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Sample records for coli quantitative analysis

  1. Quantitative Brightness Analysis of Fluorescence Intensity Fluctuations in E. Coli.

    Directory of Open Access Journals (Sweden)

    Kwang-Ho Hur

    Full Text Available The brightness measured by fluorescence fluctuation spectroscopy specifies the average stoichiometry of a labeled protein in a sample. Here we extended brightness analysis, which has been mainly applied in eukaryotic cells, to prokaryotic cells with E. coli serving as a model system. The small size of the E. coli cell introduces unique challenges for applying brightness analysis that are addressed in this work. Photobleaching leads to a depletion of fluorophores and a reduction of the brightness of protein complexes. In addition, the E. coli cell and the point spread function of the instrument only partially overlap, which influences intensity fluctuations. To address these challenges we developed MSQ analysis, which is based on the mean Q-value of segmented photon count data, and combined it with the analysis of axial scans through the E. coli cell. The MSQ method recovers brightness, concentration, and diffusion time of soluble proteins in E. coli. We applied MSQ to measure the brightness of EGFP in E. coli and compared it to solution measurements. We further used MSQ analysis to determine the oligomeric state of nuclear transport factor 2 labeled with EGFP expressed in E. coli cells. The results obtained demonstrate the feasibility of quantifying the stoichiometry of proteins by brightness analysis in a prokaryotic cell.

  2. Segmentation-based retrospective shading correction in fluorescence microscopy E. coli images for quantitative analysis

    Science.gov (United States)

    Mai, Fei; Chang, Chunqi; Liu, Wenqing; Xu, Weichao; Hung, Yeung S.

    2009-10-01

    Due to the inherent imperfections in the imaging process, fluorescence microscopy images often suffer from spurious intensity variations, which is usually referred to as intensity inhomogeneity, intensity non uniformity, shading or bias field. In this paper, a retrospective shading correction method for fluorescence microscopy Escherichia coli (E. Coli) images is proposed based on segmentation result. Segmentation and shading correction are coupled together, so we iteratively correct the shading effects based on segmentation result and refine the segmentation by segmenting the image after shading correction. A fluorescence microscopy E. Coli image can be segmented (based on its intensity value) into two classes: the background and the cells, where the intensity variation within each class is close to zero if there is no shading. Therefore, we make use of this characteristics to correct the shading in each iteration. Shading is mathematically modeled as a multiplicative component and an additive noise component. The additive component is removed by a denoising process, and the multiplicative component is estimated using a fast algorithm to minimize the intra-class intensity variation. We tested our method on synthetic images and real fluorescence E.coli images. It works well not only for visual inspection, but also for numerical evaluation. Our proposed method should be useful for further quantitative analysis especially for protein expression value comparison.

  3. Synergism between ultraviolet radiation and reductone in Escherichia coli UVR: quantitative analysis of produced injuries

    International Nuclear Information System (INIS)

    Mota, H.C.

    1980-01-01

    The relationship between cell viability and DNA-single and double-strand breaks induced by UV-reductone treatment of E.coli AB1157 and AB1886 cells was studied. A molecular and quantitative analysis was done by sedimentation in sucrose gradients. Bacteriophage T4-DNA was submitted to similar conditions. The two bacterial strains showed the same kinetics of single strand-breaks induction by reductone, in agreement with the hypothesis that the repair of these lesion is independent of uvr A uvr B genes product. This paper suggests that the 'UV-sensibilization' to reductone action is linked to a synergistic process between reductone induced single breaks and the enzymatic incisions accumulated by modification in the excision repair, during the treatment. (author)

  4. Quantitative analysis of relationships between fluxome and metabolome in Escherichia coli

    OpenAIRE

    Taymaz Nikerel, H.

    2010-01-01

    Kinetic models, which predict the behaviour of metabolic reaction networks under different conditions, are indispensible to fully and quantitatively understand the relation between a product pathway and connected central metabolism. In this thesis the focus was to develop tools for future in vivo kinetic modeling in Escherichia coli. The relations between fluxome and metabolome at steady-state or transient state but where enzyme levels can be assumed constant are investigated. In addition, we...

  5. Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction.

    Science.gov (United States)

    Kuwahara, Hiroyuki; Myers, Chris J; Samoilov, Michael S

    2010-03-26

    Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element-the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase) of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies that this down

  6. Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction.

    Directory of Open Access Journals (Sweden)

    Hiroyuki Kuwahara

    2010-03-01

    Full Text Available Uropathogenic Escherichia coli (UPEC represent the predominant cause of urinary tract infections (UTIs. A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element-the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies

  7. Quantitative analysis of an engineered CO2-fixing Escherichia coli reveals great potential of heterotrophic CO2 fixation.

    Science.gov (United States)

    Gong, Fuyu; Liu, Guoxia; Zhai, Xiaoyun; Zhou, Jie; Cai, Zhen; Li, Yin

    2015-01-01

    Production of fuels from the abundant and wasteful CO2 is a promising approach to reduce carbon emission and consumption of fossil fuels. Autotrophic microbes naturally assimilate CO2 using energy from light, hydrogen, and/or sulfur. However, their slow growth rates call for investigation of the possibility of heterotrophic CO2 fixation. Although preliminary research has suggested that CO2 fixation in heterotrophic microbes is feasible after incorporation of a CO2-fixing bypass into the central carbon metabolic pathway, it remains unclear how much and how efficient that CO2 can be fixed by a heterotrophic microbe. A simple metabolic flux index was developed to indicate the relative strength of the CO2-fixation flux. When two sequential enzymes of the cyanobacterial Calvin cycle were incorporated into an E. coli strain, the flux of the CO2-fixing bypass pathway accounts for 13 % of that of the central carbon metabolic pathway. The value was increased to 17 % when the carbonic anhydrase involved in the cyanobacterial carbon concentrating mechanism was introduced, indicating that low intracellular CO2 concentration is one limiting factor for CO2 fixation in E. coli. The engineered CO2-fixing E. coli with carbonic anhydrase was able to fix CO2 at a rate of 19.6 mg CO2 L(-1) h(-1) or the specific rate of 22.5 mg CO2 g DCW(-1) h(-1). This CO2-fixation rate is comparable with the reported rates of 14 autotrophic cyanobacteria and algae (10.5-147.0 mg CO2 L(-1) h(-1) or the specific rates of 3.5-23.7 mg CO2 g DCW(-1) h(-1)). The ability of CO2 fixation was created and improved in E. coli by incorporating partial cyanobacterial Calvin cycle and carbon concentrating mechanism, respectively. Quantitative analysis revealed that the CO2-fixation rate of this strain is comparable with that of the autotrophic cyanobacteria and algae, demonstrating great potential of heterotrophic CO2 fixation.

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

    Science.gov (United States)

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

    2014-12-01

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

  9. Quantitative analysis of relationships between fluxome and metabolome in Escherichia coli

    NARCIS (Netherlands)

    Taymaz Nikerel, H.

    2010-01-01

    Kinetic models, which predict the behaviour of metabolic reaction networks under different conditions, are indispensible to fully and quantitatively understand the relation between a product pathway and connected central metabolism. In this thesis the focus was to develop tools for future in vivo

  10. Prediction of Salmonella carcass contamination by a comparative quantitative analysis of E. coli and Salmonella during pig slaughter

    DEFF Research Database (Denmark)

    Nauta, Maarten; Barfod, Kristen; Hald, Tine

    2013-01-01

    Salmonella concentrations. It is concluded that the faecal carriage of Salmonella together with the faecal contamination of carcasses, as predicted from E. coli data in the animal faeces and hygiene performance of the slaughterhouse, is not sufficient to explain carcass contamination with Salmonella. Our...... extensive data set showed that other factors than the observed faecal carriage of Salmonella by the individual animals brought to slaughter, play a more important role in the Salmonella carcass contamination of pork.......Faecal contamination of carcasses in the slaughterhouse is generally considered to be the source of Salmonella on pork. In this study the hygiene indicator Escherichia coli is used to quantify faecal contamination of carcasses and it is hypothesized that it can be used to predict the quantitative...

  11. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli.

    Science.gov (United States)

    Sashital, Dipali G; Greeman, Candacia A; Lyumkis, Dmitry; Potter, Clinton S; Carragher, Bridget; Williamson, James R

    2014-10-14

    Ribosome assembly is a complex process involving the folding and processing of ribosomal RNAs (rRNAs), concomitant binding of ribosomal proteins (r-proteins), and participation of numerous accessory cofactors. Here, we use a quantitative mass spectrometry/electron microscopy hybrid approach to determine the r-protein composition and conformation of 30S ribosome assembly intermediates in Escherichia coli. The relative timing of assembly of the 3' domain and the formation of the central pseudoknot (PK) structure depends on the presence of the assembly factor RimP. The central PK is unstable in the absence of RimP, resulting in the accumulation of intermediates in which the 3'-domain is unanchored and the 5'-domain is depleted for r-proteins S5 and S12 that contact the central PK. Our results reveal the importance of the cofactor RimP in central PK formation, and introduce a broadly applicable method for characterizing macromolecular assembly in cells.

  12. Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level

    OpenAIRE

    Smati, Mounira; Clermont, Olivier; Bleibtreu, Alexandre; Fourreau, Frédéric; David, Anthony; Daubié, Anne-Sophie; Hignard, Cécile; Loison, Odile; Picard, Bertrand; Denamur, Erick

    2015-01-01

    The primary habitat of the Escherichia coli species is the gut of warm-blooded vertebrates. The E. coli species is structured into four main phylogenetic groups A, B1, B2, and D. We estimated the relative proportions of these phylogroups in the feces of 137 wild and domesticated animals with various diets living in the Ile de France (Paris) region by real-time PCR. We distinguished three main clusters characterized by a particular abundance of two or more phylogroups within the E. coli animal...

  13. Quantitative risk analysis for potentially resistant E. coli in surface waters caused by antibiotic use in agricultural systems.

    Science.gov (United States)

    Limayem, Alya; Martin, Elizabeth M

    2014-01-01

    Antibiotics are frequently used in agricultural systems to promote livestock health and to control bacterial contaminants. Given the upsurge of the resistant fecal indicator bacteria (FIB) in the surface waters, a novel statistical method namely, microbial risk assessment (MRA) was performed, to evaluate the probability of infection by resistant FIB on populations exposed to recreational waters. Diarrheagenic Escherichia coli, except E. coli O157:H7, were selected for their prevalence in aquatic ecosystem. A comparative study between a typical E. coli pathway and a case scenario aggravated by antibiotic use has been performed via Crystal Ball® software in an effort to analyze a set of available inputs provided by the US institutions including E. coli concentrations in US Great Lakes through using random sampling and probability distributions. Results from forecasting a possible worst-case scenario dose-response, accounted for an approximate 50% chance for 20% of the exposed human populations to be infected by recreational water in the U.S. However, in a typical scenario, there is a 50% chance of infection for only 1% of the exposed human populations. The uncertain variable, E. coli concentration accounted for approximately 92.1% in a typical scenario as the major contributing factor of the dose-response model. Resistant FIB in recreational waters that are exacerbated by a low dose of antibiotic pollutants would increase the adverse health effects in exposed human populations by 10 fold.

  14. Synergism between ultraviolet radiation and reductone in Escherichia coli UVR: quantitative analysis of produced injuries; Sinergismo entre radiacao ultravioleta e redutona em Escherichia coli UVR: analise quantitativa das lesoes produzidas

    Energy Technology Data Exchange (ETDEWEB)

    Mota, H C

    1981-12-31

    The relationship between cell viability and DNA-single and double-strand breaks induced by UV-reductone treatment of E.coli AB1157 and AB1886 cells was studied. A molecular and quantitative analysis was done by sedimentation in sucrose gradients. Bacteriophage T4-DNA was submitted to similar conditions. The two bacterial strains showed the same kinetics of single strand-breaks induction by reductone, in agreement with the hypothesis that the repair of these lesion is independent of uvr A uvr B genes product. This paper suggests that the `UV-sensibilization` to reductone action is linked to a synergistic process between reductone induced single breaks and the enzymatic incisions accumulated by modification in the excision repair, during the treatment. (author).

  15. Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level.

    Science.gov (United States)

    Smati, Mounira; Clermont, Olivier; Bleibtreu, Alexandre; Fourreau, Frédéric; David, Anthony; Daubié, Anne-Sophie; Hignard, Cécile; Loison, Odile; Picard, Bertrand; Denamur, Erick

    2015-08-01

    The primary habitat of the Escherichia coli species is the gut of warm-blooded vertebrates. The E. coli species is structured into four main phylogenetic groups A, B1, B2, and D. We estimated the relative proportions of these phylogroups in the feces of 137 wild and domesticated animals with various diets living in the Ile de France (Paris) region by real-time PCR. We distinguished three main clusters characterized by a particular abundance of two or more phylogroups within the E. coli animal commensal populations, which we called "enterocolitypes" by analogy with the enterotypes defined in the human gut microbiota at the genus level. These enterocolitypes were characterized by a dominant (>50%) B2, B1, or A phylogroup and were associated with different host species, diets, and habitats: wild and herbivorous species (wild rabbits and deer), domesticated herbivorous species (domesticated rabbits, horses, sheep, and cows), and omnivorous species (boar, pigs, and chickens), respectively. By analyzing retrospectively the data obtained using the same approach from 98 healthy humans living in Ile de France (Smati et al. 2013, Appl. Environ. Microbiol. 79, 5005-5012), we identified a specific human enterocolitype characterized by the dominant and/or exclusive (>90%) presence of phylogroup B2. We then compared B2 strains isolated from animals and humans, and revealed that human and animal strains differ regarding O-type and B2 subgroup. Moreover, two genes, sfa/foc and clbQ, were associated with the exclusive character of strains, observed only in humans. In conclusion, a complex network of interactions exists at several levels (genus and intra-species) within the intestinal microbiota. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  16. A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

    DEFF Research Database (Denmark)

    McCloskey, Douglas; Gangoiti, Jon A.; King, Zachary A.

    2014-01-01

    in metabolomes between anaerobic and aerobic growth of Escherichia coli. Constraint‐based modeling was utilized to deduce a target list of compounds for downstream method development. An analytical and experimental methodology was developed and tailored to the compound chemistry and growth conditions of interest....... This included the construction of a rapid sampling apparatus for use with anaerobic cultures. The resulting genome‐scale data sets for anaerobic and aerobic growth were validated by comparison to previous small‐scale studies comparing growth of E. coli under the same conditions. The metabolomics data were......‐oxidation pathway for synthesis of fatty acids. This analysis also identified enzyme promiscuity for the pykA gene, that is critical for anaerobic growth, and which has not been previously incorporated into metabolic models of E coli. Biotechnol....

  17. Quantitative analysis chemistry

    International Nuclear Information System (INIS)

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

    1995-02-01

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

  18. Quantitative investment analysis

    CERN Document Server

    DeFusco, Richard

    2007-01-01

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

  19. Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR

    Directory of Open Access Journals (Sweden)

    Zou Ruiyang

    2011-04-01

    Full Text Available Abstract Background Accurate interpretation of quantitative PCR (qPCR data requires normalization using constitutively expressed reference genes. Ribosomal RNA is often used as a reference gene for transcriptional studies in E. coli. However, the choice of reliable reference genes has not been systematically validated. The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in E. coli. Results In this study, the meta-analysis of 240 sets of single-channel Affymetrix microarray data representing over-expressions of 63 distinct recombinant proteins in various E. coli strains identified twenty candidate reference genes that were stably expressed across all conditions. The expression of these twenty genes and two commonly used reference genes, rrsA encoding ribosomal RNA 16S and ihfB, was quantified by qPCR in E. coli cells over-expressing four genes of the 1-Deoxy-D-Xylulose 5-Phosphate pathway. From these results, two independent statistical algorithms identified three novel reference genes cysG, hcaT, and idnT but not rrsA and ihfB as highly invariant in two E. coli strains, across different growth temperatures and induction conditions. Transcriptomic data normalized by the geometric average of these three genes demonstrated that genes of the lycopene synthetic pathway maintained steady expression upon enzyme overexpression. In contrast, the use of rrsA or ihfB as reference genes led to the mis-interpretation that lycopene pathway genes were regulated during enzyme over-expression. Conclusion This study identified cysG/hcaT/idnT to be reliable novel reference genes for transcription analysis in recombinant protein producing E. coli.

  20. Quantitative Moessbauer analysis

    International Nuclear Information System (INIS)

    Collins, R.L.

    1978-01-01

    The quantitative analysis of Moessbauer data, as in the measurement of Fe 3+ /Fe 2+ concentration, has not been possible because of the different mean square velocities (x 2 ) of Moessbauer nuclei at chemically different sites. A method is now described which, based on Moessbauer data at several temperatures, permits the comparison of absorption areas at (x 2 )=0. (Auth.)

  1. Quantitative Analysis of Renogram

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Keun Chul [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1969-03-15

    value are useful for the differentiation of various renal diseases, however, qualitative analysis of the renogram with one or two parameters is not accurate. 3) In bilateral non-functioning kidney groups, a positive correlation between anemia and nitrogen retention was observed, although the quantitative assessment of the degree of non-functioning was impossible.

  2. Quantitative Analysis of Renogram

    International Nuclear Information System (INIS)

    Choi, Keun Chul

    1969-01-01

    are useful for the differentiation of various renal diseases, however, qualitative analysis of the renogram with one or two parameters is not accurate. 3) In bilateral non-functioning kidney groups, a positive correlation between anemia and nitrogen retention was observed, although the quantitative assessment of the degree of non-functioning was impossible.

  3. Quantitative analysis of receptor imaging

    International Nuclear Information System (INIS)

    Fu Zhanli; Wang Rongfu

    2004-01-01

    Model-based methods for quantitative analysis of receptor imaging, including kinetic, graphical and equilibrium methods, are introduced in detail. Some technical problem facing quantitative analysis of receptor imaging, such as the correction for in vivo metabolism of the tracer and the radioactivity contribution from blood volume within ROI, and the estimation of the nondisplaceable ligand concentration, is also reviewed briefly

  4. Quantitative assessment of faecal shedding of β-lactam-resistant Escherichia coli and enterococci in dogs

    DEFF Research Database (Denmark)

    Gongora, Carmen Espinosa; Shah, Syed Qaswar Ali; Jessen, Lisbeth Rem

    2015-01-01

    Quantitative data on faecal shedding of antimicrobial resistant bacteria are crucial to assess the risk of transmission from dogs to other animals as well as humans. In this study we investigated prevalence and concentrations of β-lactam-resistant Escherichia coli and enterococci in the faeces...... of 108 dogs presenting at a veterinary hospital in Denmark. The dogs had not been treated with antimicrobials for 4 weeks prior to the study. Total E. coli and enterococci were quantified by counts on MacConkey and Slanetz-Bartley, respectively. Resistant E. coli and enterococci were counted on the same...... media containing relevant antibiotic concentrations, followed by species identification using MALDI-TOF. Ampicillin- and cefotaxime-resistant E. coli were detected in 40% and 8% of the dogs, respectively, whereas approximately 15% carried ampicillin-resistant enterococci, mainly Enterococcus faecium...

  5. Monotowns: A Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Shastitko Andrei

    2016-06-01

    Full Text Available The authors propose an empirical analysis of the current situation in monotowns. The study questions the perceived seriousness of the ‘monotown problem’ as well as the actual challenges it presents. The authors use a cluster analysis to divide monotowns into groups for further structural comparison. The structural differences in the available databases limit the possibilities of empirical analysis. Hence, alternative approaches are required. The authors consider possible reasons for the limitations identified. Special attention is paid to the monotowns that were granted the status of advanced development territories. A comparative analysis makes it possible to study their general characteristics and socioeconomic indicators. The authors apply the theory of opportunistic behaviour to describe potential problems caused by the lack of unified criteria for granting monotowns the status of advanced development territories. The article identifies the main stakeholders and the character of their interaction; it desc ribes a conceptual model built on the principal/agent interactions, and identifies the parametric space of mutually beneficial cooperation. The solution to the principal/agent problem suggested in the article contributes to the development of an alternative approach to the current situation and a rational approach to overcoming the ‘monotown problem’.

  6. Quantitative Concept Analysis

    NARCIS (Netherlands)

    Pavlovic, Dusko; Domenach, Florent; Ignatov, Dmitry I.; Poelmans, Jonas

    2012-01-01

    Formal Concept Analysis (FCA) begins from a context, given as a binary relation between some objects and some attributes, and derives a lattice of concepts, where each concept is given as a set of objects and a set of attributes, such that the first set consists of all objects that satisfy all

  7. Quantitative Analysis of cardiac SPECT

    International Nuclear Information System (INIS)

    Nekolla, S.G.; Bengel, F.M.

    2004-01-01

    The quantitative analysis of myocardial SPECT images is a powerful tool to extract the highly specific radio tracer uptake in these studies. If compared to normal data bases, the uptake values can be calibrated on an individual basis. Doing so increases the reproducibility of the analysis substantially. Based on the development over the last three decades starting from planar scinitigraphy, this paper discusses the methods used today incorporating the changes due to tomographic image acquisitions. Finally, the limitations of these approaches as well as consequences from most recent hardware developments, commercial analysis packages and a wider view of the description of the left ventricle are discussed. (orig.)

  8. Portable and quantitative point-of-care monitoring of Escherichia coli O157:H7 using a personal glucose meter based on immunochromatographic assay.

    Science.gov (United States)

    Huang, Haoran; Zhao, Guangying; Dou, Wenchao

    2018-06-01

    Here we innovate a portable and quantitative immunochromatographic assay (ICA) with a personal glucose meter (PGM) as readout for the detection of Escherichia coli O157:H7 (E. coli O157:H7). The carboxyl group coated Fe 3 O 4 nanoparticles (MNPs) were synthesized by a one pot method and used as carriers of invertase and monoclonal antibody against E. coli O157:H7. Initially, the invertase and antibody double functionalized MNPs (Invertase-MNPs-IgG) conjugates were prepared and used as label probe in this assay system. Before laminating onto the baking card, the absorbent pad was soaked in sucrose solution and desiccated. MNPs produced brown band at the detection zone of the ICA when acting as direct labels. As they were also coupled with invertase, the invertase catalyzed the hydrolysis of sucrose on the absorbent pad into glucose, which was detected by the PGM. To increase the sensitivity, antibody functionalized MNPs were used to enrich E. coli O157:H7 from sample solution. The innovative aspect of this approach lies in the visualization and quantification of E. coli O157:H7 through Invertase-MNPs-IgG and the detection of glucose concentration using PGM. Although the feasibility is demonstrated using E. coli O157:H7 as a model analyte, this approach can be easily developed to be a universal analysis system and applied to detection of a wide variety of foodborne pathogens and protein biomarkers. This study proposed a qualitative and quantitative analysis device for the clinic diagnostics and food safety analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Quantitative pulsed eddy current analysis

    International Nuclear Information System (INIS)

    Morris, R.A.

    1975-01-01

    The potential of pulsed eddy current testing for furnishing more information than conventional single-frequency eddy current methods has been known for some time. However, a fundamental problem has been analyzing the pulse shape with sufficient precision to produce accurate quantitative results. Accordingly, the primary goal of this investigation was to: demonstrate ways of digitizing the short pulses encountered in PEC testing, and to develop empirical analysis techniques that would predict some of the parameters (e.g., depth) of simple types of defect. This report describes a digitizing technique using a computer and either a conventional nuclear ADC or a fast transient analyzer; the computer software used to collect and analyze pulses; and some of the results obtained. (U.S.)

  10. Quantitative Microbial Risk Assessment for Escherichia coli O157:H7 in Fresh-Cut Lettuce.

    Science.gov (United States)

    Pang, Hao; Lambertini, Elisabetta; Buchanan, Robert L; Schaffner, Donald W; Pradhan, Abani K

    2017-02-01

    Leafy green vegetables, including lettuce, are recognized as potential vehicles for foodborne pathogens such as Escherichia coli O157:H7. Fresh-cut lettuce is potentially at high risk of causing foodborne illnesses, as it is generally consumed without cooking. Quantitative microbial risk assessments (QMRAs) are gaining more attention as an effective tool to assess and control potential risks associated with foodborne pathogens. This study developed a QMRA model for E. coli O157:H7 in fresh-cut lettuce and evaluated the effects of different potential intervention strategies on the reduction of public health risks. The fresh-cut lettuce production and supply chain was modeled from field production, with both irrigation water and soil as initial contamination sources, to consumption at home. The baseline model (with no interventions) predicted a mean probability of 1 illness per 10 million servings and a mean of 2,160 illness cases per year in the United States. All intervention strategies evaluated (chlorine, ultrasound and organic acid, irradiation, bacteriophage, and consumer washing) significantly reduced the estimated mean number of illness cases when compared with the baseline model prediction (from 11.4- to 17.9-fold reduction). Sensitivity analyses indicated that retail and home storage temperature were the most important factors affecting the predicted number of illness cases. The developed QMRA model provided a framework for estimating risk associated with consumption of E. coli O157:H7-contaminated fresh-cut lettuce and can guide the evaluation and development of intervention strategies aimed at reducing such risk.

  11. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2014-02-01

    Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

  12. Meta-regression analysis of commensal and pathogenic Escherichia coli survival in soil and water.

    Science.gov (United States)

    Franz, Eelco; Schijven, Jack; de Roda Husman, Ana Maria; Blaak, Hetty

    2014-06-17

    The extent to which pathogenic and commensal E. coli (respectively PEC and CEC) can survive, and which factors predominantly determine the rate of decline, are crucial issues from a public health point of view. The goal of this study was to provide a quantitative summary of the variability in E. coli survival in soil and water over a broad range of individual studies and to identify the most important sources of variability. To that end, a meta-regression analysis on available literature data was conducted. The considerable variation in reported decline rates indicated that the persistence of E. coli is not easily predictable. The meta-analysis demonstrated that for soil and water, the type of experiment (laboratory or field), the matrix subtype (type of water and soil), and temperature were the main factors included in the regression analysis. A higher average decline rate in soil of PEC compared with CEC was observed. The regression models explained at best 57% of the variation in decline rate in soil and 41% of the variation in decline rate in water. This indicates that additional factors, not included in the current meta-regression analysis, are of importance but rarely reported. More complete reporting of experimental conditions may allow future inference on the global effects of these variables on the decline rate of E. coli.

  13. Quantitative risk assessment of E. coli in street-vended cassava-based delicacies in the Philippines

    Science.gov (United States)

    Mesias, I. C. P.

    2018-01-01

    In the Philippines, rootcrop-based food products are gaining popularity in street food trade. However, a number of street-vended food products in the country are reported to be contaminated with E. coli posing possible risk among consumers. In this study, information on quantitative risk assessment of E. coli in street-vended cassava-based delicacies was generated. The assessment started with the prevalence and concentration of E. coli at post production in packages of the cassava-based delicacies. Combase growth predictor was used to trace the microbial population of E. coli in each step of the food chain. The @Risk software package, version 6 (Palisade USA) was used to run the simulations. Scenarios in the post-production to consumption pathway were simulated. The effect was then assessed in relation to exposure to the defined infective dose. In the worst case scenario, a minimum and most likely concentration of 6.3 and 7.8 log CFU of E. coli per serving respectively were observed. The simulation revealed that lowering the temperature in the chain considerably decreased the E. coli concentration prior to consumption and subsequently decreased the percentage of exposure to the infective dose. Exposure to infective dose however was increased with longer lag time from postproduction to consumption.

  14. Quantitative PCR Profiling of Escherichia coli in Livestock Feces Reveals Increased Population Resilience Relative to Culturable Counts under Temperature Extremes.

    Science.gov (United States)

    Oliver, David M; Bird, Clare; Burd, Emmy; Wyman, Michael

    2016-09-06

    The relationship between culturable counts (CFU) and quantitative PCR (qPCR) cell equivalent counts of Escherichia coli in dairy feces exposed to different environmental conditions and temperature extremes was investigated. Fecal samples were collected in summer and winter from dairy cowpats held under two treatments: field-exposed versus polytunnel-protected. A significant correlation in quantified E. coli was recorded between the qPCR and culture-based methods (r = 0.82). Evaluation of the persistence profiles of E. coli over time revealed no significant difference in the E. coli numbers determined as either CFU or gene copies during the summer for the field-exposed cowpats, whereas significantly higher counts were observed by qPCR for the polytunnel-protected cowpats, which were exposed to higher ambient temperatures. In winter, the qPCR returned significantly higher counts of E. coli for the field-exposed cowpats, thus representing a reversal of the findings from the summer sampling campaign. Results from this study suggest that with increasing time post-defecation and with the onset of challenging environmental conditions, such as extremes in temperature, culture-based counts begin to underestimate the true resilience of viable E. coli populations in livestock feces. This is important not only in the long term as the Earth changes in response to climate-change drivers but also in the short term during spells of extremely cold or hot weather.

  15. Quantitative analysis of coupler tuning

    International Nuclear Information System (INIS)

    Zheng Shuxin; Cui Yupeng; Chen Huaibi; Xiao Liling

    2001-01-01

    The author deduces the equation of coupler frequency deviation Δf and coupling coefficient β instead of only giving the adjusting direction in the process of matching coupler, on the basis of coupling-cavity chain equivalent circuits model. According to this equation, automatic measurement and quantitative display are realized on a measuring system. It contributes to industrialization of traveling-wave accelerators for large container inspection systems

  16. DNA microarray analysis of fim mutations in Escherichia coli

    DEFF Research Database (Denmark)

    Schembri, Mark; Ussery, David; Workman, Christopher

    2002-01-01

    Bacterial adhesion is often mediated by complex polymeric surface structures referred to as fimbriae. Type I fimbriae of Escherichia coli represent the archetypical and best characterised fimbrial system. These adhesive organelles mediate binding to D-mannose and are directly associated...... we have used DNA microarray analysis to examine the molecular events involved in response to fimbrial gene expression in E. coli K-12. Observed differential expression levels of the fim genes were in good agreement with our current knowledge of the stoichiometry of type I fimbriae. Changes in fim...

  17. Quantitative real-time PCR technique for the identification of E. coli residual DNA in streptokinase recombinant product.

    Science.gov (United States)

    Fazelahi, Mansoureh; Kia, Vahid; Kaghazian, Hooman; Paryan, Mahdi

    2017-11-26

    Recombinant streptokinase is a biopharmaceutical which is usually produced in E. coli. Residual DNA as a contamination and risk factor may remain in the product. It is necessary to control the production procedure to exclude any possible contamination. The aim of the present study was to develop a highly specific and sensitive quantitative real-time PCR-based method to determine the amount of E. coli DNA in recombinant streptokinase. A specific primers and a probe was designed to detect all strains of E. coli. To determine the specificity, in addition to using NCBI BLASTn, 28 samples including human, bacterial, and viral genomes were used. The results confirmed that the assay detects no genomic DNA but E. coli's and the specificity was determined to be 100%. To determine the sensitivity and limit of detection of the assay, a 10-fold serial dilution (10 1 to 10 7 copies/µL) was tested in triplicate. The sensitivity of the test was determined to be 101 copies/µL or 35 fg/µL. Inter-assay and intra-assay were determined to be 0.86 and 1.69%, respectively. Based on the results, this assay can be used as an accurate method to evaluate the contamination of recombinant streptokinase in E. coli.

  18. Quantitative analysis of boron by neutron radiography

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  19. Reactor applications of quantitative diffraction analysis

    International Nuclear Information System (INIS)

    Feguson, I.F.

