tandem Mass Spectral Data, MSforID' (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the 'NIST/NIH/EPA Mass Spectral Library' (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross-validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.

Updating the Inductee Delivery Schedule.

DTIC Science & Technology

1987-03-01

deployed forces at risk with the anticipated opposing forces for the expected level of combat intensity. An estimate of the number of individuals who...identification of shortfalls in critical skills. It prescribes the anticipation of requirements and return of personnel resources to military control as...with the Time Phased Force Deployment Data lists the forces that will be deployed over time. Each unit is then assigned to a risk group (forces

Identification and Evaluation of Underground Obstacle Sensor Embodiments for Their Applicability to the Combat Engineers’ Rapid Excavation Mission(s),

DTIC Science & Technology

1980-01-01

November 1976. 11. Ohio State University, Electroscience Laboratory, Electromagnetic Pulse Sounding for Geological Surveying with Application in Rock...Peters, L. and Moffatt, D. L., Electromagnetic Pulse Sounding for Geological Surveying with Application in Rock Mechanics and Rapid Excavation... Electromagnetic Pulse Sounding for Geolog- ical Surveying with Application in Rock Mechanics and Rapid Excava- tion Program, Ohio State University, Report

VHSIC Electronics and the Cost of Air Force Avionics in the 1990s

DTIC Science & Technology

1990-11-01

circuit. LRM Line replaceable module. LRU Line replaceable unit. LSI Large-scale integration. LSTTL Tow-power Schottky Transitor -to-Transistor Logic...displays, communications/navigation/identification, electronic combat equipment, dispensers, and computers. These CERs, which statistically relate the...some of the reliability numbers, and adding the F-15 and F-16 to obtain the data sample shown in Table 6. Both suite costs and reliability statistics

Reinforcement Learning Applications to Combat Identification

DTIC Science & Technology

2017-03-01

Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Paperwork...DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) Crucial to the safe and effective operation of U.S. Navy vessels is the quick and accurate...abilities of a human operator . While this research does focus on a sea-based, naval, application, the findings can also be expanded to DOD-wide

Rapid Prototype Development of a Remotely-Piloted Aircraft Powered by a Hybrid-Electric Propulsion System

DTIC Science & Technology

2012-03-01

ch1) IED Improvised Explosive Device (ch1) IMS Integrated Master Schedule (ch3) ISR Intelligence Surveillance Reconnaissance (ch1...including the locating, monitoring, and neutralizing of enemy combatants, identification of and detonation of improvised explosive devices (IED...typically high altitude) necessitating the use of costly optics and sensors for ISR data collection. These features preclude long endurance RPAs from being

Identification and Validation of Established and Novel Biomarkers for Infections in Burns

DTIC Science & Technology

2017-10-01

in burn patients have been proposed, but not validated. In our four site study , we are enrolling severely burned adults and children , and...identify the early stages of infection prior to clinical detection. This multicenter study will enable us to identify novel biomarkers, validate whether...a multicenter study 3. Develop a model of prediction of infection using clinical data and proteomic information. Relevance: 5% of combat-sustained

Charge-injection-device 2 x 64 element infrared array performance

NASA Technical Reports Server (NTRS)

Mckelvey, M. E.; Mccreight, C. R.; Goebel, J. H.; Reeves, A. A.

1985-01-01

Three 2 x 64 element Si:Bi accumulation-mode charge-injection-device (CID) arrays were tested at low and moderate background to evaluate their usefulness for space-based astronomical observations. Testing was conducted both in the laboratory and in ground-based telescope IR observations. The devices showed an average readout noise level below 200 equivalent electrons, a peak responsivity of 4 A/W, and a noise equivalent power of 3 x 10 to the -17th W/sq rt Hz. This sensitivity compares well with that of nonintegrating discrete extrinsic silicon photoconductors. The array well capacity was significantly smaller than predicted. The measured sensitivity makes extrinsic silicon CID arrays useful for certain astronomical applications. However, their readout efficiency and frequency response represent serious limitations in low-background applications.

Our On-Its-Head-and-In-Your-Dreams Approach Leads to Clean Energy

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

Kazmerski, Lawrence; Gwinner, Don; Hicks, Al

Representing the Center for Inverse Design (CID), this document is one of the entries in the Ten Hundred and One Word Challenge. As part of the challenge, the 46 Energy Frontier Research Centers were invited to represent their science in images, cartoons, photos, words and original paintings, but any descriptions or words could only use the 1000 most commonly used words in the English language, with the addition of one word important to each of the EFRCs and the mission of DOE: energy. The mission of the CID is to revolutionize the discovery of new materials by design with tailoredmore » properties through the development and application of a novel inverse design approach powered by theory guiding experiment with an initial focus on solar energy conversion.« less

Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods

NASA Astrophysics Data System (ADS)

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

2016-12-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.

Impact of red and processed meat and fibre intake on treatment outcomes among patients with chronic inflammatory diseases: protocol for a prospective cohort study of prognostic factors and personalised medicine

PubMed Central

Heitmann, Berit L; Andersen, Karina Winther; Nielsen, Ole Haagen; Sørensen, Signe Bek; Jawhara, Mohamad; Bygum, Anette; Hvid, Lone; Grauslund, Jakob; Wied, Jimmi; Glerup, Henning; Fredberg, Ulrich; Villadsen, Jan Alexander; Kjær, Søren Geill; Fallingborg, Jan; Moghadd, Seyed A G R; Knudsen, Torben; Brodersen, Jacob; Frøjk, Jesper; Dahlerup, Jens Frederik; Bojesen, Anders Bo; Sorensen, Grith Lykke; Thiel, Steffen; Færgeman, Nils J; Brandslund, Ivan; Bennike, Tue Bjerg; Stensballe, Allan; Schmidt, Erik Berg; Franke, Andre; Ellinghaus, David; Rosenstiel, Philip; Raes, Jeroen; Boye, Mette; Werner, Lars; Nielsen, Charlotte Lindgaard; Munk, Heidi Lausten; Nexøe, Anders Bathum; Ellingsen, Torkell; Holmskov, Uffe; Kjeldsen, Jens

2018-01-01

Introduction Chronic inflammatory diseases (CIDs) are frequently treated with biological medications, specifically tumour necrosis factor inhibitors (TNFi)). These medications inhibit the pro-inflammatory molecule TNF alpha, which has been strongly implicated in the aetiology of these diseases. Up to one-third of patients do not, however, respond to biologics, and lifestyle factors are assumed to affect treatment outcomes. Little is known about the effects of dietary lifestyle as a prognostic factor that may enable personalised medicine. The primary outcome of this multidisciplinary collaborative study will be to identify dietary lifestyle factors that support optimal treatment outcomes. Methods and analysis This prospective cohort study will enrol 320 patients with CID who are prescribed a TNFi between June 2017 and March 2019. Included among the patients with CID will be patients with inflammatory bowel disease (Crohn’s disease and ulcerative colitis), rheumatic disorders (rheumatoid arthritis, axial spondyloarthritis, psoriatic arthritis), inflammatory skin diseases (psoriasis, hidradenitis suppurativa) and non-infectious uveitis. At baseline (pretreatment), patient characteristics will be assessed using patient-reported outcome measures, clinical assessments of disease activity, quality of life and lifestyle, in addition to registry data on comorbidity and concomitant medication(s). In accordance with current Danish standards, follow-up will be conducted 14–16 weeks after treatment initiation. For each disease, evaluation of successful treatment response will be based on established primary and secondary endpoints, including disease-specific core outcome sets. The major outcome of the analyses will be to detect variability in treatment effectiveness between patients with different lifestyle characteristics. Ethics and dissemination The principle goal of this project is to improve the quality of life of patients suffering from CID by providing evidence to support dietary and other lifestyle recommendations that may improve clinical outcomes. The study is approved by the Ethics Committee (S-20160124) and the Danish Data Protecting Agency (2008-58-035). Study findings will be disseminated through peer-reviewed journals, patient associations and presentations at international conferences. Trial registration number NCT03173144; Pre-results. PMID:29439003

Impact of depressive symptoms on prosthetic status--results of the study of health in Pomerania (SHIP).

PubMed

Samietz, Stefanie A; Kindler, Stefan; Schwahn, Christian; Polzer, Ines; Hoffmann, Wolfgang; Kocher, Thomas; Grabe, Hans Jörgen; Mundt, Torsten; Biffar, Reiner

2013-05-01

Previous investigations have confirmed that every fifth dental patient suffers from clinically significant depressive symptoms. However, the putative impact of depressive symptoms on the prosthetic status has not been addressed in these studies. The objective of this study was to investigate the association between depressive symptoms and prosthetic status based on data from the Study of Health in Pomerania (SHIP-0). Data from 2,135 participants aged 30 to 59 years were analyzed. A classification (six classes regarding the number and position of missing teeth per jaw) was used to identify the degree of prosthetic status (no/suboptimal/optimal tooth replacement). The presence of depressive symptoms was assessed with a modified version of von Zerssen's complaints scale. Screening for lifetime diagnoses of mental disorders was performed with the Composite International Diagnostic-Screener (CID-S). Multivariable logistic regressions including several confounders were calculated. A significant protective dose-response effect of depressive symptoms on prosthetic status was found only in men for the lower jaw [0-1 depressive symptoms: odds ratio (OR) = 3.84, 95 % confidence interval (CI, 1.65-8.92), p < 0.01; 2-3: OR = 2.87 (CI, 1.22-6.74), p < 0.05; reference, ≥8; adjusted for age, school education, smoking status, household income, marital status, living without a partner, risky alcohol consumption, obesity, diabetes, and physical activity]. There was no such association in women or for the upper jaw. The analyses using the CID-S confirmed these results. In the lower jaw, men with depressive symptoms had a better prosthetic status than men without depressive symptoms suggesting a higher level of concern regarding their personal health. If dentists might have an opportunity to identify men with depressive symptoms they can provide a wide range of treatment options that may enhance patients' self-esteem and contribute to the patient' well-being. Furthermore, depressive symptoms could indicate a discrepancy between self-perception of the dental health and the actual status which influence the dentists' treatment decision making.

Impact of Increasing Age on Cause-Specific Mortality and Morbidity in Patients With Stage I Non-Small-Cell Lung Cancer: A Competing Risks Analysis.

PubMed

Eguchi, Takashi; Bains, Sarina; Lee, Ming-Ching; Tan, Kay See; Hristov, Boris; Buitrago, Daniel H; Bains, Manjit S; Downey, Robert J; Huang, James; Isbell, James M; Park, Bernard J; Rusch, Valerie W; Jones, David R; Adusumilli, Prasad S

2017-01-20

Purpose To perform competing risks analysis and determine short- and long-term cancer- and noncancer-specific mortality and morbidity in patients who had undergone resection for stage I non-small-cell lung cancer (NSCLC). Patients and Methods Of 5,371 consecutive patients who had undergone curative-intent resection of primary lung cancer at our institution (2000 to 2011), 2,186 with pathologic stage I NSCLC were included in the analysis. All preoperative clinical variables known to affect outcomes were included in the analysis, specifically, Charlson comorbidity index, predicted postoperative (ppo) diffusing capacity of the lung for carbon monoxide, and ppo forced expiratory volume in 1 second. Cause-specific mortality analysis was performed with competing risks analysis. Results Of 2,186 patients, 1,532 (70.1%) were ≥ 65 years of age, including 638 (29.2%) ≥ 75 years of age. In patients < 65, 65 to 74, and ≥ 75 years of age, 5-year lung cancer-specific cumulative incidence of death (CID) was 7.5%, 10.7%, and 13.2%, respectively (overall, 10.4%); noncancer-specific CID was 1.8%, 4.9%, and 9.0%, respectively (overall, 5.3%). In patients ≥ 65 years of age, for up to 2.5 years after resection, noncancer-specific CID was higher than lung cancer-specific CID; the higher noncancer-specific, early-phase mortality was enhanced in patients ≥ 75 years of age than in those 65 to 74 years of age. Multivariable analysis showed that low ppo diffusing capacity of lung for carbon monoxide was an independent predictor of severe morbidity ( P < .001), 1-year mortality ( P < .001), and noncancer-specific mortality ( P < .001), whereas low ppo forced expiratory volume in 1 second was an independent predictor of lung cancer-specific mortality ( P = .002). Conclusion In patients who undergo curative-intent resection of stage I NSCLC, noncancer-specific mortality is a significant competing event, with an increasing impact as patient age increases.

Identification and characterization of miRNAs transcriptome in the South African abalone, Haliotis midae.