    1976-09-01

    Current work in quantitative diffraction analysis was presented under the main headings of: thermal systems, fast reactor systems, SGHWR applications and irradiation damage. Preliminary results are included on a comparison of various new instrumental methods of boron analysis as well as preliminary new results on Zircaloy corrosion, and materials transfer in liquid sodium. (author)

  20. Quantitative image analysis of synovial tissue

    NARCIS (Netherlands)

    van der Hall, Pascal O.; Kraan, Maarten C.; Tak, Paul Peter

    2007-01-01

    Quantitative image analysis is a form of imaging that includes microscopic histological quantification, video microscopy, image analysis, and image processing. Hallmarks are the generation of reliable, reproducible, and efficient measurements via strict calibration and step-by-step control of the

  1. Methods in quantitative image analysis.

    Science.gov (United States)

    Oberholzer, M; Ostreicher, M; Christen, H; Brühlmann, M

    1996-05-01

    The main steps of image analysis are image capturing, image storage (compression), correcting imaging defects (e.g. non-uniform illumination, electronic-noise, glare effect), image enhancement, segmentation of objects in the image and image measurements. Digitisation is made by a camera. The most modern types include a frame-grabber, converting the analog-to-digital signal into digital (numerical) information. The numerical information consists of the grey values describing the brightness of every point within the image, named a pixel. The information is stored in bits. Eight bits are summarised in one byte. Therefore, grey values can have a value between 0 and 256 (2(8)). The human eye seems to be quite content with a display of 5-bit images (corresponding to 64 different grey values). In a digitised image, the pixel grey values can vary within regions that are uniform in the original scene: the image is noisy. The noise is mainly manifested in the background of the image. For an optimal discrimination between different objects or features in an image, uniformity of illumination in the whole image is required. These defects can be minimised by shading correction [subtraction of a background (white) image from the original image, pixel per pixel, or division of the original image by the background image]. The brightness of an image represented by its grey values can be analysed for every single pixel or for a group of pixels. The most frequently used pixel-based image descriptors are optical density, integrated optical density, the histogram of the grey values, mean grey value and entropy. The distribution of the grey values existing within an image is one of the most important characteristics of the image. However, the histogram gives no information about the texture of the image. The simplest way to improve the contrast of an image is to expand the brightness scale by spreading the histogram out to the full available range. Rules for transforming the grey value

  2. Effects of Bos taurus autosome 9-located quantitative trait loci haplotypes on enzymatic mastitis indicators of milk from dairy cows experimentally inoculated with Escherichia coli

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Engberg, Ricarda Greuel; Løvendahl, Peter

    2015-01-01

    The aim of this study was to investigate the effect of a quantitative trait locus associated with mastitis caused by Escherichia coli, with one haplotype being more susceptible (HH) and another being more resistant (HL) to E. coli mastitis, on the activity of 4 inflammatory related milk enzymes....... In particular, we investigated the suitability of β-glucuronidase (GLU) as an early indicator of E. coli mastitis. Besides GLU, the enzymes l-lactate dehydrogenase (LDH), N-acetyl-β-d-glucosaminidase (NAGase), and alkaline phosphatase were included. The study was conducted in an experimental setup with 31...... Holstein cows divided into 4 groups representing repeated experiments and, within group, divided according to quantitative trait locus haplotype. All cows were inoculated with viable E. coli, and milk samples were collected 27 times from −6 to 396 h post-E. coli inoculation (PI). Activity of the 4 enzymes...

  3. Quantitative X-ray analysis of pigments

    International Nuclear Information System (INIS)

    Araujo, M. Marrocos de

    1987-01-01

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

  4. Uncertainties in elemental quantitative analysis by PIXE

    International Nuclear Information System (INIS)

    Montenegro, E.C.; Baptista, G.B.; Paschoa, A.S.; Barros Leite, C.V.

    1979-01-01

    The effects of the degree of non-uniformity of the particle beam, matrix composition and matrix thickness in a quantitative elemental analysis by particle induced X-ray emission (PIXE) are discussed and a criterion to evaluate the resulting degree of uncertainty in the mass determination by this method is established. (Auth.)

  5. Quantitative microbial risk assessment for Escherichia coli O157:H7, salmonella, and Listeria monocytogenes in leafy green vegetables consumed at salad bars.

    Science.gov (United States)

    Franz, E; Tromp, S O; Rijgersberg, H; van der Fels-Klerx, H J

    2010-02-01

    Fresh vegetables are increasingly recognized as a source of foodborne outbreaks in many parts of the world. The purpose of this study was to conduct a quantitative microbial risk assessment for Escherichia coli O157:H7, Salmonella, and Listeria monocytogenes infection from consumption of leafy green vegetables in salad from salad bars in The Netherlands. Pathogen growth was modeled in Aladin (Agro Logistics Analysis and Design Instrument) using time-temperature profiles in the chilled supply chain and one particular restaurant with a salad bar. A second-order Monte Carlo risk assessment model was constructed (using @Risk) to estimate the public health effects. The temperature in the studied cold chain was well controlled below 5 degrees C. Growth of E. coli O157:H7 and Salmonella was minimal (17 and 15%, respectively). Growth of L. monocytogenes was considerably greater (194%). Based on first-order Monte Carlo simulations, the average number of cases per year in The Netherlands associated the consumption leafy greens in salads from salad bars was 166, 187, and 0.3 for E. coli O157:H7, Salmonella, and L. monocytogenes, respectively. The ranges of the average number of annual cases as estimated by second-order Monte Carlo simulation (with prevalence and number of visitors as uncertain variables) were 42 to 551 for E. coli O157:H7, 81 to 281 for Salmonella, and 0.1 to 0.9 for L. monocytogenes. This study included an integration of modeling pathogen growth in the supply chain of fresh leafy vegetables destined for restaurant salad bars using software designed to model and design logistics and modeling the public health effects using probabilistic risk assessment software.

  6. Comparison of the quantitative dry culture methods with both conventional media and most probable number method for the enumeration of coliforms and Escherichia coli/coliforms in food.

    Science.gov (United States)

    Teramura, H; Sota, K; Iwasaki, M; Ogihara, H

    2017-07-01

    Sanita-kun™ CC (coliform count) and EC (Escherichia coli/coliform count), sheet quantitative culture systems which can avoid chromogenic interference by lactase in food, were evaluated in comparison with conventional methods for these bacteria. Based on the results of inclusivity and exclusivity studies using 77 micro-organisms, sensitivity and specificity of both Sanita-kun™ met the criteria for ISO 16140. Both media were compared with deoxycholate agar, violet red bile agar, Merck Chromocult™ coliform agar (CCA), 3M Petrifilm™ CC and EC (PEC) and 3-tube MPN, as reference methods, in 100 naturally contaminated food samples. The correlation coefficients of both Sanita-kun™ for coliform detection were more than 0·95 for all comparisons. For E. coli detection, Sanita-kun™ EC was compared with CCA, PEC and MPN in 100 artificially contaminated food samples. The correlation coefficients for E. coli detection of Sanita-kun™ EC were more than 0·95 for all comparisons. There were no significant differences in all comparisons when conducting a one-way analysis of variance (anova). Both Sanita-kun™ significantly inhibited colour interference by lactase when inhibition of enzymatic staining was assessed using 40 natural cheese samples spiked with coliform. Our results demonstrated Sanita-kun™ CC and EC are suitable alternatives for the enumeration of coliforms and E. coli/coliforms, respectively, in a variety of foods, and specifically in fermented foods. Current chromogenic media for coliforms and Escherichia coli/coliforms have enzymatic coloration due to breaking down of chromogenic substrates by food lactase. The novel sheet culture media which have film layer to avoid coloration by food lactase have been developed for enumeration of coliforms and E. coli/coliforms respectively. In this study, we demonstrated these media had comparable performance with reference methods and less interference by food lactase. These media have a possibility not only

  7. Quantitative possibility analysis. Present status in ESCA

    International Nuclear Information System (INIS)

    Brion, D.

    1981-01-01

    A short review of the recent developments in quantification of X-ray photoelectron spectroscopy or ESCA is presented. The basic equations are reminded. Each involved parameter (photoionisation, inelastic mean free paths, 'response function' of the instruments, intensity measurement) is separately discussed in relation with the accuracy and the precision of the method. Other topics are considered such as roughness, surface contamination, matrix effect and inhomogeneous composition. Some aspects of the quantitative ESCA analysis and AES analysis are compared [fr

  8. Quantitative phase analysis in industrial research

    International Nuclear Information System (INIS)

    Ahmad Monshi

    1996-01-01

    X-Ray Diffraction (XRD) is the only technique able to identify phase and all the other analytical techniques give information about the elements. Quantitative phase analysis of minerals and industrial products is logically the next step after a qualitative examination and is of great importance in industrial research. Since the application of XRD in industry, early in this century, workers were trying to develop quantitative XRD methods. In this paper some of the important methods are briefly discussed and partly compared. These methods are Internal Standard, Known Additions, Double Dilution, External Standard, Direct Comparison, Diffraction Absorption and Ratio of Slopes

  9. Analysis and Design of Stimulus Response Curves of E. coli

    Directory of Open Access Journals (Sweden)

    Andreas Kremling

    2012-11-01

    Full Text Available Metabolism and signalling are tightly coupled in bacteria. Combining several theoretical approaches, a core model is presented that describes transcriptional and allosteric control of glycolysis in Escherichia coli. Experimental data based on microarrays, signalling components and extracellular metabolites are used to estimate kinetic parameters. A newly designed strain was used that adjusts the incoming glucose flux into the system and allows a kinetic analysis. Based on the results, prediction for intracelluar metabolite concentrations over a broad range of the growth rate could be performed and compared with data from literature.

  10. Quantitative analysis of untreated bio-samples

    International Nuclear Information System (INIS)

    Sera, K.; Futatsugawa, S.; Matsuda, K.

    1999-01-01

    A standard-free method of quantitative analysis for untreated samples has been developed. For hair samples, measurements were performed by irradiating with a proton beam a few hairs as they are, and quantitative analysis was carried out by means of a standard-free method developed by ourselves. First, quantitative values of concentration of zinc were derived, then concentration of other elements was obtained by regarding zinc as an internal standard. As the result, values of concentration of sulphur for 40 samples agree well with the average value for a typical Japanese and also with each other within 20%, and validity of the present method could be confirmed. Accuracy was confirmed by comparing the results with those obtained by the usual internal standard method, too. For the purpose of a surface analysis of a bone sample, a very small incidence angle of the proton beam was used, so that both energy loss of the projectile and self-absorption of X-rays become negligible. As the result, consistent values of concentration for many elements were obtained by the standard-free method

  11. Quantitative analysis of thallium-201 myocardial scintigraphy

    International Nuclear Information System (INIS)

    Kanemoto, Nariaki; Hoer, G.; Johost, S.; Maul, F.-D.; Standke, R.

    1981-01-01

    The method of quantitative analysis of thallium-201 myocardial scintigraphy using computer assisted technique was described. Calculated indices are washout factor, vitality index and redistribution factor. Washout factor is the ratio of counts at certain period of time after exercise and immediately after exercise. This value is neccessary for the evaluation of redistribution to the ischemic areas in serial imagings to correct the Tl-201 washout from the myocardium under the assumption that the washout is constant in the whole myocardium. Vitality index is the ratio between the Tl-201 uptake in the region of interest and that of the maximum. Redistribution factor is the ratio of the redistribution in the region of interest in serial imagings after exercise to that of immediately after exercise. Four examples of exercise Tl-201 myocardial scintigrams and the quantitative analyses before and after the percutaneous transluminal coronary angioplasty were presented. (author)

  12. Quantitative analysis by nuclear magnetic resonance spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Wainai, T; Mashimo, K [Nihon Univ., Tokyo. Coll. of Science and Engineering

    1976-04-01

    Recent papers on the practical quantitative analysis by nuclear magnetic resonance spectroscopy (NMR) are reviewed. Specifically, the determination of moisture in liquid N/sub 2/O/sub 4/ as an oxidizing agent for rocket propulsion, the analysis of hydroperoxides, the quantitative analysis using a shift reagent, the analysis of aromatic sulfonates, and the determination of acids and bases are reviewed. Attention is paid to the accuracy. The sweeping velocity and RF level in addition to the other factors must be on the optimal condition to eliminate the errors, particularly when computation is made with a machine. Higher sweeping velocity is preferable in view of S/N ratio, but it may be limited to 30 Hz/s. The relative error in the measurement of area is generally 1%, but when those of dilute concentration and integrated, the error will become smaller by one digit. If impurities are treated carefully, the water content on N/sub 2/O/sub 4/ can be determined with accuracy of about 0.002%. The comparison method between peak heights is as accurate as that between areas, when the uniformity of magnetic field and T/sub 2/ are not questionable. In the case of chemical shift movable due to content, the substance can be determined by the position of the chemical shift. Oil and water contents in rape-seed, peanuts, and sunflower-seed are determined by measuring T/sub 1/ with 90 deg pulses.

  13. Quantitative analysis method for ship construction quality

    Directory of Open Access Journals (Sweden)

    FU Senzong

    2017-03-01

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

  14. Quantitative phase analysis by neutron diffraction

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-06-01

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

  15. Good practices for quantitative bias analysis.

    Science.gov (United States)

    Lash, Timothy L; Fox, Matthew P; MacLehose, Richard F; Maldonado, George; McCandless, Lawrence C; Greenland, Sander

    2014-12-01

    Quantitative bias analysis serves several objectives in epidemiological research. First, it provides a quantitative estimate of the direction, magnitude and uncertainty arising from systematic errors. Second, the acts of identifying sources of systematic error, writing down models to quantify them, assigning values to the bias parameters and interpreting the results combat the human tendency towards overconfidence in research results, syntheses and critiques and the inferences that rest upon them. Finally, by suggesting aspects that dominate uncertainty in a particular research result or topic area, bias analysis can guide efficient allocation of sparse research resources. The fundamental methods of bias analyses have been known for decades, and there have been calls for more widespread use for nearly as long. There was a time when some believed that bias analyses were rarely undertaken because the methods were not widely known and because automated computing tools were not readily available to implement the methods. These shortcomings have been largely resolved. We must, therefore, contemplate other barriers to implementation. One possibility is that practitioners avoid the analyses because they lack confidence in the practice of bias analysis. The purpose of this paper is therefore to describe what we view as good practices for applying quantitative bias analysis to epidemiological data, directed towards those familiar with the methods. We focus on answering questions often posed to those of us who advocate incorporation of bias analysis methods into teaching and research. These include the following. When is bias analysis practical and productive? How does one select the biases that ought to be addressed? How does one select a method to model biases? How does one assign values to the parameters of a bias model? How does one present and interpret a bias analysis?. We hope that our guide to good practices for conducting and presenting bias analyses will encourage

  16. Immune adherence: a quantitative and kinetic analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sekine, T [National Cancer Center, Tokyo (Japan). Research Inst.

    1978-09-01

    Quantitative and kinetic analysis of the immune-adherence reaction (IA) between C3b fragments and IA receptors as an agglutination reaction is difficult. Analysis is possible, however, by use of radio-iodinated bovine serum albumin as antigen at low concentrations (less than 200 ng/ml) and optimal concentration of antibody to avoid precipitation of antigen-antibody complexes with human erythrocytes without participation of complement. Antigen and antibody are reacted at 37/sup 0/C, complement is added, the mixture incubated and human erythrocytes added; after further incubation, ice-cold EDTA containing buffer is added and the erythrocytes centrifuged and assayed for radioactivity. Control cells reacted with heated guinea pig serum retained less than 5% of the added radioactivity. The method facilitates measurement of IA reactivity and permits more detailed analysis of the mechanism underlying the reaction.

  17. Micro photometer's automation for quantitative spectrograph analysis

    International Nuclear Information System (INIS)

    Gutierrez E, C.Y.A.

    1996-01-01

    A Microphotometer is used to increase the sharpness of dark spectral lines. Analyzing these lines one sample content and its concentration could be determined and the analysis is known as Quantitative Spectrographic Analysis. The Quantitative Spectrographic Analysis is carried out in 3 steps, as follows. 1. Emulsion calibration. This consists of gauging a photographic emulsion, to determine the intensity variations in terms of the incident radiation. For the procedure of emulsion calibration an adjustment with square minimum to the data obtained is applied to obtain a graph. It is possible to determine the density of dark spectral line against the incident light intensity shown by the microphotometer. 2. Working curves. The values of known concentration of an element against incident light intensity are plotted. Since the sample contains several elements, it is necessary to find a work curve for each one of them. 3. Analytical results. The calibration curve and working curves are compared and the concentration of the studied element is determined. The automatic data acquisition, calculation and obtaining of resulting, is done by means of a computer (PC) and a computer program. The conditioning signal circuits have the function of delivering TTL levels (Transistor Transistor Logic) to make the communication between the microphotometer and the computer possible. Data calculation is done using a computer programm

  18. Quantitative standard-less XRF analysis

    International Nuclear Information System (INIS)

    Ulitzka, S.

    2002-01-01

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

  19. Quantitative proteomic analysis of intact plastids.

    Science.gov (United States)

    Shiraya, Takeshi; Kaneko, Kentaro; Mitsui, Toshiaki

    2014-01-01

    Plastids are specialized cell organelles in plant cells that are differentiated into various forms including chloroplasts, chromoplasts, and amyloplasts, and fulfill important functions in maintaining the overall cell metabolism and sensing environmental factors such as sunlight. It is therefore important to grasp the mechanisms of differentiation and functional changes of plastids in order to enhance the understanding of vegetality. In this chapter, details of a method for the extraction of intact plastids that makes analysis possible while maintaining the plastid functions are provided; in addition, a quantitative shotgun method for analyzing the composition and changes in the content of proteins in plastids as a result of environmental impacts is described.

  20. Quantitative texture analysis of electrodeposited line patterns

    DEFF Research Database (Denmark)

    Pantleon, Karen; Somers, Marcel A.J.

    2005-01-01

    Free-standing line patterns of Cu and Ni were manufactured by electrochemical deposition into lithographically prepared patterns. Electrodeposition was carried out on top of a highly oriented Au-layer physically vapor deposited on glass. Quantitative texture analysis carried out by means of x......-ray diffraction for both the substrate layer and the electrodeposits yielded experimental evidence for epitaxy between Cu and Au. An orientation relation between film and substrate was discussed with respect to various concepts of epitaxy. While the conventional mode of epitaxy fails for the Cu...

  1. Analysis of genes involved in glycogen degradation in Escherichia coli.

    Science.gov (United States)

    Strydom, Lindi; Jewell, Jonathan; Meier, Michael A; George, Gavin M; Pfister, Barbara; Zeeman, Samuel; Kossmann, Jens; Lloyd, James R

    2017-02-01

    Escherichia coli accumulate or degrade glycogen depending on environmental carbon supply. Glycogen phosphorylase (GlgP) and glycogen debranching enzyme (GlgX) are known to act on the glycogen polymer, while maltodextrin phosphorylase (MalP) is thought to remove maltodextrins released by GlgX. To examine the roles of these enzymes in more detail, single, double and triple mutants lacking all their activities were produced. GlgX and GlgP were shown to act directly on the glycogen polymer, while MalP most likely catabolised soluble malto-oligosaccharides. Interestingly, analysis of a triple mutant lacking all three enzymes indicates the presence of another enzyme that can release maltodextrins from glycogen. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions

    Directory of Open Access Journals (Sweden)

    Edwards Jeremy S

    2000-07-01

    Full Text Available Abstract Background Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in silico representations of integrated metabolic functions can be constructed and analyzed using flux balance analysis (FBA. FBA is particularly well-suited to study metabolic networks based on genomic, biochemical, and strain specific information. Results Herein, we have utilized FBA to interpret and analyze the metabolic capabilities of Escherichia coli. We have computationally mapped the metabolic capabilities of E. coli using FBA and examined the optimal utilization of the E. coli metabolic pathways as a function of environmental variables. We have used an in silico analysis to identify seven gene products of central metabolism (glycolysis, pentose phosphate pathway, TCA cycle, electron transport system essential for aerobic growth of E. coli on glucose minimal media, and 15 gene products essential for anaerobic growth on glucose minimal media. The in silico tpi-, zwf, and pta- mutant strains were examined in more detail by mapping the capabilities of these in silico isogenic strains. Conclusions We found that computational models of E. coli metabolism based on physicochemical constraints can be used to interpret mutant behavior. These in silica results lead to a further understanding of the complex genotype-phenotype relation. Supplementary information: http://gcrg.ucsd.edu/supplementary_data/DeletionAnalysis/main.htm

  3. Inspection, visualisation and analysis of quantitative proteomics data

    OpenAIRE

    Gatto, Laurent

    2016-01-01

    Material Quantitative Proteomics and Data Analysis Course. 4 - 5 April 2016, Queen Hotel, Chester, UK Table D - Inspection, visualisation and analysis of quantitative proteomics data, Laurent Gatto (University of Cambridge)

  4. Effects of Bos taurus autosome 9-located quantitative trait loci haplotypes on the disease phenotypes of dairy cows with experimentally induced Escherichia coli mastitis

    DEFF Research Database (Denmark)

    Khatun, Momena; Sørensen, Peter; Jørgensen, Hanne Birgitte Hede

    2013-01-01

    Several quantitative trait loci (QTL) affecting mastitis incidence and mastitis-related traits such as somatic cell score exist in dairy cows. Previously, QTL haplotypes associated with susceptibility to Escherichia coli mastitis in Nordic Holstein-Friesian (HF) cows were identified on Bos taurus...... autosome 9. In the present study, we induced experimental E. coli mastitis in Danish HF cows to investigate the effect of 2 E. coli mastitis-associated QTL haplotypes on the cows' disease phenotypes and recovery in early lactation. Thirty-two cows were divided in 2 groups bearing haplotypes with either low...... the HH group did. However, we also found interactions between the effects of haplotype and biopsy for body temperature, heart rate, and PMNL. In conclusion, when challenged with E. coli mastitis, HF cows with the specific Bos taurus autosome 9-located QTL haplotypes were associated with differences...

  5. Analytical performance of reciprocal isotope labeling of proteome digests for quantitative proteomics and its application for comparative studies of aerobic and anaerobic Escherichia coli proteomes

    International Nuclear Information System (INIS)

    Lo, Andy; Weiner, Joel H.; Li, Liang

    2013-01-01

    Graphical abstract: -- Highlights: •Investigating a strategy of reciprocal isotope labeling of comparative samples. •Filtering out incorrect peptide identification or quantification values. •Analyzing the proteome changes of E. coli cells grown aerobically or anaerobically. •Presenting guidelines for reciprocal labeling experimental design. -- Abstract: Due to limited sample amounts, instrument time considerations, and reagent costs, only a small number of replicate experiments are typically performed for quantitative proteome analyses. Generation of reproducible data that can be readily assessed for consistency within a small number of datasets is critical for accurate quantification. We report our investigation of a strategy using reciprocal isotope labeling of two comparative samples as a tool for determining proteome changes. Reciprocal labeling was evaluated to determine the internal consistency of quantified proteome changes from Escherichia coli grown under aerobic and anaerobic conditions. Qualitatively, the peptide overlap between replicate analyses of the same sample and reverse labeled samples were found to be within 8%. Quantitatively, reciprocal analyses showed only a slight increase in average overall inconsistency when compared with replicate analyses (1.29 vs. 1.24-fold difference). Most importantly, reverse labeling was successfully used to identify spurious values resulting from incorrect peptide identifications and poor peak fitting. After removal of 5% of the peptide data with low reproducibility, a total of 275 differentially expressed proteins (>1.50-fold difference) were consistently identified and were then subjected to bioinformatics analysis. General considerations and guidelines for reciprocal labeling experimental design and biological significance of obtained results are discussed

  6. Quantitative Microbial Risk Assessment for Escherichia coli O157 : H7, Salmonella, and Listeria monocytogenes in Leafy Green Vegetables Consumed at Salad Bars

    NARCIS (Netherlands)

    Franz, E.; Tromp, S.O.; Rijgersberg, H.; Fels-Klerx, van der H.J.

    2010-01-01

    Fresh vegetables are increasingly recognized as a source of foodborne outbreaks in many parts of the world. The purpose of this study was to conduct a quantitative microbial risk assessment for Escherichia coli O157:H7, Salmonella, and Listeria monocytogenes infection from consumption of leafy green

  7. A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport

    Science.gov (United States)

    Chopra, Paras; Bender, Andreas

    The bgl operon is responsible for the metabolism of β-glucoside sugars such as salicin or arbutin in E. coli. Its regulatory system involves both positive and negative feedback mechanisms and it can be assumed to be more complex than that of the more closely studied lac and trp operons. We have developed a quantitative model for the regulation of the bgl operon which is subject to in silico experiments investigating its behavior under different hypothetical conditions. Upon administration of 5mM salicin as an inducer our model shows 80-fold induction, which compares well with the 60-fold induction measured experimentally. Under practical conditions 5-10mM inducer are employed, which is in line with the minimum inducer concentration of 1mM required by our model. The necessity of BglF conformational change for sugar transport has been hypothesized previously, and in line with those hypotheses our model shows only minor induction if conformational change is not allowed. Overall, this first quantitative model for the bgl operon gives reasonable predictions that are close to experimental results (where measured). It will be further refined as values of the parameters are determined experimentally. The model was developed in Systems Biology Markup Language (SBML) and it is available from the authors and from the Biomodels repository [www.ebi.ac.uk/biomodels].

  8. Diagnostic performance of semi-quantitative and quantitative stress CMR perfusion analysis: a meta-analysis.

    Science.gov (United States)

    van Dijk, R; van Assen, M; Vliegenthart, R; de Bock, G H; van der Harst, P; Oudkerk, M

    2017-11-27

    Stress cardiovascular magnetic resonance (CMR) perfusion imaging is a promising modality for the evaluation of coronary artery disease (CAD) due to high spatial resolution and absence of radiation. Semi-quantitative and quantitative analysis of CMR perfusion are based on signal-intensity curves produced during the first-pass of gadolinium contrast. Multiple semi-quantitative and quantitative parameters have been introduced. Diagnostic performance of these parameters varies extensively among studies and standardized protocols are lacking. This study aims to determine the diagnostic accuracy of semi- quantitative and quantitative CMR perfusion parameters, compared to multiple reference standards. Pubmed, WebOfScience, and Embase were systematically searched using predefined criteria (3272 articles). A check for duplicates was performed (1967 articles). Eligibility and relevance of the articles was determined by two reviewers using pre-defined criteria. The primary data extraction was performed independently by two researchers with the use of a predefined template. Differences in extracted data were resolved by discussion between the two researchers. The quality of the included studies was assessed using the 'Quality Assessment of Diagnostic Accuracy Studies Tool' (QUADAS-2). True positives, false positives, true negatives, and false negatives were subtracted/calculated from the articles. The principal summary measures used to assess diagnostic accuracy were sensitivity, specificity, andarea under the receiver operating curve (AUC). Data was pooled according to analysis territory, reference standard and perfusion parameter. Twenty-two articles were eligible based on the predefined study eligibility criteria. The pooled diagnostic accuracy for segment-, territory- and patient-based analyses showed good diagnostic performance with sensitivity of 0.88, 0.82, and 0.83, specificity of 0.72, 0.83, and 0.76 and AUC of 0.90, 0.84, and 0.87, respectively. In per territory

  9. Winston-Lutz Test: A quantitative analysis

    International Nuclear Information System (INIS)

    Pereira, Aline Garcia; Nandi, Dorival Menegaz; Saraiva, Crystian Wilian Chagas

    2017-01-01

    Objective: Describe a method of quantitative analysis for the Winston-Lutz test. Materials and methods The research is a qualitative exploratory study. The materials used were: portal film; Winston- Lutz test tools and Omni Pro software. Sixteen portal films were used as samples and were analyzed by five different technicians to measure the deviation between the radiation isocenters and mechanic. Results: Among the results were identified two combinations with offset values greater than 1 mm. In addition, when compared the method developed with the previously studied, it was observed that the data obtained are very close, with the maximum percentage deviation of 32.5%, which demonstrates its efficacy in reducing dependence on the performer. Conclusion: The results show that the method is reproducible and practical, which constitutes one of the fundamental factors for its implementation. (author)

  10. Quantitative Analysis in Nuclear Medicine Imaging

    CERN Document Server

    2006-01-01

    This book provides a review of image analysis techniques as they are applied in the field of diagnostic and therapeutic nuclear medicine. Driven in part by the remarkable increase in computing power and its ready and inexpensive availability, this is a relatively new yet rapidly expanding field. Likewise, although the use of radionuclides for diagnosis and therapy has origins dating back almost to the discovery of natural radioactivity itself, radionuclide therapy and, in particular, targeted radionuclide therapy has only recently emerged as a promising approach for therapy of cancer and, to a lesser extent, other diseases. As effort has, therefore, been made to place the reviews provided in this book in a broader context. The effort to do this is reflected by the inclusion of introductory chapters that address basic principles of nuclear medicine imaging, followed by overview of issues that are closely related to quantitative nuclear imaging and its potential role in diagnostic and therapeutic applications. ...

  11. Investment appraisal using quantitative risk analysis.

    Science.gov (United States)

    Johansson, Henrik

    2002-07-01

    Investment appraisal concerned with investments in fire safety systems is discussed. Particular attention is directed at evaluating, in terms of the Bayesian decision theory, the risk reduction that investment in a fire safety system involves. It is shown how the monetary value of the change from a building design without any specific fire protection system to one including such a system can be estimated by use of quantitative risk analysis, the results of which are expressed in terms of a Risk-adjusted net present value. This represents the intrinsic monetary value of investing in the fire safety system. The method suggested is exemplified by a case study performed in an Avesta Sheffield factory.

  12. Genome analysis of E. coli isolated from Crohn's disease patients.

    Science.gov (United States)

    Rakitina, Daria V; Manolov, Alexander I; Kanygina, Alexandra V; Garushyants, Sofya K; Baikova, Julia P; Alexeev, Dmitry G; Ladygina, Valentina G; Kostryukova, Elena S; Larin, Andrei K; Semashko, Tatiana A; Karpova, Irina Y; Babenko, Vladislav V; Ismagilova, Ruzilya K; Malanin, Sergei Y; Gelfand, Mikhail S; Ilina, Elena N; Gorodnichev, Roman B; Lisitsyna, Eugenia S; Aleshkin, Gennady I; Scherbakov, Petr L; Khalif, Igor L; Shapina, Marina V; Maev, Igor V; Andreev, Dmitry N; Govorun, Vadim M

    2017-07-19

    Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.

  13. Expanded flux variability analysis on metabolic network of Escherichia coli

    Institute of Scientific and Technical Information of China (English)

    CHEN Tong; XIE ZhengWei; OUYANG Qi

    2009-01-01

    Flux balance analysis,based on the mass conservation law in a cellular organism,has been extensively employed to study the interplay between structures and functions of cellular metabolic networks.Consequently,the phenotypes of the metabolism can be well elucidated.In this paper,we introduce the Expanded Flux Variability Analysis (EFVA) to characterize the intrinsic nature of metabolic reactions,such as flexibility,modularity and essentiality,by exploring the trend of the range,the maximum and the minimum flux of reactions.We took the metabolic network of Escherichia coli as an example and analyzed the variability of reaction fluxes under different growth rate constraints.The average variability of all reactions decreases dramatically when the growth rate increases.Consider the noise effect on the metabolic system,we thus argue that the microorganism may practically grow under a suboptimal state.Besides,under the EFVA framework,the reactions are easily to be grouped into catabolic and anabolic groups.And the anabolic groups can be further assigned to specific biomass constitute.We also discovered the growth rate dependent essentiality of reactions.

  14. Universal platform for quantitative analysis of DNA transposition

    Directory of Open Access Journals (Sweden)

    Pajunen Maria I

    2010-11-01

    Full Text Available Abstract Background Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition. Results Here we developed a universal in vivo platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable lacZ-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish Escherichia coli colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS903 transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne E. coli arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level. Conclusions The established universal papillation assay platform should be widely applicable to a

  15. Quantitative Analysis of Thallium-201 Myocardial Tomograms

    International Nuclear Information System (INIS)

    Kim, Sang Eun; Nam, Gi Byung; Choi, Chang Woon

    1991-01-01

    The purpose of this study was to assess the ability of quantitative Tl-201 tomography to identify and localize coronary artery disease (CAD). The study population consisted of 41 patients (31 males, 10 females; mean age 55 ± 7 yr) including 14 with prior myocardial infarction who underwent both exercise Tl-201 myocardium SPECT and coronary angiography for the evaluation of chest pain. From the short axis and vertical long axis tomograms, stress extent polar maps were generated by Cedars-Sinai Medical Center program, and the 9 stress defect extent (SDE) was quantified for each coronary artery territory. For the purpose of this study, the coronary circulation was divided into 6 arterial segments, and the myocardial ischemic score (MIS) was calculated from the coronary angiogram. Sensitivity for the detection of CAD (>50% coronary stenosis by angiography) by stress extent polar map was 95% in single vessel disease, and 100% in double and triple vessel diseases. Overall sensitivity was 97%<. Sensitivity and specificity for the detection of individual diseased vessels were, respectively, 87% and 90% for the left anterior descending artery (LAD), 36% and 93% for the left circumflex artery (LCX), and 71% and 70%, for the right coronary artery (RCA). Concordance for the detection of individual diseased vessels between the coronary angiography and stress polar map was fair for the LAD (kappa=0.70), and RCA (kappa=0.41) lesions, whereas it was poor for the LCK lesions (kappa =0.32) There were significant correlations between the MIS and SDE in LAD (rs=0. 56, p=0.0027), and RCA territory (rs=0.60, p=0.0094). No significant correlation was found in LCX territory. When total vascular territories were combined, there was a significant correlation between the MIS and SDE (rs=0.42, p=0,0116). In conclusion, the quantitative analysis of Tl-201 tomograms appears to be accurate for determining the presence and location of CAD.