PubMed

Picone, Barbara; Rhode, Clint; Roodt-Wilding, Rouvay

2017-02-01

Aquatic animal diseases are one of the most important limitations to the growth of aquaculture. miRNAs represent an important class of small ncRNAs able to modulate host immune and stress responses. In Mollusca, a large phylum of invertebrates, miRNAs have been identified in several species. The current preliminary study identified known miRNAs from the South African abalone, Haliotis midae. The economic and ecological importance of abalone makes this species a suitable model for studying and understanding stress response in marine gastropods. Furthermore, the identification of miRNA, represents an alternative and powerful tool to combat infectious disease. Copyright © 2016 Elsevier B.V. All rights reserved.

Does money work? Cash transfers to ex-combatants in disarmament, demobilisation and reintegration processes.

PubMed

Willibald, Sigrid

2006-09-01

This paper analyses the relevance and potential of cash transfers as part of the disarmament, demobilisation and reintegration (DDR) assistance packages provided to ex-combatants in transitions from war to peace. To this end, a theoretical framework is established that permits the identification of the advantages and disadvantages of using cash in DDR. Subsequently, an empirical analysis is carried out to compare selected theoretical assumptions on the use of cash with the reality of lessons learned from recent experience in Sierra Leone and other African countries. The study shows that some theoretical drawbacks commonly associated with the use of cash in DDR processes may indeed bear out in practice. At the same time, though, the paper argues that the utility of cash transfers in DDR is affected by a variety of factors that go far beyond the simple choice of employing cash, most notably decisions on payment location, eligibility criteria and targeting.

Recent patents therapeutic agents for cancer.

PubMed

Li, Xun; Xu, Wenfang

2006-06-01

Cancer is one of the most dreaded diseases with a complex pathogenesis, which threats human life greatly. Multidisciplinary scientific investigations are making best efforts to combat this disease and put to the identification of novel anticancer agents. Patent anticancer agents registered in China are therefore increasing dramatically during the past ten years, which will be reviewed briefly in this article. platinum complexes anthracycline analogs (including doxorubicin derivatives) quinoline analogs podophyllotoxins analogs taxane analogs camptothecin (CPT) analogs.

US Army Medical Bioengineering Research and Development Laboratory Annual Progress Report for FY 84. Volume 2

DTIC Science & Technology

1984-10-01

29 030 Bioassay for Mycotoxins in Water Using 29 Brine Shrimp Larvae ... .. ’ .- ,. ,. 031 Chemical Detection and Identification of 31 Trichothecene... Mycotoxins in Field Water Supplies 032 Microbial Degradation and Yeast Bioassay 33 of Trichothecene Mycotoxins DA Project 832 Combat Medical Materiel 35... mycotoxins in field water supplies treated with hypochlorite. 24. (U) The reaction products are to be separated by chromatographic procedures, and their

U.S. Army/FRG Army Mobility Symposium Proceedings held in April 1975

DTIC Science & Technology

1975-11-01

widths, etC.--and their interactions with soil strength, tree stems of various sizes and spacings, approach angles in ditches and streams, etc. At the...provides for their specific identification and user control so that the effects of various levels of driver motivation, associated with combat or...prevailing in the areal unit (braking-visility limit). d. Maneuvering to avoid trees and/or obstacles. e. Acceleration and deceleration between obstacles

Identification of Combat Unit Leader Skills and Leader-Group Interaction Processes

DTIC Science & Technology

1980-01-01

Categories of human learning. New York: Academic Press, 1964. Galton , (Sir) Francis . Hereditary genius. l-itmillan and Company, London, 1879. Garland...naissance tEam was given the mission to acquire intelligence on enemy activities in a particular area of operation (Jones, 1969). The team was to avoid...contact as the mission was strictly one of gathering intelligence . The team operating in the assigned reconnaisspnce zone came upon approximately 15 NVA

41 CFR 101-29.303 - All Federal executive agencies.

Code of Federal Regulations, 2010 CFR

2010-07-01

... present form and scope or whether a more simplified one can be used; (2) The existence of voluntary... CID's; and (4) The currency and applicability of reference documents included in the product...

Psychosocial Adaptation to Chronic Illness and Disability: A Virtue Based Model.

PubMed

Kim, Jeong Han; McMahon, Brian T; Hawley, Carolyn; Brickham, Dana; Gonzalez, Rene; Lee, Dong-Hun

2016-03-01

Psychosocial adaptation to chronic illness and disability (CID) is an area of study where a positive psychology perspective, especially the study of virtues and character strengths, can be implemented within the rehabilitation framework. A carefully developed theory to guide future interdisciplinary research is now timely. A traditional literature review between philosophy and rehabilitation psychology was conducted in order to develop a virtue-based psychosocial adaptation theory, merging important perspectives from the fields of rehabilitation and positive psychology. The virtue-based psychosocial adaptation model (V-PAM) to CID is proposed in the present study. The model involves five qualities or constructs: courage, practical wisdom, commitment to action, integrity and emotional transcendence. Each of these components of virtue contributes to an understanding of psychosocial adaptation. The present study addresses the implications and applications of V-PAM that will advance this understanding.

On-Line Electrochemical Reduction of Disulfide Bonds: Improved FTICR-CID and -ETD Coverage of Oxytocin and Hepcidin

NASA Astrophysics Data System (ADS)

Nicolardi, Simone; Giera, Martin; Kooijman, Pieter; Kraj, Agnieszka; Chervet, Jean-Pierre; Deelder, André M.; van der Burgt, Yuri E. M.

2013-12-01

Particularly in the field of middle- and top-down peptide and protein analysis, disulfide bridges can severely hinder fragmentation and thus impede sequence analysis (coverage). Here we present an on-line/electrochemistry/ESI-FTICR-MS approach, which was applied to the analysis of the primary structure of oxytocin, containing one disulfide bridge, and of hepcidin, containing four disulfide bridges. The presented workflow provided up to 80 % (on-line) conversion of disulfide bonds in both peptides. With minimal sample preparation, such reduction resulted in a higher number of peptide backbone cleavages upon CID or ETD fragmentation, and thus yielded improved sequence coverage. The cycle times, including electrode recovery, were rapid and, therefore, might very well be coupled with liquid chromatography for protein or peptide separation, which has great potential for high-throughput analysis.

Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods.

PubMed

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P

2016-12-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H 2 O, are present in PSD, photodissociation, and charge tagging. c • +57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. Graphical Abstract ᅟ.

Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer

PubMed Central

Gardner, Myles W.; Smith, Suncerae I.; Ledvina, Aaron R.; Madsen, James A.; Coon, Joshua J.; Schwartz, Jae C.; Stafford, George C.; Brodbelt, Jennifer S.

2009-01-01

A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells - the first a high pressure cell operated at nominally 5 × 10-3 Torr and the second a low pressure cell operated at nominally 3 × 10-4 Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y1 fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of ~100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra. PMID:19739654

Fragmentation study of iridoid glucosides through positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry.

PubMed

Es-Safi, Nour-Eddine; Kerhoas, Lucien; Ducrot, Paul-Henri

2007-01-01

Mass spectrometric methodology based on the combined use of positive and negative electrospray ionization, collision-induced dissociation (CID) and tandem mass spectrometry (MS/MS) has been applied to the mass spectral study of a series of six naturally occurring iridoids through in-source fragmentation of the protonated [M+H]+, deprotonated [M--H]- and sodiated [M+Na]+ ions. This led to the unambiguous determination of the molecular masses of the studied compounds and allowed CID spectra of the molecular ions to be obtained. Valuable structural information regarding the nature of both the glycoside and the aglycone moiety was thus obtained. Glycosidic cleavage and ring cleavages of both aglycone and sugar moieties were the major fragmentation pathways observed during CID, where the losses of small molecules, the cinnamoyl and the cinnamate parts were also observed. The formation of the ionized aglycones, sugars and their product ions was thus obtained giving information on their basic skeleton. The protonated, i.e. [M+H]+ and deprotonated [M--H]-, ions were found to fragment mainly by glycosidic cleavages. MS/MS spectra of the [M+Na]+ ions gave complementary information for the structural characterization of the studied compounds. Unlike the dissociation of protonated molecular ions, that of sodiated molecules also provided sodiated sugar fragments where the C0+ fragment corresponding to the glucose ion was obtained as base peak for all the studied compounds. Copyright (c) 2007 John Wiley & Sons, Ltd.

Sequence analysis of the pyruvylated galactan sulfate-derived oligosaccharides by negative-ion electrospray tandem mass spectrometry.

PubMed

Li, Na; Mao, Wenjun; Liu, Xue; Wang, Shuyao; Xia, Zheng; Cao, Sujian; Li, Lin; Zhang, Qi; Liu, Shan

2016-10-04

Five sulfated oligosaccharide fragments, F1-F5, were prepared from a pyruvylated galactan sulfate from the green alga Codium divaricatum, by partial depolymerization using mild acid hydrolysis and purification with gel-permeation chromatography. Negative-ion electrospray tandem mass spectrometry with collision-induced dissociation (ES-CID-MS/MS) is attempted for sequence determination of the sulfated oligosaccharides. The sequence of F1 with homogeneous disaccharide composition was first characterized to be Galp-(4SO4)-(1 → 3)-Galp by detailed nuclear magnetic resonance spectroscopic analyses. The fragmentation pattern of F1 in the product ion spectra was established on the basis of negative-ion ES-CID MS/MS, which was then applied to sequence analysis of other sulfated oligosaccharides. The sequences of F2 and F3 were deduced to be Galp-(4SO4)-(1 → 3)-Galp-(1 → 3)-Galp-(1 → 3)-Galp and 3,4-O-(1-carboxyethylidene)-Galp-(6SO4)-(1 → 3)-Galp, respectively. The sequences of major fragments in F4 and F5 were also deduced. The investigation demonstrated that negative-ion ES-CID-MS/MS was an efficient method for the sequence analysis of the pyruvylated galactan sulfate-derived oligosaccharides which revealed the patterns of substitution and glycosidic linkages. The pyruvylated galactan sulfate-derived oligosaccharides were novel sulfated oligosaccharides different from other algal polysaccharide-derived oligosaccharides. Copyright © 2016 Elsevier Ltd. All rights reserved.

Surface Induced Dissociation Yields Quaternary Substructure of Refractory Noncovalent Phosphorylase B and Glutamate Dehydrogenase Complexes

NASA Astrophysics Data System (ADS)

Ma, Xin; Zhou, Mowei; Wysocki, Vicki H.

2014-03-01

Ion mobility (IM) and tandem mass spectrometry (MS/MS) coupled with native MS are useful for studying noncovalent protein complexes. Collision induced dissociation (CID) is the most common MS/MS dissociation method. However, some protein complexes, including glycogen phosphorylase B kinase (PHB) and L-glutamate dehydrogenase (GDH) examined in this study, are resistant to dissociation by CID at the maximum collision energy available in the instrument. Surface induced dissociation (SID) was applied to dissociate the two refractory protein complexes. Different charge state precursor ions of the two complexes were examined by CID and SID. The PHB dimer was successfully dissociated to monomers and the GDH hexamer formed trimeric subcomplexes that are informative of its quaternary structure. The unfolding of the precursor and the percentages of the distinct products suggest that the dissociation pathways vary for different charge states. The precursors at lower charge states (+21 for PHB dimer and +27 for GDH hexamer) produce a higher percentage of folded fragments and dissociate more symmetrically than the precusors at higher charge states (+29 for PHB dimer and +39 for GDH hexamer). The precursors at lower charge state may be more native-like than the higher charge state because a higher percentage of folded fragments and a lower percentage of highly charged unfolded fragments are detected. The combination of SID and charge reduction is shown to be a powerful tool for quaternary structure analysis of refractory noncovalent protein complexes, as illustrated by the data for PHB dimer and GDH hexamer.

Is the presence of AA amyloidosis associated with impaired coronary flow reserve?

PubMed

Bulut, Mustafa; Keles, Nursen; Caliskan, Zuhal; Kostek, Osman; Aksu, Feyza; Ozdil, Kamil; Akcakoyun, Mustafa; Demircioglu, Kenan; Yilmaz, Yusuf; Kanbay, Mehmet; Caliskan, Mustafa

2016-08-01

Systemic amyloid A protein (AA) amyloidosis may occur as a complication of many chronic inflammatory disorders. Patients receiving inadequate anti-inflammatory and immunosuppressive therapies have an increased risk of developing systemic AA amyloidosis. Inflammation plays a role in all stages and the thrombotic complications of atherosclerosis. In the absence of epicardial coronary stenosis, coronary flow reserve (CFR) reflects coronary microvascular dysfunction. In the present study, we hypothesized that amyloid advanced subclinical inflammation in chronic inflammatory diseases (CID) patients may further affect coronary microcirculation. Thirty-two patients with biopsy-diagnosed renal AA, 73 patients with non-amyloid CID, and a group of healthy volunteers were included in the study. The measurements of coronary flow velocity were performed by a single investigator with expertise in transthoracic Doppler harmonic echocardiography (TTDE). The AA amyloidosis subgroup had significantly lower CFR values than other non-amyloid CID patients and the control individuals (1.8 (1.5-2.1) vs. 2.1 (2.0-2.4) and 3.0 (2.8-3.2), p < 0.001). Multivariate logistic regression analysis indicated that the presence of AA amyloidosis and elevated hs - CRP independently predict impairment of the CFR (p < 0.05). The presence of AA amyloidosis is related to decreased CFR values and the presence of AA amyloidosis and elevated hs - CRP independently predict impairment of the CFR. Therefore, patients with AA amyloidosis may have an increased risk of developing coronary artery diseases. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

STARR: shortwave-targeted agile Raman robot for the detection and identification of emplaced explosives

NASA Astrophysics Data System (ADS)

Gomer, Nathaniel R.; Gardner, Charles W.

2014-05-01

In order to combat the threat of emplaced explosives (land mines, etc.), ChemImage Sensor Systems (CISS) has developed a multi-sensor, robot mounted sensor capable of identification and confirmation of potential threats. The system, known as STARR (Shortwave-infrared Targeted Agile Raman Robot), utilizes shortwave infrared spectroscopy for the identification of potential threats, combined with a visible short-range standoff Raman hyperspectral imaging (HSI) system for material confirmation. The entire system is mounted onto a Talon UGV (Unmanned Ground Vehicle), giving the sensor an increased area search rate and reducing the risk of injury to the operator. The Raman HSI system utilizes a fiber array spectral translator (FAST) for the acquisition of high quality Raman chemical images, allowing for increased sensitivity and improved specificity. An overview of the design and operation of the system will be presented, along with initial detection results of the fusion sensor.

Training Strategies to Mitigate Expectancy-Induced Response Bias in Combat Identification: A Research Agenda

DTIC Science & Technology

2010-01-01

effects on troops in addition to the tragic loss of life. Data collected through the U.S. Army’s Center for Army Lessons Learned (CALL) suggest 10...stress (from Kavanagh, 2005, p. 3) Several investigations have shown that tasks that are well- learned tend to be more resistant to the effects of...automaticity and the proceduralization of tasks. These over- learned behaviors tend to require less attentional control and fewer mental resources

Proceedings: User’s Workshop on Combat Stress Held at Fort Sam Houston, Texas on 2-4 September 1981.

DTIC Science & Technology

1983-12-01

Primary Treatment Principle * Clinical Picture: Tremors, Paralysis, Mutism , Ganser Syndrome 5. WW II * No Effective Treatment-Evacuation Policy Existed...there is a lack of specific detailed tasks and the amount of time expended in these tasks for selected specialty skill identifiers. Information is...The study objective is the identification of the various tasks to be per- formed by selected specialty skill identifiers dealing with psychiatric

Statistical Analysis of Warfare: Identification of Winning Factors with a Focus on Irregular Warfare

DTIC Science & Technology

2015-09-01

Defense HERO Historical Evaluation and Research Organization IDPs Internally Displaced Persons IFR Initial Force Ratio INITA Relative Imitative...armies started combating non-state, widely dispersed groups. Although this change appears to be quite simple, it has had a deep impact on military...1789–1961: A Study of the Impact of the French, Industrial, and Russian Revolutions on War and its Conduct (Boston, MA: Da Capo Press, 1992). 10 Ibid

Developing Human-Machine Interfaces to Support Appropriate Trust and Reliance on Automated Combat Identification Systems

DTIC Science & Technology

2007-09-17

Signal Detection Theory (SDT) (Macmillan & Creelman , 1991; Wickens & Hollands, 2000). In SDT, the participants’ performance is characterized by two...probability, whereas their sensitivity will stay constant (Macmillan & Creelman , 1991; Wickens & Hollands, 2000). If this hypothesis holds, it will...Macmillan & Creelman , 1991, p273), and it was also the measure used in Dzindolet et al.’s study (2001a). Thus, C was used in the analysis HMIs for Trust and

Identification of Text and Symbols on a Liquid Crystal Display Part 2: Contrast and Luminance Settings to Optimise Legibility

DTIC Science & Technology

2009-02-01

Measurements on Chart Design and Scoring Rule. Optometry and Vision Science, 79(12), 768-792. ISO. (1998). EN ISO 9241-11. Ergonomic Requirements for...Human Factors from the University of Queensland. He began his career designing and building computerised electronics for the theatre. Following this...to optical detection. Recent work includes the assessment of networked naval gunfire support, ergonomic assessments of combat system consoles and

A composite CBRN surveillance and testing service

NASA Astrophysics Data System (ADS)

Niemeyer, Debra M.

2004-08-01

The terrorist threat coupled with a global military mission necessitates quick and accurate identification of environmental hazards, and CBRN early warning. The Air Force Institute for Operational Health (AFIOH) provides fundamental support to protect personnel from and mitigate the effects of untoward hazards exposures. Sustaining healthy communities since 1955, the organizational charter is to enhance warfighter mission effectiveness, protect health, improve readiness and reduce costs, assess and manage risks to human heath and safety, operational performance and the environment. The AFIOH Surveillance Directorate provides forward deployed and reach-back surveillance, agent identification, and environ-mental regulatory compliance testing. Three unique laboratories process and analyze over two million environmental samples and clinical specimens per year, providing analytical chemistry, radiological assessment, and infectious disease testing, in addition to supporting Air Force and Department of Defense (DoD) clinical reference laboratory and force health protection testing. Each laboratory has an applied or investigational testing section where new technologies and techniques are evaluated, and expert consultative support to assist in technology assessments and test analyses. The Epidemiology Surveillance Laboratory and Analytical Chemistry Laboratory are critical assets of the Centers for Disease Control and Prevention (CDC) National Laboratory Response Network. Deployable assets provide direct support to the Combatant Commander and include the Air Force Radiological Assessment Team, and the Biological Augmentation Team. A diverse directorate, the synergistic CBRN response capabilities are a commander"s force protection tool, critical to maintaining combat power.

Alcohol Use Among Active Duty Women: Analysis AUDIT Scores From the 2011 Health-Related Behavior Survey of Active Duty Military Personnel.

PubMed

Jeffery, Diana D; Mattiko, Mark

2016-01-01

Numerous studies document higher substance use among military men after deployment; similar studies focused on military women are limited. This study examines alcohol use of active duty women and deployment factors, social/environmental/attitudinal factors, and psychological/intrapersonal factors. Secondary data analysis of the 2011 Survey of Health-Related Behavior of active duty military personnel was conducted using bivariate statistics and multiple regression analyses with Alcohol Use Disorders Identification Test scores as the dependent variable. Nearly 94% had low risk for alcohol use disorders. Length of combat experience and extent of combat exposure were unrelated to Alcohol Use Disorders Identification Test scores; noncombat deployment was unrelated after controlling for marital status, age of first drink, pay grade, and branch of service. Significant motivators (p < 0.001) for drinking were "like/enjoy drinking," "drink to cheer up," "drink to forget problems," and significant deterrents were "cost of alcohol" and "fear of upsetting family/friends if used alcohol." Anger propensity, risk propensity, lifetime prevalence of suicidal ideation, and depressed mood were significant predictors in the regression model after controlling for covariates. Findings suggest that some active duty women use alcohol to cope with adverse emotional states, whereas others use alcohol consistent with propensity for high-risk behaviors. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

Chemical investigation of saponins in different parts of Panax notoginseng by pressurized liquid extraction and liquid chromatography-electrospray ionization-tandem mass spectrometry.

PubMed

Wan, Jian-Bo; Zhang, Qing-Wen; Hong, Si-Jia; Li, Peng; Li, Shao-Ping; Wang, Yi-Tao

2012-05-16

A pressurized liquid extraction (PLE) and high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) method was developed for the qualitative determination of saponins in different parts of P. notoginseng, including rhizome, root, fibre root, seed, stem, leaf and flower. The samples were extracted using PLE. The analysis was achieved on a Zorbax SB-C18 column with gradient elution of acetonitrile and 8 mM aqueous ammonium acetate as mobile phase. The mass spectrometer was operated in the negative ion mode using the electrospray ionization, and a collision induced dissociation (CID) experiment was also carried out to aid the identification of compounds. Forty one saponins were identified in different parts of P. notoginseng according to the fragmentation patterns and literature reports, among them, 21 saponins were confirmed by comparing the retention time and ESI-MS data with those of standard compounds. The results showed that the chemical characteristics were obviously diverse in different parts of P. notoginseng, which is helpful for pharmacological evaluation and quality control of P. notoginseng.

Analysis of human serum phosphopeptidome by a focused database searching strategy.

PubMed

Zhu, Jun; Wang, Fangjun; Cheng, Kai; Song, Chunxia; Qin, Hongqiang; Hu, Lianghai; Figeys, Daniel; Ye, Mingliang; Zou, Hanfa

2013-01-14

As human serum is an important source for early diagnosis of many serious diseases, analysis of serum proteome and peptidome has been extensively performed. However, the serum phosphopeptidome was less explored probably because the effective method for database searching is lacking. Conventional database searching strategy always uses the whole proteome database, which is very time-consuming for phosphopeptidome search due to the huge searching space resulted from the high redundancy of the database and the setting of dynamic modifications during searching. In this work, a focused database searching strategy using an in-house collected human serum pro-peptidome target/decoy database (HuSPep) was established. It was found that the searching time was significantly decreased without compromising the identification sensitivity. By combining size-selective Ti (IV)-MCM-41 enrichment, RP-RP off-line separation, and complementary CID and ETD fragmentation with the new searching strategy, 143 unique endogenous phosphopeptides and 133 phosphorylation sites (109 novel sites) were identified from human serum with high reliability. Copyright © 2012 Elsevier B.V. All rights reserved.

Tandem mass spectrometry approach for the investigation of the steroidal metabolism: structure-fragmentation relationship (SFR) in anabolic steroids and their metabolites by ESI-MS/MS analysis.

PubMed

Musharraf, Syed Ghulam; Ali, Arslan; Khan, Naik Tameem; Yousuf, Maria; Choudhary, Muhammad Iqbal; Atta-ur-Rahman

2013-02-01

Electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to investigate the effect of different substitutions introduced during metabolism on fragmentation patterns of four anabolic steroids including methyltestosterone, methandrostenolone, cis-androsterone and adrenosterone, along with their metabolites. Collision-induced dissociation (CID) analysis was performed to correlate the major product ions of 19 steroids with structural features. The analysis is done to portray metabolic alteration, such as incorporation or reduction of double bonds, hydroxylations, and/or oxidation of hydroxyl moieties to keto functional group on steroidal skeleton which leads to drastically changed product ion spectra from the respective classes of steroids, therefore, making them difficult to identify. The comparative ESI-MS/MS study also revealed some characteristic peaks to differentiate different steroidal metabolites and can be useful for the unambiguous identification of anabolic steroids in biological fluid. Moreover, LC-ESI-MS/MS analysis of fermented extract of methyltestosterone, obtained by Macrophomina phaseolina was also investigated. Copyright © 2012 Elsevier Inc. All rights reserved.

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments

NASA Astrophysics Data System (ADS)

Harvey, David J.; Seabright, Gemma E.; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B.

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man8GlcNAc2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. [Figure not available: see fulltext.

Annotation and Structural Analysis of Sialylated Human Milk Oligosaccharides

PubMed Central

Wu, Shuai; Grimm, Rudolf; German, J. Bruce; Lebrilla, Carlito B.