  16. Quantitative risk analysis preoperational of gas pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Manfredi, Carlos; Bispo, Gustavo G.; Esteves, Alvaro [Gie S.A., Buenos Aires (Argentina)

    2009-07-01

    The purpose of this analysis is to predict how it can be affected the individual risk and the public's general security due to the operation of a gas pipeline. In case that the single or social risks are considered intolerable, compared with the international standards, to be recommended measures of mitigation of the risk associated to the operation until levels that can be considered compatible with the best practices in the industry. The quantitative risk analysis calculates the probability of occurrence of an event based on the frequency of occurrence of the same one and it requires a complex mathematical treatment. The present work has as objective to develop a calculation methodology based on the previously mentioned publication. This calculation methodology is centered in defining the frequencies of occurrence of events, according to representative database of each case in study. Besides, it settles down the consequences particularly according to the considerations of each area and the different possibilities of interferences with the gas pipeline in study. For each one of the interferences a typical curve of ignition probabilities is developed in function from the distance to the pipe. (author)

  17. Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai-Tibet plateau of China.

    Science.gov (United States)

    Lu, Shan; Jin, Dong; Wu, Shusheng; Yang, Jing; Lan, Ruiting; Bai, Xiangning; Liu, Sha; Meng, Qiong; Yuan, Xuejiao; Zhou, Juan; Pu, Ji; Chen, Qiang; Dai, Hang; Hu, Yuanyuan; Xiong, Yanwen; Ye, Changyun; Xu, Jianguo

    2016-12-07

    Escherichia coli is both of a widespread harmless gut commensal and a versatile pathogen of humans. Domestic animals are a well-known reservoir for pathogenic E. coli. However, studies of E. coli populations from wild animals that have been separated from human activities had been very limited. Here we obtained 580 isolates from intestinal contents of 116 wild Marmot Marmota himalayana from Qinghai-Tibet plateau, China, with five isolates per animal. We selected 125 (hereinafter referred to as strains) from the 580 isolates for genome sequencing, based on unique pulse field gel electrophoresis patterns and at least one isolate per animal. Whole genome sequence analysis revealed that all 125 strains carried at least one and the majority (79.2%) carried multiple virulence genes based on the analysis of 22 selected virulence genes. In particular, the majority of the strains carried virulence genes from different pathovars as potential 'hybrid pathogens'. The alleles of eight virulence genes from the Marmot E. coli were found to have diverged earlier than all known alleles from human and other animal E. coli. Phylogenetic analysis of the 125 Marmot E. coli genomes and 355 genomes selected from 1622 human and other E. coli strains identified two new phylogroups, G and H, both of which diverged earlier than the other phylogroups. Eight of the 12 well-known pathogenic E. coli lineages were found to share a most recent common ancestor with one or more Marmot E. coli strains. Our results suggested that the intestinal E. coli of the Marmots contained a diverse virulence gene pool and is potentially pathogenic to humans. These findings provided a new understanding of the evolutionary origin of pathogenic E. coli.

  18. An unconventional method of quantitative microstructural analysis

    International Nuclear Information System (INIS)

    Rastani, M.

    1995-01-01

    The experiment described here introduces a simple methodology which could be used to replace the time-consuming and expensive conventional methods of metallographic and quantitative analysis of thermal treatment effect on microstructure. The method is ideal for the microstructural evaluation of tungsten filaments and other wire samples such as copper wire which can be conveniently coiled. Ten such samples were heat treated by ohmic resistance at temperatures which were expected to span the recrystallization range. After treatment, the samples were evaluated in the elastic recovery test. The normalized elastic recovery factor was defined in terms of these deflections. Experimentally it has shown that elastic recovery factor depends on the degree of recrystallization. In other words this factor is used to determine the fraction of unrecrystallized material. Because the elastic recovery method examines the whole filament rather than just one section through the filament as in metallographical method, it more accurately measures the degree of recrystallization. The method also takes a considerably shorter time and cost compared to the conventional method

  19. Quantitative Analysis of Retrieved Glenoid Liners

    Directory of Open Access Journals (Sweden)

    Katelyn Childs

    2016-02-01

    Full Text Available Revision of orthopedic surgeries is often expensive and involves higher risk from complications. Since most total joint replacement devices use a polyethylene bearing, which serves as a weak link, the assessment of damage to the liner due to in vivo exposure is very important. The failures often are due to excessive polyethylene wear. The glenoid liners are complex and hemispherical in shape and present challenges while assessing the damage. Therefore, the study on the analysis of glenoid liners retrieved from revision surgery may lend insight into common wear patterns and improve future product designs. The purpose of this pilot study is to further develop the methods of segmenting a liner into four quadrants to quantify the damage in the liner. Different damage modes are identified and statistically analyzed. Multiple analysts were recruited to conduct the damage assessments. In this paper, four analysts evaluated nine glenoid liners, retrieved from revision surgery, two of whom had an engineering background and two of whom had a non-engineering background. Associated human factor mechanisms are reported in this paper. The wear patterns were quantified using the Hood/Gunther, Wasielewski, Brandt, and Lombardi methods. The quantitative assessments made by several observers were analyzed. A new, composite damage parameter was developed and applied to assess damage. Inter-observer reliability was assessed using a paired t-test. Data reported by four analysts showed a high standard deviation; however, only two analysts performed the tests in a significantly similar way and they had engineering backgrounds.

  20. Meta-Analysis of Transcriptional Responses to Mastitis-Causing Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Sidra Younis

    Full Text Available Bovine mastitis is a widespread disease in dairy cows, and is often caused by bacterial mammary gland infection. Mastitis causes reduced milk production and leads to excessive use of antibiotics. We present meta-analysis of transcriptional profiles of bovine mastitis from 10 studies and 307 microarrays, allowing identification of much larger sets of affected genes than any individual study. Combining multiple studies provides insight into the molecular effects of Escherichia coli infection in vivo and uncovers differences between the consequences of E. coli vs. Staphylococcus aureus infection of primary mammary epithelial cells (PMECs. In udders, live E. coli elicits inflammatory and immune defenses through numerous cytokines and chemokines. Importantly, E. coli infection causes downregulation of genes encoding lipid biosynthesis enzymes that are involved in milk production. Additionally, host metabolism is generally suppressed. Finally, defensins and bacteria-recognition genes are upregulated, while the expression of the extracellular matrix protein transcripts is silenced. In PMECs, heat-inactivated E. coli elicits expression of ribosomal, cytoskeletal and angiogenic signaling genes, and causes suppression of the cell cycle and energy production genes. We hypothesize that heat-inactivated E. coli may have prophylactic effects against mastitis. Heat-inactivated S. aureus promotes stronger inflammatory and immune defenses than E. coli. Lipopolysaccharide by itself induces MHC antigen presentation components, an effect not seen in response to E. coli bacteria. These results provide the basis for strategies to prevent and treat mastitis and may lead to the reduction in the use of antibiotics.

  1. Quantitative Risk Analysis: Method And Process

    Directory of Open Access Journals (Sweden)

    Anass BAYAGA

    2010-03-01

    Full Text Available Recent and past studies (King III report, 2009: 73-75; Stoney 2007;Committee of Sponsoring Organisation-COSO, 2004, Bartell, 2003; Liebenberg and Hoyt, 2003; Reason, 2000; Markowitz 1957 lament that although, the introduction of quantifying risk to enhance degree of objectivity in finance for instance was quite parallel to its development in the manufacturing industry, it is not the same in Higher Education Institution (HEI. In this regard, the objective of the paper was to demonstrate the methods and process of Quantitative Risk Analysis (QRA through likelihood of occurrence of risk (phase I. This paper serves as first of a two-phased study, which sampled hundred (100 risk analysts in a University in the greater Eastern Cape Province of South Africa.The analysis of likelihood of occurrence of risk by logistic regression and percentages were conducted to investigate whether there were a significant difference or not between groups (analyst in respect of QRA.The Hosmer and Lemeshow test was non-significant with a chi-square(X2 =8.181; p = 0.300, which indicated that there was a good model fit, since the data did not significantly deviate from the model. The study concluded that to derive an overall likelihood rating that indicated the probability that a potential risk may be exercised within the construct of an associated threat environment, the following governing factors must be considered: (1 threat source motivation and capability (2 nature of the vulnerability (3 existence and effectiveness of current controls (methods and process.

  2. Network analysis of metabolic enzyme evolution in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Kraulis Per

    2004-02-01

    Full Text Available Abstract Background The two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate specificity, and the retrograde evolution model, according to which enzymes evolve in response to substrate depletion. Analysis of the distribution of homologous enzyme pairs in the metabolic network can shed light on the respective importance of the two models. We here investigate the evolution of the metabolism in E. coli viewed as a single network using EcoCyc. Results Sequence comparison between all enzyme pairs was performed and the minimal path length (MPL between all enzyme pairs was determined. We find a strong over-representation of homologous enzymes at MPL 1. We show that the functionally similar and functionally undetermined enzyme pairs are responsible for most of the over-representation of homologous enzyme pairs at MPL 1. Conclusions The retrograde evolution model predicts that homologous enzymes pairs are at short metabolic distances from each other. In general agreement with previous studies we find that homologous enzymes occur close to each other in the network more often than expected by chance, which lends some support to the retrograde evolution model. However, we show that the homologous enzyme pairs which may have evolved through retrograde evolution, namely the pairs that are functionally dissimilar, show a weaker over-representation at MPL 1 than the functionally similar enzyme pairs. Our study indicates that, while the retrograde evolution model may have played a small part, the patchwork evolution model is the predominant process of metabolic enzyme evolution.

  3. Drug Resistance Patterns of Escherichia coli in Ethiopia: A Meta-Analysis.

    Science.gov (United States)

    Tuem, Kald Beshir; Gebre, Abadi Kahsu; Atey, Tesfay Mehari; Bitew, Helen; Yimer, Ebrahim M; Berhe, Derbew Fikadu

    2018-01-01

    Antimicrobial drug resistance is a global threat for treatment of infectious diseases and costs life and money and threatens health delivery system's effectiveness. The resistance of E. coli to frequently utilized antimicrobial drugs is becoming a major challenge in Ethiopia. However, there is no inclusive countrywide study. Therefore, this study intended to assess the prevalence of E. coli resistance and antimicrobial-specific resistance pattern among E. coli clinical isolates in Ethiopia. Articles were retrieved from PubMed, Embase, and grey literature from 2007 to 2017. The main outcome measures were overall E. coli and drug-specific resistance patterns. A random-effects model was used to determine pooled prevalence with 95% confidence interval (CI), using DerSimonian and Laird method. In addition, subgroup analysis was conducted to improve the outcome. The study bias was assessed by Begg's funnel plot. This study was registered in PROSPERO as follows: PROSPERO 2017: CRD42017070106. Of 164 articles retrieved, 35 articles were included. A total of 19,235 study samples participated in the studies and 2,635 E. coli strains were isolated. Overall, E. coli antibacterial resistance was 45.38% (95% confidence interval (CI): 33.50 to 57.27). The resistance pattern ranges from 62.55% in Addis Ababa to 27.51% in Tigray region. The highest resistance of E. coli reported was to ampicillin (83.81%) and amoxicillin (75.79%), whereas only 13.55% of E. coli isolates showed resistance to nitrofurantoin. E. coli antimicrobial resistance remains high with disparities observed among regions. The bacterium was found to be highly resistant to aminopenicillins. The finding implies the need for effective prevention strategies for the E. coli drug resistance and calls for multifaceted approaches with full involvement of all stakeholders.

  4. Quantitative assessment of human exposure to extended spectrum and AmpC β-lactamases bearing E. coli in lettuce attributable to irrigation water and subsequent horizontal gene transfer.

    Science.gov (United States)

    Njage, P M K; Buys, E M

    2017-01-02

    The contribution of the fresh produce production environment to human exposure with bacteria bearing extended spectrum β-lactamases and AmpC β-lactamases (ESBL/AmpC) has not been reported. High prevalence of ESBLs/AmpC bearing E. coli as well as a high gene transfer efficiency of lettuce and irrigation water E. coli isolates was previously reported. This stochastic modeling was aimed at quantitatively assessing human exposure to ESBL/AmpC bearing E. coli through lettuce attributable to irrigation water and subsequent horizontal gene transfer. Modular process risk approach was used for the quantitative exposure assessment and models were constructed in Ms. Excel spreadsheet with farm to consumption chain accounted for by primary production, processing, retail and consumer storage. Probability distributions were utilised to take into account the variability of the exposure estimates. Exposure resulting from ESBL/AmpC positive E. coli and gene transfer was taken into account. Monte Carlo simulation was carried out using @Risk software followed by sensitivity and scenario analysis to assess most effective single or combinations of mitigation strategies for the ESBL/AmpC positive E. coli events from farm to fork. Three percent of South African lettuce consumers are exposed to lettuce contaminated with about 10 6.4 ±10 6.7 (95% CI: 10 5.1 -10 7 ) cfu of ESBL/AmpC positive E. coli per serving. The contribution of originally positive isolates and conjugative genetic transfer was 10 6 ±10 6.7 (95% CI: 10 5 -10 7 ) and 10 5.2 ±10 5.6 (95% CI: 10 3.9 -10 5.8 ) cfu per serving respectively. Proportion of ESBL/AmpC positive E. coli (Spearman's correlation coefficient (ρ)=0.85), conjugative gene transfer (ρ=0.05-0.14), washing in chlorine water (ρ=0.18), further rinsing (ρ=0.15), and prevalence of E. coli in irrigation water (ρ=0.16) had highest influence on consumer exposure. The most effective single methods in reducing consumer exposure were reduction in irrigation

  5. Genetic and biochemical analysis of peptide transport in Escherichia coli

    International Nuclear Information System (INIS)

    Andrews, J.C.

    1986-01-01

    E. coli peptide transport mutants have been isolated based on their resistance to toxic tripeptides. These genetic defects were found to map in two distinct chromosomal locations. The transport systems which require expression of the trp-linked opp genes and the oppE gene(s) for activity were shown to have different substrate preferences. Growth of E. coli in medium containing leucine results in increased entry of exogenously supplied tripeptides into the bacterial cell. This leucine-mediated elevation of peptide transport required expression of the trp-linked opp operon and was accompanied by increased sensitivity to toxic tripeptides, by an enhanced capacity to utilize nutritional peptides, and by an increase in both the velocity and apparent steady-state level of L-(U- 14 C)alanyl-L-alanyl-L-alanine accumulation for E. coli grown in leucine-containing medium relative to these parameters of peptide transport measured with bacteria grown in media lacking leucine. Direct measurement of opp operon expression by pulse-labeling experiments demonstrated that growth of E. coli in the presence of leucine resulted in increased synthesis of the oppA-encoded periplasmic binding protein. The transcriptional regulation of the trp-linked opp operon of E. coli was investigated using λ placMu51-generated lac operon fusions. Synthesis of β-galactosidase by strains harboring oppA-lac, oppB-lac, and oppD-lac fusions occurred at a basal level when the fusion-containing strains were grown in minimal medium

  6. Quantitative Auger analysis of Nb-Ge superconducting alloys

    International Nuclear Information System (INIS)

    Buitrago, R.H.

    1980-01-01

    The feasibility of using Auger electron analysis for quantitative analysis was investigated by studying Nb 3 Ge thin-film Auger data with different approaches. A method base on elemental standards gave consistent quantitative values with reported Nb-Ge data. Alloy sputter yields were also calculated and results were consistent with those for pure elements

  7. Quantitative Data Analysis--In the Graduate Curriculum

    Science.gov (United States)

    Albers, Michael J.

    2017-01-01

    A quantitative research study collects numerical data that must be analyzed to help draw the study's conclusions. Teaching quantitative data analysis is not teaching number crunching, but teaching a way of critical thinking for how to analyze the data. The goal of data analysis is to reveal the underlying patterns, trends, and relationships of a…

  8. Quantitative Real-time Polymerase Chain Reaction for Enteropathogenic Escherichia coli: A Tool for Investigation of Asymptomatic Versus Symptomatic Infections

    Science.gov (United States)

    Barletta, Francesca; Mercado, Erik; Ruiz, Joaquim; Ecker, Lucie; Lopez, Giovanni; Mispireta, Monica; Gil, Ana I.; Lanata, Claudio F.; Cleary, Thomas G.

    2011-01-01

    Background. Enteropathogenic Escherichia coli (EPEC) strains are pediatric pathogens commonly isolated from both healthy and sick children with diarrhea in areas of endemicity. The aim of this study was to compare the bacterial load of EPEC isolated from stool samples from children with and without diarrhea to determine whether bacterial load might be a useful tool for further study of this phenomenon. Methods. EPEC was detected by polymerase chain reaction (PCR) of colonies isolated on MacConkey plates from 53 diarrheal and 90 healthy children aged <2 years. DNA was isolated from stool samples by cetyltrimethylammonium bromide extraction. To standardize quantification by quantitative real-time PCR (qRT-PCR), the correlation between fluorescence threshold cycle and copy number of the intimin gene of EPEC E2348/69 was determined. Results. The detection limit of qRT-PCR was 5 bacteria/mg stool. The geometric mean load in diarrhea was 299 bacteria/mg (95% confidence interval [CI], 77–1164 bacteria/mg), compared with 29 bacteria/mg (95% CI, 10–87 bacteria/mg) in control subjects (P = .016). Bacterial load was significantly higher in children with diarrhea than in control subjects among children <12 months of age (178 vs 5 bacteria/mg; P = .006) and among children with EPEC as the sole pathogen (463 vs 24 bacteria/mg; P = .006). Conclusions. EPEC load measured by qRT-PCR is higher in diarrheal than in healthy children. qRT-PCR may be useful to study the relationship between disease and colonization in settings of endemicity. PMID:22028433

  9. Critical Race Quantitative Intersections: A "testimonio" Analysis

    Science.gov (United States)

    Covarrubias, Alejandro; Nava, Pedro E.; Lara, Argelia; Burciaga, Rebeca; Vélez, Verónica N.; Solorzano, Daniel G.

    2018-01-01

    The educational pipeline has become a commonly referenced depiction of educational outcomes for racialized groups across the country. While visually impactful, an overreliance on decontextualized quantitative data often leads to majoritarian interpretations. Without sociohistorical contexts, these interpretations run the risk of perpetuating…

  10. Quantitative Models and Analysis for Reactive Systems

    DEFF Research Database (Denmark)

    Thrane, Claus

    phones and websites. Acknowledging that now more than ever, systems come in contact with the physical world, we need to revise the way we construct models and verification algorithms, to take into account the behavior of systems in the presence of approximate, or quantitative information, provided...

  11. Automated approach to quantitative error analysis

    International Nuclear Information System (INIS)

    Bareiss, E.H.

    1977-04-01

    A method is described how a quantitative measure for the robustness of a given neutron transport theory code for coarse network calculations can be obtained. A code that performs this task automatically and at only nominal cost is described. This code also generates user-oriented benchmark problems which exhibit the analytic behavior at interfaces. 5 figures, 1 table

  12. Quantitative blood flow analysis with digital techniques

    International Nuclear Information System (INIS)

    Forbes, G.

    1984-01-01

    The general principles of digital techniques in quantitating absolute blood flow during arteriography are described. Results are presented for a phantom constructed to correlate digitally calculated absolute flow with direct flow measurements. The clinical use of digital techniques in cerebrovascular angiography is briefly described. (U.K.)

  13. Combination and Integration of Qualitative and Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Philipp Mayring

    2001-02-01

    Full Text Available In this paper, I am going to outline ways of combining qualitative and quantitative steps of analysis on five levels. On the technical level, programs for the computer-aided analysis of qualitative data offer various combinations. Where the data are concerned, the employment of categories (for instance by using qualitative content analysis allows for combining qualitative and quantitative forms of data analysis. On the individual level, the creation of types and the inductive generalisation of cases allow for proceeding from individual case material to quantitative generalisations. As for research design, different models can be distinguished (preliminary study, generalisation, elaboration, triangulation which combine qualitative and quantitative steps of analysis. Where the logic of research is concerned, it can be shown that an extended process model which combined qualitative and quantitative research can be appropriate and thus lead to an integration of the two approaches. URN: urn:nbn:de:0114-fqs010162

  14. Detection of diarrheagenic Escherichia coli by use of melting-curve analysis and real-time multiplex PCR.

    Science.gov (United States)

    Guion, Chase E; Ochoa, Theresa J; Walker, Christopher M; Barletta, Francesca; Cleary, Thomas G

    2008-05-01

    Diarrheagenic Escherichia coli strains are important causes of diarrhea in children from the developing world and are now being recognized as emerging enteropathogens in the developed world. Current methods of detection are too expensive and labor-intensive for routine detection of these organisms to be practical. We developed a real-time fluorescence-based multiplex PCR for the detection of all six of the currently recognized classes of diarrheagenic E. coli. The primers were designed to specifically amplify eight different virulence genes in the same reaction: aggR for enteroaggregative E. coli, stIa/stIb and lt for enterotoxigenic E. coli, eaeA for enteropathogenic E. coli and Shiga toxin-producing E. coli (STEC), stx(1) and stx(2) for STEC, ipaH for enteroinvasive E. coli, and daaD for diffusely adherent E. coli (DAEC). Eighty-nine of ninety diarrheagenic E. coli and 36/36 nonpathogenic E. coli strains were correctly identified using this approach (specificity, 1.00; sensitivity, 0.99). The single false negative was a DAEC strain. The total time between preparation of DNA from E. coli colonies on agar plates and completion of PCR and melting-curve analysis was less than 90 min. The cost of materials was low. Melting-point analysis of real-time multiplex PCR is a rapid, sensitive, specific, and inexpensive method for detection of diarrheagenic E. coli.

  15. [Rapid analysis of suppositories by quantitative 1H NMR spectroscopy].

    Science.gov (United States)

    Abramovich, R A; Kovaleva, S A; Goriainov, S V; Vorob'ev, A N; Kalabin, G A

    2012-01-01

    Rapid analysis of suppositories with ibuprofen and arbidol by quantitative 1H NMR spectroscopy was performed. Optimal conditions for the analysis were developed. The results are useful for design of rapid methods for quality control of suppositories with different components

  16. Compilation and analysis of Escherichia coli promoter DNA sequences.

    OpenAIRE

    Hawley, D K; McClure, W R

    1983-01-01

    The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter ...

  17. Application of quantitative real-time PCR compared to filtration methods for the enumeration of Escherichia coli in surface waters within Vietnam.

    Science.gov (United States)

    Vital, Pierangeli G; Van Ha, Nguyen Thi; Tuyet, Le Thi Hong; Widmer, Kenneth W

    2017-02-01

    Surface water samples in Vietnam were collected from the Saigon River, rural and suburban canals, and urban runoff canals in Ho Chi Minh City, Vietnam, and were processed to enumerate Escherichia coli. Quantification was done through membrane filtration and quantitative real-time polymerase chain reaction (PCR). Mean log colony-forming unit (CFU)/100 ml E. coli counts in the dry season for river/suburban canals and urban canals were log 2.8 and 3.7, respectively, using a membrane filtration method, while using Taqman quantitative real-time PCR they were log 2.4 and 2.8 for river/suburban canals and urban canals, respectively. For the wet season, data determined by the membrane filtration method in river/suburban canals and urban canals samples had mean counts of log 3.7 and 4.1, respectively. While mean log CFU/100 ml counts in the wet season using quantitative PCR were log 3 and 2, respectively. Additionally, the urban canal samples were significantly lower than those determined by conventional culture methods for the wet season. These results show that while quantitative real-time PCR can be used to determine levels of fecal indicator bacteria in surface waters, there are some limitations to its application and it may be impacted by sources of runoff based on surveyed samples.

  18. Molecular analysis of formaldehyde-induced mutations in human lymphoblasts and E. coli

    International Nuclear Information System (INIS)

    Crosby, R.M.; Richardson, K.K.; Craft, T.R.; Benforado, K.B.; Liber, H.L.; Skopek, T.R.

    1988-01-01

    The molecular nature of formaldehyde (HCHO)-induced mutations was studied in both human lymphoblasts and E. coli. Thirty HPRT - human lymphoblast colonies induced by eight repetitive 150 μM HCHO treatments were characterized by Southern blot analysis. Fourteen of these mutants (47%) had visible deletions of some or all of the X-linked HPRT bands, indicating that HCHO can induce large losses of DNA in human lymphoblasts. In E. coli., DNA alterations induced by HCHO were characterized with use of the xanthine guanine phosphoribosyl transferase (gpt) gene as the genetic target. Exposure of E. coli to 4 mM HCHO for 1 hr induced large insertions (41%), large deletions (18%), and point mutations (41%). Dideoxy DNA sequencing revealed that most of the point mutations were transversions at GC base pairs. In contrast, exposure of E. coli to 40 mM HCHO for 1 hr produced 92% point mutations, 62% of which were transitions at a single AT base pair in the gene. Therefore, HCHO is capable of producing different genetic alterations in E. coli at different concentrations, suggesting fundamental differences in the mutagenic mechanisms operating at the two concentrations used. Naked pSV2gpt plasmid DNA was exposed to 3.3 or 10 mM HCHO and transformed into E. coli. Most of the resulting mutations were frameshifts, again suggesting a different mutagenic mechanism

  19. Analysis of Ingredient Lists to Quantitatively Characterize ...

    Science.gov (United States)

    The EPA’s ExpoCast program is developing high throughput (HT) approaches to generate the needed exposure estimates to compare against HT bioactivity data generated from the US inter-agency Tox21 and the US EPA ToxCast programs. Assessing such exposures for the thousands of chemicals in consumer products requires data on product composition. This is a challenge since quantitative product composition data are rarely available. We developed methods to predict the weight fractions of chemicals in consumer products from weight fraction-ordered chemical ingredient lists, and curated a library of such lists from online manufacturer and retailer sites. The probabilistic model predicts weight fraction as a function of the total number of reported ingredients, the rank of the ingredient in the list, the minimum weight fraction for which ingredients were reported, and the total weight fraction of unreported ingredients. Weight fractions predicted by the model compared very well to available quantitative weight fraction data obtained from Material Safety Data Sheets for products with 3-8 ingredients. Lists were located from the online sources for 5148 products containing 8422 unique ingredient names. A total of 1100 of these names could be located in EPA’s HT chemical database (DSSTox), and linked to 864 unique Chemical Abstract Service Registration Numbers (392 of which were in the Tox21 chemical library). Weight fractions were estimated for these 864 CASRN. Using a

  20. Quantitative phosphoproteomic analysis of postmortem muscle development

    DEFF Research Database (Denmark)

    Huang, Honggang

    Meat quality development is highly dependent on postmortem (PM) metabolism and rigor mortis development in PM muscle. PM glycometabolism and rigor mortis fundamentally determine most of the important qualities of raw meat, such as ultimate pH, tenderness, color and water-holding capacity. Protein...... phosphorylation is known to play essential roles on regulating metabolism, contraction and other important activities in muscle systems. However, protein phosphorylation has rarely been systematically explored in PM muscle in relation to meat quality. In this PhD project, both gel-based and mass spectrometry (MS......)-based quantitative phosphoproteomic strategies were employed to analyze PM muscle with the aim to intensively characterize the protein phosphorylation involved in meat quality development. Firstly, gel-based phosphoproteomic studies were performed to analyze the protein phosphorylation in both sarcoplasmic proteins...

  1. Energy Dispersive Spectrometry and Quantitative Analysis Short Course. Introduction to X-ray Energy Dispersive Spectrometry and Quantitative Analysis

    Science.gov (United States)

    Carpenter, Paul; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    This course will cover practical applications of the energy-dispersive spectrometer (EDS) to x-ray microanalysis. Topics covered will include detector technology, advances in pulse processing, resolution and performance monitoring, detector modeling, peak deconvolution and fitting, qualitative and quantitative analysis, compositional mapping, and standards. An emphasis will be placed on use of the EDS for quantitative analysis, with discussion of typical problems encountered in the analysis of a wide range of materials and sample geometries.

  2. Quantitative Analysis of Complex Tropical Forest Stands: A Review ...

    African Journals Online (AJOL)

    FIRST LADY

    The importance of data analysis in quantitative assessment of natural resources .... Data collection design is an important process in complex forest statistical ... Ideally, the sample size should be equal among groups and sufficiently large.

  3. Quantitative Structure-Activity Relationship Analysis of the ...

    African Journals Online (AJOL)

    Erah

    Quantitative Structure-Activity Relationship Analysis of the Anticonvulsant ... Two types of molecular descriptors, including the 2D autocorrelation ..... It is based on the simulation of natural .... clustering anticonvulsant, antidepressant, and.

  4. Quantitative-genetic analysis of wing form and bilateral asymmetry ...

    Indian Academy of Sciences (India)

    Unknown

    lines; Procrustes analysis; wing shape; wing size. ... Models of stochastic gene expression pre- dict that intrinsic noise ... Quantitative parameters of wing size and shape asymmetries ..... the residuals of a regression on centroid size produced.

  5. Analysis association of milk fat and protein percent in quantitative ...

    African Journals Online (AJOL)

    Analysis association of milk fat and protein percent in quantitative trait locus ... African Journal of Biotechnology ... Protein and fat percent as content of milk are high-priority criteria for financial aims and selection of programs in dairy cattle.

  6. Quantitative analysis of some brands of chloroquine tablets ...

    African Journals Online (AJOL)

    Quantitative analysis of some brands of chloroquine tablets marketed in Maiduguri using spectrophotometric ... and compared with that of the standard, wavelength of maximum absorbance at 331nm for chloroquine. ... HOW TO USE AJOL.

  7. Quantitative data analysis in education a critical introduction using SPSS

    CERN Document Server

    Connolly, Paul

    2007-01-01

    This book provides a refreshing and user-friendly guide to quantitative data analysis in education for students and researchers. It assumes absolutely no prior knowledge of quantitative methods or statistics. Beginning with the very basics, it provides the reader with the knowledge and skills necessary to be able to undertake routine quantitative data analysis to a level expected of published research. Rather than focusing on teaching statistics through mathematical formulae, the book places an emphasis on using SPSS to gain a real feel for the data and an intuitive grasp of t

  8. Implementing quantitative analysis and its complement

    International Nuclear Information System (INIS)

    Rasmuson, D.M.; Nelson, W.R.; Shepherd, J.C.

    1982-01-01

    This paper presents an application of risk analysis for the evaluation of nuclear reactor facility operation. Common cause failure analysis (CCFA) techniques to identify potential problem areas are discussed. Integration of CCFA and response trees, a particular form of the path sets of a success tree, to gain significant insight into the operation of the facility is also demonstrated. An example illustrating the development of the risk analysis methodology, development of the fault trees, generation of response trees, and evaluation of the CCFA is presented to explain the technique

  9. Quantitative multi-modal NDT data analysis

    International Nuclear Information System (INIS)

    Heideklang, René; Shokouhi, Parisa

    2014-01-01

    A single NDT technique is often not adequate to provide assessments about the integrity of test objects with the required coverage or accuracy. In such situations, it is often resorted to multi-modal testing, where complementary and overlapping information from different NDT techniques are combined for a more comprehensive evaluation. Multi-modal material and defect characterization is an interesting task which involves several diverse fields of research, including signal and image processing, statistics and data mining. The fusion of different modalities may improve quantitative nondestructive evaluation by effectively exploiting the augmented set of multi-sensor information about the material. It is the redundant information in particular, whose quantification is expected to lead to increased reliability and robustness of the inspection results. There are different systematic approaches to data fusion, each with its specific advantages and drawbacks. In our contribution, these will be discussed in the context of nondestructive materials testing. A practical study adopting a high-level scheme for the fusion of Eddy Current, GMR and Thermography measurements on a reference metallic specimen with built-in grooves will be presented. Results show that fusion is able to outperform the best single sensor regarding detection specificity, while retaining the same level of sensitivity

  10. Quantitative infrared analysis of hydrogen fluoride

    International Nuclear Information System (INIS)

    Manuta, D.M.

    1997-04-01

    This work was performed at the Portsmouth Gaseous Diffusion Plant where hydrogen fluoride is produced upon the hydrolysis of UF 6 . This poses a problem for in this setting and a method for determining the mole percent concentration was desired. HF has been considered to be a non-ideal gas for many years. D. F. Smith utilized complex equations in his HF studies in the 1950s. We have evaluated HF behavior as a function of pressure from three different perspectives. (1) Absorbance at 3877 cm -1 as a function of pressure for 100% HF. (2) Absorbance at 3877 cm -1 as a function of increasing partial pressure HF. Total pressure = 300 mm HgA maintained with nitrogen. (3) Absorbance at 3877 cm -1 for constant partial pressure HF. Total pressure is increased to greater than 800 mm HgA with nitrogen. These experiments have shown that at partial pressures up to 35mm HgA, HIF follows the ideal gas law. The absorbance at 3877 cm -1 can be quantitatively analyzed via infrared methods

  11. Quantitative assessment of the role played by plasmid R446b in the overall U. V. response in EscHer-ICHIA COLI ymel

    Energy Technology Data Exchange (ETDEWEB)

    Farhan, A A

    1987-01-01

    The present study concerned with the quantitative assessment of the role of plasmid R446b in the overall U.V. response in E.Coli ymel. The plasmid was, therefore, transferred to the strain by mating. The transfer of the plasmid has no influence on the microbioloicaLl characteristics evaluated from growth profiles under the rigorously controlled experimental conditions. On the other hand, the plasmid reduced the typical U.V. response of mor than 40 as measured by inactivation constant values to the dose in survival curves. (19 figs., 4 tabs., 99 refs.).

  12. Quantitative risk assessment for Escherichia coli O157:H7 in frozen ground beef patties consumed by young children in French households.

    Science.gov (United States)

    Delignette-Muller, M L; Cornu, M

    2008-11-30

    A quantitative risk assessment for Escherichia coli O157:H7 in frozen ground beef patties consumed by children under 10 years of age in French households was conducted by a national study group describing an outbreak which occurred in France in 2005. Our exposure assessment model incorporates results from French surveys on consumption frequency of ground beef patties, serving size and consumption preference, microbial destruction experiments and microbial counts on patties sampled from the industrial batch which were responsible for the outbreak. Two different exposure models were proposed, respectively for children under the age of 5 and for children between 5 and 10 years. For each of these two age groups, a single-hit dose-response model was proposed to describe the probability of hemolytic and uremic syndrome (HUS) as a function of the ingested dose. For each group, the single parameter of this model was estimated by Bayesian inference, using the results of the exposure assessment and the epidemiological data collected during the outbreak. Results show that children under 5 years of age are roughly 5 times more susceptible to the pathogen than children over 5 years. Exposure and dose-response models were used in a scenario analysis in order to validate the use of the model and to propose appropriate guidelines in order to prevent new outbreaks. The impact of the cooking preference was evaluated, showing that only a well-done cooking notably reduces the HUS risk, without annulling it. For each age group, a relation between the mean individual HUS risk per serving and the contamination level in a ground beef batch was proposed, as a tool to help French risk managers.

  13. Quantitative genetic analysis of total glucosinolate, oil and protein ...

    African Journals Online (AJOL)

    Quantitative genetic analysis of total glucosinolate, oil and protein contents in Ethiopian mustard ( Brassica carinata A. Braun) ... Seeds were analyzed using HPLC (glucosinolates), NMR (oil) and NIRS (protein). Analyses of variance, Hayman's method of diallel analysis and a mixed linear model of genetic analysis were ...

  14. Applied quantitative analysis in the social sciences

    CERN Document Server

    Petscher, Yaacov; Compton, Donald L

    2013-01-01

    To say that complex data analyses are ubiquitous in the education and social sciences might be an understatement. Funding agencies and peer-review journals alike require that researchers use the most appropriate models and methods for explaining phenomena. Univariate and multivariate data structures often require the application of more rigorous methods than basic correlational or analysis of variance models. Additionally, though a vast set of resources may exist on how to run analysis, difficulties may be encountered when explicit direction is not provided as to how one should run a model

  15. Qualitative and quantitative analysis of detonation products

    International Nuclear Information System (INIS)

    Xie Yun

    2005-01-01

    Different sampling and different injection method were used during analyzing unknown detonation products in a obturator. The sample analyzed by gas chromatography and gas chromatography/mass spectrum. Qualitative analysis was used with CO, NO, C 2 H 2 , C 6 H 6 and so on, qualitative analysis was used with C 3 H 5 N, C 10 H 10 , C 8 H 8 N 2 and so on. The method used in the article is feasible. The results show that the component of detonation in the study is negative oxygen balance, there were many pollutants in the detonation products. (authors)

  16. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

    We present a framework for modelling and analysis of realworld business workflows. We present a formalised core subset of the Business Process Modelling and Notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations...... of events, reward-based properties and best- and worst- case scenarios. We develop a simple example of medical workflow and demonstrate the utility of this analysis in accurate provisioning of drug stocks. Finally, we suggest a path to building upon these techniques to cover the entire BPMN language, allow...

  17. The quantitative failure of human reliability analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, C.T.

    1995-07-01

    This philosophical treatise argues the merits of Human Reliability Analysis (HRA) in the context of the nuclear power industry. Actually, the author attacks historic and current HRA as having failed in informing policy makers who make decisions based on risk that humans contribute to systems performance. He argues for an HRA based on Bayesian (fact-based) inferential statistics, which advocates a systems analysis process that employs cogent heuristics when using opinion, and tempers itself with a rational debate over the weight given subjective and empirical probabilities.

  18. Quantitative Determination of Aluminum in Deodorant Brands: A Guided Inquiry Learning Experience in Quantitative Analysis Laboratory

    Science.gov (United States)

    Sedwick, Victoria; Leal, Anne; Turner, Dea; Kanu, A. Bakarr

    2018-01-01

    The monitoring of metals in commercial products is essential for protecting public health against the hazards of metal toxicity. This article presents a guided inquiry (GI) experimental lab approach in a quantitative analysis lab class that enabled students' to determine the levels of aluminum in deodorant brands. The utility of a GI experimental…

  19. Fundamentals of quantitative PET data analysis

    NARCIS (Netherlands)

    Willemsen, ATM; van den Hoff, J

    2002-01-01

    Drug analysis and development with PET should fully exhaust the ability of this tomographic technique to quantify regional tracer concentrations in vivo. Data evaluation based on visual inspection or assessment of regional image contrast is not sufficient for this purpose since much of the

  20. Event History Analysis in Quantitative Genetics

    DEFF Research Database (Denmark)

    Maia, Rafael Pimentel

    Event history analysis is a clas of statistical methods specially designed to analyze time-to-event characteristics, e.g. the time until death. The aim of the thesis was to present adequate multivariate versions of mixed survival models that properly represent the genetic aspects related to a given...

  1. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

    We present a framework for modelling and analysis of realworld business workflows. We present a formalised core subset of the Business Process Modelling and Notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations...... of events, reward-based properties and best- and worst- case scenarios. We develop a simple example of medical workflow and demonstrate the utility of this analysis in accurate provisioning of drug stocks. Finally, we suggest a path to building upon these techniques to cover the entire BPMN language, allow...... for more complex annotations and ultimately to automatically synthesise workflows by composing predefined sub-processes, in order to achieve a configuration that is optimal for parameters of interest....

  2. Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

    Directory of Open Access Journals (Sweden)

    Thomas Jensen

    2016-01-01

    Full Text Available Background: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including staining may benefit. Methods: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm are presented. Results: It is shown that the autofluorescence intensity of unstained microsections at two different wavelengths is a suitable starting point for automated digital analysis of myocytes, fibrous tissue, lipofuscin, and the extracellular compartment. The output of the method is absolute quantitation along with accurate outlines of above-mentioned components. The digital quantitations are verified by comparison to point grid quantitations performed on the microsections after Van Gieson staining. Conclusion: The presented method is amply described as a prestain multicomponent quantitation and outlining tool for histological sections of cardiac tissue. The main perspective is the opportunity for combination with digital analysis of stained microsections, for which the method may provide an accurate digital framework.

  3. Crystallization and preliminary X-ray analysis of Escherichia coli RNase G

    International Nuclear Information System (INIS)

    Fang, Pengfei; Wang, Jing; Li, Xu; Guo, Min; Xing, Li; Cao, Xu; Zhu, Yi; Gao, Yan; Niu, Liwen; Teng, Maikun

    2009-01-01

    Full-length E. coli RNase G was overexpressed, purified and crystallized. Diffraction data were collected to a resolution of 3.4 Å. The homologous RNases RNase E and RNase G are widely distributed in bacteria and function in many important physiological processes, including mRNA degradation, rRNA maturation and so on. In this study, the crystallization and preliminary X-ray analysis of RNase G from Escherichia coli is described. Purified recombinant E. coli RNase G, which has 497 amino acids, was crystallized in the cubic space group F432, with unit-cell parameters a = b = c = 219.84 Å. X-ray diffraction data were collected to a resolution of 3.4 Å

  4. Chromatic Image Analysis For Quantitative Thermal Mapping

    Science.gov (United States)

    Buck, Gregory M.

    1995-01-01

    Chromatic image analysis system (CIAS) developed for use in noncontact measurements of temperatures on aerothermodynamic models in hypersonic wind tunnels. Based on concept of temperature coupled to shift in color spectrum for optical measurement. Video camera images fluorescence emitted by phosphor-coated model at two wavelengths. Temperature map of model then computed from relative brightnesses in video images of model at those wavelengths. Eliminates need for intrusive, time-consuming, contact temperature measurements by gauges, making it possible to map temperatures on complex surfaces in timely manner and at reduced cost.

  5. Segmentation and Quantitative Analysis of Epithelial Tissues.

    Science.gov (United States)

    Aigouy, Benoit; Umetsu, Daiki; Eaton, Suzanne

    2016-01-01

    Epithelia are tissues that regulate exchanges with the environment. They are very dynamic and can acquire virtually any shape; at the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the large number of cells composing an epithelium and the absence of informatics tools dedicated to epithelial analysis largely prevented tissue scale studies. Here we present Tissue Analyzer, a free tool that can be used to segment and analyze epithelial cells and monitor tissue dynamics.

  6. Quantitative analysis of deuterium by gas chromatography

    International Nuclear Information System (INIS)

    Isomura, Shohei; Kaetsu, Hayato

    1981-01-01

    An analytical method for the determination of deuterium concentration in water and hydrogen gas by gas chromatography is described. HD and D 2 in a hydrogen gas sample were separated from H 2 by a column packed with Molecular Sieve 13X, using extra pure hydrogen gas as carrier. A thermal conductivity detector was used. Concentrations of deuterium were determined by comparison with standard samples. The error inherent to the present method was less a 1% on the basis of the calibration curves obtained with the standard samples. The average time required for the analysis was about 3 minutes. (author)

  7. Influence of corrosion layers on quantitative analysis

    International Nuclear Information System (INIS)

    Denker, A.; Bohne, W.; Opitz-Coutureau, J.; Rauschenberg, J.; Roehrich, J.; Strub, E.

    2005-01-01

    Art historians and restorers in charge of ancient metal objects are often reluctant to remove the corrosion layer evolved over time, as this would change the appearance of the artefact dramatically. Therefore, when an elemental analysis of the objects is required, this has to be done by penetrating the corrosion layer. In this work the influence of corrosion was studied on Chinese and Roman coins, where removal of oxidized material was possible. Measurements on spots with and without corrosion are presented and the results discussed

  8. Genetic analysis of the SOS response of Escherichia coli

    International Nuclear Information System (INIS)

    Mount, D.W.; Wertman, K.F.; Ennis, D.G.; Peterson, K.R.; Fisher, B.L.; Lyons, G.

    1983-01-01

    In the SOS response, a large number of E. coli genes having different functions are derepressed when the cellular DNA is damaged. This derepression occurs through inactivation of a repressor, the product of the lexA gene, by a protease activity of the recA gene product. The protease is thought to be activated in response to changes in DNA metabolism which follow the damage. After the SOS functions have acted, the protease activity declines and repression is again established. Because the DNA sequence of both lexA and recA have been determined, it is possible to induce many mutations in their regulatory and structural regions in order to analyze further the control of the SOS response. We are studying the effects of mutations in both the lexA and recA regulatory regions, and mutations which affect the protease activity or the sensitivity of repressor to the protease. Finally, we are using genetic methods to analyze a newly identified requirement for recA protein, induced mutagenesis in cells lacking repressor. 16 references, 3 figures

  9. Structural model analysis of multiple quantitative traits.

    Directory of Open Access Journals (Sweden)

    Renhua Li

    2006-07-01

    Full Text Available We introduce a method for the analysis of multilocus, multitrait genetic data that provides an intuitive and precise characterization of genetic architecture. We show that it is possible to infer the magnitude and direction of causal relationships among multiple correlated phenotypes and illustrate the technique using body composition and bone density data from mouse intercross populations. Using these techniques we are able to distinguish genetic loci that affect adiposity from those that affect overall body size and thus reveal a shortcoming of standardized measures such as body mass index that are widely used in obesity research. The identification of causal networks sheds light on the nature of genetic heterogeneity and pleiotropy in complex genetic systems.

  10. Human eyeball model reconstruction and quantitative analysis.

    Science.gov (United States)

    Xing, Qi; Wei, Qi

    2014-01-01

    Determining shape of the eyeball is important to diagnose eyeball disease like myopia. In this paper, we present an automatic approach to precisely reconstruct three dimensional geometric shape of eyeball from MR Images. The model development pipeline involved image segmentation, registration, B-Spline surface fitting and subdivision surface fitting, neither of which required manual interaction. From the high resolution resultant models, geometric characteristics of the eyeball can be accurately quantified and analyzed. In addition to the eight metrics commonly used by existing studies, we proposed two novel metrics, Gaussian Curvature Analysis and Sphere Distance Deviation, to quantify the cornea shape and the whole eyeball surface respectively. The experiment results showed that the reconstructed eyeball models accurately represent the complex morphology of the eye. The ten metrics parameterize the eyeball among different subjects, which can potentially be used for eye disease diagnosis.

  11. Quantitative Image Simulation and Analysis of Nanoparticles

    DEFF Research Database (Denmark)

    Madsen, Jacob; Hansen, Thomas Willum

    Microscopy (HRTEM) has become a routine analysis tool for structural characterization at atomic resolution, and with the recent development of in-situ TEMs, it is now possible to study catalytic nanoparticles under reaction conditions. However, the connection between an experimental image, and the underlying...... physical phenomena or structure is not always straightforward. The aim of this thesis is to use image simulation to better understand observations from HRTEM images. Surface strain is known to be important for the performance of nanoparticles. Using simulation, we estimate of the precision and accuracy...... of strain measurements from TEM images, and investigate the stability of these measurements to microscope parameters. This is followed by our efforts toward simulating metal nanoparticles on a metal-oxide support using the Charge Optimized Many Body (COMB) interatomic potential. The simulated interface...

  12. Biostatistical analysis of quantitative immunofluorescence microscopy images.

    Science.gov (United States)

    Giles, C; Albrecht, M A; Lam, V; Takechi, R; Mamo, J C

    2016-12-01

    Semiquantitative immunofluorescence microscopy has become a key methodology in biomedical research. Typical statistical workflows are considered in the context of avoiding pseudo-replication and marginalising experimental error. However, immunofluorescence microscopy naturally generates hierarchically structured data that can be leveraged to improve statistical power and enrich biological interpretation. Herein, we describe a robust distribution fitting procedure and compare several statistical tests, outlining their potential advantages/disadvantages in the context of biological interpretation. Further, we describe tractable procedures for power analysis that incorporates the underlying distribution, sample size and number of images captured per sample. The procedures outlined have significant potential for increasing understanding of biological processes and decreasing both ethical and financial burden through experimental optimization. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

  13. Developments in statistical analysis in quantitative genetics

    DEFF Research Database (Denmark)

    Sorensen, Daniel

    2009-01-01

    of genetic means and variances, models for the analysis of categorical and count data, the statistical genetics of a model postulating that environmental variance is partly under genetic control, and a short discussion of models that incorporate massive genetic marker information. We provide an overview......A remarkable research impetus has taken place in statistical genetics since the last World Conference. This has been stimulated by breakthroughs in molecular genetics, automated data-recording devices and computer-intensive statistical methods. The latter were revolutionized by the bootstrap...... and by Markov chain Monte Carlo (McMC). In this overview a number of specific areas are chosen to illustrate the enormous flexibility that McMC has provided for fitting models and exploring features of data that were previously inaccessible. The selected areas are inferences of the trajectories over time...

  14. Parameter determination for quantitative PIXE analysis using genetic algorithms

    International Nuclear Information System (INIS)

    Aspiazu, J.; Belmont-Moreno, E.

    1996-01-01

    For biological and environmental samples, PIXE technique is in particular advantage for elemental analysis, but the quantitative analysis implies accomplishing complex calculations that require the knowledge of more than a dozen parameters. Using a genetic algorithm, the authors give here an account of the procedure to obtain the best values for the parameters necessary to fit the efficiency for a X-ray detector. The values for some variables involved in quantitative PIXE analysis, were manipulated in a similar way as the genetic information is treated in a biological process. The authors carried out the algorithm until they reproduce, within the confidence interval, the elemental concentrations corresponding to a reference material

  15. Quantitative assessment of human exposure to extended spectrum and AmpC β-lactamases bearing E. coli in lettuce attributable to irrigation water and subsequent horizontal gene transfer

    DEFF Research Database (Denmark)

    Njage, Patrick Murigu Kamau; Buys, E. M.

    2017-01-01

    and irrigation water E. coli isolates was previously reported. This stochastic modeling was aimed at quantitatively assessing human exposure to ESBL/AmpC bearing E. coli through lettuce attributable to irrigation water and subsequent horizontal gene transfer. Modular process risk approach was used.......15), and prevalence of E. coli in irrigation water (ρ=0.16) had highest influence on consumer exposure. The most effective single methods in reducing consumer exposure were reduction in irrigation water microbial quality variation (87.4% reduction), storage period (49.9-87.4% reduction) and growth rate reduction...... irrigation water quality variation. The exposure levels may impose higher consumer risk than acceptable for irrigation water risk. E. coli contamination and growth related measures, as well as measures to reduce contamination with antimicrobial resistant E. coli from lettuce production environment...

  16. Quantitative analysis of carbon in plutonium

    International Nuclear Information System (INIS)

    Lefevre, Chantal.

    1979-11-01

    The aim of this study is to develop a method for the determination of carbon traces (20 to 400 ppm) in plutonium. The development of a carbon in plutonium standard is described, then the content of this substance is determined and its validity as a standard shown by analysis in two different ways. In the first method used, reaction of the metal with sulphur and determination of carbon as carbon sulphide, the following parameters were studied: influence of excess reagent, surface growth of samples in contact with sulphur, temperature and reaction time. The results obtained are in agreement with those obtained by the conventional method of carbon determination, combustion in oxygen and measurement of carbon in the form of carbon dioxide. Owing to the presence of this standard we were then able to study the different parameters involved in plutonium combustion so that the reaction can be made complete: temperature reached during combustion, role of flux, metal surface in contact with oxygen and finally method of cleaning plutonium samples [fr

  17. Quantitative analysis of forest fire extinction efficiency

    Directory of Open Access Journals (Sweden)

    Miguel E. Castillo-Soto

    2015-08-01

    Full Text Available Aim of study: Evaluate the economic extinction efficiency of forest fires, based on the study of fire combat undertaken by aerial and terrestrial means. Area of study, materials and methods: Approximately 112,000 hectares in Chile. Records of 5,876 forest fires that occurred between 1998 and 2009 were analyzed. The area further provides a validation sector for results, by incorporating databases for the years 2010 and 2012. The criteria used for measuring extinction efficiency were economic value of forestry resources, Contraction Factor analysis and definition of the extinction costs function. Main results: It is possible to establish a relationship between burnt area, extinction costs and economic losses. The method proposed may be used and adapted to other fire situations, requiring unit costs for aerial and terrestrial operations, economic value of the property to be protected and speed attributes of fire spread in free advance. Research highlights: The determination of extinction efficiency in containment works of forest fires and potential projection of losses, different types of plant fuel and local conditions favoring the spread of fire broaden the admissible ranges of a, φ and Ce considerably.

  18. [Quantitative data analysis for live imaging of bone.

    Science.gov (United States)

    Seno, Shigeto

    Bone tissue is a hard tissue, it was difficult to observe the interior of the bone tissue alive. With the progress of microscopic technology and fluorescent probe technology in recent years, it becomes possible to observe various activities of various cells forming bone society. On the other hand, the quantitative increase in data and the diversification and complexity of the images makes it difficult to perform quantitative analysis by visual inspection. It has been expected to develop a methodology for processing microscopic images and data analysis. In this article, we introduce the research field of bioimage informatics which is the boundary area of biology and information science, and then outline the basic image processing technology for quantitative analysis of live imaging data of bone.

  19. Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

    Science.gov (United States)

    Gunar, O V; Sakhno, N G

    2015-12-30

    The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Quantiprot - a Python package for quantitative analysis of protein sequences.

    Science.gov (United States)

    Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

    2017-07-17

    The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

  1. Quantitative methods for the analysis of electron microscope images

    DEFF Research Database (Denmark)

    Skands, Peter Ulrik Vallø

    1996-01-01

    The topic of this thesis is an general introduction to quantitative methods for the analysis of digital microscope images. The images presented are primarily been acquired from Scanning Electron Microscopes (SEM) and interfermeter microscopes (IFM). The topic is approached though several examples...... foundation of the thesis fall in the areas of: 1) Mathematical Morphology; 2) Distance transforms and applications; and 3) Fractal geometry. Image analysis opens in general the possibility of a quantitative and statistical well founded measurement of digital microscope images. Herein lies also the conditions...

  2. SILAC-based comparative analysis of pathogenic Escherichia coli secretomes

    DEFF Research Database (Denmark)

    Boysen, Anders; Borch, Jonas; Krogh, Thøger Jensen

    2015-01-01

    Comparative studies of pathogenic bacteria and their non-pathogenic counterparts has led to the discovery of important virulence factors thereby generating insight into mechanisms of pathogenesis. Protein-based antigens for vaccine development are primarily selected among unique virulence...... experimental approach. In addition we find proteins that are not unique to the pathogenic strains but expressed at levels different from the commensal strain, including the colonization factor YghJ and the surface adhesin antigen 43, which is involved in pathogenesis of other Gram-negative bacteria......-related factors produced by the pathogen of interest. However, recent work indicates that proteins that are not unique to the pathogen but instead selectively expressed compared to its non-pathogenic counterpart could also be vaccine candidates or targets for drug development. Modern methods in quantitative...

  3. Original methods of quantitative analysis developed for diverse samples in various research fields. Quantitative analysis at NMCC

    International Nuclear Information System (INIS)

    Sera, Koichiro

    2003-01-01

    Nishina Memorial Cyclotron Center (NMCC) has been opened for nationwide-common utilization of positron nuclear medicine (PET) and PIXE since April 1993. At the present time, nearly 40 subjects of PIXE in various research fields are pursued here, and more than 50,000 samples have been analyzed up to the present. In order to perform quantitative analyses of diverse samples, technical developments in sample preparation, measurement and data analysis have been continuously carried out. Especially, a standard-free method for quantitative analysis'' made it possible to perform analysis of infinitesimal samples, powdered samples and untreated bio samples, which could not be well analyzed quantitatively in the past. The standard-free method'' and a ''powdered internal standard method'' made the process for target preparation quite easier. It has been confirmed that results obtained by these methods show satisfactory accuracy and reproducibility preventing any ambiguity coming from complicated target preparation processes. (author)

  4. Quantitative scenario analysis of low and intermediate level radioactive repository

    International Nuclear Information System (INIS)

    Lee, Keon Jae; Lee, Sang Yoon; Park, Keon Baek; Song, Min Cheon; Lee, Ho Jin

    1998-03-01

    Derivation of hypothetical radioactive waste disposal facility os conducted through sub-component characteristic analysis and conceptual modeling. It is studied that quantitative analysis of constructed scenario in terms of annual effective dose equivalent. This study is sequentially conducted according to performance assessment of radioactive waste disposal facility such as : ground water flow analysis, source term analysis, ground water transport, surface water transport, dose and pathways. The routine program module such as VAM2D-PAGAN-GENII is used for quantitative scenario analysis. Detailed data used in this module are come from experimental data of Korean territory and default data given within this module. Is case of blank data for code execution, it is estimated through reasonable engineering sense

  5. Issues in Quantitative Analysis of Ultraviolet Imager (UV) Data: Airglow

    Science.gov (United States)

    Germany, G. A.; Richards, P. G.; Spann, J. F.; Brittnacher, M. J.; Parks, G. K.

    1999-01-01

    The GGS Ultraviolet Imager (UVI) has proven to be especially valuable in correlative substorm, auroral morphology, and extended statistical studies of the auroral regions. Such studies are based on knowledge of the location, spatial, and temporal behavior of auroral emissions. More quantitative studies, based on absolute radiometric intensities from UVI images, require a more intimate knowledge of the instrument behavior and data processing requirements and are inherently more difficult than studies based on relative knowledge of the oval location. In this study, UVI airglow observations are analyzed and compared with model predictions to illustrate issues that arise in quantitative analysis of UVI images. These issues include instrument calibration, long term changes in sensitivity, and imager flat field response as well as proper background correction. Airglow emissions are chosen for this study because of their relatively straightforward modeling requirements and because of their implications for thermospheric compositional studies. The analysis issues discussed here, however, are identical to those faced in quantitative auroral studies.

  6. Quantitative Proteomic Analysis of Sulfolobus solfataricus Membrane Proteins

    NARCIS (Netherlands)

    Pham, T.K.; Sierocinski, P.; Oost, van der J.; Wright, P.C.

    2010-01-01

    A quantitative proteomic analysis of the membrane of the archaeon Sulfolobus solfataricus P2 using iTRAQ was successfully demonstrated in this technical note. The estimated number of membrane proteins of this organism is 883 (predicted based on Gravy score), corresponding to 30 % of the total

  7. Data from quantitative label free proteomics analysis of rat spleen

    Directory of Open Access Journals (Sweden)

    Khadar Dudekula

    2016-09-01

    Full Text Available The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides. A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis. Keywords: Spleen, Rat, Protein extraction, Label-free quantitative proteomics

  8. Quantitative Analysis of Complex Tropical Forest Stands: A Review ...

    African Journals Online (AJOL)

    The importance of data analysis in quantitative assessment of natural resources remains significant in the sustainable management of complex tropical forest resources. Analyses of data from complex tropical forest stands have not been easy or clear due to improper data management. It is pivotal to practical researches ...

  9. Proteomic analysis of the response of Escherichia coli to short-chain fatty acids.

    Science.gov (United States)

    Rodríguez-Moyá, María; Gonzalez, Ramon

    2015-06-03

    Given their simple and easy-to-manipulate chemical structures, short-chain fatty acids (SCFAs) are valuable feedstocks for many industrial applications. While the microbial production of SCFAs by engineered Escherichia coli has been demonstrated recently, productivity and yields are limited by their antimicrobial properties. In this work, we performed a comparative proteomic analysis of E. coli under octanoic acid stress (15 mM) and identified the underlying mechanisms of SCFA toxicity. Out of a total of 33 spots differentially expressed at a p-value ≤ 0.05, nine differentially expressed proteins involved in transport and structural roles (OmpF, HPr, and FliC), oxidative stress (SodA, SodB, and TrxA), protein synthesis (PPiB and RpsA) and metabolic functions (HPr, PflB) were selected for further investigation. Our studies suggest that membrane damage and oxidative stress are the main routes of inhibition by SCFAs in E. coli. The outer membrane porin OmpF had the greatest impact on SCFA tolerance. Intracellular pH analysis on ompF mutants grown under octanoic acid stress indicated that this porin facilitates transport of SCFAs into the cell. The same response was observed under hexanoic acid stress, further supporting the role of OmpF in response to the presence of SCFAs. Furthermore, analysis of membrane protein expression revealed that other outer membrane porins are also involved in the response of E. coli to SCFAs. This work covers the first known proteomic analysis to assess the inhibitory effect of SCFAs in E. coli. SCFAs are molecules of great interest in the industry, but their microbial production is limited by their antimicrobial properties. This work allowed identification of differentially expressed proteins in response to SCFA stress and demonstrated the relevance of short- and medium-chain FA transport across the cell membrane via outer membrane porins, providing valuable insights on the toxicity mechanism of SCFAs in E. coli. These results could

  10. Quantitative analysis of regional myocardial performance in coronary artery disease

    Science.gov (United States)

    Stewart, D. K.; Dodge, H. T.; Frimer, M.

    1975-01-01

    Findings from a group of subjects with significant coronary artery stenosis are given. A group of controls determined by use of a quantitative method for the study of regional myocardial performance based on the frame-by-frame analysis of biplane left ventricular angiograms are presented. Particular emphasis was placed upon the analysis of wall motion in terms of normalized segment dimensions, timing and velocity of contraction. The results were compared with the method of subjective assessment used clinically.

  11. Quantitative measurement of damage caused by 1064-nm wavelength optical trapping of Escherichia coli cells using on-chip single cell cultivation system

    International Nuclear Information System (INIS)

    Ayano, Satoru; Wakamoto, Yuichi; Yamashita, Shinobu; Yasuda, Kenji

    2006-01-01

    We quantitatively examined the possible damage to the growth and cell division ability of Escherichia coli caused by 1064-nm optical trapping. Using the synchronous behavior of two sister E. coli cells, the growth and interdivision times between those two cells, one of which was trapped by optical tweezers, the other was not irradiated, were compared using an on-chip single cell cultivation system. Cell growth stopped during the optical trapping period, even with the smallest irradiated power on the trapped cells. Moreover, the damage to the cell's growth and interdivision period was proportional to the total irradiated energy (work) on the cell, i.e., irradiation time multiplied by irradiation power. The division ability was more easily affected by a smaller energy, 0.36 J, which was 30% smaller than the energy that adversely affected growth, 0.54 J. The results indicate that the damage caused by optical trapping can be estimated from the total energy applied to cells, and furthermore, that the use of optical trapping for manipulating cells might cause damage to cell division and growth mechanisms, even at wavelengths under 1064 nm, if the total irradiation energy is excessive

  12. Quantitative analysis of culture using millions of digitized books.

    Science.gov (United States)

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva Presser; Veres, Adrian; Gray, Matthew K; Pickett, Joseph P; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A; Aiden, Erez Lieberman

    2011-01-14

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of 'culturomics,' focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.