2011-01-01

Sialylated human milk oligosaccharides (SHMOs) are important components of human milk oligosaccharides. Sialic acids are typically found on the nonreducing end and are known binding sites for pathogens and aid in neonates’ brain development. Due to their negative charge and hydrophilic nature, they also help modulate cell-cell interactions. It has also been shown that sialic acids are involved in regulating the immune response and aid in brain development. In this study, the enriched SHMOs from pooled milk sample were analyzed by HPLC-Chip/QTOF MS. The instrument employs a microchip-based nano-LC column packed with porous graphitized carbon (PGC) to provide excellent isomer separation for SHMOs with highly reproducible retention time. The precursor ions were further examined with collision-induced dissociation (CID). By applying the proper collision energy, isomers can be readily differentiated by diagnostic peaks and characteristic fragmentation patterns. A set of 30 SHMO structures with retention times, accurate masses and MS/MS spectra was deduced and incorporated into an HMO library. When combined with previously determined neutral components, a library with over 70 structures is obtained allowing high-throughput oligosaccharide structure identification. PMID:21133381

30 CFR 550.200 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... OPERATIONS IN THE OUTER CONTINENTAL SHELF Plans and Information General Information § 550.200 Definitions... of Safety and Environmental Enforcement. CID means Conservation Information Document. CZMA means Coastal Zone Management Act. DOCD means Development Operations Coordination Document. DPP means...

An automated testing tool for traffic signal controller functionalities.

DOT National Transportation Integrated Search

2010-03-01

The purpose of this project was to develop an automated tool that facilitates testing of traffic controller functionality using controller interface device (CID) technology. Benefits of such automated testers to traffic engineers include reduced test...

78 FR 29019 - Individual Requests for Access or Amendment of CID Reports of Investigation

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-17

... Interference With Constitutionally Protected Property Rights) The Department of the Army has determined that Executive Order 12630 does not apply because the rule change does not impair private property rights. G...

30 CFR 250.298 - How long will MMS take to evaluate and make a decision on the CID?

Code of Federal Regulations, 2011 CFR

2011-07-01

..., REGULATION, AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE... economically producible reservoirs according to sound conservation, engineering, and economic practices. ...

Tandem SAM Domain Structure of Human Caskin1: A Presynaptic, Self-Assembling Scaffold for CASK

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

Stafford, Ryan L.; Hinde, Elizabeth; Knight, Mary Jane

2012-02-07

The synaptic scaffolding proteins CASK and Caskin1 are part of the fibrous mesh of proteins that organize the active zones of neural synapses. CASK binds to a region of Caskin1 called the CASK interaction domain (CID). Adjacent to the CID, Caskin1 contains two tandem sterile a motif (SAM) domains. Many SAM domains form polymers so they are good candidates for forming the fibrous structures seen in the active zone. We show here that the SAM domains of Caskin1 form a new type of SAM helical polymer. The Caskin1 polymer interface exhibits a remarkable segregation of charged residues, resulting in amore » high sensitivity to ionic strength in vitro. The Caskin1 polymers can be decorated with CASK proteins, illustrating how these proteins may work together to organize the cytomatrix in active zones.« less

Comparison of experimental and calculated chiroptical spectra for chiral molecular structure determination.

PubMed

Polavarapu, Prasad L; Covington, Cody L

2014-09-01

For three different chiroptical spectroscopic methods, namely, vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and Raman optical activity (ROA), the measures of similarity of the experimental spectra to the corresponding spectra predicted using quantum chemical theories are summarized. In determining the absolute configuration and/or predominant conformations of chiral molecules, these similarity measures provide numerical estimates of agreement between experimental observations and theoretical predictions. Selected applications illustrating the similarity measures for absorption, circular dichroism, and corresponding dissymmetry factor (DF) spectra, in the case of VCD and ECD, and for Raman, ROA, and circular intensity differential (CID) spectra in the case of ROA, are presented. The analysis of similarity in DF or CID spectra is considered to be much more discerning and accurate than that in absorption (or Raman) and circular dichroism (or ROA) spectra, undertaken individually. © 2014 Wiley Periodicals, Inc.

Perceptual Color Characterization of Cameras

PubMed Central

Vazquez-Corral, Javier; Connah, David; Bertalmío, Marcelo

2014-01-01

Color camera characterization, mapping outputs from the camera sensors to an independent color space, such as XY Z, is an important step in the camera processing pipeline. Until now, this procedure has been primarily solved by using a 3 × 3 matrix obtained via a least-squares optimization. In this paper, we propose to use the spherical sampling method, recently published by Finlayson et al., to perform a perceptual color characterization. In particular, we search for the 3 × 3 matrix that minimizes three different perceptual errors, one pixel based and two spatially based. For the pixel-based case, we minimize the CIE ΔE error, while for the spatial-based case, we minimize both the S-CIELAB error and the CID error measure. Our results demonstrate an improvement of approximately 3% for the ΔE error, 7% for the S-CIELAB error and 13% for the CID error measures. PMID:25490586

Design and tritium permeation analysis of China HCCB TBM port cell

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

Jiangfeng, S.; Guoqiang, H.; Zhiyong, H.

2015-03-15

China is planning to develop a helium-cooled ceramic breeder (HCCB) test blanket module (TBM) on ITER to test key blanket technologies. In this paper, the design and tritium permeation analysis of China HCCB TBM port cell are introduced. A theoretical model has been developed to estimate tritium permeation rates and leak rates from the components and pipes which China has scheduled to house in the port cell. It is shown that on normal working conditions, the permeation and leak rate of the systems in the port cell will be no higher than 1.58 Ci/d without the use of tritium permeationmore » barriers, and 0.10 Ci/d with the use of tritium permeation barriers. It also appears that tritium permeation barriers are necessary for high temperature components such as the reduction bed and the heater.« less

Rapid ultra-trace analysis of sucralose in multiple-origin aqueous samples by online solid-phase extraction coupled to high-resolution mass spectrometry.

PubMed

Batchu, Sudha Rani; Ramirez, Cesar E; Gardinali, Piero R

2015-05-01

Because of its widespread consumption and its persistence during wastewater treatment, the artificial sweetener sucralose has gained considerable interest as a proxy to detect wastewater intrusion into usable water resources. The molecular resilience of this compound dictates that coastal and oceanic waters are the final recipient of this compound with unknown effects on ecosystems. Furthermore, no suitable methodologies have been reported for routine, ultra-trace detection of sucralose in seawater as the sensitivity of traditional liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis is limited by a low yield of product ions upon collision-induced dissociation (CID). In this work, we report the development and field test of an alternative analysis tool for sucralose in environmental waters, with enough sensitivity for the proper quantitation and confirmation of this analyte in seawater. The methodology is based on automated online solid-phase extraction (SPE) and high-resolving-power orbitrap MS detection. Operating in full scan (no CID), detection of the unique isotopic pattern (100:96:31 for [M-H](-), [M-H+2](-), and [M-H+4](-), respectively) was used for ultra-trace quantitation and analyte identification. The method offers fast analysis (14 min per run) and low sample consumption (10 mL per sample) with method detection and confirmation limits (MDLs and MCLs) of 1.4 and 5.7 ng/L in seawater, respectively. The methodology involves low operating costs due to virtually no sample preparation steps or consumables. As an application example, samples were collected from 17 oceanic and estuarine sites in Broward County, FL, with varying salinity (6-40 PSU). Samples included the ocean outfall of the Southern Regional Wastewater Treatment Plant (WWTP) that serves Hollywood, FL. Sucralose was detected above MCL in 78% of the samples at concentrations ranging from 8 to 148 ng/L, with the exception of the WWTP ocean outfall (at pipe end, 28 m below the surface) where the measured concentration was 8418 ± 3813 ng/L. These results demonstrate the applicability of this monitoring tool for the trace-level detection of this wastewater marker in very dilute environmental waters.

American College of Rheumatology provisional criteria for defining clinical inactive disease in select categories of juvenile idiopathic arthritis.

PubMed

Wallace, Carol A; Giannini, Edward H; Huang, Bin; Itert, Lukasz; Ruperto, Nicolino

2011-07-01

To prospectively validate the preliminary criteria for clinical inactive disease (CID) in patients with select categories of juvenile idiopathic arthritis (JIA). We used the process for development of classification and response criteria recommended by the American College of Rheumatology Quality of Care Committee. Patient-visit profiles were extracted from the phase III randomized controlled trial of infliximab in polyarticular-course JIA (i.e., patients considered to resemble those with select categories of JIA) and sent to an international group of expert physician raters. Using the physician ratings as the gold standard, the sensitivity and specificity were calculated using the preliminary criteria. Modifications to the criteria were made, and these were sent to a larger group of pediatric rheumatologists to determine quantitative, face, and content validity. Variables weighted heaviest by physicians when making their judgment were the number of joints with active arthritis, erythrocyte sedimentation rate (ESR), physician's global assessment, and duration of morning stiffness. Three modifications were made: the definition of uveitis, the definition of abnormal ESR, and the addition of morning stiffness. These changes did not alter the accuracy of the preliminary set. The modified criteria, termed the "criteria for CID in select categories of JIA," have excellent feasibility and face, content, criterion, and discriminant validity to detect CID in select categories of JIA. The small changes made to the preliminary criteria set did not alter the area under the receiver operating characteristic curve (0.954) or accuracy (91%), but have increased face and content validity. Copyright © 2011 by the American College of Rheumatology.

Determination of patulin in apple juice by high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry.

PubMed

Sewram, V; Nair, J J; Nieuwoudt, T W; Leggott, N L; Shephard, G S

2000-11-03

An HPLC-MS-MS method with selected reaction monitoring (SRM) for the determination of patulin in apple juice samples is described. Mass spectrometric detection was accomplished following atmospheric pressure chemical ionization (APCI) in both positive and negative ion modes. Collision induced dissociation (CID) of the protonated molecular ion led initially to the loss of H2O (fragment m/z 137). At higher energies CO is lost from both the protonated parent molecule (fragment m/z 127) and the dehydrated molecular ion (fragment m/z 109). In contrast, CID of the deprotonated molecular ion led initially to the fragment at m/z 109 corresponding to the loss of either CO2 or acetaldehyde, followed at higher CID energy by the loss of H2O (fragment m/z 135) and CO (fragment m/z 125) from the deprotonated molecular ion. Detection in the negative ion mode proved superior and a linear response was observed over the injected range from 6 to 200 ng patulin. Apple juice samples spiked with patulin between 10 and 135 microg/l were analyzed following liquid-liquid extraction with ethyl acetate and clean up with sodium carbonate. Utilizing reversed-phase HPLC with acetonitrile-water (10:90) at 0.5 ml/min, levels down to 10 microg/l were readily quantified and a detection limit of 4 microg/l was attainable at a signal-to-noise (SIN) ratio of 4. The MS data for the spiked samples compared well to the UV data and when plotted against each other displayed a correlation coefficient (R) of 0.99.

Electron Transfer Dissociation of iTRAQ Labeled Peptide Ions

PubMed Central

Han, Hongling; Pappin, Darryl J.; Ross, Philip L; McLuckey, Scott A.

2009-01-01

Triply and doubly charged iTRAQ (isobaric tagging for relative and absolute quantitation) labeled peptide cations from a tryptic peptide mixture of bovine carbonic anhydrase II were subjected to electron transfer ion/ion reactions to investigate the effect of charge bearing modifications associated with iTRAQ on the fragmentation pattern. It was noted that electron transfer dissociation (ETD) of triply charged or activated ETD (ETD + supplemental collisional activation of intact electron transfer species) of doubly charged iTRAQ tagged peptide ions yielded extensive sequence information, in analogy with ETD of unmodified peptide ions. That is, addition of the fixed charge iTRAQ tag showed relatively little deleterious effect on the ETD performance of the modified peptides. ETD of the triply charged iTRAQ labeled peptide ions followed by collision-induced dissociation (CID) of the product ion at m/z 162 yielded the reporter ion at m/z 116, which is the reporter ion used for quantitation via CID of the same precursor ions. The reporter ion formed via the two-step activation process is expected to provide quantitative information similar to that directly produced from CID. A 103 Da neutral loss species observed in the ETD spectra of all the triply and doubly charged iTRAQ labeled peptide ions is unique to the 116 Da iTRAQ reagent, which implies that this process also has potential for quantitation of peptides/proteins. Therefore, ETD with or without supplemental collisional activation, depending on the precursor ion charge state, has the potential to directly identify and quantify the peptides/proteins simultaneously using existing iTRAQ reagents. PMID:18646790

Collision-Induced Dissociation of Electrosprayed NaCl Clusters: Using Molecular Dynamics Simulations to Visualize Reaction Cascades in the Gas Phase

NASA Astrophysics Data System (ADS)

Schachel, Tilo D.; Metwally, Haidy; Popa, Vlad; Konermann, Lars

2016-11-01

Infusion of NaCl solutions into an electrospray ionization (ESI) source produces [Na( n+1)Cl n ]+ and other gaseous clusters. The n = 4, 13, 22 magic number species have cuboid ground state structures and exhibit elevated abundance in ESI mass spectra. Relatively few details are known regarding the mechanisms whereby these clusters undergo collision-induced dissociation (CID). The current study examines to what extent molecular dynamics (MD) simulations can be used to garner insights into the sequence of events taking place during CID. Experiments on singly charged clusters reveal that the loss of small neutrals is the dominant fragmentation pathway. MD simulations indicate that the clusters undergo extensive structural fluctuations prior to decomposition. Consistent with the experimentally observed behavior, most of the simulated dissociation events culminate in ejection of small neutrals ([NaCl] i , with i = 1, 2, 3). The MD data reveal that the prevalence of these dissociation channels is linked to the presence of short-lived intermediates where a relatively compact core structure carries a small [NaCl] i protrusion. The latter can separate from the parent cluster via cleavage of a single Na-Cl contact. Fragmentation events of this type are kinetically favored over other dissociation channels that would require the quasi-simultaneous rupture of multiple electrostatic contacts. The CID behavior of NaCl cluster ions bears interesting analogies to that of collisionally activated protein complexes. Overall, it appears that MD simulations represent a valuable tool for deciphering the dissociation of noncovalently bound systems in the gas phase.