  13. Quantitative analysis of culture using millions of digitized books

    Science.gov (United States)

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva P.; Veres, Adrian; Gray, Matthew K.; Pickett, Joseph P.; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A.; Aiden, Erez Lieberman

    2011-01-01

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics’, focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. ‘Culturomics’ extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities. PMID:21163965

  14. Epidemic potential of Escherichia coli ST131 and Klebsiella pneumoniae ST258: a systematic review and meta-analysis

    Science.gov (United States)

    Dautzenberg, M J D; Haverkate, M R; Bonten, M J M; Bootsma, M C J

    2016-01-01

    Objectives Observational studies have suggested that Escherichia coli sequence type (ST) 131 and Klebsiella pneumoniae ST258 have hyperendemic properties. This would be obvious from continuously high incidence and/or prevalence of carriage or infection with these bacteria in specific patient populations. Hyperendemicity could result from increased transmissibility, longer duration of infectiousness, and/or higher pathogenic potential as compared with other lineages of the same species. The aim of our research is to quantitatively estimate these critical parameters for E. coli ST131 and K. pneumoniae ST258, in order to investigate whether E. coli ST131 and K. pneumoniae ST258 are truly hyperendemic clones. Primary outcome measures A systematic literature search was performed to assess the evidence of transmissibility, duration of infectiousness, and pathogenicity for E. coli ST131 and K. pneumoniae ST258. Meta-regression was performed to quantify these characteristics. Results The systematic literature search yielded 639 articles, of which 19 data sources provided information on transmissibility (E. coli ST131 n=9; K. pneumoniae ST258 n=10)), 2 on duration of infectiousness (E. coli ST131 n=2), and 324 on pathogenicity (E. coli ST131 n=285; K. pneumoniae ST258 n=39). Available data on duration of carriage and on transmissibility were insufficient for quantitative assessment. In multivariable meta-regression E. coli isolates causing infection were associated with ST131, compared to isolates only causing colonisation, suggesting that E. coli ST131 can be considered more pathogenic than non-ST131 isolates. Date of isolation, location and resistance mechanism also influenced the prevalence of ST131. E. coli ST131 was 3.2 (95% CI 2.0 to 5.0) times more pathogenic than non-ST131. For K. pneumoniae ST258 there were not enough data for meta-regression assessing the influence of colonisation versus infection on ST258 prevalence. Conclusions With the currently available data

  15. Flux Balance Analysis of Escherichia coli under Temperature and pH Stress Conditions

    KAUST Repository

    Xu, Xiaopeng

    2015-05-12

    An interesting discovery in biology is that most genes in an organism are dispensable. That means these genes have minor effects on survival of the organism in standard laboratory conditions. One explanation of this discovery is that some genes play important roles in specific conditions and are essential genes under those conditions. E. coli is a model organism, which is widely used. It can adapt to many stress conditions, including temperature, pH, osmotic, antibiotic, etc. Underlying mechanisms and associated genes of each stress condition responses are usually different. In our analysis, we combined protein abundance data and mutant conditional fitness data into E. coli constraint-based metabolic models to study conditionally essential metabolic genes under temperature and pH stress conditions. Flux Balance Analysis was employed as the modeling method to analysis these data. We discovered lists of metabolic genes, which are E. coli dispensable genes, but conditionally essential under some stress conditions. Among these conditionally essential genes, atpA in low pH stress and nhaA in high pH stress found experimental evidences from previous studies. Our study provides new conditionally essential gene candidates for biologists to explore stress condition mechanisms.

  16. Quantitative analysis by computer controlled X-ray fluorescence spectrometer

    International Nuclear Information System (INIS)

    Balasubramanian, T.V.; Angelo, P.C.

    1981-01-01

    X-ray fluorescence spectroscopy has become a widely accepted method in the metallurgical field for analysis of both minor and major elements. As encountered in many other analytical techniques, the problem of matrix effect generally known as the interelemental effects is to be dealt with effectively in order to make the analysis accurate. There are several methods by which the effects of matrix on the analyte are minimised or corrected for and the mathematical correction is one among them. In this method the characteristic secondary X-ray intensities are measured from standard samples and correction coefficients. If any, for interelemental effects are evaluated by mathematical calculations. This paper describes attempts to evaluate the correction coefficients for interelemental effects by multiple linear regression programmes using a computer for the quantitative analysis of stainless steel and a nickel base cast alloy. The quantitative results obtained using this method for a standard stainless steel sample are compared with the given certified values. (author)

  17. Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages.

    Science.gov (United States)

    Cowley, Lauren A; Beckett, Stephen J; Chase-Topping, Margo; Perry, Neil; Dallman, Tim J; Gally, David L; Jenkins, Claire

    2015-04-08

    Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age groups and disease severity. The aim of this study was to analyse the genome sequences of 16 (fourteen T4 and two T7) E. coli O157 typing phages and to determine the genes responsible for the subtle differences in phage type profiles. The typing phages were sequenced using paired-end Illumina sequencing at The Genome Analysis Centre and the Animal Health and Veterinary Laboratories Agency and bioinformatics programs including Velvet, Brig and Easyfig were used to analyse them. A two-way Euclidian cluster analysis highlighted the associations between groups of phage types and typing phages. The analysis showed that the T7 typing phages (9 and 10) differed by only three genes and that the T4 typing phages formed three distinct groups of similar genomic sequences: Group 1 (1, 8, 11, 12 and 15, 16), Group 2 (3, 6, 7 and 13) and Group 3 (2, 4, 5 and 14). The E. coli O157 phage typing scheme exhibited a significantly modular network linked to the genetic similarity of each group showing that these groups are specialised to infect a subset of phage types. Sequencing the typing phage has enabled us to identify the variable genes within each group and to determine how this corresponds to changes in phage type.

  18. Data from quantitative label free proteomics analysis of rat spleen.

    Science.gov (United States)

    Dudekula, Khadar; Le Bihan, Thierry

    2016-09-01

    The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

  19. Accurate quantitative XRD phase analysis of cement clinkers

    International Nuclear Information System (INIS)

    Kern, A.

    2002-01-01

    Full text: Knowledge about the absolute phase abundance in cement clinkers is a requirement for both, research and quality control. Traditionally, quantitative analysis of cement clinkers has been carried out by theoretical normative calculation from chemical analysis using the so-called Bogue method or by optical microscopy. Therefore chemical analysis, mostly performed by X-ray fluorescence (XRF), forms the basis of cement plan control by providing information for proportioning raw materials, adjusting kiln and burning conditions, as well as cement mill feed proportioning. In addition, XRF is of highest importance with respect to the environmentally relevant control of waste recovery raw materials and alternative fuels, as well as filters, plants and sewage. However, the performance of clinkers and cements is governed by the mineralogy and not the elemental composition, and the deficiencies and inherent errors of Bogue as well as microscopic point counting are well known. With XRD and Rietveld analysis a full quantitative analysis of cement clinkers can be performed providing detailed mineralogical information about the product. Until recently several disadvantages prevented the frequent application of the Rietveld method in the cement industry. As the measurement of a full pattern is required, extended measurement times made an integration of this method into existing automation environments difficult. In addition, several drawbacks of existing Rietveld software such as complexity, low performance and severe numerical instability were prohibitive for automated use. The latest developments of on-line instrumentation, as well as dedicated Rietveld software for quantitative phase analysis (TOPAS), now make a decisive breakthrough possible. TOPAS not only allows the analysis of extremely complex phase mixtures in the shortest time possible, but also a fully automated online phase analysis for production control and quality management, free of any human interaction

  20. Functional Analysis of Genes Comprising the Locus of Heat Resistance in Escherichia coli.

    Science.gov (United States)

    Mercer, Ryan; Nguyen, Oanh; Ou, Qixing; McMullen, Lynn; Gänzle, Michael G

    2017-10-15

    The locus of heat resistance (LHR) is a 15- to 19-kb genomic island conferring exceptional heat resistance to organisms in the family Enterobacteriaceae , including pathogenic strains of Salmonella enterica and Escherichia coli The complement of LHR-comprising genes that is necessary for heat resistance and the stress-induced or growth-phase-induced expression of LHR-comprising genes are unknown. This study determined the contribution of the seven LHR-comprising genes yfdX1 GI , yfdX2 , hdeD GI , orf11 , trx GI , kefB , and psiE GI by comparing the heat resistances of E. coli strains harboring plasmid-encoded derivatives of the different LHRs in these genes. (Genes carry a subscript "GI" [genomic island] if an ortholog of the same gene is present in genomes of E. coli ) LHR-encoded heat shock proteins sHSP20, ClpK GI , and sHSP GI are not sufficient for the heat resistance phenotype; YfdX1, YfdX2, and HdeD are necessary to complement the LHR heat shock proteins and to impart a high level of resistance. Deletion of trx GI , kefB , and psiE GI from plasmid-encoded copies of the LHR did not significantly affect heat resistance. The effect of the growth phase and the NaCl concentration on expression from the putative LHR promoter p2 was determined by quantitative reverse transcription-PCR and by a plasmid-encoded p2:GFP promoter fusion. The expression levels of exponential- and stationary-phase E. coli cells were not significantly different, but the addition of 1% NaCl significantly increased LHR expression. Remarkably, LHR expression in E. coli was dependent on a chromosomal copy of evgA In conclusion, this study improved our understanding of the genes required for exceptional heat resistance in E. coli and factors that increase their expression in food. IMPORTANCE The locus of heat resistance (LHR) is a genomic island conferring exceptional heat resistance to several foodborne pathogens. The exceptional level of heat resistance provided by the LHR questions the

  1. Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

    DEFF Research Database (Denmark)

    Jensen, Thomas; Holten-Rossing, Henrik; Svendsen, Ida M H

    2016-01-01

    to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including...... staining may benefit. METHODS: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm......BACKGROUND: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar...

  2. Quantitative high-resolution genomic analysis of single cancer cells.

    Science.gov (United States)

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

    2011-01-01

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

  3. Quantitative high-resolution genomic analysis of single cancer cells.

    Directory of Open Access Journals (Sweden)

    Juliane Hannemann

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

  4. A quantitative analysis of coupled oscillations using mobile accelerometer sensors

    International Nuclear Information System (INIS)

    Castro-Palacio, Juan Carlos; Velázquez-Abad, Luisberis; Giménez, Fernando; Monsoriu, Juan A

    2013-01-01

    In this paper, smartphone acceleration sensors were used to perform a quantitative analysis of mechanical coupled oscillations. Symmetric and asymmetric normal modes were studied separately in the first two experiments. In the third, a coupled oscillation was studied as a combination of the normal modes. Results indicate that acceleration sensors of smartphones, which are very familiar to students, represent valuable measurement instruments for introductory and first-year physics courses. (paper)

  5. A quantitative analysis of coupled oscillations using mobile accelerometer sensors

    Science.gov (United States)

    Castro-Palacio, Juan Carlos; Velázquez-Abad, Luisberis; Giménez, Fernando; Monsoriu, Juan A.

    2013-05-01

    In this paper, smartphone acceleration sensors were used to perform a quantitative analysis of mechanical coupled oscillations. Symmetric and asymmetric normal modes were studied separately in the first two experiments. In the third, a coupled oscillation was studied as a combination of the normal modes. Results indicate that acceleration sensors of smartphones, which are very familiar to students, represent valuable measurement instruments for introductory and first-year physics courses.

  6. Quantitative analysis of the ATV data base, Stage 2

    International Nuclear Information System (INIS)

    Stenquist, C.; Kjellbert, N.A.

    1981-01-01

    A supplementary study of the Swedish ATV data base was carried out. The study was limited to an analysis of the quantitative coverage of component failures from 1979 through 1980. The results indicate that the coverage of component failures is about 75-80 per cent related to the failure reports and work order sheets at the reactor sites together with SKI's ''Safety Related Occurrences''. In general there has been an improvement compared to previous years. (Auth.)

  7. Quantitative analysis of culture using millions of digitized books

    OpenAIRE

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva P.; Veres, Adrian; Gray, Matthew K.; Pickett, Joseph P.; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A.; Aiden, Erez Lieberman

    2010-01-01

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics’, focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pu...

  8. Quantitative Analysis of Culture Using Millions of Digitized Books

    OpenAIRE

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva Presser; Veres, Adrian; Gray, Matthew K.; Google Books Team; Pickett, Joseph; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A.; Aiden, Erez Lieberman

    2011-01-01

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics,’ focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pu...

  9. Quantitative risk analysis of a space shuttle subsystem

    International Nuclear Information System (INIS)

    Frank, M.V.

    1989-01-01

    This paper reports that in an attempt to investigate methods for risk management other than qualitative analysis techniques, NASA has funded pilot study quantitative risk analyses for space shuttle subsystems. The authors performed one such study of two shuttle subsystems with McDonnell Douglas Astronautics Company. The subsystems were the auxiliary power units (APU) on the orbiter, and the hydraulic power units on the solid rocket booster. The technology and results of the APU study are presented in this paper. Drawing from a rich in-flight database as well as from a wealth of tests and analyses, the study quantitatively assessed the risk of APU-initiated scenarios on the shuttle during all phases of a flight mission. Damage states of interest were loss of crew/vehicle, aborted mission, and launch scrub. A quantitative risk analysis approach to deciding on important items for risk management was contrasted with the current NASA failure mode and effects analysis/critical item list approach

  10. The use of quantitative PCR for identification and quantification of Brachyspira pilosicoli, Lawsonia intracellularis and Escherichia coli fimbrial types F4 and F18 in pig feces

    DEFF Research Database (Denmark)

    Ståhl, Marie; Kokotovic, Branko; Hjulsager, Charlotte Kristiane

    2011-01-01

    Four quantitative PCR (qPCR) assays were evaluated for quantitative detection of Brachyspira pilosicoli, Lawsonia intracellularis, and E. coli fimbrial types F4 and F18 in pig feces. Standard curves were based on feces spiked with the respective reference strains. The detection limits from...... the spiking experiments were 102 bacteria/g feces for BpiloqPCR and Laws-qPCR, 103 CFU/g feces for F4-qPCR and F18-qPCR. The PCR efficiency for all four qPCR assays was between 0.91 and 1.01 with R2 above 0.993. Standard curves, slopes and elevation, varied between assays and between measurements from pure...... DNA from reference strains and feces spiked with the respective strains. The linear ranges found for spiked fecal samples differed both from the linear ranges from pure culture of the reference strains and between the qPCR tests. The linear ranges were five log units for F4- qPCR, and Laws-qPCR, six...

  11. Analysis of early-onset bloodstream infection due to Escherichia coli infection in premature babies

    OpenAIRE

    Chen, I-Lun; Huang, Hsin-Chun; Wu, Chih-Te; Ou-Yang, Mei-Chen; Chung, Mei-Yung; Chen, Chih-Cheng; Suen, Jau-Ling; Hung, Chih-Hsing

    2017-01-01

    Abstract In early-onset bacteremia among preterm neonates, Escherichia coli (E. coli) is the main pathogen and can cause a high mortality rate. Thus, the predictive factors of mortality and extended-spectrum ?-lactamase (ESBL)-producing E. coli in preterm babies with E. coli early-onset bacteremia were reported. We retrospectively reviewed preterm neonates who had E. coli bacteremia occurring within 3 days after birth between 2004 and 2015. Maternal and perinatal information were collected fr...

  12. MraZ from Escherichia coli: cloning, purification, crystallization and preliminary X-ray analysis

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Melanie A.; Udell, Christian M.; Pal, Gour Pada; Jia, Zongchao, E-mail: jia@post.queensu.ca [Department of Biochemistry, Queen’s University, Kingston, Ontario K7L 3N6 (Canada)

    2005-04-01

    The crystallization and preliminary X-ray diffraction analysis of MraZ, formerly known as hypothetical protein YabB, from Escherichia coli K-12 is presented. The MraZ family of proteins, also referred to as the UPF0040 family, are highly conserved in bacteria and are thought to play a role in cell-wall biosynthesis and cell division. The murein region A (mra) gene cluster encodes MraZ proteins along with a number of other proteins involved in this complex process. To date, there has been no clear functional assignment provided for MraZ proteins and the structure of a homologue from Mycoplasma pneumoniae, MPN314, failed to suggest a molecular function. The b0081 gene from Escherichia coli that encodes the MraZ protein was cloned and the protein was overexpressed, purified and crystallized. This data is presented along with evidence that the E. coli homologue exists in a different oligomeric state to the MPN314 protein.

  13. MraZ from Escherichia coli: cloning, purification, crystallization and preliminary X-ray analysis

    International Nuclear Information System (INIS)

    Adams, Melanie A.; Udell, Christian M.; Pal, Gour Pada; Jia, Zongchao

    2005-01-01

    The crystallization and preliminary X-ray diffraction analysis of MraZ, formerly known as hypothetical protein YabB, from Escherichia coli K-12 is presented. The MraZ family of proteins, also referred to as the UPF0040 family, are highly conserved in bacteria and are thought to play a role in cell-wall biosynthesis and cell division. The murein region A (mra) gene cluster encodes MraZ proteins along with a number of other proteins involved in this complex process. To date, there has been no clear functional assignment provided for MraZ proteins and the structure of a homologue from Mycoplasma pneumoniae, MPN314, failed to suggest a molecular function. The b0081 gene from Escherichia coli that encodes the MraZ protein was cloned and the protein was overexpressed, purified and crystallized. This data is presented along with evidence that the E. coli homologue exists in a different oligomeric state to the MPN314 protein

  14. Comparative sequence analysis of acid sensitive/resistance proteins in Escherichia coli and Shigella flexneri

    Science.gov (United States)

    Manikandan, Selvaraj; Balaji, Seetharaaman; Kumar, Anil; Kumar, Rita

    2007-01-01

    The molecular basis for the survival of bacteria under extreme conditions in which growth is inhibited is a question of great current interest. A preliminary study was carried out to determine residue pattern conservation among the antiporters of enteric bacteria, responsible for extreme acid sensitivity especially in Escherichia coli and Shigella flexneri. Here we found the molecular evidence that proved the relationship between E. coli and S. flexneri. Multiple sequence alignment of the gadC coded acid sensitive antiporter showed many conserved residue patterns at regular intervals at the N-terminal region. It was observed that as the alignment approaches towards the C-terminal, the number of conserved residues decreases, indicating that the N-terminal region of this protein has much active role when compared to the carboxyl terminal. The motif, FHLVFFLLLGG, is well conserved within the entire gadC coded protein at the amino terminal. The motif is also partially conserved among other antiporters (which are not coded by gadC) but involved in acid sensitive/resistance mechanism. Phylogenetic cluster analysis proves the relationship of Escherichia coli and Shigella flexneri. The gadC coded proteins are converged as a clade and diverged from other antiporters belongs to the amino acid-polyamine-organocation (APC) superfamily. PMID:21670792

  15. Flux balance analysis of ammonia assimilation network in E. coli predicts preferred regulation point.

    Science.gov (United States)

    Wang, Lu; Lai, Luhua; Ouyang, Qi; Tang, Chao

    2011-01-25

    Nitrogen assimilation is a critical biological process for the synthesis of biomolecules in Escherichia coli. The central ammonium assimilation network in E. coli converts carbon skeleton α-ketoglutarate and ammonium into glutamate and glutamine, which further serve as nitrogen donors for nitrogen metabolism in the cell. This reaction network involves three enzymes: glutamate dehydrogenase (GDH), glutamine synthetase (GS) and glutamate synthase (GOGAT). In minimal media, E. coli tries to maintain an optimal growth rate by regulating the activity of the enzymes to match the availability of the external ammonia. The molecular mechanism and the strategy of the regulation in this network have been the research topics for many investigators. In this paper, we develop a flux balance model for the nitrogen metabolism, taking into account of the cellular composition and biosynthetic requirements for nitrogen. The model agrees well with known experimental results. Specifically, it reproduces all the (15)N isotope labeling experiments in the wild type and the two mutant (ΔGDH and ΔGOGAT) strains of E. coli. Furthermore, the predicted catalytic activities of GDH, GS and GOGAT in different ammonium concentrations and growth rates for the wild type, ΔGDH and ΔGOGAT strains agree well with the enzyme concentrations obtained from western blots. Based on this flux balance model, we show that GS is the preferred regulation point among the three enzymes in the nitrogen assimilation network. Our analysis reveals the pattern of regulation in this central and highly regulated network, thus providing insights into the regulation strategy adopted by the bacteria. Our model and methods may also be useful in future investigations in this and other networks.

  16. Transcriptomic analysis displays the effect of (-)-roemerine on the motility and nutrient uptake in Escherichia coli.

    Science.gov (United States)

    Ayyildiz, Dilara; Arga, Kazim Yalcin; Avci, Fatma Gizem; Altinisik, Fatma Ece; Gurer, Caglayan; Gulsoy Toplan, Gizem; Kazan, Dilek; Wozny, Katharina; Brügger, Britta; Mertoglu, Bulent; Sariyar Akbulut, Berna

    2017-08-01

    Among the different families of plant alkaloids, (-)-roemerine, an aporphine type, was recently shown to possess significant antibacterial activity in Escherichia coli. Based on the increasing demand for antibacterials with novel mechanisms of action, the present work investigates the potential of the plant-derived alkaloid (-)-roemerine as an antibacterial in E. coli cells using microarray technology. Analysis of the genome-wide transcriptional reprogramming in cells after 60 min treatment with 100 μg/mL (-)-roemerine showed significant changes in the expression of 241 genes (p value 2). Expression of selected genes was confirmed by qPCR. Differentially expressed genes were classified into functional categories to map biological processes and molecular pathways involved. Cellular activities with roles in carbohydrate transport and metabolism, energy production and conversion, lipid transport and metabolism, amino acid transport and metabolism, two-component signaling systems, and cell motility (in particular, the flagellar organization and motility) were among metabolic processes altered in the presence of (-)-roemerine. The down-regulation of the outer membrane proteins probably led to a decrease in carbohydrate uptake rate, which in turn results in nutrient limitation. Consequently, energy metabolism is slowed down. Interestingly, the majority of the expressional alterations were found in the flagellar system. This suggested reduction in motility and loss in the ability to form biofilms, thus affecting protection of E. coli against host cell defense mechanisms. In summary, our findings suggest that the antimicrobial action of (-)-roemerine in E. coli is linked to disturbances in motility and nutrient uptake.

  17. Flux balance analysis of ammonia assimilation network in E. coli predicts preferred regulation point.

    Directory of Open Access Journals (Sweden)

    Lu Wang

    Full Text Available Nitrogen assimilation is a critical biological process for the synthesis of biomolecules in Escherichia coli. The central ammonium assimilation network in E. coli converts carbon skeleton α-ketoglutarate and ammonium into glutamate and glutamine, which further serve as nitrogen donors for nitrogen metabolism in the cell. This reaction network involves three enzymes: glutamate dehydrogenase (GDH, glutamine synthetase (GS and glutamate synthase (GOGAT. In minimal media, E. coli tries to maintain an optimal growth rate by regulating the activity of the enzymes to match the availability of the external ammonia. The molecular mechanism and the strategy of the regulation in this network have been the research topics for many investigators. In this paper, we develop a flux balance model for the nitrogen metabolism, taking into account of the cellular composition and biosynthetic requirements for nitrogen. The model agrees well with known experimental results. Specifically, it reproduces all the (15N isotope labeling experiments in the wild type and the two mutant (ΔGDH and ΔGOGAT strains of E. coli. Furthermore, the predicted catalytic activities of GDH, GS and GOGAT in different ammonium concentrations and growth rates for the wild type, ΔGDH and ΔGOGAT strains agree well with the enzyme concentrations obtained from western blots. Based on this flux balance model, we show that GS is the preferred regulation point among the three enzymes in the nitrogen assimilation network. Our analysis reveals the pattern of regulation in this central and highly regulated network, thus providing insights into the regulation strategy adopted by the bacteria. Our model and methods may also be useful in future investigations in this and other networks.

  18. Ratio of slopes method for quantitative analysis in ceramic bodies

    International Nuclear Information System (INIS)

    Zainal Arifin Ahmad; Ahmad Fauzi Mohd Noor; Radzali Othman; Messer, P.F.

    1996-01-01

    A quantitative x-ray diffraction analysis technique developed at University of Sheffield was adopted, rather than the previously widely used internal standard method, to determine the amount of the phases present in a reformulated whiteware porcelain and a BaTiO sub 3 electrochemical material. This method, although still employs an internal standard, was found to be very easy and accurate. The required weight fraction of a phase in the mixture to be analysed is determined from the ratio of slopes of two linear plots, designated as the analysis and reference lines, passing through their origins using the least squares method

  19. QUANTITATIVE ANALYSIS OF FLUX REGULATION THROUGH HIERARCHICAL REGULATION ANALYSIS

    NARCIS (Netherlands)

    van Eunen, Karen; Rossell, Sergio; Bouwman, Jildau; Westerhoff, Hans V.; Bakker, Barbara M.; Jameson, D; Verma, M; Westerhoff, HV

    2011-01-01

    Regulation analysis is a methodology that quantifies to what extent a change in the flux through a metabolic pathway is regulated by either gene expression or metabolism. Two extensions to regulation analysis were developed over the past years: (i) the regulation of V(max) can be dissected into the

  20. Quantitative analysis of flux regulation through hierarchical regulation analysis

    NARCIS (Netherlands)

    Eunen, K. van; Rossell, S.; Bouwman, J.; Westerhoff, H.V.; Bakker, B.M.

    2011-01-01

    Regulation analysis is a methodology that quantifies to what extent a change in the flux through a metabolic pathway is regulated by either gene expression or metabolism. Two extensions to regulation analysis were developed over the past years: (i) the regulation of Vmax can be dissected into the

  1. Novel approach in quantitative analysis of shearography method

    International Nuclear Information System (INIS)

    Wan Saffiey Wan Abdullah

    2002-01-01

    The application of laser interferometry in industrial non-destructive testing and material characterization is becoming more prevalent since this method provides non-contact full-field inspection of the test object. However their application only limited to the qualitative analysis, current trend has changed to the development of this method by the introduction of quantitative analysis, which attempts to detail the defect examined. This being the design feature for a ranges of object size to be examined. The growing commercial demand for quantitative analysis for NDT and material characterization is determining the quality of optical and analysis instrument. However very little attention is currently being paid to understanding, quantifying and compensating for the numerous error sources which are a function of interferometers. This paper presents a comparison of measurement analysis using the established theoretical approach and the new approach, taken into account the factor of divergence illumination and other geometrical factors. The difference in the measurement system could be associated in the error factor. (Author)

  2. Quantitative subsurface analysis using frequency modulated thermal wave imaging

    Science.gov (United States)

    Subhani, S. K.; Suresh, B.; Ghali, V. S.

    2018-01-01

    Quantitative depth analysis of the anomaly with an enhanced depth resolution is a challenging task towards the estimation of depth of the subsurface anomaly using thermography. Frequency modulated thermal wave imaging introduced earlier provides a complete depth scanning of the object by stimulating it with a suitable band of frequencies and further analyzing the subsequent thermal response using a suitable post processing approach to resolve subsurface details. But conventional Fourier transform based methods used for post processing unscramble the frequencies with a limited frequency resolution and contribute for a finite depth resolution. Spectral zooming provided by chirp z transform facilitates enhanced frequency resolution which can further improves the depth resolution to axially explore finest subsurface features. Quantitative depth analysis with this augmented depth resolution is proposed to provide a closest estimate to the actual depth of subsurface anomaly. This manuscript experimentally validates this enhanced depth resolution using non stationary thermal wave imaging and offers an ever first and unique solution for quantitative depth estimation in frequency modulated thermal wave imaging.

  3. Quantitative analysis of patient-specific dosimetric IMRT verification

    International Nuclear Information System (INIS)

    Budgell, G J; Perrin, B A; Mott, J H L; Fairfoul, J; Mackay, R I

    2005-01-01

    Patient-specific dosimetric verification methods for IMRT treatments are variable, time-consuming and frequently qualitative, preventing evidence-based reduction in the amount of verification performed. This paper addresses some of these issues by applying a quantitative analysis parameter to the dosimetric verification procedure. Film measurements in different planes were acquired for a series of ten IMRT prostate patients, analysed using the quantitative parameter, and compared to determine the most suitable verification plane. Film and ion chamber verification results for 61 patients were analysed to determine long-term accuracy, reproducibility and stability of the planning and delivery system. The reproducibility of the measurement and analysis system was also studied. The results show that verification results are strongly dependent on the plane chosen, with the coronal plane particularly insensitive to delivery error. Unexpectedly, no correlation could be found between the levels of error in different verification planes. Longer term verification results showed consistent patterns which suggest that the amount of patient-specific verification can be safely reduced, provided proper caution is exercised: an evidence-based model for such reduction is proposed. It is concluded that dose/distance to agreement (e.g., 3%/3 mm) should be used as a criterion of acceptability. Quantitative parameters calculated for a given criterion of acceptability should be adopted in conjunction with displays that show where discrepancies occur. Planning and delivery systems which cannot meet the required standards of accuracy, reproducibility and stability to reduce verification will not be accepted by the radiotherapy community

  4. Multivariate analysis of quantitative traits can effectively classify rapeseed germplasm

    Directory of Open Access Journals (Sweden)

    Jankulovska Mirjana

    2014-01-01

    Full Text Available In this study, the use of different multivariate approaches to classify rapeseed genotypes based on quantitative traits has been presented. Tree regression analysis, PCA analysis and two-way cluster analysis were applied in order todescribe and understand the extent of genetic variability in spring rapeseed genotype by trait data. The traits which highly influenced seed and oil yield in rapeseed were successfully identified by the tree regression analysis. Principal predictor for both response variables was number of pods per plant (NP. NP and 1000 seed weight could help in the selection of high yielding genotypes. High values for both traits and oil content could lead to high oil yielding genotypes. These traits may serve as indirect selection criteria and can lead to improvement of seed and oil yield in rapeseed. Quantitative traits that explained most of the variability in the studied germplasm were classified using principal component analysis. In this data set, five PCs were identified, out of which the first three PCs explained 63% of the total variance. It helped in facilitating the choice of variables based on which the genotypes’ clustering could be performed. The two-way cluster analysissimultaneously clustered genotypes and quantitative traits. The final number of clusters was determined using bootstrapping technique. This approach provided clear overview on the variability of the analyzed genotypes. The genotypes that have similar performance regarding the traits included in this study can be easily detected on the heatmap. Genotypes grouped in the clusters 1 and 8 had high values for seed and oil yield, and relatively short vegetative growth duration period and those in cluster 9, combined moderate to low values for vegetative growth duration and moderate to high seed and oil yield. These genotypes should be further exploited and implemented in the rapeseed breeding program. The combined application of these multivariate methods

  5. Quantitative microbial risk assessment for Escherichia coli O157 on lettuce, based on survival data from controlled studies in a climate chamber.

    Science.gov (United States)

    Ottoson, Jakob R; Nyberg, Karin; Lindqvist, Roland; Albihn, Ann

    2011-12-01

    The aims of the study were to determine the survival of Escherichia coli O157 on lettuce as a function of temperature and light intensity, and to use that information in a screening-level quantitative microbial risk assessment (QMRA) in order to evaluate risk-reducing strategies including irrigation water quality guidelines, rinsing, and holding time between last irrigation and harvest. Iceberg lettuce was grown in a climate chamber and inoculated with E. coli O157. Bacterial numbers were determined with the standard plate count method after inoculation and 1, 2, 4, and 7 day(s) postinoculation. The experiments were carried out at 11, 18, and 25°C in light intensities of 0, 400, and 600 mmol (m(2))(-1) s(-1). There was a significant effect of temperature and light intensity on survival, with less bacteria isolated from lettuce incubated at 25 and 18°C compared with 11°C (P < 0.0001), and in light intensities of 400 and 600 mmol (m(2))(-1) s(-1) compared with 0 mmol (m(2))(-1) s(-1) (P < 0.001). The average log reductions after 1, 2, 4, and 7 day(s) were 1.14, 1.71, 2.04, and 3.0, respectively. The QMRA compared the relative risk with lettuce consumption from 20 scenarios. A stricter water quality guideline gave a mean fivefold risk reduction. Holding times of 1, 2, 4, and 7 day(s) reduced the risk 3, 8, 8, and 18 times, respectively, compared with harvest the same day as the last irrigation. Finally, rinsing lettuce for 15 s in cold tap water prior to consumption gave a sixfold risk reduction compared with eating unrinsed lettuce. Sensitivity analyses indicated that variation in bacterial inactivation had the most significant effect on the risk outcome. A QMRA determining the relative risks between scenarios reduces uncertainty and can provide risk managers with decision support.

  6. Quantitative analysis of microtubule orientation in interdigitated leaf pavement cells.

    Science.gov (United States)

    Akita, Kae; Higaki, Takumi; Kutsuna, Natsumaro; Hasezawa, Seiichiro

    2015-01-01

    Leaf pavement cells are shaped like a jigsaw puzzle in most dicotyledon species. Molecular genetic studies have identified several genes required for pavement cells morphogenesis and proposed that microtubules play crucial roles in the interdigitation of pavement cells. In this study, we performed quantitative analysis of cortical microtubule orientation in leaf pavement cells in Arabidopsis thaliana. We captured confocal images of cortical microtubules in cotyledon leaf epidermis expressing GFP-tubulinβ and quantitatively evaluated the microtubule orientations relative to the pavement cell growth axis using original image processing techniques. Our results showed that microtubules kept parallel orientations to the growth axis during pavement cell growth. In addition, we showed that immersion treatment of seed cotyledons in solutions containing tubulin polymerization and depolymerization inhibitors decreased pavement cell complexity. Treatment with oryzalin and colchicine inhibited the symmetric division of guard mother cells.

  7. Risk prediction, safety analysis and quantitative probability methods - a caveat

    International Nuclear Information System (INIS)

    Critchley, O.H.

    1976-01-01

    Views are expressed on the use of quantitative techniques for the determination of value judgements in nuclear safety assessments, hazard evaluation, and risk prediction. Caution is urged when attempts are made to quantify value judgements in the field of nuclear safety. Criteria are given the meaningful application of reliability methods but doubts are expressed about their application to safety analysis, risk prediction and design guidances for experimental or prototype plant. Doubts are also expressed about some concomitant methods of population dose evaluation. The complexities of new designs of nuclear power plants make the problem of safety assessment more difficult but some possible approaches are suggested as alternatives to the quantitative techniques criticized. (U.K.)

  8. Quantitative analysis of macro-ARG using IP system

    International Nuclear Information System (INIS)

    Nakajima, Eiichi; Kawai, Kenji; Furuta, Yoshitake

    1997-01-01

    Recent progress in imaging plate (IP) system allow us to analyze autoradiographic images quantitatively. In the 'whole-body autoradiography', a method clarify the distribution of radioisotope or labeled compounds in the tissues and organs in a freeze-dried whole-body section of small animals such as rats and mice, the sections are pressed against a IP for exposure and the IP is scanned by Bio-Imaging Analyzer (Fuji Photo Film Co., Ltd) and a digital autoradiographic image is given. Quantitative data concerning the activity in different tissues can be obtained using an isotope scale as a reference source. Fading effect, application of IP system for distribution of receptor binding ARG, analysis of radio-spots on TLC and radioactive concentration in liquid such as blood are also discussed. (author)

  9. What Really Happens in Quantitative Group Research? Results of a Content Analysis of Recent Quantitative Research in "JSGW"

    Science.gov (United States)

    Boyle, Lauren H.; Whittaker, Tiffany A.; Eyal, Maytal; McCarthy, Christopher J.

    2017-01-01

    The authors conducted a content analysis on quantitative studies published in "The Journal for Specialists in Group Work" ("JSGW") between 2012 and 2015. This brief report provides a general overview of the current practices of quantitative group research in counseling. The following study characteristics are reported and…

  10. Scientific aspects of urolithiasis: quantitative stone analysis and crystallization experiments

    International Nuclear Information System (INIS)

    Wandt, M.A.E.

    1986-03-01

    The theory, development and results of three quantitative analytical procedures are described and the crystallization experiments in a rotary evaporator are presented. Of the different methods of quantitative X-ray powder diffraction analyses, the 'internal standard method' and a microanalytical technique were identified as the two most useful procedures for the quantitative analysis of urinary calculi. 'Reference intensity ratios' for 6 major stone phases were determined and were used in the analysis of 20 calculi by the 'internal standard method'. Inductively coupled plasma atomic emission spectroscopic (ICP-AES) methods were also investigated, developed and used in this study. Various procedures for the digestion of calculi were tested and a mixture of HNO 3 and HC1O 4 was eventually found to be the most successful. The major elements Ca, Mg, and P in 41 calculi were determined. For the determination of trace elements, a new microwave-assisted digestion procedure was developed and used for the digestion of 100 calculi. Fluoride concentrations in two stone collections were determined using a fluoride-ion sensitive electrode and the HNO 3 /HC1O 4 digestion prodecure used for the ICP study. A series of crystallization experiments involving a standard reference artificial urine was carried out in a rotary evaporator. The effect of pH and urine composition was studied by varying the former and by including uric acid, urea, creatinine, MgO, methylene blue, chondroitin sulphate A, and fluoride in the reference solution. Crystals formed in these experiments were subjected to qualitative and semi-quantitative X-ray powder diffraction analyses. Scanning electron microscopy of several deposits was also carried out. Similar deposits to those observed in calculi were obtained with the fast evaporator. The results presented suggest that this system provides a simple, yet very useful means for studying the crystallization characteristics of urine solutions

  11. Quantitative risk analysis as a basis for emergency planning

    Energy Technology Data Exchange (ETDEWEB)

    Yogui, Regiane Tiemi Teruya [Bureau Veritas do Brasil, Rio de Janeiro, RJ (Brazil); Macedo, Eduardo Soares de [Instituto de Pesquisas Tecnologicas (IPT), Sao Paulo, SP (Brazil)

    2009-07-01

    Several environmental accidents happened in Brazil and in the world during the 70's and 80's. This strongly motivated the preparation for emergencies in the chemical and petrochemical industries. Environmental accidents affect the environment and the communities that are neighbor to the industrial facilities. The present study aims at subsidizing and providing orientation to develop Emergency Planning from the data obtained on Quantitative Risk Analysis, elaborated according to the Technical Standard P4.261/03 from CETESB (Sao Paulo Environmental Agency). It was observed, during the development of the research, that the data generated on these studies need a complementation and a deeper analysis, so that it is possible to use them on the Emergency Plans. The main issues that were analyzed and discussed on this study were the reevaluation of hazard identification for the emergency plans, the consequences and vulnerability analysis for the response planning, the risk communication, and the preparation to respond to the emergencies of the communities exposed to manageable risks. As a result, the study intends to improve the interpretation and use of the data deriving from the Quantitative Risk Analysis to develop the emergency plans. (author)

  12. Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli.

    Science.gov (United States)

    Hasanpour, Mojtaba; Najafi, Akram

    2017-06-01

    Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (T m ) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Fluorescent foci quantitation for high-throughput analysis

    Directory of Open Access Journals (Sweden)

    Elena Ledesma-Fernández

    2015-06-01

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

  14. Quantitative x-ray fractographic analysis of fatigue fractures

    International Nuclear Information System (INIS)

    Saprykin, Yu.V.

    1983-01-01

    The study deals with quantitative X-ray fractographic investigation of fatigue fractures of samples with sharp notches tested at various stresses and temperatures with the purpose of establishing a connection between material crack resistance parameters and local plastic instability zones restraining and controlling the crack growth. At fatigue fractures of notched Kh18N9T steel samples tested at +20 and -196 deg C a zone of sharp ring notch effect being analogous to the zone in which crack growth rate is controlled by the microshifting mechanisms is singled out. The size of the notched effect zone in the investigate steel is unambiguosly bound to to the stress amplitude. This provides the possibility to determine the stress value by the results of quantitative fractographic analysis of notched sample fractures. A possibility of determining one of the threshold values of cyclic material fracture toughness by the results of fatigue testing and fractography of notched sample fractures is shown. Correlation between the size of the hsub(s) crack effect zone in the notched sample, delta material yield limit and characteristic of cyclic Ksub(s) fracture toughness has been found. Such correlation widens the possibilities of quantitative diagnostics of fractures by the methods of X-ray fractography

  15. High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis

    DEFF Research Database (Denmark)

    Williamson, James C; Edwards, Alistair V G; Verano-Braga, Thiago

    2016-01-01

    We present basic workups and quantitative comparisons for two current generation Orbitrap mass spectrometers, the Q Exactive Plus and Orbitrap Fusion Tribrid, which are widely considered two of the highest performing instruments on the market. We assessed the performance of two quantitative methods...... on both instruments, namely label-free quantitation and stable isotope labeling using isobaric tags, for studying the heat shock response in Escherichia coli. We investigated the recently reported MS3 method on the Fusion instrument and the potential of MS3-based reporter ion isolation Synchronous...... Precursor Selection (SPS) and its impact on quantitative accuracy. We confirm that the label-free approach offers a more linear response with a wider dynamic range than MS/MS-based isobaric tag quantitation and that the MS3/SPS approach alleviates but does not eliminate dynamic range compression. We...

  16. The cost of electricity distribution in Italy: a quantitative analysis

    International Nuclear Information System (INIS)

    Scarpa, C.

    1998-01-01

    This paper presents a quantitative analysis of the cost of medium and low tension electricity distribution in Italy. An econometric analysis of the cost function is proposed, on the basis of data on 147 zones of the dominant firm, ENEL. Data are available only for 1996, which has forced to carry out only a cross-section OLS analysis. The econometric estimate shows the existence of significant scale economies, that the current organisational structure does not exploit. On this basis is also possible to control to what extent exogenous cost drivers affect costs. The role of numerous exogenous factors considered seems however quite limited. The area of the distribution zone and an indicator of quality are the only elements that appear significant from an economic viewpoint [it

  17. Quantitative multiphase analysis of archaeological bronzes by neutron diffraction

    CERN Document Server

    Siano, S; Celli, M; Pini, R; Salimbeni, R; Zoppi, M; Kockelmann, W A; Iozzo, M; Miccio, M; Moze, O

    2002-01-01

    In this paper, we report the first investigation on the potentials of neutron diffraction to characterize archaeological bronze artifacts. The preliminary feasibility of phase and structural analysis was demonstrated on standardised specimens with a typical bronze alloy composition. These were realised through different hardening and annealing cycles, simulating possible ancient working techniques. The Bragg peak widths that resulted were strictly dependent on the working treatment, thus providing an important analytical element to investigate ancient making techniques. The diagnostic criteria developed on the standardised specimens were then applied to study two Etruscan museum pieces. Quantitative multiphase analysis by Rietveld refinement of the diffraction patterns was successfully demonstrated. Furthermore, the analysis of patterns associated with different artifact elements also yielded evidence for some peculiar perspective of the neutron diffraction diagnostics in archeometric applications. (orig.)

  18. Quantitative surface analysis using deuteron-induced nuclear reactions

    International Nuclear Information System (INIS)

    Afarideh, Hossein

    1991-01-01

    The nuclear reaction analysis (NRA) technique consists of looking at the energies of the reaction products which uniquely define the particular elements present in the sample and it analysis the yield/energy distribution to reveal depth profiles. A summary of the basic features of the nuclear reaction analysis technique is given, in particular emphasis is placed on quantitative light element determination using (d,p) and (d,alpha) reactions. The experimental apparatus is also described. Finally a set of (d,p) spectra for the elements Z=3 to Z=17 using 2 MeV incident deutrons is included together with example of more applications of the (d,alpha) spectra. (author)

  19. Program for the quantitative and qualitative analysis of

    International Nuclear Information System (INIS)

    Tepelea, V.; Purice, E.; Dan, R.; Calcev, G.; Domnisan, M.; Galis, V.; Teodosiu, G.; Debert, C.; Mocanu, N.; Nastase, M.

    1985-01-01

    A computer code for processing of data from neutron activation analysis is described. The code is capable of qualitative and quantitative analysis of regular spectra from neutron irradiated samples, measured by a Ge(li) detector. Multichannel analysers with 1024 channels, such as TN 1705 or a Romanian made MCA 79, and an ITC interface can be used. The code is implemented on FELIX M118 and FELIX M216 microcomputers. Spectrum processing is performed off line, after storing the data on a floppy disk. The background is assumed to be a polynomial of first, second or third degree. Qualitative analysis is performed by recursive least square, Gaussian curve fitting. The elements are identified using a polynomial relation between energy and channel, obtained by calibration with a standard sample

  20. Quantitative analysis of light elements in aerosol samples by PIGE

    International Nuclear Information System (INIS)

    Mateus, R.; Reis, M.A.; Jesus, A.P.; Ribeiro, J.P.

    2006-01-01

    Quantitative PIGE analysis of aerosol samples collected on nuclepore polycarbonate filters was performed by a method that avoids the use of comparative standards. Nuclear cross sections and calibration parameters established before in an extensive work on thick and intermediate samples were employed. For these samples, the excitation functions of nuclear reactions, induced by the incident protons on target's light elements, were used as input for a code that evaluates the gamma-ray yield integrating along the depth of the sample. In the present work we apply the same code to validate the use of an effective energy for thin sample analysis. Results pertaining to boron, fluorine and sodium concentrations are presented. In order to establish a correlation with sodium values, PIXE results related to chlorine are also presented, giving support to the reliability of this PIGE method for thin film analysis

  1. Some selected quantitative methods of thermal image analysis in Matlab.

    Science.gov (United States)

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

    Science.gov (United States)

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

  3. Quantitative analysis method for niobium in lead zirconate titanate

    International Nuclear Information System (INIS)

    Hara, Hideo; Hashimoto, Toshio

    1986-01-01

    Lead zirconate titanate (PZT) is a strong dielectric ceramic having piezoelectric and pyroelectric properties, and is used most as a piezoelectric material. Also it is a main component of lead lanthanum zirconate titanate (PLZT), which is a typical electrical-optical conversion element. Since these have been developed, the various electronic parts utilizing the piezoelectric characteristics have been put in practical use. The characteristics can be set up by changing the composition of PZT and the kinds and amount of additives. Among the additives, niobium has the action to make metallic ion vacancy in crystals, and by the formation of this vacancy, to ease the movement of domain walls in crystal grains, and to increase resistivity. Accordingly, it is necessary to accurately determine the niobium content for the research and development, quality control and process control. The quantitative analysis methods for niobium used so far have respective demerits, therefore, the authors examined the quantitative analysis of niobium in PZT by using an inductively coupled plasma emission spectro-analysis apparatus which has remarkably developed recently. As the result, the method of dissolving a specimen with hydrochloric acid and hydrofluoric acid, and masking unstable lead with ethylene diamine tetraacetic acid 2 sodium and fluoride ions with boric acid was established. The apparatus, reagents, the experiment and the results are reported. (Kako, I.)

  4. Correlative SEM SERS for quantitative analysis of dimer nanoparticles.

    Science.gov (United States)

    Timmermans, F J; Lenferink, A T M; van Wolferen, H A G M; Otto, C

    2016-11-14

    A Raman microscope integrated with a scanning electron microscope was used to investigate plasmonic structures by correlative SEM-SERS analysis. The integrated Raman-SEM microscope combines high-resolution electron microscopy information with SERS signal enhancement from selected nanostructures with adsorbed Raman reporter molecules. Correlative analysis is performed for dimers of two gold nanospheres. Dimers were selected on the basis of SEM images from multi aggregate samples. The effect of the orientation of the dimer with respect to the polarization state of the laser light and the effect of the particle gap size on the Raman signal intensity is observed. Additionally, calculations are performed to simulate the electric near field enhancement. These simulations are based on the morphologies observed by electron microscopy. In this way the experiments are compared with the enhancement factor calculated with near field simulations and are subsequently used to quantify the SERS enhancement factor. Large differences between experimentally observed and calculated enhancement factors are regularly detected, a phenomenon caused by nanoscale differences between the real and 'simplified' simulated structures. Quantitative SERS experiments reveal the structure induced enhancement factor, ranging from ∼200 to ∼20 000, averaged over the full nanostructure surface. The results demonstrate correlative Raman-SEM microscopy for the quantitative analysis of plasmonic particles and structures, thus enabling a new analytical method in the field of SERS and plasmonics.

  5. Quantitative imaging analysis of posterior fossa ependymoma location in children.

    Science.gov (United States)

    Sabin, Noah D; Merchant, Thomas E; Li, Xingyu; Li, Yimei; Klimo, Paul; Boop, Frederick A; Ellison, David W; Ogg, Robert J

    2016-08-01

    Imaging descriptions of posterior fossa ependymoma in children have focused on magnetic resonance imaging (MRI) signal and local anatomic relationships with imaging location only recently used to classify these neoplasms. We developed a quantitative method for analyzing the location of ependymoma in the posterior fossa, tested its effectiveness in distinguishing groups of tumors, and examined potential associations of distinct tumor groups with treatment and prognostic factors. Pre-operative MRI examinations of the brain for 38 children with histopathologically proven posterior fossa ependymoma were analyzed. Tumor margin contours and anatomic landmarks were manually marked and used to calculate the centroid of each tumor. Landmarks were used to calculate a transformation to align, scale, and rotate each patient's image coordinates to a common coordinate space. Hierarchical cluster analysis of the location and morphological variables was performed to detect multivariate patterns in tumor characteristics. The ependymomas were also characterized as "central" or "lateral" based on published radiological criteria. Therapeutic details and demographic, recurrence, and survival information were obtained from medical records and analyzed with the tumor location and morphology to identify prognostic tumor characteristics. Cluster analysis yielded two distinct tumor groups based on centroid location The cluster groups were associated with differences in PFS (p = .044), "central" vs. "lateral" radiological designation (p = .035), and marginally associated with multiple operative interventions (p = .064). Posterior fossa ependymoma can be objectively classified based on quantitative analysis of tumor location, and these classifications are associated with prognostic and treatment factors.

  6. Application of harmonic analysis in quantitative heart scintigraphy

    International Nuclear Information System (INIS)

    Fischer, P.; Knopp, R.; Breuel, H.P.

    1979-01-01

    Quantitative scintigraphy of the heart after equilibrium distribution of a radioactive tracer permits the measurement of time activity curves in the left ventricle during a representative heart cycle with great statistical accuracy. By application of Fourier's analysis, criteria are to be attained in addition for evaluation of the volume curve as a whole. Thus the entire information contained in the volume curve is completely described in a Fourier spectrum. Resynthesis after Fourier transformation seems to be an ideal method of smoothing because of its convergence in the minimum quadratic error for the type of function concerned. (orig./MG) [de

  7. Quantitative analysis of tritium distribution in austenitic stainless steels welds

    International Nuclear Information System (INIS)

    Roustila, A.; Kuromoto, N.; Brass, A.M.; Chene, J.

    1994-01-01

    Tritium autoradiography was used to study the tritium distribution in laser and arc (TIG) weldments performed on tritiated AISI 316 samples. Quantitative values of the local tritium concentration were obtained from the microdensitometric analysis of the autoradiographs. This procedure was used to map the tritium concentration in the samples before and after laser and TIG treatments. The effect of the detritiation conditions and of welding on the tritium distribution in the material is extensively characterized. The results illustrate the interest of the technique for predicting a possible embrittlement of the material associated with a local enhancement of the tritium concentration and the presence of helium 3 generated by tritium decay. ((orig.))

  8. Quantitative x-ray fluorescent analysis using fundamental parameters

    International Nuclear Information System (INIS)

    Sparks, C.J. Jr.

    1976-01-01

    A monochromatic source of x-rays for sample excitation permits the use of pure elemental standards and relatively simple calculations to convert the measured fluorescent intensities to an absolute basis of weight per unit weight of sample. Only the mass absorption coefficients of the sample for the exciting and the fluorescent radiation need be determined. Besides the direct measurement of these absorption coefficients in the sample, other techniques are considered which require fewer sample manipulations and measurements. These fundamental parameters methods permit quantitative analysis without recourse to the time-consuming process of preparing nearly identical standards

  9. Quantitative analysis with energy dispersive X-ray fluorescence analyser

    International Nuclear Information System (INIS)

    Kataria, S.K.; Kapoor, S.S.; Lal, M.; Rao, B.V.N.

    1977-01-01

    Quantitative analysis of samples using radioisotope excited energy dispersive x-ray fluorescence system is described. The complete set-up is built around a locally made Si(Li) detector x-ray spectrometer with an energy resolution of 220 eV at 5.94 KeV. The photopeaks observed in the x-ray fluorescence spectra are fitted with a Gaussian function and the intensities of the characteristic x-ray lines are extracted, which in turn are used for calculating the elemental concentrations. The results for a few typical cases are presented. (author)

  10. Computer compensation for NMR quantitative analysis of trace components

    International Nuclear Information System (INIS)

    Nakayama, T.; Fujiwara, Y.

    1981-01-01

    A computer program has been written that determines trace components and separates overlapping components in multicomponent NMR spectra. This program uses the Lorentzian curve as a theoretical curve of NMR spectra. The coefficients of the Lorentzian are determined by the method of least squares. Systematic errors such as baseline/phase distortion are compensated and random errors are smoothed by taking moving averages, so that there processes contribute substantially to decreasing the accumulation time of spectral data. The accuracy of quantitative analysis of trace components has been improved by two significant figures. This program was applied to determining the abundance of 13C and the saponification degree of PVA

  11. Stochastic filtering of quantitative data from STR DNA analysis

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt

    due to the apparatus used for measurements). Pull-up effects (more systematic increase caused by overlap in the spectrum) Stutters (peaks located four basepairs before the true peak). We present filtering techniques for all three technical artifacts based on statistical analysis of data from......The quantitative data observed from analysing STR DNA is a mixture of contributions from various sources. Apart from the true allelic peaks, the observed signal consists of at least three components resulting from the measurement technique and the PCR amplification: Background noise (random noise...... controlled experiments conducted at The Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, Universityof Copenhagen, Denmark....

  12. Paediatric HUS Cases Related to the Consumption of Raw Milk Sold by Vending Machines in Italy: Quantitative Risk Assessment Based on Escherichia coli O157 Official Controls over 7 years.

    Science.gov (United States)

    Giacometti, F; Bonilauri, P; Piva, S; Scavia, G; Amatiste, S; Bianchi, D M; Losio, M N; Bilei, S; Cascone, G; Comin, D; Daminelli, P; Decastelli, L; Merialdi, G; Mioni, R; Peli, A; Petruzzelli, A; Tonucci, F; Liuzzo, G; Serraino, A

    2017-11-01

    A quantitative risk assessment (RA) was developed to estimate haemolytic-uremic syndrome (HUS) cases in paediatric population associated with the consumption of raw milk sold in vending machines in Italy. The historical national evolution of raw milk consumption phenomenon since 2008, when consumer interest started to grow, and after 7 years of marketing adjustment, is outlined. Exposure assessment was based on the official Shiga toxin-producing Escherichia coli O157:H7 (STEC) microbiological records of raw milk samples from vending machines monitored by the regional Veterinary Authorities from 2008 to 2014, microbial growth during storage, consumption frequency of raw milk, serving size, consumption preference and age of consumers. The differential risk considered milk handled under regulation conditions (4°C throughout all phases) and the worst time-temperature field handling conditions detected. In case of boiling milk before consumption, we assumed that the risk of HUS is fixed at zero. The model estimates clearly show that the public health significance of HUS cases due to raw milk STEC contamination depends on the current variability surrounding the risk profile of the food and the consumer behaviour has more impact than milk storage scenario. The estimated HUS cases predicted by our model are roughly in line with the effective STEC O157-associated HUS cases notified in Italy only when the proportion of consumers not boiling milk before consumption is assumed to be 1%. Raw milk consumption remains a source of E. coli O157:H7 for humans, but its overall relevance is likely to have subsided and significant caution should be exerted for temporal, geographical and consumers behaviour analysis. Health education programmes and regulatory actions are required to educate people, primarily children, on other STEC sources. © 2016 Blackwell Verlag GmbH.

  13. Control analysis of the dependence of Escherichia coli physiology on the H+ -ATPase

    DEFF Research Database (Denmark)

    Jensen, Peter Ruhdal; Michelsen, Ole; Westerhoff, Hans V.

    1993-01-01

    The H+-ATPase plays a central role in Escherichia coli free-energy transduction and hence in E. coli physiology. We here investigate the extent to which this enzyme also controls the growth rate, growth yield, and respiratory rate of E. coli. We modulate the expression of the atp operon and deter...

  14. Absorption correction factor in X-ray fluorescent quantitative analysis

    International Nuclear Information System (INIS)

    Pimjun, S.

    1994-01-01

    An experiment on absorption correction factor in X-ray fluorescent quantitative analysis were carried out. Standard samples were prepared from the mixture of Fe 2 O 3 and tapioca flour at various concentration of Fe 2 O 3 ranging from 5% to 25%. Unknown samples were kaolin containing 3.5% to-50% of Fe 2 O 3 Kaolin samples were diluted with tapioca flour in order to reduce the absorption of FeK α and make them easy to prepare. Pressed samples with 0.150 /cm 2 and 2.76 cm in diameter, were used in the experiment. Absorption correction factor is related to total mass absorption coefficient (χ) which varied with sample composition. In known sample, χ can be calculated by conveniently the formula. However in unknown sample, χ can be determined by Emission-Transmission method. It was found that the relationship between corrected FeK α intensity and contents of Fe 2 O 3 in these samples was linear. This result indicate that this correction factor can be used to adjust the accuracy of X-ray intensity. Therefore, this correction factor is essential in quantitative analysis of elements comprising in any sample by X-ray fluorescent technique

  15. Developments in Dynamic Analysis for quantitative PIXE true elemental imaging

    International Nuclear Information System (INIS)

    Ryan, C.G.

    2001-01-01

    Dynamic Analysis (DA) is a method for projecting quantitative major and trace element images from PIXE event data-streams (off-line or on-line) obtained using the Nuclear Microprobe. The method separates full elemental spectral signatures to produce images that strongly reject artifacts due to overlapping elements, detector effects (such as escape peaks and tailing) and background. The images are also quantitative, stored in ppm-charge units, enabling images to be directly interrogated for the concentrations of all elements in areas of the images. Recent advances in the method include the correction for changing X-ray yields due to varying sample compositions across the image area and the construction of statistical variance images. The resulting accuracy of major element concentrations extracted directly from these images is better than 3% relative as determined from comparisons with electron microprobe point analysis. These results are complemented by error estimates derived from the variance images together with detection limits. This paper provides an update of research on these issues, introduces new software designed to make DA more accessible, and illustrates the application of the method to selected geological problems.

  16. Quantitative XPS analysis of high Tc superconductor surfaces

    International Nuclear Information System (INIS)

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

    1993-01-01

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

  17. Quantitative analysis on electrooculography (EOG) for neurodegenerative disease

    Science.gov (United States)

    Liu, Chang-Chia; Chaovalitwongse, W. Art; Pardalos, Panos M.; Seref, Onur; Xanthopoulos, Petros; Sackellares, J. C.; Skidmore, Frank M.

    2007-11-01

    Many studies have documented abnormal horizontal and vertical eye movements in human neurodegenerative disease as well as during altered states of consciousness (including drowsiness and intoxication) in healthy adults. Eye movement measurement may play an important role measuring the progress of neurodegenerative diseases and state of alertness in healthy individuals. There are several techniques for measuring eye movement, Infrared detection technique (IR). Video-oculography (VOG), Scleral eye coil and EOG. Among those available recording techniques, EOG is a major source for monitoring the abnormal eye movement. In this real-time quantitative analysis study, the methods which can capture the characteristic of the eye movement were proposed to accurately categorize the state of neurodegenerative subjects. The EOG recordings were taken while 5 tested subjects were watching a short (>120 s) animation clip. In response to the animated clip the participants executed a number of eye movements, including vertical smooth pursued (SVP), horizontal smooth pursued (HVP) and random saccades (RS). Detection of abnormalities in ocular movement may improve our diagnosis and understanding a neurodegenerative disease and altered states of consciousness. A standard real-time quantitative analysis will improve detection and provide a better understanding of pathology in these disorders.

  18. Quantitative analysis of infantile ureteropelvic junction obstruction by diuretic renography

    International Nuclear Information System (INIS)

    Ueno, Shigeru; Suzuki, Yutaka; Murakami, Takeshi; Yokoyama, Seishichi; Hirakawa, Hitoshi; Tajima, Tomoo; Makuuchi, Hiroyasu

    2001-01-01

    Infantile hydronephrosis detected by ultrasonography poses a clinical dilemma on how to treat the condition. This article reports a retrospective study to evaluate infantile hydronephrosis due to suspected ureteropelvic junction (UPJ) obstruction by means of standardized diuretic renography and to speculate its usefulness for quantitative assessment and management of this condition. Between November 1992 and July 1999, 43 patients who had the disease detected in their fetal or infantile period were submitted to this study. Standardized diuretic renograms were obtained with 99m Tc-labeled diethylene-triaminepenta-acetate (Tc-99m-DTPA) or 99m Tc-labeled mercaptoacetyl triglycine (Tc-99m-MAG3) as radiopharmaceuticals. Drainage half-time clearance (T 1/2) of the activity at each region of interest set to encompass the entire kidney and the dilated pelvis was used as an index of quantitative analysis of UPJ obstruction. Initial T 1/2s of 32 kidneys with suspected UPJ obstruction were significantly longer than those of 37 without obstruction. T 1/2s of kidneys which had undergone pyeloplasty decreased promptly after surgery whereas those of units followed up without surgery decreased more sluggishly. These findings demonstrate that a standardized diuretic renographic analysis with T 1/2 can reliably assess infantile hydronephrosis with UPJ obstruction and be helpful in making a decision on surgical intervention. (author)

  19. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    Directory of Open Access Journals (Sweden)

    Venkatesha R. Hathwar

    2015-09-01

    Full Text Available Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

  20. Quantitative analysis of infantile ureteropelvic junction obstruction by diuretic renography

    Energy Technology Data Exchange (ETDEWEB)

    Ueno, Shigeru; Suzuki, Yutaka; Murakami, Takeshi; Yokoyama, Seishichi; Hirakawa, Hitoshi; Tajima, Tomoo; Makuuchi, Hiroyasu [Tokai Univ., Isehara, Kanagawa (Japan). School of Medicine

    2001-04-01

    Infantile hydronephrosis detected by ultrasonography poses a clinical dilemma on how to treat the condition. This article reports a retrospective study to evaluate infantile hydronephrosis due to suspected ureteropelvic junction (UPJ) obstruction by means of standardized diuretic renography and to speculate its usefulness for quantitative assessment and management of this condition. Between November 1992 and July 1999, 43 patients who had the disease detected in their fetal or infantile period were submitted to this study. Standardized diuretic renograms were obtained with {sup 99m}Tc-labeled diethylene-triaminepenta-acetate (Tc-99m-DTPA) or {sup 99m}Tc-labeled mercaptoacetyl triglycine (Tc-99m-MAG3) as radiopharmaceuticals. Drainage half-time clearance (T 1/2) of the activity at each region of interest set to encompass the entire kidney and the dilated pelvis was used as an index of quantitative analysis of UPJ obstruction. Initial T 1/2s of 32 kidneys with suspected UPJ obstruction were significantly longer than those of 37 without obstruction. T 1/2s of kidneys which had undergone pyeloplasty decreased promptly after surgery whereas those of units followed up without surgery decreased more sluggishly. These findings demonstrate that a standardized diuretic renographic analysis with T 1/2 can reliably assess infantile hydronephrosis with UPJ obstruction and be helpful in making a decision on surgical intervention. (author)

  1. Quantitative analysis of tellurium in simple substance sulfur

    International Nuclear Information System (INIS)

    Arikawa, Yoshiko

    1976-01-01

    The MIBK extraction-bismuthiol-2 absorptiometric method for the quantitative analysis of tellurium was studied. The method and its limitation were compared with the atomic absorption method. The period of time required to boil the solution in order to decompose excess hydrogen peroxide and to reduce tellurium from 6 valance to 4 valance was examined. As a result of experiment, the decomposition was fast in the alkaline solution. It takes 30 minutes with alkaline solution and 40 minutes with acid solution to indicate constant absorption. A method of analyzing the sample containing tellurium less than 5 ppm was studied. The experiment revealed that the sample containing a very small amount of tellurium can be analyzed when concentration by extraction is carried out for the sample solutions which are divided into one gram each because it is difficult to treat several grams of the sample at one time. This method also is suitable for the quantitative analysis of selenium. This method showed good addition effect and reproducibility within the relative error of 5%. The comparison between the calibration curve of the standard solution of tellurium 4 subjected to the reaction with bismuthiol-2 and the calibration curve obtained from the extraction of tellurium 4 with MIBK indicated that the extraction is perfect. The result by bismuthiol-2 method and that by atom absorption method coincided quite well on the same sample. (Iwakiri, K.)