Quantitative analysis of polyethylene glycol (PEG) and PEGylated proteins in animal tissues by LC-MS/MS coupled with in-source CID.

PubMed

Gong, Jiachang; Gu, Xiaomei; Achanzar, William E; Chadwick, Kristina D; Gan, Jinping; Brock, Barry J; Kishnani, Narendra S; Humphreys, W Griff; Iyer, Ramaswamy A

2014-08-05

The covalent conjugation of polyethylene glycol (PEG, typical MW > 10k) to therapeutic peptides and proteins is a well-established approach to improve their pharmacokinetic properties and diminish the potential for immunogenicity. Even though PEG is generally considered biologically inert and safe in animals and humans, the slow clearance of large PEGs raises concerns about potential adverse effects resulting from PEG accumulation in tissues following chronic administration, particularly in the central nervous system. The key information relevant to the issue is the disposition and fate of the PEG moiety after repeated dosing with PEGylated proteins. Here, we report a novel quantitative method utilizing LC-MS/MS coupled with in-source CID that is highly selective and sensitive to PEG-related materials. Both (40K)PEG and a tool PEGylated protein (ATI-1072) underwent dissociation in the ionization source of mass spectrometer to generate a series of PEG-specific ions, which were subjected to further dissociation through conventional CID. To demonstrate the potential application of the method to assess PEG biodistribution following PEGylated protein administration, a single dose study of ATI-1072 was conducted in rats. Plasma and various tissues were collected, and the concentrations of both (40K)PEG and ATI-1072 were determined using the LC-MS/MS method. The presence of (40k)PEG in plasma and tissue homogenates suggests the degradation of PEGylated proteins after dose administration to rats, given that free PEG was absent in the dosing solution. The method enables further studies for a thorough characterization of disposition and fate of PEGylated proteins.

Phenological adjustment in arctic bird species: relative importance of snow melt and ecological factors

USGS Publications Warehouse

Liebezeit, Joseph R.; Gurney, K. E. B.; Budde, Michael E.; Zack, Steve; Ward, David H.

2014-01-01

Previous studies have documented advancement in clutch initiation dates (CIDs) in response to climate change, most notably for temperate-breeding passerines. Despite accelerated climate change in the Arctic, few studies have examined nest phenology shifts in arctic breeding species. We investigated whether CIDs have advanced for the most abundant breeding shorebird and passerine species at a long-term monitoring site in arctic Alaska. We pooled data from three additional nearby sites to determine the explanatory power of snow melt and ecological variables (predator abundance, green-up) on changes in breeding phenology. As predicted, all species (semipalmated sandpiper, Calidris pusilla, pectoral sandpiper, Calidris melanotos, red-necked phalarope, Phalaropus lobatus, red phalarope, Phalaropus fulicarius, Lapland longspur, Calcarius lapponicus) exhibited advanced CIDs ranging from 0.40 to 0.80 days/year over 9 years. Timing of snow melt was the most important variable in explaining clutch initiation advancement (“climate/snow hypothesis”) for four of the five species, while green-up was a much less important explanatory factor. We found no evidence that high predator abundances led to earlier laying dates (“predator/re-nest hypothesis”). Our results support previous arctic studies in that climate change in the cryosphere will have a strong impact on nesting phenology although factors explaining changes in nest phenology are not necessarily uniform across the entire Arctic. Our results suggest some arctic-breeding shorebird and passerine species are altering their breeding phenology to initiate nesting earlier enabling them to, at least temporarily, avoid the negative consequences of a trophic mismatch.

Effect of enrofloxacin-Na against pathogens related to the respiratory and alimentary diseases in suckling and weanling piglets.

PubMed

Yoo, H S; Lee, B J; Chang, B S; Lee, Y S; Park, B K

2001-01-01

A field trial was conducted to evaluate effect of enrofloxacin-Na against pathogens related to the respiratory and alimentary diseases in eighty suckling piglets (6-7 days old) and eighty weanling piglets (5-6 weeks old). Respective twenty of the suckling and weanling piglets were assigned to each of 4 experimental groups; control (non-treated), clinical injection dose (CID), 2x clinical injection dose (2CID). and premix. A 0.05 ml (2.5 mg) of enrofloxacin-Na injection (5% solution, 1 ml) per kg body weight of piglets as CID was injected intramuscularly for 3 days and the clinical signs were observed for 9 days. The premix (150 ppm) of enrofloxacin-Na was administered with feed for 7 days ad libitum and the clinical signs were observed for 13 days. The enrofloxacin-Na-treated piglets showed a higher increase in body weight and a lower feed per gain than the control piglets. In addition, the treatment of enrofloxacin-Na, regardless of the route of administration, decreased the incidence rate of diarrhea in suckling piglets and respiratory symptoms in weanling piglets. The isolation index of E. coli and Cl. perfringens during the treatment periods was also lowered by the enrofloxacin-Na treatment in both suckling and weanling piglets. The antibiotics was also evaluated as safe locally and whole bodily as treated by injection or feeding. These results indicate that the newly developed antibiotics, enrofloxacin-Na, is very useful for the prevention and therapy of swine diseases in the pig industry.

Generation and collision-induced dissociation of ammonium tetrafluoroborate cluster ions.

PubMed

Dain, Ryan P; Van Stipdonk, Michael J

2008-07-01

Singly and doubly charged cluster ions of ammonium tetrafluoroborate (NH4BF4) with general formula [(NH4BF4)nNH4]+ and [(NH4BF4)m(NH4)2]2+, respectively, were generated by electrospray ionization (ESI) and their fragmentation examined using collision-induced dissociation (CID) and ion-trap tandem mass spectrometry. CID of [(NH4BF4)nNH4]+ caused the loss of one or more neutral NH4BF4 units. The n = 2 cluster, [(NH4BF4)2NH4]+, was unique in that it also exhibited a dissociation pathway in which HBF4 was eliminated to create [(NH4BF4)(NH3)NH4]+. Dissociation of [(NH4BF4)m(NH4)2]2+ occurred through two general pathways: (a) 'fission' to produce singly charged cluster ions and (b) elimination of one or more neutral NH4BF4 units to leave doubly charged product ions. CID profiles, and measurements of changing precursor and product ion signal intensity as a function of applied collision voltage, were collected for [(NH4BF4)nNH4]+ and compared with those for analogous [(NaBF4)nNa]+ and [(KBF4)nK]+ ions to determine the influence of the cation on the relative stability of cluster ions. In general, the [(NH4BF4)nNH4]+ clusters were found to be easier to dissociate than both the sodium and potassium clusters of comparable size, with [(KBF4)nK]+ ions the most difficult to dissociate.

Engine Performance Test of the 1975 GM 140-CID

DOT National Transportation Integrated Search

1976-06-01

An engine test of the 1975 GM 140 cubic-inch-displacement, 4-cylinder engine was performed to determine its steady-state fuel consumption and emissions (HC, CO, and NO/sub x/) maps. The data acquired are summarized.

Unimolecular reactivity of organotrifluoroborate anions, RBF3- , and their alkali metal cluster ions, M(RBF3 )2- (M = Na, K; R = CH3 , CH3 CH2 , CH3 (CH2 )3 , CH3 (CH2 )5 , c-C3 H5 , C6 H5 , C6 H5 CH2 , CH2 CHCH2 , CH2 CH, C6 H5 CO).

PubMed

Bathie, Fiona L B; Bowen, Chris J; Hutton, Craig A; O'Hair, Richard A J

2018-07-15

Potassium organotrifluoroborates (RBF 3 K) are important reagents used in organic synthesis. Although mass spectrometry is commonly used to confirm their molecular formulae, the gas-phase fragmentation reactions of organotrifluoroborates and their alkali metal cluster ions have not been previously reported. Negative-ion mode electrospray ionization (ESI) together with collision-induced dissociation (CID) using a triple quadrupole mass spectrometer were used to examine the fragmentation pathways for RBF 3 - (where R = CH 3 , CH 3 CH 2 , CH 3 (CH 2 ) 3 , CH 3 (CH 2 ) 5 , c-C 3 H 5 , C 6 H 5 , C 6 H 5 CH 2 , CH 2 CHCH 2 , CH 2 CH, C 6 H 5 CO) and M(RBF 3 ) 2 - (M = Na, K), while density functional theory (DFT) calculations at the M06/def2-TZVP level were used to examine the structures and energies associated with fragmentation reactions for R = Me and Ph. Upon CID, preferentially elimination of HF occurs for RBF 3 - ions for systems where R = an alkyl anion, whereas R - formation is favoured when R = a stabilized anion. At higher collision energies loss of F - and additional HF losses are sometimes observed. Upon CID of M(RBF 3 ) 2 - , formation of RBF 3 - is the preferred pathway with some fluoride transfer observed only when M = Na. The DFT-calculated relative thermochemistry for competing fragmentation pathways is consistent with the experiments. The main fragmentation pathways of RBF 3 - are HF elimination and/or R - loss. This contrasts with the fragmentation reactions of other organometallate anions, where reductive elimination, beta hydride transfer and bond homolysis are often observed. The presence of fluoride transfer upon CID of Na(RBF 3 ) 2 - but not K(RBF 3 ) 2 - is in agreement with the known fluoride affinities of Na + and K + and can be rationalized by Pearson's HSAB theory. Copyright © 2018 John Wiley & Sons, Ltd.

Collaborator Support: Identification of Fundamental Visual, Auditory, and Cognitive Requirements for Command and Control Environments

DTIC Science & Technology

2009-04-01

generally involve display design for combat vehicles, such as aircraft or tanks. The strength of such displays is their non-intrusive nature , which...level .05 was used. 7 Table 1: ANOVA Summary Table for Reaction Time Due to a significant violation of the assumption of sphericity (p=.041...the Greenhouse- Geiser test was used to adjust the degrees of freedom. A significant main effect for cue type was found, F(1.693, 15.233) = 9.077

Two Birds With One Stone: Application of Fundamental Cognitive Theory of Visual Perception Supporting Fratricide Prevention and Sensor Modeling Experimentation

DTIC Science & Technology

2008-12-01

tools capable of reducing fratricide and collateral damage. The theory of recognition-by-components developed by Dr. Irving Biederman presented a...trainer. The key to thermal combat identification was discovered in an unusual place: chick sexing. Biederman and Shiffrar [11] conducted object...professional sexers was .82. Biederman and Shiffrar conclude that “…after instruction the performance of the naïve subjects more closely resemble that of the

An intervention to decrease patient identification band errors in a children's hospital.

PubMed

Hain, Paul D; Joers, B; Rush, M; Slayton, J; Throop, P; Hoagg, S; Allen, L; Grantham, J; Deshpande, J K

2010-06-01

Patient misidentification continues to be a quality and safety issue. There is a paucity of US data describing interventions to reduce identification band error rates. Monroe Carell Jr Children's Hospital at Vanderbilt. Percentage of patients with defective identification bands. Web-based surveys were sent, asking hospital personnel to anonymously identify perceived barriers to reaching zero defects with identification bands. Corrective action plans were created and implemented with ideas from leadership, front-line staff and the online survey. Data from unannounced audits of patient identification bands were plotted on statistical process control charts and shared monthly with staff. All hospital personnel were expected to "stop the line" if there were any patient identification questions. The first audit showed a defect rate of 20.4%. The original mean defect rate was 6.5%. After interventions and education, the new mean defect rate was 2.6%. (a) The initial rate of patient identification band errors in the hospital was higher than expected. (b) The action resulting in most significant improvement was staff awareness of the problem, with clear expectations to immediately stop the line if a patient identification error was present. (c) Staff surveys are an excellent source of suggestions for combating patient identification issues. (d) Continued audit and data collection is necessary for sustainable staff focus and continued improvement. (e) Statistical process control charts are both an effective method to track results and an easily understood tool for sharing data with staff.