  2. Multivariate calibration applied to the quantitative analysis of infrared spectra

    Energy Technology Data Exchange (ETDEWEB)

    Haaland, D.M.

    1991-01-01

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

  3. Quantitative CT analysis of small pulmonary vessels in lymphangioleiomyomatosis

    International Nuclear Information System (INIS)

    Ando, Katsutoshi; Tobino, Kazunori; Kurihara, Masatoshi; Kataoka, Hideyuki; Doi, Tokuhide; Hoshika, Yoshito; Takahashi, Kazuhisa; Seyama, Kuniaki

    2012-01-01

    Backgrounds: Lymphangioleiomyomatosis (LAM) is a destructive lung disease that share clinical, physiologic, and radiologic features with chronic obstructive pulmonary disease (COPD). This study aims to identify those features that are unique to LAM by using quantitative CT analysis. Methods: We measured total cross-sectional areas of small pulmonary vessels (CSA) less than 5 mm 2 and 5–10 mm 2 and calculated percentages of those lung areas (%CSA), respectively, in 50 LAM and 42 COPD patients. The extent of cystic destruction (LAA%) and mean parenchymal CT value were also calculated and correlated with pulmonary function. Results: The diffusing capacity for carbon monoxide/alveolar volume (DL CO /VA %predicted) was similar for both groups (LAM, 44.4 ± 19.8% vs. COPD, 45.7 ± 16.0%, p = 0.763), but less tissue damage occurred in LAM than COPD (LAA% 21.7 ± 16.3% vs. 29.3 ± 17.0; p CO /VA %predicted, %CSA and mean parenchymal CT value were still greater for LAM than COPD (p < 0.05). Conclusions: Quantitative CT analysis revealing a correlation between cystic destruction and CSA in COPD but not LAM indicates that this approach successfully reflects different mechanisms governing the two pathologic courses. Such determinations of small pulmonary vessel density may serve to differentiate LAM from COPD even in patients with severe lung destruction.

  4. Hydrogen production and metabolic flux analysis of metabolically engineered Escherichia coli strains

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seohyoung; Seol, Eunhee; Park, Sunghoon [Department of Chemical and Biochemical Engineering, Pusan National University, Busan 609-735 (Korea); Oh, You-Kwan [Bioenergy Research Center, Korea Institute of Energy Research, Daejeon 305-543 (Korea); Wang, G.Y. [Department of Oceanography, University of Hawaii at Manoa Honolulu, HI 96822 (United States)

    2009-09-15

    Escherichia coli can produce H{sub 2} from glucose via formate hydrogen lyase (FHL). In order to improve the H{sub 2} production rate and yield, metabolically engineered E. coli strains, which included pathway alterations in their H{sub 2} production and central carbon metabolism, were developed and characterized by batch experiments and metabolic flux analysis. Deletion of hycA, a negative regulator for FHL, resulted in twofold increase of FHL activity. Deletion of two uptake hydrogenases (1 (hya) and hydrogenase 2 (hyb)) increased H{sub 2} production yield from 1.20 mol/mol glucose to 1.48 mol/mol glucose. Deletion of lactate dehydrogenase (ldhA) and fumarate reductase (frdAB) further improved the H{sub 2} yield; 1.80 mol/mol glucose under high H{sub 2} pressure or 2.11 mol/mol glucose under reduced H{sub 2} pressure. Several batch experiments at varying concentrations of glucose (2.5-10 g/L) and yeast extract (0.3 or 3.0 g/L) were conducted for the strain containing all these genetic alternations, and their carbon and energy balances were analyzed. The metabolic flux analysis revealed that deletion of ldhA and frdAB directed most of the carbons from glucose to the glycolytic pathway leading to H{sub 2} production by FHL, not to the pentose phosphate pathway. (author)

  5. Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coli

    International Nuclear Information System (INIS)

    Hor, Lilian; Dobson, Renwick C. J.; Dogovski, Con; Hutton, Craig A.; Perugini, Matthew A.

    2009-01-01

    Diaminopimelate (DAP) epimerase, an enzyme in the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the cloning, expression, purification, crystallization and preliminary diffraction analysis of DAP epimerase from E. coli are reported. Diaminopimelate (DAP) epimerase (EC 5.1.1.7) catalyzes the penultimate step of lysine biosynthesis in bacteria and plants, converting l,l-diaminopimelate to meso-diaminopimelate. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DAP epimerase from Escherichia coli are presented. Crystals were obtained in space group P4 1 2 1 2 and diffracted to 2.0 Å resolution, with unit-cell parameters a = b = 89.4, c = 179.6 Å. Molecular replacement was conducted using Bacillus anthracis DAP epimerase as a search model and showed the presence of two molecules in the asymmetric unit, with an initial R free of 0.456 and R work of 0.416

  6. Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

    Science.gov (United States)

    Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

    2006-01-01

    A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

  7. Quantitative morphometric analysis for the tectonic characterisation of northern Tunisia.

    Science.gov (United States)

    Camafort, Miquel; Pérez-Peña, José Vicente; Booth-Rea, Guillermo; Ranero, César R.; Gràcia, Eulàlia; Azañón, José Miguel; Melki, Fetheddine; Ouadday, Mohamed

    2016-04-01

    Northern Tunisia is characterized by low deformation rates and low to moderate seismicity. Although instrumental seismicity reaches maximum magnitudes of Mw 5.5, some historical earthquakes have occurred with catastrophic consequences in this region. Aiming to improve our knowledge of active tectonics in Tunisia, we carried out both a quantitative morphometric analysis and field study in the north-western region. We applied different morphometric tools, like river profiles, knickpoint analysis, hypsometric curves and integrals and drainage pattern anomalies in order to differentiate between zones with high or low recent tectonic activity. This analysis helps identifying uplift and subsidence zones, which we relate to fault activity. Several active faults in a sparse distribution were identified. A selected sector was studied with a field campaign to test the results obtained with the quantitative analysis. During the fieldwork we identified geological evidence of recent activity and a considerable seismogenic potential along El Alia-Teboursouk (ETF) and Dkhila (DF) faults. The ETF fault could be responsible of one of the most devastating historical earthquakes in northern Tunisia that destroyed Utique in 412 A.D. Geological evidence include fluvial terraces folded by faults, striated and cracked pebbles, clastic dikes, sand volcanoes, coseismic cracks, etc. Although not reflected in the instrumental seismicity, our results support an important seismic hazard, evidenced by the several active tectonic structures identified and the two seismogenic faults described. After obtaining the current active tectonic framework of Tunisia we discuss our results within the western Mediterranean trying to contribute to the understanding of the western Mediterranean tectonic context. With our results, we suggest that the main reason explaining the sparse and scarce seismicity of the area in contrast with the adjacent parts of the Nubia-Eurasia boundary is due to its extended

  8. Comparison of different surface quantitative analysis methods. Application to corium

    International Nuclear Information System (INIS)

    Guilbaud, N.; Blin, D.; Perodeaud, Ph.; Dugne, O.; Gueneau, Ch.

    2000-01-01

    In case of a severe hypothetical accident in a pressurized water reactor, the reactor assembly melts partially or completely. The material formed, called corium, flows out and spreads at the bottom of the reactor. To limit and control the consequences of such an accident, the specifications of the O-U-Zr basic system must be known accurately. To achieve this goal, the corium mix was melted by electron bombardment at very high temperature (3000 K) followed by quenching of the ingot in the Isabel 1 evaporator. Metallographic analyses were then required to validate the thermodynamic databases set by the Thermo-Calc software. The study consists in defining an overall surface quantitative analysis method that is fast and reliable, in order to determine the overall corium composition. The analyzed ingot originated in a [U+Fe+Y+UO 2 +ZrO 2 ) mix, with a total mass of 2253.7 grams. Several successive heating with average power were performed before a very brief plateau at very high temperature, so that the ingot was formed progressively and without any evaporation liable to modify its initial composition. The central zone of the ingot was then analyzed by qualitative and quantitative global surface methods, to yield the volume composition of the analyzed zone. Corium sample analysis happens to be very complex because of the variety and number of elements present, and also because of the presence of oxygen in a heavy element like the uranium based matrix. Three different global quantitative surface analysis methods were used: global EDS analysis (Energy Dispersive Spectrometry), with SEM, global WDS analysis (Wavelength Dispersive Spectrometry) with EPMA, and coupling of image analysis with EDS or WDS point spectroscopic analyses. The difficulties encountered during the study arose from sample preparation (corium is very sensitive to oxidation), and the choice of acquisition parameters of the images and analyses. The corium sample studied consisted of two zones displaying

  9. Quantitative image analysis in sonograms of the thyroid gland

    Energy Technology Data Exchange (ETDEWEB)

    Catherine, Skouroliakou [A' Department of Radiology, University of Athens, Vas.Sophias Ave, Athens 11528 (Greece); Maria, Lyra [A' Department of Radiology, University of Athens, Vas.Sophias Ave, Athens 11528 (Greece)]. E-mail: mlyra@pindos.uoa.gr; Aristides, Antoniou [A' Department of Radiology, University of Athens, Vas.Sophias Ave, Athens 11528 (Greece); Lambros, Vlahos [A' Department of Radiology, University of Athens, Vas.Sophias Ave, Athens 11528 (Greece)

    2006-12-20

    High-resolution, real-time ultrasound is a routine examination for assessing the disorders of the thyroid gland. However, the current diagnosis practice is based mainly on qualitative evaluation of the resulting sonograms, therefore depending on the physician's experience. Computerized texture analysis is widely employed in sonographic images of various organs (liver, breast), and it has been proven to increase the sensitivity of diagnosis by providing a better tissue characterization. The present study attempts to characterize thyroid tissue by automatic texture analysis. The texture features that are calculated are based on co-occurrence matrices as they have been proposed by Haralick. The sample consists of 40 patients. For each patient two sonographic images (one for each lobe) are recorded in DICOM format. The lobe is manually delineated in each sonogram, and the co-occurrence matrices for 52 separation vectors are calculated. The texture features extracted from each one of these matrices are: contrast, correlation, energy and homogeneity. Primary component analysis is used to select the optimal set of features. The statistical analysis resulted in the extraction of 21 optimal descriptors. The optimal descriptors are all co-occurrence parameters as the first-order statistics did not prove to be representative of the images characteristics. The bigger number of components depends mainly on correlation for very close or very far distances. The results indicate that quantitative analysis of thyroid sonograms can provide an objective characterization of thyroid tissue.

  10. Primary and secondary cases in Escherichia coli O157 outbreaks: a statistical analysis.

    LENUS (Irish Health Repository)

    Snedeker, Kate G

    2009-01-01

    BACKGROUND: Within outbreaks of Escherichia coli O157 (E. coli O157), at least 10-15% of cases are thought to have been acquired by secondary transmission. However, there has been little systematic quantification or characterisation of secondary outbreak cases worldwide. The aim of this study was to characterise secondary outbreak cases, estimate the overall proportion of outbreak cases that were the result of secondary transmission and to analyse the relationships between primary and secondary outbreak cases by mode of transmission, country and median age. METHODS: Published data was obtained from 90 confirmed Escherichia coli O157 outbreaks in Great Britain, Ireland, Scandinavia, Canada, the United States and Japan, and the outbreaks were described in terms of modes of primary and secondary transmission, country, case numbers and median case age. Outbreaks were tested for statistically significant differences in the number of ill, confirmed, primary and secondary cases (analysis of variance and Kruskal-Wallis) and in the rate of secondary cases between these variables (Generalised Linear Models). RESULTS: The outbreaks had a median of 13.5 confirmed cases, and mean proportion of 0.195 secondary cases. There were statistically significant differences in the numbers of ill, confirmed, primary and secondary cases between modes of primary transmission (p < 0.021), and in primary and secondary cases between median age categories (p < 0.039) and modes of secondary transmission (p < 0.001).Secondary case rates differed statistically significantly between modes of secondary and primary transmission and median age categories (all p < 0.001), but not between countries (p = 0.23). Statistically significantly higher rates of secondary transmission were found in outbreaks with a median age <6 years and those with secondary transmission via person to person spread in nurseries. No statistically significant interactions were found between country, mode of transmission and age

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

    Science.gov (United States)

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

    2015-08-01

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

  12. The Quantitative Analysis of Chennai Automotive Industry Cluster

    Science.gov (United States)

    Bhaskaran, Ethirajan

    2016-07-01

    Chennai, also called as Detroit of India due to presence of Automotive Industry producing over 40 % of the India's vehicle and components. During 2001-2002, the Automotive Component Industries (ACI) in Ambattur, Thirumalizai and Thirumudivakkam Industrial Estate, Chennai has faced problems on infrastructure, technology, procurement, production and marketing. The objective is to study the Quantitative Performance of Chennai Automotive Industry Cluster before (2001-2002) and after the CDA (2008-2009). The methodology adopted is collection of primary data from 100 ACI using quantitative questionnaire and analyzing using Correlation Analysis (CA), Regression Analysis (RA), Friedman Test (FMT), and Kruskall Wallis Test (KWT).The CA computed for the different set of variables reveals that there is high degree of relationship between the variables studied. The RA models constructed establish the strong relationship between the dependent variable and a host of independent variables. The models proposed here reveal the approximate relationship in a closer form. KWT proves, there is no significant difference between three locations clusters with respect to: Net Profit, Production Cost, Marketing Costs, Procurement Costs and Gross Output. This supports that each location has contributed for development of automobile component cluster uniformly. The FMT proves, there is no significant difference between industrial units in respect of cost like Production, Infrastructure, Technology, Marketing and Net Profit. To conclude, the Automotive Industries have fully utilized the Physical Infrastructure and Centralised Facilities by adopting CDA and now exporting their products to North America, South America, Europe, Australia, Africa and Asia. The value chain analysis models have been implemented in all the cluster units. This Cluster Development Approach (CDA) model can be implemented in industries of under developed and developing countries for cost reduction and productivity

  13. Functional linear models for association analysis of quantitative traits.

    Science.gov (United States)

    Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

    2013-11-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. © 2013 WILEY

  14. Quantitative CT analysis of small pulmonary vessels in lymphangioleiomyomatosis

    Energy Technology Data Exchange (ETDEWEB)

    Ando, Katsutoshi, E-mail: kando@juntendo.ac.jp [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Tobino, Kazunori [Department of Respiratory Medicine, Iizuka Hospital, 3-83 Yoshio-Machi, Iizuka-City, Fukuoka 820-8505 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Kurihara, Masatoshi; Kataoka, Hideyuki [Pneumothorax Center, Nissan Tamagawa Hospital, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Doi, Tokuhide [Fukuoka Clinic, 7-18-11 Umeda, Adachi-Ku, Tokyo 123-0851 (Japan); Hoshika, Yoshito [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Takahashi, Kazuhisa [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); Seyama, Kuniaki [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan)

    2012-12-15

    Backgrounds: Lymphangioleiomyomatosis (LAM) is a destructive lung disease that share clinical, physiologic, and radiologic features with chronic obstructive pulmonary disease (COPD). This study aims to identify those features that are unique to LAM by using quantitative CT analysis. Methods: We measured total cross-sectional areas of small pulmonary vessels (CSA) less than 5 mm{sup 2} and 5–10 mm{sup 2} and calculated percentages of those lung areas (%CSA), respectively, in 50 LAM and 42 COPD patients. The extent of cystic destruction (LAA%) and mean parenchymal CT value were also calculated and correlated with pulmonary function. Results: The diffusing capacity for carbon monoxide/alveolar volume (DL{sub CO}/VA %predicted) was similar for both groups (LAM, 44.4 ± 19.8% vs. COPD, 45.7 ± 16.0%, p = 0.763), but less tissue damage occurred in LAM than COPD (LAA% 21.7 ± 16.3% vs. 29.3 ± 17.0; p < 0.05). Pulmonary function correlated negatively with LAA% (p < 0.001) in both groups, yet the correlation with %CSA was significant only in COPD (p < 0.001). When the same analysis was conducted in two groups with equal levels of LAA% and DL{sub CO}/VA %predicted, %CSA and mean parenchymal CT value were still greater for LAM than COPD (p < 0.05). Conclusions: Quantitative CT analysis revealing a correlation between cystic destruction and CSA in COPD but not LAM indicates that this approach successfully reflects different mechanisms governing the two pathologic courses. Such determinations of small pulmonary vessel density may serve to differentiate LAM from COPD even in patients with severe lung destruction.

  15. QuASAR: quantitative allele-specific analysis of reads.

    Science.gov (United States)

    Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-04-15

    Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Quantitative Analysis of TDLUs using Adaptive Morphological Shape Techniques.

    Science.gov (United States)

    Rosebrock, Adrian; Caban, Jesus J; Figueroa, Jonine; Gierach, Gretchen; Linville, Laura; Hewitt, Stephen; Sherman, Mark

    2013-03-29

    Within the complex branching system of the breast, terminal duct lobular units (TDLUs) are the anatomical location where most cancer originates. With aging, TDLUs undergo physiological involution, reflected in a loss of structural components (acini) and a reduction in total number. Data suggest that women undergoing benign breast biopsies that do not show age appropriate involution are at increased risk of developing breast cancer. To date, TDLU assessments have generally been made by qualitative visual assessment, rather than by objective quantitative analysis. This paper introduces a technique to automatically estimate a set of quantitative measurements and use those variables to more objectively describe and classify TDLUs. To validate the accuracy of our system, we compared the computer-based morphological properties of 51 TDLUs in breast tissues donated for research by volunteers in the Susan G. Komen Tissue Bank and compared results to those of a pathologist, demonstrating 70% agreement. Secondly, in order to show that our method is applicable to a wider range of datasets, we analyzed 52 TDLUs from biopsies performed for clinical indications in the National Cancer Institute's Breast Radiology Evaluation and Study of Tissues (BREAST) Stamp Project and obtained 82% correlation with visual assessment. Lastly, we demonstrate the ability to uncover novel measures when researching the structural properties of the acini by applying machine learning and clustering techniques. Through our study we found that while the number of acini per TDLU increases exponentially with the TDLU diameter, the average elongation and roundness remain constant.

  17. MR imaging of Minamata disease. Qualitative and quantitative analysis

    International Nuclear Information System (INIS)

    Korogi, Yukunori; Takahashi, Mutsumasa; Sumi, Minako; Hirai, Toshinori; Okuda, Tomoko; Shinzato, Jintetsu; Okajima, Toru.

    1994-01-01

    Minamata disease (MD), a result of methylmercury poisoning, is a neurological illness caused by ingestion of contaminated seafood. We evaluated MR findings of patients with MD qualitatively and quantitatively. Magnetic resonance imaging at 1.5 Tesla was performed in seven patients with MD and in eight control subjects. All of our patients showed typical neurological findings like sensory disturbance, constriction of the visual fields, and ataxia. In the quantitative image analysis, inferior and middle parts of the cerebellar vermis and cerebellar hemispheres were significantly atrophic in comparison with the normal controls. There were no significant differences in measurements of the basis pontis, middle cerebellar peduncles, corpus callosum, or cerebral hemispheres between MD and the normal controls. The calcarine sulci and central sulci were significantly dilated, reflecting atrophy of the visual cortex and postcentral cortex, respectively. The lesions located in the calcarine area, cerebellum, and postcentral gyri were related to three characteristic manifestations of this disease, constriction of the visual fields, ataxia, and sensory disturbance, respectively. MR imaging has proved to be useful in evaluating the CNS abnormalities of methylmercury poisoning. (author)

  18. Analysis of different DNA fragments of Corynebacterium glutamicum complementing dapE of Escherichia coli.

    Science.gov (United States)

    Wehrmann, A; Eggeling, L; Sahm, H

    1994-12-01

    In Corynebacterium glutamicum L-lysine is synthesized simultaneously via the succinylase and dehydrogenase variant of the diaminopimelate pathway. Starting from a strain with a disrupted dehydrogenase gene, three different-sized DNA fragments were isolated which complemented defective Escherichia coli mutants in the succinylase pathway. Enzyme studies revealed that in one case the dehydrogenase gene had apparently been reconstituted in the heterologous host. The two other fragments resulted in desuccinylase activity; one of them additionally in succinylase activity. However, the physical analysis showed that structural changes had taken place in all fragments. Using a probe derived from one of the fragments we isolated a 3.4 kb BamHI DNA fragment without selective pressure (by colony hybridization). This was structurally intact and proved functionally to result in tenfold desuccinylase overexpression. The nucleotide sequence of a 1966 bp fragment revealed the presence of one truncated open reading frame of unknown function and that of dapE encoding N-succinyl diaminopimelate desuccinylase (EC 3.5.1.18). The deduced amino acid sequence of the dapE gene product shares 23% identical residues with that from E. coli. The C. glutamicum gene now available is the first gene from the succinylase branch of lysine synthesis of this biotechnologically important organism.

  19. Qualitative and quantitative reliability analysis of safety systems

    International Nuclear Information System (INIS)

    Karimi, R.; Rasmussen, N.; Wolf, L.

    1980-05-01

    A code has been developed for the comprehensive analysis of a fault tree. The code designated UNRAC (UNReliability Analysis Code) calculates the following characteristics of an input fault tree: (1) minimal cut sets; (2) top event unavailability as point estimate and/or in time dependent form; (3) quantitative importance of each component involved; and, (4) error bound on the top event unavailability. UNRAC can analyze fault trees, with any kind of gates (EOR, NAND, NOR, AND, OR), up to a maximum of 250 components and/or gates. The code is benchmarked against WAMCUT, MODCUT, KITT, BIT-FRANTIC, and PL-MODT. The results showed that UNRAC produces results more consistent with the KITT results than either BIT-FRANTIC or PL-MODT. Overall it is demonstrated that UNRAC is an efficient easy-to-use code and has the advantage of being able to do a complete fault tree analysis with this single code. Applications of fault tree analysis to safety studies of nuclear reactors are considered

  20. Quantitative analysis and classification of AFM images of human hair.

    Science.gov (United States)

    Gurden, S P; Monteiro, V F; Longo, E; Ferreira, M M C

    2004-07-01

    The surface topography of human hair, as defined by the outer layer of cellular sheets, termed cuticles, largely determines the cosmetic properties of the hair. The condition of the cuticles is of great cosmetic importance, but also has the potential to aid diagnosis in the medical and forensic sciences. Atomic force microscopy (AFM) has been demonstrated to offer unique advantages for analysis of the hair surface, mainly due to the high image resolution and the ease of sample preparation. This article presents an algorithm for the automatic analysis of AFM images of human hair. The cuticular structure is characterized using a series of descriptors, such as step height, tilt angle and cuticle density, allowing quantitative analysis and comparison of different images. The usefulness of this approach is demonstrated by a classification study. Thirty-eight AFM images were measured, consisting of hair samples from (a) untreated and bleached hair samples, and (b) the root and distal ends of the hair fibre. The multivariate classification technique partial least squares discriminant analysis is used to test the ability of the algorithm to characterize the images according to the properties of the hair samples. Most of the images (86%) were found to be classified correctly.

  1. Large-scale quantitative analysis of painting arts.

    Science.gov (United States)

    Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

    2014-12-11

    Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images - the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances.

  2. Quali- and quantitative analysis of commercial coffee by NMR

    International Nuclear Information System (INIS)

    Tavares, Leila Aley; Ferreira, Antonio Gilberto

    2006-01-01

    Coffee is one of the beverages most widely consumed in the world and the 'cafezinho' is normally prepared from a blend of roasted powder of two species, Coffea arabica and Coffea canephora. Each one exhibits differences in their taste and in the chemical composition, especially in the caffeine percentage. There are several procedures proposed in the literature for caffeine determination in different samples like soft drinks, coffee, medicines, etc but most of them need a sample workup which involves at least one step of purification. This work describes the quantitative analysis of caffeine using 1 H NMR and the identification of the major components in commercial coffee samples using 1D and 2D NMR techniques without any sample pre-treatment. (author)

  3. Automated quantitative cytological analysis using portable microfluidic microscopy.

    Science.gov (United States)

    Jagannadh, Veerendra Kalyan; Murthy, Rashmi Sreeramachandra; Srinivasan, Rajesh; Gorthi, Sai Siva

    2016-06-01

    In this article, a portable microfluidic microscopy based approach for automated cytological investigations is presented. Inexpensive optical and electronic components have been used to construct a simple microfluidic microscopy system. In contrast to the conventional slide-based methods, the presented method employs microfluidics to enable automated sample handling and image acquisition. The approach involves the use of simple in-suspension staining and automated image acquisition to enable quantitative cytological analysis of samples. The applicability of the presented approach to research in cellular biology is shown by performing an automated cell viability assessment on a given population of yeast cells. Further, the relevance of the presented approach to clinical diagnosis and prognosis has been demonstrated by performing detection and differential assessment of malaria infection in a given sample. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Quantitative image analysis of WE43-T6 cracking behavior

    International Nuclear Information System (INIS)

    Ahmad, A; Yahya, Z

    2013-01-01

    Environment-assisted cracking of WE43 cast magnesium (4.2 wt.% Yt, 2.3 wt.% Nd, 0.7% Zr, 0.8% HRE) in the T6 peak-aged condition was induced in ambient air in notched specimens. The mechanism of fracture was studied using electron backscatter diffraction, serial sectioning and in situ observations of crack propagation. The intermetallic (rare earthed-enriched divorced intermetallic retained at grain boundaries and predominantly at triple points) material was found to play a significant role in initiating cracks which leads to failure of this material. Quantitative measurements were required for this project. The populations of the intermetallic and clusters of intermetallic particles were analyzed using image analysis of metallographic images. This is part of the work to generate a theoretical model of the effect of notch geometry on the static fatigue strength of this material.

  5. Quantitative analysis of spatial variability of geotechnical parameters

    Science.gov (United States)

    Fang, Xing

    2018-04-01

    Geotechnical parameters are the basic parameters of geotechnical engineering design, while the geotechnical parameters have strong regional characteristics. At the same time, the spatial variability of geotechnical parameters has been recognized. It is gradually introduced into the reliability analysis of geotechnical engineering. Based on the statistical theory of geostatistical spatial information, the spatial variability of geotechnical parameters is quantitatively analyzed. At the same time, the evaluation of geotechnical parameters and the correlation coefficient between geotechnical parameters are calculated. A residential district of Tianjin Survey Institute was selected as the research object. There are 68 boreholes in this area and 9 layers of mechanical stratification. The parameters are water content, natural gravity, void ratio, liquid limit, plasticity index, liquidity index, compressibility coefficient, compressive modulus, internal friction angle, cohesion and SP index. According to the principle of statistical correlation, the correlation coefficient of geotechnical parameters is calculated. According to the correlation coefficient, the law of geotechnical parameters is obtained.

  6. Quantitative analysis of lead in polysulfide-based impression material

    Directory of Open Access Journals (Sweden)

    Aparecida Silva Braga

    2007-06-01

    Full Text Available Permlastic® is a polysulfide-based impression material widely used by dentists in Brazil. It is composed of a base paste and a catalyzer containing lead dioxide. The high toxicity of lead to humans is ground for much concern, since it can attack various systems and organs. The present study involved a quantitative analysis of the concentration of lead in the material Permlastic®. The lead was determined by plasma-induced optical emission spectrometry (Varian model Vista. The percentages of lead found in the two analyzed lots were 38.1 and 40.8%. The lead concentrations in the material under study were high, but the product’s packaging contained no information about these concentrations.

  7. Quantitative analysis of fission products by γ spectrography

    International Nuclear Information System (INIS)

    Malet, G.

    1962-01-01

    The activity of the fission products present in treated solutions of irradiated fuels is given as a function of the time of cooling and of the irradiation time. The variation of the ratio ( 144 Ce + 144 Pr activity)/ 137 Cs activity) as a function of these same parameters is also given. From these results a method is deduced giving the 'age' of the solution analyzed. By γ-scintillation spectrography it was possible to estimate the following elements individually: 141 Ce, 144 Ce + 144 Pr, 103 Ru, 106 Ru + 106 Rh, 137 Cs, 95 Zr + 95 Nb. Yield curves are given for the case of a single emitter. Of the various existing methods, that of the least squares was used for the quantitative analysis of the afore-mentioned fission products. The accuracy attained varies from 3 to 10%. (author) [fr

  8. Quantitative image analysis for investigating cell-matrix interactions

    Science.gov (United States)

    Burkel, Brian; Notbohm, Jacob

    2017-07-01

    The extracellular matrix provides both chemical and physical cues that control cellular processes such as migration, division, differentiation, and cancer progression. Cells can mechanically alter the matrix by applying forces that result in matrix displacements, which in turn may localize to form dense bands along which cells may migrate. To quantify the displacements, we use confocal microscopy and fluorescent labeling to acquire high-contrast images of the fibrous material. Using a technique for quantitative image analysis called digital volume correlation, we then compute the matrix displacements. Our experimental technology offers a means to quantify matrix mechanics and cell-matrix interactions. We are now using these experimental tools to modulate mechanical properties of the matrix to study cell contraction and migration.

  9. Quantitative analysis of secretome from adipocytes regulated by insulin

    Institute of Scientific and Technical Information of China (English)

    Hu Zhou; Yuanyuan Xiao; Rongxia Li; Shangyu Hong; Sujun Li; Lianshui Wang; Rong Zeng; Kan Liao

    2009-01-01

    Adipocyte is not only a central player involved in storage and release of energy, but also in regulation of energy metabolism in other organs via secretion of pep-tides and proteins. During the pathogenesis of insulin resistance and type 2 diabetes, adipocytes are subjected to the increased levels of insulin, which may have a major impact on the secretion of adipokines. We have undertaken cleavable isotope-coded affinity tag (clCAT) and label-free quantitation approaches to identify and quantify secretory factors that are differen-tially secreted by 3T3-LI adipocytes with or without insulin treatment. Combination of clCAT and label-free results, there are 317 proteins predicted or annotated as secretory proteins. Among these secretory proteins, 179 proteins and 53 proteins were significantly up-regulated and down-regulated, respectively. A total of 77 reported adipokines were quantified in our study, such as adiponectin, cathepsin D, cystatin C, resistin, and transferrin. Western blot analysis of these adipo-kines confirmed the quantitative results from mass spectrometry, and revealed individualized secreting pat-terns of these proteins by increasing insulin dose. In addition, 240 proteins were newly identified and quanti-fied as secreted proteins from 3T3-L1 adipocytes in our study, most of which were up-regulated upon insulin treatment. Further comprehensive bioinformatics analysis revealed that the secretory proteins in extra-cellular matrix-receptor interaction pathway and glycan structure degradation pathway were significantly up-regulated by insulin stimulation.

  10. Qualitative and quantitative analysis of women's perceptions of transvaginal surgery.

    Science.gov (United States)

    Bingener, Juliane; Sloan, Jeff A; Ghosh, Karthik; McConico, Andrea; Mariani, Andrea

    2012-04-01

    Prior surveys evaluating women's perceptions of transvaginal surgery both support and refute the acceptability of transvaginal access. Most surveys employed mainly quantitative analysis, limiting the insight into the women's perspective. In this mixed-methods study, we include qualitative and quantitative methodology to assess women's perceptions of transvaginal procedures. Women seen at the outpatient clinics of a tertiary-care center were asked to complete a survey. Demographics and preferences for appendectomy, cholecystectomy, and tubal ligation were elicited, along with open-ended questions about concerns or benefits of transvaginal access. Multivariate logistic regression models were constructed to examine the impact of age, education, parity, and prior transvaginal procedures on preferences. For the qualitative evaluation, content analysis by independent investigators identified themes, issues, and concerns raised in the comments. The completed survey tool was returned by 409 women (grouped mean age 53 years, mean number of 2 children, 82% ≥ some college education, and 56% with previous transvaginal procedure). The transvaginal approach was acceptable for tubal ligation to 59%, for appendectomy to 43%, and for cholecystectomy to 41% of the women. The most frequently mentioned factors that would make women prefer a vaginal approach were decreased invasiveness (14.4%), recovery time (13.9%), scarring (13.7%), pain (6%), and surgical entry location relative to organ removed (4.4%). The most frequently mentioned concerns about the vaginal approach were the possibility of complications/safety (14.7%), pain (9%), infection (5.6%), and recovery time (4.9%). A number of women voiced technical concerns about the vaginal approach. As in prior studies, scarring and pain were important issues to be considered, but recovery time and increased invasiveness were also in the "top five" list. The surveyed women appeared to actively participate in evaluating the technical

  11. Quantitative analysis of protein-ligand interactions by NMR.

    Science.gov (United States)

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  12. Development of an Escherichia coli K12-specific quantitative polymerase chain reaction assay and DNA isolation suited to biofilms associated with iron drinking water pipe corrosion products

    Science.gov (United States)

    Escherichia coli is one of the most commonly used fecal indicator organisms for drinking water and groundwater systems. In order to understand various biogeochemical and biophysical factors affecting its interactions with biofilms, E. coli K12 was chosen as a model organism. A Ta...