Transformation of Human Cathelicidin LL-37 into Selective, Stable, and Potent Antimicrobial Compounds

PubMed Central

2015-01-01

This Letter reports a family of novel antimicrobial compounds obtained by combining peptide library screening with structure-based design. Library screening led to the identification of a human LL-37 peptide resistant to chymotrypsin. This d-amino-acid-containing peptide template was active against Escherichia coli but not methicillin-resistant Staphylococcus aureus (MRSA). It possesses a unique nonclassic amphipathic structure with hydrophobic defects. By repairing the hydrophobic defects, the peptide (17BIPHE2) gained activity against the ESKAPE pathogens, including Enterococcus faecium, S. aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter species. In vitro, 17BIPHE2 could disrupt bacterial membranes and bind to DNA. In vivo, the peptide prevented staphylococcal biofilm formation in a mouse model of catheter-associated infection. Meanwhile, it boosted the innate immune response to further combat the infection. Because these peptides are potent, cell-selective, and stable to several proteases, they may be utilized to combat one or more ESKAPE pathogens. PMID:25061850

A review of existing and emerging digital technologies to combat the global trade in fake medicines.

PubMed

Mackey, Tim K; Nayyar, Gaurvika

2017-05-01

The globalization of the pharmaceutical supply chain has introduced new challenges, chief among them, fighting the international criminal trade in fake medicines. As the manufacture, supply, and distribution of drugs becomes more complex, so does the need for innovative technology-based solutions to protect patients globally. Areas covered: We conducted a multidisciplinary review of the science/health, information technology, computer science, and general academic literature with the aim of identifying cutting-edge existing and emerging 'digital' solutions to combat fake medicines. Our review identified five distinct categories of technology including mobile, radio frequency identification, advanced computational methods, online verification, and blockchain technology. Expert opinion: Digital fake medicine solutions are unifying platforms that integrate different types of anti-counterfeiting technologies as complementary solutions, improve information sharing and data collection, and are designed to overcome existing barriers of adoption and implementation. Investment in this next generation technology is essential to ensure the future security and integrity of the global drug supply chain.

Integrated Detection of Pathogens and Host Biomarkers for Wounds

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

Jaing, C

2012-03-19

The increasing incidence and complications arising from combat wounds has necessitated a reassessment of methods for effective treatment. Infection, excessive inflammation, and incidence of drug-resistant organisms all contribute toward negative outcomes for afflicted individuals. The organisms and host processes involved in wound progression, however, are incompletely understood. We therefore set out, using our unique technical resources, to construct a profile of combat wounds which did or did not successfully resolve. We employed the Lawrence Livermore Microbial Detection Array and identified a number of nosocomial pathogens present in wound samples. Some of these identities corresponded with bacterial isolates previously cultured, whilemore » others were not obtained via standard microbiology. Further, we optimized proteomics protocols for the identification of host biomarkers indicative of various stages in wound progression. In combination with our pathogen data, our biomarker discovery efforts will provide a profile corresponding to wound complications, and will assist significantly in treatment of these complex cases.« less

Microbial Profiling of Combat Wound Infection through Detection Microarray and Next-Generation Sequencing

PubMed Central

Allen, Jonathan E.; Brown, Trevor S.; Gardner, Shea N.; McLoughlin, Kevin S.; Forsberg, Jonathan A.; Kirkup, Benjamin C.; Chromy, Brett A.; Luciw, Paul A.; Elster, Eric A.

2014-01-01

Combat wound healing and resolution are highly affected by the resident microbial flora. We therefore sought to achieve comprehensive detection of microbial populations in wounds using novel genomic technologies and bioinformatics analyses. We employed a microarray capable of detecting all sequenced pathogens for interrogation of 124 wound samples from extremity injuries in combat-injured U.S. service members. A subset of samples was also processed via next-generation sequencing and metagenomic analysis. Array analysis detected microbial targets in 51% of all wound samples, with Acinetobacter baumannii being the most frequently detected species. Multiple Pseudomonas species were also detected in tissue biopsy specimens. Detection of the Acinetobacter plasmid pRAY correlated significantly with wound failure, while detection of enteric-associated bacteria was associated significantly with successful healing. Whole-genome sequencing revealed broad microbial biodiversity between samples. The total wound bioburden did not associate significantly with wound outcome, although temporal shifts were observed over the course of treatment. Given that standard microbiological methods do not detect the full range of microbes in each wound, these data emphasize the importance of supplementation with molecular techniques for thorough characterization of wound-associated microbes. Future application of genomic protocols for assessing microbial content could allow application of specialized care through early and rapid identification and management of critical patterns in wound bioburden. PMID:24829242

Open Globe Injury Patient Identification in Warfare Clinical Notes1

PubMed Central

Apostolova, Emilia; White, Helen A.; Morris, Patty A.; Eliason, David A.; Velez, Tom

2017-01-01

The aim of this study is to utilize the Defense and Veterans Eye Injury and Vision Registry clinical data derived from DoD and VA medical systems which include documentation of care while in combat, and develop methods for comprehensive and reliable Open Globe Injury (OGI) patient identification. In particular, we focus on the use of free-form clinical notes, since structured data, such as diagnoses or procedure codes, as found in early post-trauma clinical records, may not be a comprehensive and reliable indicator of OGIs. The challenges of the task include low incidence rate (few positive examples), idiosyncratic military ophthalmology vocabulary, extreme brevity of notes, specialized abbreviations, typos and misspellings. We modeled the problem as a text classification task and utilized a combination of supervised learning (SVMs) and word embeddings learnt in a unsupervised manner, achieving a precision of 92.50% and a recall of89.83%o. The described techniques are applicable to patient cohort identification with limited training data and low incidence rate. PMID:29854104

ANALYSIS OF POLYCYCLIC AROMATIC HYDROCARBONS BY ION TRAP TANDEM MASS SPECTROMETRY

EPA Science Inventory

An ion-trap mass spectrometer with a wave board and tandem mass spectrometry software was used to analyze gas chromatographically separated polycyclic aromatic hydrocarbons (PAHs) by using collision-induced dissociation (CID). The nonresonant (multiple collision) mode was used to...

30 CFR 250.200 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... OPERATIONS IN THE OUTER CONTINENTAL SHELF Plans and Information General Information § 250.200 Definitions... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Definitions. 250.200 Section 250.200 Mineral... subpart are listed alphabetically below: CID means Conservation Information Document CZMA means Coastal...

Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution.

PubMed

Harper, Brett; Neumann, Elizabeth K; Stow, Sarah M; May, Jody C; McLean, John A; Solouki, Touradj

2016-10-05

Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting "pure" IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810-1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) "shift factors" to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.8 Å(2), 295.1 Å(2), 296.8 Å(2), and 300.1 Å(2); all four of these CCS values were within 1.5% of independently measured DTIM-MS values. Copyright © 2016 Elsevier B.V. All rights reserved.

Primary fragmentation pathways of gas phase [M(uracil-H)(uracil)]+ complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): loss of uracil versus HNCO.

PubMed

Ali, Osama Y; Randell, Nicholas M; Fridgen, Travis D

2012-04-23

Complexes formed between metal dications, the conjugate base of uracil, and uracil are investigated by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Positive-ion electrospray spectra show that [M(Ura-H)(Ura)](+) (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd, Mg, Ca, Sr, Ba, or Pb) is the most abundant ion even at low concentrations of uracil. SORI-CID experiments show that the main primary decomposition pathway for all [M(Ura-H)(Ura)](+) , except where M=Ca, Sr, Ba, or Pb, is the loss of HNCO. Under the same SORI-CID conditions, when M is Ca, Sr, Ba, or Pb, [M(Ura-H)(Ura)](+) are shown to lose a molecule of uracil. Similar results were observed under infrared multiple-photon dissociation excitation conditions, except that [Ca(Ura-H)(Ura)](+) was found to lose HNCO as the primary fragmentation product. The binding energies between neutral uracil and [M(Ura-H)](+) (M=Zn, Cu, Ni, Fe, Cd, Pd ,Mg, Ca, Sr Ba, or Pb) are calculated by means of electronic-structure calculations. The differences in the uracil binding energies between complexes which lose uracil and those which lose HNCO are consistent with the experimentally observed differences in fragmentation pathways. A size dependence in the binding energies suggests that the interaction between uracil and [M(Ura-H)](+) is ion-dipole complexation and the experimental evidence presented supports this. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of the measurement model and clinically important differences for menopause-specific quality of life associated with bazedoxifene/conjugated estrogens.

PubMed

Bushmakin, Andrew G; Abraham, Lucy; Pinkerton, JoAnn V; Cappelleri, Joseph C; Mirkin, Sebastian

2014-08-01

This study aims to confirm the factor structure of the Menopause-Specific Quality of Life (MENQOL) questionnaire by using confirmatory factor analysis (CFA) and to determine whether improvements in menopause-specific health-related quality of life (HRQOL) observed with bazedoxifene (BZA)/conjugated estrogens (CE) relative to placebo are clinically meaningful. Postmenopausal women with seven or more moderate to severe hot flushes per day (or ≥50 per wk) received BZA 20 mg/CE 0.45 mg, BZA 20 mg/CE 0.625 mg, or placebo for 12 weeks. HRQOL and treatment satisfaction were evaluated using the MENQOL questionnaire and the Menopause Symptoms Treatment Satisfaction Questionnaire, respectively. The structure of the MENQOL questionnaire was evaluated using CFA. To estimate clinically important differences (CIDs) in HRQOL, we used a repeated-measures model to estimate changes in MENQOL domain and total scores using Menopause Symptoms Treatment Satisfaction Questionnaire items as anchors. The CFA model fits the MENQOL data (Bentler's comparative fit index >0.9). CID estimates ranged from 0.5 to 1.2 for the MENQOL domains and total score. Change from baseline in MENQOL vasomotor domain score for BZA 20 mg/CE 0.45 mg and BZA 20 mg/CE 0.625 mg compared with placebo was greater than the estimated CID, as were changes in MENQOL physical domain and total scores for BZA 20 mg/CE 0.625 mg compared with placebo. CFA confirms the factor structure of the MENQOL questionnaire. Treatment with BZA/CE provides clinically meaningful improvements in HRQOL in a population of postmenopausal women with bothersome vasomotor symptoms.

Analysis of antioxidants in insulation cladding of copper wire: a comparison of different mass spectrometric techniques (ESI-IT, MALDI-RTOF and RTOF-SIMS).

PubMed

Schnöller, Johannes; Pittenauer, Ernst; Hutter, Herbert; Allmaier, Günter

2009-12-01

Commercial copper wire and its polymer insulation cladding was investigated for the presence of three synthetic antioxidants (ADK STAB AO412S, Irganox 1010 and Irganox MD 1024) by three different mass spectrometric techniques including electrospray ionization-ion trap-mass spectrometry (ESI-IT-MS), matrix-assisted laser desorption/ionization reflectron time-of-flight (TOF) mass spectrometry (MALDI-RTOF-MS) and reflectron TOF secondary ion mass spectrometry (RTOF-SIMS). The samples were analyzed either directly without any treatment (RTOF-SIMS) or after a simple liquid/liquid extraction step (ESI-IT-MS, MALDI-RTOF-MS and RTOF-SIMS). Direct analysis of the copper wire itself or of the insulation cladding by RTOF-SIMS allowed the detection of at least two of the three antioxidants but at rather low sensitivity as molecular radical cations and with fairly strong fragmentation (due to the highly energetic ion beam of the primary ion gun). ESI-IT- and MALDI-RTOF-MS-generated abundant protonated and/or cationized molecules (ammoniated or sodiated) from the liquid/liquid extract. Only ESI-IT-MS allowed simultaneous detection of all three analytes in the extract of insulation claddings. The latter two so-called 'soft' desorption/ionization techniques exhibited intense fragmentation only by applying low-energy collision-induced dissociation (CID) tandem MS on a multistage ion trap-instrument and high-energy CID on a tandem TOF-instrument (TOF/RTOF), respectively. Strong differences in the fragmentation behavior of the three analytes could be observed between the different CID spectra obtained from either the IT-instrument (collision energy in the very low eV range) or the TOF/RTOF-instrument (collision energy 20 keV), but both delivered important structural information. Copyright 2009 John Wiley & Sons, Ltd.

Simultaneous Quantification of Free Cholesterol, Cholesteryl Esters, and Triglycerides without Ester Hydrolysis by UHPLC Separation and In-Source Collision Induced Dissociation Coupled MS/MS

NASA Astrophysics Data System (ADS)

Gardner, Michael S.; McWilliams, Lisa G.; Jones, Jeffrey I.; Kuklenyik, Zsuzsanna; Pirkle, James L.; Barr, John R.

2017-08-01

We demonstrate the application of in-source nitrogen collision-induced dissociation (CID) that eliminates the need for ester hydrolysis before simultaneous analysis of esterified cholesterol (EC) and triglycerides (TG) along with free cholesterol (FC) from human serum, using normal phase liquid chromatography (LC) coupled to atmospheric pressure chemical ionization (APCI) tandem mass spectrometry (MS/MS). The analysis requires only 50 μL of 1:100 dilute serum with a high-throughput, precipitation/evaporation/extraction protocol in one pot. Known representative mixtures of EC and TG species were used as calibrators with stable isotope labeled analogs as internal standards. The APCI MS source was operated with nitrogen source gas. Reproducible in-source CID was achieved with the use of optimal cone voltage (declustering potential), generating FC, EC, and TG lipid class-specific precursor fragment ions for multiple reaction monitoring (MRM). Using a representative mixture of purified FC, CE, and TG species as calibrators, the method accuracy was assessed with analysis of five inter-laboratory standardization materials, showing -10% bias for Total-C and -3% for Total-TG. Repeated duplicate analysis of a quality control pool showed intra-day and inter-day variation of 5% and 5.8% for FC, 5.2% and 8.5% for Total-C, and 4.1% and 7.7% for Total-TG. The applicability of the method was demonstrated on 32 serum samples and corresponding lipoprotein sub-fractions collected from normolipidemic, hypercholesterolemic, hypertriglyceridemic, and hyperlipidemic donors. The results show that in-source CID coupled with isotope dilution UHPLC-MS/MS is a viable high precision approach for translational research studies where samples are substantially diluted or the amounts of archived samples are limited. [Figure not available: see fulltext.

Strategies for generating peptide radical cations via ion/ion reactions.

PubMed

Gilbert, Joshua D; Fisher, Christine M; Bu, Jiexun; Prentice, Boone M; Redwine, James G; McLuckey, Scott A

2015-02-01

Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon-iodine (C-I) bond are subjected to UVPD with 266-nm photons, which selectively cleaves the C-I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even-electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non-covalent complexes in the electrospray process. Copyright © 2015 John Wiley & Sons, Ltd.

Investigation of some biologically relevant redox reactions using electrochemical mass spectrometry interfaced by desorption electrospray ionization.

PubMed

Lu, Mei; Wolff, Chloe; Cui, Weidong; Chen, Hao

2012-04-01

Recently we have shown that, as a versatile ionization technique, desorption electrospray ionization (DESI) can serve as a useful interface to combine electrochemistry (EC) with mass spectrometry (MS). In this study, the EC/DESI-MS method has been further applied to investigate some aqueous phase redox reactions of biological significance, including the reduction of peptide disulfide bonds and nitroaromatics as well as the oxidation of phenothiazines. It was found that knotted/enclosed disulfide bonds in the peptides apamin and endothelin could be electrochemically cleaved. Subsequent tandem MS analysis of the resulting reduced peptide ions using collision-induced dissociation (CID) and electron-capture dissociation (ECD) gave rise to extensive fragment ions, providing a fast protocol for sequencing peptides with complicated disulfide bond linkages. Flunitrazepam and clonazepam, a class of nitroaromatic drugs, are known to undergo reduction into amines which was proposed to involve nitroso and N-hydroxyl intermediates. Now in this study, these corresponding intermediate ions were successfully intercepted and their structures were confirmed by CID. This provides mass spectrometric evidence for the mechanism of the nitro to amine conversion process during nitroreduction, an important redox reaction involved in carcinogenesis. In addition, the well-known oxidation reaction of chlorpromazine was also examined. The putative transient one-electron transfer product, the chlorpromazine radical cation (m/z 318), was captured by MS, for the first time, and its structure was also verified by CID. In addition to these observations, some features of the DESI-interfaced electrochemical mass spectrometry were discussed, such as simple instrumentation and the lack of background signal. These results further demonstrate the feasibility of EC/DESI-MS for the study of the biology-relevant redox chemistry and would find applications in proteomics and drug development research.

Molecular Docking and Pharmacological Investigations of Rivastigmine-Fluoxetine and Coumarin-Tacrine hybrids against Acetyl Choline Esterase.

PubMed

Babitha, Pallikkara Pulikkal; Sahila, Mohammed Marunnan; Bandaru, Srinivas; Nayarisseri, Anuraj; Sureshkumar, Sivanpillai

2015-01-01

The present AChE inhibitors have been successful in the treatment of Alzheimer׳s Diseases however suffers serious side effects. Therefore in this view, the present study was sought to identify compounds with appreciable pharmacological profile targeting AChE. Analogue of Rivastigmine and Fluoxetine hybrid synthesized by Toda et al, 2003 (dataset1), and Coumarin-Tacrine hybrids synthesized by Qi Sun et al (dataset2) formed the test compounds for the present pharmacological evaluation. p-cholorophenyl substituted Rivastigmine and Fluoxetine hybrid compound (26d) from dataset 1 and -OCH3 substitute Coumarin-Tacrine hybrids (1h) from dataset 2 demonstrated superior pharmacological profile. 26 d showed superior pharmacological profile comparison to the entire compounds in either dataset owing to its better electrostatic interactions and hydrogen bonding patterns. In order to identify still better compound with pharmacological profile than 26 d and 1h, virtual screening was performed. The best docked compound (PubCId: PubCid: 68874404) showed better affinity than its parent 26 d, however showed poor ADME profile and AMES toxicity. CHEMBL2391475 (PubCid: 71699632) similar to 1h had reduced affinity in comparison to its parent compound 1h. From, our extensive analysis involving binding affinity analysis, ADMET properties predictions and pharmacophoric mappings, we report p-cholorophenyl substituted rivastigmine and fluoxetine hybrid (26d) to be a potential candidate for AcHE inhibition which in addition can overcome narrow therapeutic window of present AChE inhibitors in clinical treatment of Alzheimer׳s disease. AD - Alzheimer׳s Disease, AChE - Acetyl Choline Estarase, OPLS - Optimized Potentials for Liquid Simulations, PDB - Protein Data Bank.

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries.

PubMed

do Rosário, Denes Kaic Alves; da Silva Mutz, Yhan; Peixoto, Jaqueline Moreira Curtis; Oliveira, Syllas Borburema Silva; de Carvalho, Raquel Vieira; Carneiro, Joel Camilo Souza; de São José, Jackline Freitas Brilhante; Bernardes, Patrícia Campos

2017-01-16

New sanitization methods have been evaluated to improve food safety and food quality and to replace chlorine compounds. However, these new methods can lead to physicochemical and sensory changes in fruits and vegetables. The present study evaluated the effects of acetic acid, peracetic acid, and sodium dodecylbenzenesulfonate isolated or combined with 5min of ultrasound treatment (40kHz, 500W) on strawberry quality over 9days of storage at 8°C. The strawberry natural contaminant microbiota (molds and yeasts, mesophilic aerobic and lactic acid bacteria), physicochemical quality (pH, total titratable acidity, total soluble solids, vitamin C, and color), sensory quality (triangle test) and inactivation of Salmonella enterica subsp. enterica intentionally inoculated onto strawberries were analyzed. Ultrasound increased the effect of all chemical compounds in the reduction of aerobic mesophilic, molds and yeasts. The best treatment for those groups of microorganisms was ultrasound combined with peracetic acid (US+PA) that reduced 1.8 and 2.0logcfu/g during 9days of storage. Bactericidal effect of peracetic acid was also improved by ultrasound inactivation of S. enterica, reaching a decimal reduction of 2.1logcfu/g. Moreover, synergistic effects were observed in contaminant natural microbiota inactivation for all tested compounds during storage, without any major physicochemical or sensory alteration to the strawberries. Therefore, ultrasound treatment can improve the effect of sanitizers that are substitutes of chlorine compounds without altering the quality of strawberries during storage. Acetic acid (PubChem CID: 176); Peracetic acid (PubChem CID: 6585); Sodium dodecylbenzenesulfonate (PubChem CID: 18372154). Copyright © 2016 Elsevier B.V. All rights reserved.

32 CFR 637.6 - Customs investigations.

Code of Federal Regulations, 2010 CFR

2010-07-01

... CRIMINAL INVESTIGATIONS MILITARY POLICE INVESTIGATION Investigations § 637.6 Customs investigations. (a... to the military police and investigated by CID or the military police, as appropriate. (b) Military police will receipt for all seized or confiscated U.S. Government property and contraband shipped by U.S...

Colloquy to Paul Musset

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

None

2007-12-13

En honneur de Paul Musset il a été décidé de faire plutôt un colloque scientifique à la place d'une cérémonie. Plusieurs personnes temoignent de leurs estime et amitié pour ce physicien et ses activités

Controlled information destruction: the final frontier in preserving information security for every organisation

NASA Astrophysics Data System (ADS)

Curiac, Daniel-Ioan; Pachia, Mihai

2015-05-01

Information security represents the cornerstone of every data processing system that resides in an organisation's trusted network, implementing all necessary protocols, mechanisms and policies to be one step ahead of possible threats. Starting from the need to strengthen the set of security services, in this article we introduce a new and innovative process named controlled information destruction (CID) that is meant to secure sensitive data that are no longer needed for the organisation's future purposes but would be very damaging if revealed. The disposal of this type of data has to be controlled carefully in order to delete not only the information itself but also all its splinters spread throughout the network, thus denying any possibility of recovering the information after its alleged destruction. This process leads to a modified model of information assurance and also reconfigures the architecture of any information security management system. The scheme we envisioned relies on a reshaped information lifecycle, which reveals the impact of the CID procedure directly upon the information states.

Analysis of phenolic choline esters from seeds of Arabidopsis thaliana and Brassica napus by capillary liquid chromatography/electrospray- tandem mass spectrometry.

PubMed

Böttcher, Christoph; von Roepenack-Lahaye, Edda; Schmidt, Jürgen; Clemens, Stephan; Scheel, Dierk

2009-04-01

Total phenolic choline ester fractions prepared from seeds of Arabidopsis thaliana and Brassica napus were analyzed by capillary LC/ESI-QTOF-MS and direct infusion ESI-FTICR-MS. In addition to the dominating sinapoylcholine, 30 phenolic choline esters could be identified based on accurate mass measurements, interpretation of collision-induced dissociation (CID) mass spectra, and synthesis of selected representatives. The compounds identified so far include substituted hydroxycinnamoyl- and hydroxybenzoylcholines, respective monohexosides as well as oxidative coupling products of phenolic choline esters and monolignols. Phenolic choline esters are well separable by reversed-phase liquid chromatography and sensitively detectable using electrospray ionization mass spectrometry in positive ion mode. CID mass spectra obtained from molecular ions facilitate the characterization of both the type and substitution pattern of such compounds. Therefore, LC/ESI-MS/MS represents a valuable tool for comprehensive qualitative and quantitative analysis of this compound class. Copyright (c) 2009 John Wiley & Sons, Ltd.

Fragmentation studies of fulvic acids using collision induced dissociation fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Witt, Matthias; Fuchser, Jens; Koch, Boris P

2009-04-01

The complex natural organic matter standard Suwannee river fulvic acid (SRFA) was analyzed by negative ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS) using on-resonance collision induced dissociation (CID) of single ultrahigh resolved mass peaks in the ICR cell. Molecular formula assignment of precursor masses resulted in exactly one molecular formula for each of the peaks. Analyses of the corresponding fragment spectra and comparison to different standard substances revealed specific neutral losses and fragmentation patterns which result in structures consisting of a high degree of carboxyl- and fewer hydroxyl groups. The comparison of fragmented mass peaks within different pseudohomologous series (CH(2)-series, and CH(4) vs O exchange) suggested structurally based differences between these series. CID FTICR MS allowed isolating single mass peaks in a very complex natural organic matter spectrum. Subsequently, fragmentation gave structural insights into this material. Our results suggest that the structural diversity in complex humic substances is not as high as expected.

Comparison of Detector Technologies for CAPS

NASA Technical Reports Server (NTRS)

Stockum, Jana L.

2005-01-01

In this paper, several different detectors are examined for use in a Comet/Asteroid Protection System (CAPS), a conceptual study for a possible future space-based system. Each detector will be examined for its future (25 years or more in the future) ability to find and track near-Earth Objects (NEOs) from a space-based detection platform. Within the CAPS study are several teams of people who each focus on different aspects of the system concept. This study s focus is on detection devices. In particular, evaluations on the following devices have been made: charge-coupled devices (CCDs), charge-injected devices (CIDs), superconducting tunneling junctions (STJs), and transition edge sensors (TESs). These devices can be separated into two main categories; the first category includes detectors that are currently being widely utilized, such as CCDs and CIDs. The second category includes experimental detectors, such as STJs and TESs. After the discussion of the detectors themselves, there will be a section devoted to the explicit use of these detectors with CAPS.

Collision Cross Sections and Ion Mobility Separation of Fragment Ions from Complex N-Glycans.

PubMed

Harvey, David J; Watanabe, Yasunori; Allen, Joel D; Rudd, Pauline; Pagel, Kevin; Crispin, Max; Struwe, Weston B

2018-06-01

Ion mobility mass spectrometry (IM-MS) holds great potential for structural glycobiology, in particular in its ability to resolve glycan isomers. Generally, IM-MS has largely been applied to intact glycoconjugate ions with reports focusing on the separation of different adduct types. Here, we explore IM separation and report the collision cross section (CCS) of complex type N-glycans and their fragments in negative ion mode following collision-induced dissociation (CID). CCSs of isomeric fragment ions were found, in some cases, to reveal structural details that were not present in CID spectra themselves. Many fragment ions were confirmed as possessing multiple structure, details of which could be obtained by comparing their drift time profiles to different glycans. By using fragmentation both before and after mobility separation, information was gathered on the fragmentation pathways producing some of the ions. These results help demonstrate the utility of IM and will contribute to the growing use of IM-MS for glycomics. Graphical Abstract ᅟ.

Neither bridging nor bonding: A test of socialization effects by ethnically diverse voluntary associations on participants' inter-ethnic tolerance, inter-ethnic trust and intra-ethnic belonging.

PubMed

van der Meer, Tom

2016-01-01

The distinction between bridging and bonding associations is a cornerstone of social capital research. Nevertheless, this study is the first to provide a direct test of the socialization mechanism that supposedly causes ethnically mixed (bridging) associations to generate interethnic tolerance and trust, and homogenous (bonding) associations to cement self-affirming identities. This multilevel analysis of the Citizenship, Involvement & Democracy (CID) 1999/2000 survey data on Mannheim (Germany), Enschede (the Netherlands), and Aberdeen (Scotland) covers 3166 active participants in 645 associations. The CID includes objective, exogenous measures of each association's composition and aim. Socialization and self-selection effects are pulled apart through interactions with detailed measures of associational involvement. The results display no evidence for (diverse and homogenous) associations as socializing agents. Although inter-ethnic tolerance is higher in ethnically diverse associations, this should be attributed to self-selection effects. Copyright © 2015 Elsevier Inc. All rights reserved.

Design, fabrication, and delivery of a charge injection device as a stellar tracking device

NASA Technical Reports Server (NTRS)

Burke, H. K.; Michon, G. J.; Tomlinson, H. W.; Vogelsong, T. L.; Grafinger, A.; Wilson, R.

1979-01-01

Six 128 x 128 CID imagers fabricated on bulk silicon and with thin polysilicon upper-level electrodes were tested in a star tracking mode. Noise and spectral response were measured as a function of temperature over the range of +25 C to -40 C. Noise at 0 C and below was less than 40 rms carriers/pixel for all devices at an effective noise bandwidth of 150 Hz. Quantum yield for all devices averaged 40% from 0.4 to 1.0 microns with no measurable temperature dependence. Extrapolating from these performance parameters to those of a large (400 x 400) array and accounting for design and processing improvements, indicates that the larger array would show a further improvement in noise performance -- on the order of 25 carriers. A preliminary evaluation of the projected performance of the 400 x 400 array and a representative set of star sensor requirements indicates that the CID has excellent potential as a stellar tracking device.

Collision Cross Sections and Ion Mobility Separation of Fragment Ions from Complex N-Glycans

NASA Astrophysics Data System (ADS)

Harvey, David J.; Watanabe, Yasunori; Allen, Joel D.; Rudd, Pauline; Pagel, Kevin; Crispin, Max; Struwe, Weston B.

2018-04-01

Ion mobility mass spectrometry (IM-MS) holds great potential for structural glycobiology, in particular in its ability to resolve glycan isomers. Generally, IM-MS has largely been applied to intact glycoconjugate ions with reports focusing on the separation of different adduct types. Here, we explore IM separation and report the collision cross section (CCS) of complex type N-glycans and their fragments in negative ion mode following collision-induced dissociation (CID). CCSs of isomeric fragment ions were found, in some cases, to reveal structural details that were not present in CID spectra themselves. Many fragment ions were confirmed as possessing multiple structure, details of which could be obtained by comparing their drift time profiles to different glycans. By using fragmentation both before and after mobility separation, information was gathered on the fragmentation pathways producing some of the ions. These results help demonstrate the utility of IM and will contribute to the growing use of IM-MS for glycomics. [Figure not available: see fulltext.

Financial Time Series Prediction Using Elman Recurrent Random Neural Networks

PubMed Central

Wang, Jie; Wang, Jun; Fang, Wen; Niu, Hongli

2016-01-01

In recent years, financial market dynamics forecasting has been a focus of economic research. To predict the price indices of stock markets, we developed an architecture which combined Elman recurrent neural networks with stochastic time effective function. By analyzing the proposed model with the linear regression, complexity invariant distance (CID), and multiscale CID (MCID) analysis methods and taking the model compared with different models such as the backpropagation neural network (BPNN), the stochastic time effective neural network (STNN), and the Elman recurrent neural network (ERNN), the empirical results show that the proposed neural network displays the best performance among these neural networks in financial time series forecasting. Further, the empirical research is performed in testing the predictive effects of SSE, TWSE, KOSPI, and Nikkei225 with the established model, and the corresponding statistical comparisons of the above market indices are also exhibited. The experimental results show that this approach gives good performance in predicting the values from the stock market indices. PMID:27293423

Stereospecific generation and analysis of α- and β-hemiacetals of monosaccharides in gas phase.

PubMed

Shioiri, Yuki; Suzuki, Katsuhiko; Daikoku, Shusaku; Kurimoto, Ayako; Ito, Yukishige; Kanie, Osamu

2013-12-15

A series of Boc-protected 4-aminobutyl α- and β-glycosides of commonly found neutral monosaccharides were synthesized. The sodium adducted ions of these individual molecules were used in producing corresponding α- and β-anomers of hemiacetal species under collision-induced dissociation (CID) conditions. The Boc group was successfully removed under CID conditions producing 4-aminobutyl glycosides, which were then used as the precursors. An intramolecular attack of the aglyconic nitrogen atom onto C-1 position of aglycon assisted to leave hemiacetal ion species without affecting anomeric configurations. In this manner, stereospecific syntheses of sugar hemiacetals were first achieved in gas phase. The dissociation of sodium cation from a series of these hemiacetals was further studied according to energy-resolved mass spectrometry. In this study, it was found that all the sugar hemiacetals could be distinguished even if they have same m/z values. Furthermore, the order of affinity of Na(+) toward the hemiacetals was determined. Copyright © 2013 Elsevier Ltd. All rights reserved.

Antimisting kerosene JT3 engine fuel system integration study

NASA Technical Reports Server (NTRS)

Fiorentino, A.

1987-01-01

An analytical study and laboratory tests were conducted to assist NASA in determining the safety and mission suitability of the modified fuel system and flight tests for the Full-Scale Transport Controlled Impact Demonstration (CID) program. This twelve-month study reviewed and analyzed both the use of antimisting kerosene (AMK) fuel and the incorporation of a fuel degrader on the operational and performance characteristics of the engines tested. Potential deficiencies and/or failures were identified and approaches to accommodate these deficiencies were recommended to NASA Ames -Dryden Flight Research Facility. The result of flow characterization tests on degraded AMK fuel samples indicated levels of degradation satisfactory for the planned missions of the B-720 aircraft. The operability and performance with the AMK in a ground test engine and in the aircraft engines during the test flights were comparable to those with unmodified Jet A. For the final CID test, the JT-3C-7 engines performed satisfactorily while operating on AMK right up to impact.

Improved Steroids Detection and Evidence for Their Regiospecific Decompositions Using Anion Attachment Mass Spectrometry.

PubMed

Dumont, Quentin; Bárcenas, Mariana; Dossmann, Héloïse; Bailloux, Isabelle; Buisson, Corinne; Mechin, Nathalie; Molina, Adeline; Lasne, Françoise; Rannulu, Nalaka S; Cole, Richard B

2016-04-05

Nonpolar anabolic steroids are doping agents that typically do not provide strong signals by electrospray ionization-mass spectrometry (ESI-MS) owing especially to the low polarity of the functional groups present. We have investigated the addition of anions, in ammonium salt form, to anabolic steroid samples as ionization enhancers and have confirmed that lower instrumental limits of detection (as low as 10 ng/mL for fluoxymesterone-M) are obtained by fluoride anion attachment mass spectrometry, as compared to ESI(+)/(-) or atmospheric pressure photoionization (APPI)(+). Moreover, collision-induced decomposition (CID) spectra of precursor fluoride adducts of the bifunctional steroid "reduced pregnenolone" (containing two hydroxyl groups) and its d4-analogue provide evidence of regiospecific decompositions after attachment of fluoride anion to a specific hydroxyl group of the steroid. This type of charting of specific CID reaction pathways can offer value to selected reaction monitoring experiments (SRM) as it may result in a gain in selectivity in detection as well as in improvements in quantification.

Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

PubMed

Beck, Emily A; Llopart, Ana

2015-11-25

Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.

USP7 Is a Tumor-Specific WNT Activator for APC-Mutated Colorectal Cancer by Mediating β-Catenin Deubiquitination.

PubMed

Novellasdemunt, Laura; Foglizzo, Valentina; Cuadrado, Laura; Antas, Pedro; Kucharska, Anna; Encheva, Vesela; Snijders, Ambrosius P; Li, Vivian S W

2017-10-17

The tumor suppressor gene adenomatous polyposis coli (APC) is mutated in most colorectal cancers (CRCs), resulting in constitutive Wnt activation. To understand the Wnt-activating mechanism of the APC mutation, we applied CRISPR/Cas9 technology to engineer various APC-truncated isogenic lines. We find that the β-catenin inhibitory domain (CID) in APC represents the threshold for pathological levels of Wnt activation and tumor transformation. Mechanistically, CID-deleted APC truncation promotes β-catenin deubiquitination through reverse binding of β-TrCP and USP7 to the destruction complex. USP7 depletion in APC-mutated CRC inhibits Wnt activation by restoring β-catenin ubiquitination, drives differentiation, and suppresses xenograft tumor growth. Finally, the Wnt-activating role of USP7 is specific to APC mutations; thus, it can be used as a tumor-specific therapeutic target for most CRCs. Copyright © 2017 The Francis Crick Institute. Published by Elsevier Inc. All rights reserved.

Development of a Branched Radio-Frequency Ion Trap for Electron Based Dissociation and Related Applications

PubMed Central

Baba, Takashi; Campbell, J. Larry; Le Blanc, J. C. Yves; Baker, Paul R. S.; Hager, James W.; Thomson, Bruce A.

2017-01-01

Collision-induced dissociation (CID) is the most common tool for molecular analysis in mass spectrometry to date. However, there are difficulties associated with many applications because CID does not provide sufficient information to permit details of the molecular structures to be elucidated, including post-translational-modifications in proteomics, as well as isomer differentiation in metabolomics and lipidomics. To face these challenges, we are developing fast electron-based dissociation devices using a novel radio-frequency ion trap (i.e., a branched ion trap). These devices have the ability to perform electron capture dissociation (ECD) on multiply protonated peptide/proteins; in addition, the electron impact excitation of ions from organics (EIEIO) can be also performed on singly charged molecules using such a device. In this article, we review the development of this technology, in particular on how reaction speed for EIEIO analyses on singly charged ions can be improved. We also overview some unique, recently reported applications in both lipidomics and glycoproteomics. PMID:28630811