  13. Quantitative mass-spectrometric analysis of hydrogen helium isotope mixtures

    International Nuclear Information System (INIS)

    Langer, U.

    1998-12-01

    This work deals with the mass-spectrometric method for the quantitative analysis of hydrogen-helium-isotope mixtures, with special attention to fusion plasma diagnostics. The aim was to use the low-resolution mass spectrometry, a standard measuring method which is well established in science and industry. This task is solved by means of the vector mass spectrometry, where a mass spectrum is repeatedly measured, but with stepwise variation of the parameter settings of a quadruple mass spectrometer. In this way, interfering mass spectra can be decomposed and, moreover, it is possible to analyze underestimated mass spectra of complex hydrogen-helium-isotope mixtures. In this work experimental investigations are presented which show that there are different parameters which are suitable for the UMS-method. With an optimal choice of the parameter settings hydrogen-helium-isotope mixtures can be analyzed with an accuracy of 1-3 %. In practice, a low sensitivity for small helium concentration has to be noted. To cope with this task, a method for selective hydrogen pressure reduction has been developed. Experimental investigations and calculations show that small helium amounts (about 1 %) in a hydrogen atmosphere can be analyzed with an accuracy of 3 - 10 %. Finally, this work deals with the effects of the measuring and calibration error on the resulting error in spectrum decomposition. This aspect has been investigated both in general mass-spectrometric gas analysis and in the analysis of hydrogen-helium-mixtures by means of the vector mass spectrometry. (author)

  14. Quantitative charge-tags for sterol and oxysterol analysis.

    Science.gov (United States)

    Crick, Peter J; William Bentley, T; Abdel-Khalik, Jonas; Matthews, Ian; Clayton, Peter T; Morris, Andrew A; Bigger, Brian W; Zerbinati, Chiara; Tritapepe, Luigi; Iuliano, Luigi; Wang, Yuqin; Griffiths, William J

    2015-02-01

    Global sterol analysis is challenging owing to the extreme diversity of sterol natural products, the tendency of cholesterol to dominate in abundance over all other sterols, and the structural lack of a strong chromophore or readily ionized functional group. We developed a method to overcome these challenges by using different isotope-labeled versions of the Girard P reagent (GP) as quantitative charge-tags for the LC-MS analysis of sterols including oxysterols. Sterols/oxysterols in plasma were extracted in ethanol containing deuterated internal standards, separated by C18 solid-phase extraction, and derivatized with GP, with or without prior oxidation of 3β-hydroxy to 3-oxo groups. By use of different isotope-labeled GPs, it was possible to analyze in a single LC-MS analysis both sterols/oxysterols that naturally possess a 3-oxo group and those with a 3β-hydroxy group. Intra- and interassay CVs were sterols/oxysterols in a single analytical run and can be used to identify inborn errors of cholesterol synthesis and metabolism. © 2014 American Association for Clinical Chemistry.

  15. [Quantitative analysis of drug expenditures variability in dermatology units].

    Science.gov (United States)

    Moreno-Ramírez, David; Ferrándiz, Lara; Ramírez-Soto, Gabriel; Muñoyerro, M Dolores

    2013-01-01

    Variability in adjusted drug expenditures among clinical departments raises the possibility of difficult access to certain therapies at the time that avoidable expenditures may also exist. Nevertheless, drug expenditures are not usually applied to clinical practice variability analysis. To identify and quantify variability in drug expenditures in comparable dermatology department of the Servicio Andaluz de Salud. Comparative economic analysis regarding the drug expenditures adjusted to population and health care production in 18 dermatology departments of the Servicio Andaluz de Salud. The 2012 cost and production data (homogeneous production units -HPU-)were provided by Inforcoan, the cost accounting information system of the Servicio Andaluz de Salud. The observed drug expenditure ratio ranged from 0.97?/inh to 8.90?/inh and from 208.45?/HPU to 1,471.95?/ HPU. The Pearson correlation between drug expenditure and population was 0.25 and 0.35 for the correlation between expenditure and homogeneous production (p=0.32 and p=0,15, respectively), both Pearson coefficients confirming the lack of correlation and arelevant degree of variability in drug expenditures. The quantitative analysis of variability performed through Pearson correlation has confirmed the existence of drug expenditure variability among comparable dermatology departments. Copyright © 2013 SEFH. Published by AULA MEDICA. All rights reserved.

  16. Application of neural networks to quantitative spectrometry analysis

    International Nuclear Information System (INIS)

    Pilato, V.; Tola, F.; Martinez, J.M.; Huver, M.

    1999-01-01

    Accurate quantitative analysis of complex spectra (fission and activation products), relies upon experts' knowledge. In some cases several hours, even days of tedious calculations are needed. This is because current software is unable to solve deconvolution problems when several rays overlap. We have shown that such analysis can be correctly handled by a neural network, and the procedure can be automated with minimum laboratory measurements for networks training, as long as all the elements of the analysed solution figure in the training set and provided that adequate scaling of input data is performed. Once the network has been trained, analysis is carried out in a few seconds. On submitting to a test between several well-known laboratories, where unknown quantities of 57 Co, 58 Co, 85 Sr, 88 Y, 131 I, 139 Ce, 141 Ce present in a sample had to be determined, the results yielded by our network classed it amongst the best. The method is described, including experimental device and measures, training set designing, relevant input parameters definition, input data scaling and networks training. Main results are presented together with a statistical model allowing networks error prediction

  17. An approach for quantitative image quality analysis for CT

    Science.gov (United States)

    Rahimi, Amir; Cochran, Joe; Mooney, Doug; Regensburger, Joe

    2016-03-01

    An objective and standardized approach to assess image quality of Compute Tomography (CT) systems is required in a wide variety of imaging processes to identify CT systems appropriate for a given application. We present an overview of the framework we have developed to help standardize and to objectively assess CT image quality for different models of CT scanners used for security applications. Within this framework, we have developed methods to quantitatively measure metrics that should correlate with feature identification, detection accuracy and precision, and image registration capabilities of CT machines and to identify strengths and weaknesses in different CT imaging technologies in transportation security. To that end we have designed, developed and constructed phantoms that allow for systematic and repeatable measurements of roughly 88 image quality metrics, representing modulation transfer function, noise equivalent quanta, noise power spectra, slice sensitivity profiles, streak artifacts, CT number uniformity, CT number consistency, object length accuracy, CT number path length consistency, and object registration. Furthermore, we have developed a sophisticated MATLAB based image analysis tool kit to analyze CT generated images of phantoms and report these metrics in a format that is standardized across the considered models of CT scanners, allowing for comparative image quality analysis within a CT model or between different CT models. In addition, we have developed a modified sparse principal component analysis (SPCA) method to generate a modified set of PCA components as compared to the standard principal component analysis (PCA) with sparse loadings in conjunction with Hotelling T2 statistical analysis method to compare, qualify, and detect faults in the tested systems.

  18. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

    Directory of Open Access Journals (Sweden)

    Schlegel Brigitte

    2004-03-01

    Full Text Available Abstract Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.

  19. Review of Department of Defense Education Activity (DODEA) Schools. Volume II: Quantitative Analysis of Educational Quality

    National Research Council Canada - National Science Library

    Anderson, Lowell

    2000-01-01

    This volume compiles, and presents in integrated form, IDA's quantitative analysis of educational quality provided by DoD's dependent schools, It covers the quantitative aspects of volume I in greater...

  20. PIQMIe: A web server for semi-quantitative proteomics data management and analysis

    NARCIS (Netherlands)

    A. Kuzniar (Arnold); R. Kanaar (Roland)

    2014-01-01

    textabstractWe present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates

  1. Genetic analysis of an Escherichia coli urease locus: evidence of DNA rearrangement.

    OpenAIRE

    Collins, C M; Falkow, S

    1988-01-01

    Ureolytic Escherichia coli strains are uncommon clinical isolates. The urease phenotype in a large percentage of these isolates is unstable and lost upon storage. We examined two urease-positive uropathogenic E. coli isolates that give off urease-negative segregants and determined that the urease phenotype was chromosomally encoded. The urease phenotype was cloned from E. coli 1021 and found to be encoded on a 9.4-kilobase HindIII restriction fragment. Transposon mutagenesis indicated that at...

  2. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    Directory of Open Access Journals (Sweden)

    Erin M Siegel

    Full Text Available Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2. A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003. Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  3. Comparative proteomic analysis of proteins expression changes in the mammary tissue of cows infected with Escherichia coli mastitis.

    Science.gov (United States)

    Zhao, Xiao-wei; Yang, Yong-xin; Huang, Dong-wei; Cheng, Guang-long; Zhao, Hui-ling

    2015-01-01

    Cows infected with Escherichia (E.) coli usually experience severe clinical symptoms, including damage to mammary tissues, reduced milk yield, and altered milk composition. In order to investigate the host response to E. coli infection and discover novel markers for mastitis treatment, mammary tissue samples were collected from healthy cows and bovines with naturally occurring severe E. coli mastitis. Changes of mammary tissue proteins were examined using two-dimensional gel electrophoresis and label-free proteomic approaches. A total of 95 differentially expressed proteins were identified. Of these, 56 proteins were categorized according to molecular function, cellular component, and biological processes. The most frequent biological processes influenced by the proteins were response to stress, transport, and establishment of localization. Furthermore, a network analysis of the proteins with altered expression in mammary tissues demonstrated that these factors are predominantly involved with binding and structural molecule activities. Vimentin and a-enolase were central "functional hubs" in the network. Based on results from the present study, disease-induced alterations of protein expression in mammary glands and potential markers for the effective treatment of E. coli mastitis were identified. These data have also helped elucidate defense mechanisms that protect the mammary glands and promote the pathogenesis of E. coli mastitis.

  4. Optimal display conditions for quantitative analysis of stereoscopic cerebral angiograms

    International Nuclear Information System (INIS)

    Charland, P.; Peters, T.; McGill Univ., Montreal, Quebec

    1996-01-01

    For several years the authors have been using a stereoscopic display as a tool in the planning of stereotactic neurosurgical techniques. This PC-based workstation allows the surgeon to interact with and view vascular images in three dimensions, as well as to perform quantitative analysis of the three-dimensional (3-D) space. Some of the perceptual issues relevant to the presentation of medical images on this stereoscopic display were addressed in five experiments. The authors show that a number of parameters--namely the shape, color, and depth cue, associated with a cursor--as well as the image filtering and observer position, have a role in improving the observer's perception of a 3-D image and his ability to localize points within the stereoscopically presented 3-D image. However, an analysis of the results indicates that while varying these parameters can lead to an effect on the performance of individual observers, the effects are not consistent across observers, and the mean accuracy remains relatively constant under the different experimental conditions

  5. Quantitative Machine Learning Analysis of Brain MRI Morphology throughout Aging.

    Science.gov (United States)

    Shamir, Lior; Long, Joe

    2016-01-01

    While cognition is clearly affected by aging, it is unclear whether the process of brain aging is driven solely by accumulation of environmental damage, or involves biological pathways. We applied quantitative image analysis to profile the alteration of brain tissues during aging. A dataset of 463 brain MRI images taken from a cohort of 416 subjects was analyzed using a large set of low-level numerical image content descriptors computed from the entire brain MRI images. The correlation between the numerical image content descriptors and the age was computed, and the alterations of the brain tissues during aging were quantified and profiled using machine learning. The comprehensive set of global image content descriptors provides high Pearson correlation of ~0.9822 with the chronological age, indicating that the machine learning analysis of global features is sensitive to the age of the subjects. Profiling of the predicted age shows several periods of mild changes, separated by shorter periods of more rapid alterations. The periods with the most rapid changes were around the age of 55, and around the age of 65. The results show that the process of brain aging of is not linear, and exhibit short periods of rapid aging separated by periods of milder change. These results are in agreement with patterns observed in cognitive decline, mental health status, and general human aging, suggesting that brain aging might not be driven solely by accumulation of environmental damage. Code and data used in the experiments are publicly available.

  6. Automatic quantitative analysis of liver functions by a computer system

    International Nuclear Information System (INIS)

    Shinpo, Takako

    1984-01-01

    In the previous paper, we confirmed the clinical usefulness of hepatic clearance (hepatic blood flow), which is the hepatic uptake and blood disappearance rate coefficients. These were obtained by the initial slope index of each minute during a period of five frames of a hepatogram by injecting sup(99m)Tc-Sn-colloid 37 MBq. To analyze the information simply, rapidly and accurately, we developed a automatic quantitative analysis for liver functions. Information was obtained every quarter minute during a period of 60 frames of the sequential image. The sequential counts were measured for the heart, whole liver, both left lobe and right lobes using a computer connected to a scintillation camera. We measured the effective hepatic blood flow, from the disappearance rate multiplied by the percentage of hepatic uptake as follows, (liver counts)/(tatal counts of the field) Our method of analysis automatically recorded the reappearance graph of the disappearance curve and uptake curve on the basis of the heart and the whole liver, respectively; and computed using BASIC language. This method makes it possible to obtain the image of the initial uptake of sup(99m)Tc-Sn-colloid into the liver by a small dose of it. (author)

  7. Quantitative analysis of normal thallium-201 tomographic studies

    International Nuclear Information System (INIS)

    Eisner, R.L.; Gober, A.; Cerqueira, M.

    1985-01-01

    To determine the normal (nl) distribution of Tl-201 uptake post exercise (EX) and at redistribution (RD) and nl washout, Tl-201 rotational tomographic (tomo) studies were performed in 40 subjects: 16 angiographic (angio) nls and 24 nl volunteers (12 from Emory and 12 from Yale). Oblique angle short axis slices were subjected to maximal count circumferential profile analysis. Data were displayed as a ''bullseye'' functional map with the apex at the center and base at the periphery. The bullseye was not uniform in all regions because of the variable effects of attenuation and resolution at different view angles. In all studies, the septum: lateral wall ratio was 1.0 in males and approximately equal to 1.0 in females. This occurred predominantly because of anterior defects due to breast soft tissue attenuation. EX and RD bullseyes were similar. Using a bi-exponential model for Tl kinetics, 4 hour normalized washout ranged 49-54% in each group and showed minimal variation between walls throughout the bullseye. Thus, there are well defined variations in Tl-201 uptake in the nl myocardium which must be taken into consideration when analyzing pt data. Because of these defects and the lack of adequate methods for attenuation correction, quantitative analysis of Tl-201 studies must include direct comparison with gender-matched nl data sets

  8. Quantitative analysis of the security performance in wireless LANs

    Directory of Open Access Journals (Sweden)

    Poonam Jindal

    2017-07-01

    Full Text Available A comprehensive experimental study to analyze the security performance of a WLAN based on IEEE 802.11 b/g/n standards in various network scenarios is presented in this paper. By setting-up an experimental testbed we have measured results for a layered security model in terms of throughput, response time, encryption overheads, frame loss and jitter. Through numerical results obtained from the testbed, we have presented quantitative as well as realistic findings for both security mechanisms and network performance. It establishes the fact that there is always a tradeoff between the security strength and the associated network performance. It is observed that the non-roaming network always performs better than the roaming network under all network scenarios. To analyze the benefits offered by a particular security protocol a relative security strength index model is demonstrated. Further we have presented the statistical analysis of our experimental data. We found that different security protocols have different robustness against mobility. By choosing the robust security protocol, network performance can be improved. The presented analysis is significant and useful with reference to the assessment of the suitability of security protocols for given real time application.

  9. Analysis of the human intestinal epithelial cell transcriptional response to Lactobacillus acidophilus, Lactobacillus salivarius, Bifidobacterium lactis and Escherichia coli

    DEFF Research Database (Denmark)

    Putaala, H; Barrangou, R; Leyer, G J

    2010-01-01

    a comparative analysis of the global in vitro transcriptional response of human intestinal epithelial cells to Lactobacillus acidophilus NCFM™, Lactobacillus salivarius Ls-33, Bifidobacterium animalis subsp. lactis 420, and enterohaemorrhagic Escherichia coli O157:H7 (EHEC). Interestingly, L. salivarius Ls-33...

  10. Structural and Functional Analysis of the Escherichia coli Acid-Sensing Histidine Kinase EvgS.

    Science.gov (United States)

    Sen, Hrishiraj; Aggarwal, Nikhil; Ishionwu, Chibueze; Hussain, Nosheen; Parmar, Chandni; Jamshad, Mohammed; Bavro, Vassiliy N; Lund, Peter A

    2017-09-15

    The EvgS/EvgA two-component system of Escherichia coli is activated in response to low pH and alkali metals and regulates many genes, including those for the glutamate-dependent acid resistance system and a number of efflux pumps. EvgS, the sensor kinase, is one of five unconventional histidine kinases (HKs) in E. coli and has a large periplasmic domain and a cytoplasmic PAS domain in addition to phospho-acceptor, HK and dimerization, internal receiver, and phosphotransfer domains. Mutations that constitutively activate the protein at pH 7 map to the PAS domain. Here, we built a homology model of the periplasmic region of EvgS, based on the structure of the equivalent region of the BvgS homologue, to guide mutagenesis of potential key residues in this region. We show that histidine 226 is required for induction and that it is structurally colocated with a proline residue (P522) at the top of the predicted transmembrane helix that is expected to play a key role in passing information to the cytoplasmic domains. We also show that the constitutive mutations in the PAS domain can be further activated by low external pH. Expression of the cytoplasmic part of the protein alone also gives constitutive activation, which is lost if the constitutive PAS mutations are present. These findings are consistent with a model in which EvgS senses both external and internal pH and is activated by a shift from a tight inactive to a weak active dimer, and we present an analysis of the purified cytoplasmic portion of EvgS that supports this. IMPORTANCE One of the ways bacteria sense their environment is through two-component systems, which have one membrane-bound protein to do the sensing and another inside the cell to turn genes on or off in response to what the membrane-bound protein has detected. The membrane-bound protein must thus be able to detect the stress and signal this detection event to the protein inside the cell. To understand this process, we studied a protein that helps

  11. Quantitative analysis of left ventricular strain using cardiac computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Buss, Sebastian J., E-mail: sebastian.buss@med.uni-heidelberg.de [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Schulz, Felix; Mereles, Derliz [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Hosch, Waldemar [Department of Diagnostic and Interventional Radiology, University of Heidelberg, 69120 Heidelberg (Germany); Galuschky, Christian; Schummers, Georg; Stapf, Daniel [TomTec Imaging Systems GmbH, Munich (Germany); Hofmann, Nina; Giannitsis, Evangelos; Hardt, Stefan E. [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Kauczor, Hans-Ulrich [Department of Diagnostic and Interventional Radiology, University of Heidelberg, 69120 Heidelberg (Germany); Katus, Hugo A.; Korosoglou, Grigorios [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany)

    2014-03-15

    Objectives: To investigate whether cardiac computed tomography (CCT) can determine left ventricular (LV) radial, circumferential and longitudinal myocardial deformation in comparison to two-dimensional echocardiography in patients with congestive heart failure. Background: Echocardiography allows for accurate assessment of strain with high temporal resolution. A reduced strain is associated with a poor prognosis in cardiomyopathies. However, strain imaging is limited in patients with poor echogenic windows, so that, in selected cases, tomographic imaging techniques may be preferable for the evaluation of myocardial deformation. Methods: Consecutive patients (n = 27) with congestive heart failure who underwent a clinically indicated ECG-gated contrast-enhanced 64-slice dual-source CCT for the evaluation of the cardiac veins prior to cardiac resynchronization therapy (CRT) were included. All patients underwent additional echocardiography. LV radial, circumferential and longitudinal strain and strain rates were analyzed in identical midventricular short axis, 4-, 2- and 3-chamber views for both modalities using the same prototype software algorithm (feature tracking). Time for analysis was assessed for both modalities. Results: Close correlations were observed for both techniques regarding global strain (r = 0.93, r = 0.87 and r = 0.84 for radial, circumferential and longitudinal strain, respectively, p < 0.001 for all). Similar trends were observed for regional radial, longitudinal and circumferential strain (r = 0.88, r = 0.84 and r = 0.94, respectively, p < 0.001 for all). The number of non-diagnostic myocardial segments was significantly higher with echocardiography than with CCT (9.6% versus 1.9%, p < 0.001). In addition, the required time for complete quantitative strain analysis was significantly shorter for CCT compared to echocardiography (877 ± 119 s per patient versus 1105 ± 258 s per patient, p < 0.001). Conclusion: Quantitative assessment of LV strain

  12. Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in e. coli

    Science.gov (United States)

    Genome-based Flux Balance Analysis (FBA, constraints based flux analysis) and steady state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here a genome-derived model of E. coli metabol...

  13. Quantitative assessment of early diabetic retinopathy using fractal analysis.

    Science.gov (United States)

    Cheung, Ning; Donaghue, Kim C; Liew, Gerald; Rogers, Sophie L; Wang, Jie Jin; Lim, Shueh-Wen; Jenkins, Alicia J; Hsu, Wynne; Li Lee, Mong; Wong, Tien Y

    2009-01-01

    Fractal analysis can quantify the geometric complexity of the retinal vascular branching pattern and may therefore offer a new method to quantify early diabetic microvascular damage. In this study, we examined the relationship between retinal fractal dimension and retinopathy in young individuals with type 1 diabetes. We conducted a cross-sectional study of 729 patients with type 1 diabetes (aged 12-20 years) who had seven-field stereoscopic retinal photographs taken of both eyes. From these photographs, retinopathy was graded according to the modified Airlie House classification, and fractal dimension was quantified using a computer-based program following a standardized protocol. In this study, 137 patients (18.8%) had diabetic retinopathy signs; of these, 105 had mild retinopathy. Median (interquartile range) retinal fractal dimension was 1.46214 (1.45023-1.47217). After adjustment for age, sex, diabetes duration, A1C, blood pressure, and total cholesterol, increasing retinal vascular fractal dimension was significantly associated with increasing odds of retinopathy (odds ratio 3.92 [95% CI 2.02-7.61] for fourth versus first quartile of fractal dimension). In multivariate analysis, each 0.01 increase in retinal vascular fractal dimension was associated with a nearly 40% increased odds of retinopathy (1.37 [1.21-1.56]). This association remained after additional adjustment for retinal vascular caliber. Greater retinal fractal dimension, representing increased geometric complexity of the retinal vasculature, is independently associated with early diabetic retinopathy signs in type 1 diabetes. Fractal analysis of fundus photographs may allow quantitative measurement of early diabetic microvascular damage.

  14. Nanotechnology patents in the automotive industry (a quantitative & qualitative analysis).

    Science.gov (United States)

    Prasad, Raghavendra; Bandyopadhyay, Tapas K

    2014-01-01

    The aim of the article is to present a trend in patent filings for application of nanotechnology to the automobile sector across the world, using the keyword-based patent search. Overviews of the patents related to nano technology in the automobile industry have been provided. The current work has started from the worldwide patent search to find the patents on nanotechnology in the automobile industry and classify the patents according to the various parts of an automobile to which they are related and the solutions which they are providing. In the next step various graphs have been produced to get an insight into various trends. In next step, analysis of patents in various classifications, have been performed. The trends shown in graphs provide the quantitative analysis whereas; the qualitative analysis has been done in another section. The classifications of patents based on the solution they provide have been performed by reading the claims, titles, abstract and full texts separately. Patentability of nano technology inventions have been discussed in a view to give an idea of requirements and statutory bars to the patentability of nanotechnology inventions. Another objective of the current work is to suggest appropriate framework for the companies regarding use of nano technology in the automobile industry and a suggestive strategy for patenting of the inventions related to the same. For example, US Patent, with patent number US2008-019426A1 discusses the invention related to Lubricant composition. This patent has been studied and classified to fall under classification of automobile parts. After studying this patent, it is deduced that, the problem of friction in engine is being solved by this patent. One classification is the "automobile part" based while other is the basis of "problem being solved". Hence, two classifications, namely reduction in friction and engine were created. Similarly, after studying all the patents, a similar matrix has been created.

  15. Collocations and collocation types in ESP textbooks: Quantitative pedagogical analysis

    Directory of Open Access Journals (Sweden)

    Bogdanović Vesna Ž.

    2016-01-01

    Full Text Available The term collocation, even though it is rather common in the English language grammar, it is not a well known or commonly used term in the textbooks and scientific papers written in the Serbian language. Collocating is usually defined as a natural appearance of two (or more words, which are usually one next to another even though they can be separated in the text, while collocations are defined as words with natural semantic and/or syntactic relations being joined together in a sentence. Collocations are naturally used in all English written texts, including scientific texts and papers. Using two textbooks for English for Specific Purposes (ESP for intermediate students' courses, this paper presents the frequency of collocations and their typology. The paper tries to investigate the relationship between lexical and grammatical collocations written in the ESP texts and the reasons for their presence. There is an overview of the most used subtypes of lexical collocations as well. Furthermore, on applying the basic corpus analysis based on the quantitative analysis, the paper presents the number of open, restricted and bound collocations in ESP texts, trying to draw conclusions on their frequency and hence the modes for their learning. There is also a section related to the number and usage of scientific collocations, both common scientific and narrow-professional ones. The conclusion is that the number of present collocations in the selected two textbooks imposes a demand for further analysis of these lexical connections, as well as new modes for their teaching and presentations to the English learning students.

  16. The Measles Vaccination Narrative in Twitter: A Quantitative Analysis.

    Science.gov (United States)

    Radzikowski, Jacek; Stefanidis, Anthony; Jacobsen, Kathryn H; Croitoru, Arie; Crooks, Andrew; Delamater, Paul L

    2016-01-01

    The emergence of social media is providing an alternative avenue for information exchange and opinion formation on health-related issues. Collective discourse in such media leads to the formation of a complex narrative, conveying public views and perceptions. This paper presents a study of Twitter narrative regarding vaccination in the aftermath of the 2015 measles outbreak, both in terms of its cyber and physical characteristics. We aimed to contribute to the analysis of the data, as well as presenting a quantitative interdisciplinary approach to analyze such open-source data in the context of health narratives. We collected 669,136 tweets referring to vaccination from February 1 to March 9, 2015. These tweets were analyzed to identify key terms, connections among such terms, retweet patterns, the structure of the narrative, and connections to the geographical space. The data analysis captures the anatomy of the themes and relations that make up the discussion about vaccination in Twitter. The results highlight the higher impact of stories contributed by news organizations compared to direct tweets by health organizations in communicating health-related information. They also capture the structure of the antivaccination narrative and its terms of reference. Analysis also revealed the relationship between community engagement in Twitter and state policies regarding child vaccination. Residents of Vermont and Oregon, the two states with the highest rates of non-medical exemption from school-entry vaccines nationwide, are leading the social media discussion in terms of participation. The interdisciplinary study of health-related debates in social media across the cyber-physical debate nexus leads to a greater understanding of public concerns, views, and responses to health-related issues. Further coalescing such capabilities shows promise towards advancing health communication, thus supporting the design of more effective strategies that take into account the complex

  17. Lab-on-capillary: a rapid, simple and quantitative genetic analysis platform integrating nucleic acid extraction, amplification and detection.

    Science.gov (United States)

    Fu, Yu; Zhou, Xiaoming; Xing, Da

    2017-12-05

    In this work, we describe for the first time a genetic diagnosis platform employing a polydiallyldimethylammonium chloride (PDDA)-modified capillary and a liquid-based thermalization system for rapid, simple and quantitative DNA analysis with minimal user interaction. Positively charged PDDA is modified on the inner surface of the silicon dioxide capillary by using an electrostatic self-assembly approach that allows the negatively charged DNA to be separated from the lysate in less than 20 seconds. The capillary loaded with the PCR mix is incorporated in the thermalization system, which can achieve on-site real-time PCR. This system is based on the circulation of pre-heated liquids in the chamber, allowing for high-speed thermalization of the capillary and fast amplification. Multiple targets can be simultaneously analysed with multiplex spatial melting. Starting with live Escherichia coli (E. coli) cells in milk, as a realistic sample, the current method can achieve DNA extraction, amplification, and detection within 40 min.

  18. Quantitative risk analysis of urban flooding in lowland areas

    NARCIS (Netherlands)

    Ten Veldhuis, J.A.E.

    2010-01-01

    Urban flood risk analyses suffer from a lack of quantitative historical data on flooding incidents. Data collection takes place on an ad hoc basis and is usually restricted to severe events. The resulting data deficiency renders quantitative assessment of urban flood risks uncertain. The study

  19. DEVELOPMENT OF TECHNIQUES FOR QUANTITATIVE ANALYSIS OF LIME FLOWERS

    Directory of Open Access Journals (Sweden)

    Demyanenko DV

    2016-03-01

    Full Text Available Introduction. The article is devoted to the development of techniques for quantitative analysis of lime flower in order to make amendments to existing pharmacopoeian monographs for this herbal drug. Lime inflorescences contain lipophilic biologically active substances (BAS causing notable antimicrobial and anti-inflammatory effects and also more polar phenolic compounds with antiulcer activity. Considering this, it’s necessary to regulate all these groups of BAS quantitatively. Materials and methods. For this study six batches of lime flowers harvested in 2008-2009 yrs. in Kharkiv, Rivno and Zhitomir regions were used as crude herbal drug. Loss on drying was determined by routine pharmacopoeian procedures. Total content of lipophilic substances was determined gravimetrically after Soxhlet extraction of samples 1, 5, 7 and 10 g in weight with methylene chloride, considering that by its extracting ability this solvent is close to liquefied difluorochloromethane (freon R22 used by us for obtaining of lipophilic complexes. The duration of complete analytical extraction was determined by infusion of six 10 g assays of lime flowers during 1, 2, 3, 4, 5, 6 hours, then quantity of lipophilic extractives was revealed gravimetrically. Quantity of essential oil in lime flowers was evaluated under the procedure of ЕР7, 2.8.12. Weight of the herbal drug sample was 200 g, distillation rate – 2,5- 3,5 ml/min, volume of distillation liquid (water – 500 ml, volume of xylene in the graduated tube – 0,50 ml. Total flavonoid content recalculated to quercetin was determined after hydrolysis with acidified acetone, withdrawing of flavonoid aglycones with ethylacetate and by further spectrophotometry of their complexes with aluminium chloride. All quantitative determinations were replicated five times for each assay. All chemicals and reagents were of analytical grade. Results and discussion. It was found that adequate accuracy of the analysis of lipophilic

  20. A Quantitative Analysis of Photovoltaic Modules Using Halved Cells

    Directory of Open Access Journals (Sweden)

    S. Guo

    2013-01-01

    Full Text Available In a silicon wafer-based photovoltaic (PV module, significant power is lost due to current transport through the ribbons interconnecting neighbour cells. Using halved cells in PV modules is an effective method to reduce the resistive power loss which has already been applied by some major PV manufacturers (Mitsubishi, BP Solar in their commercial available PV modules. As a consequence, quantitative analysis of PV modules using halved cells is needed. In this paper we investigate theoretically and experimentally the difference between modules made with halved and full-size solar cells. Theoretically, we find an improvement in fill factor of 1.8% absolute and output power of 90 mW for the halved cell minimodule. Experimentally, we find an improvement in fill factor of 1.3% absolute and output power of 60 mW for the halved cell module. Also, we investigate theoretically how this effect confers to the case of large-size modules. It is found that the performance increment of halved cell PV modules is even higher for high-efficiency solar cells. After that, the resistive loss of large-size modules with different interconnection schemes is analysed. Finally, factors influencing the performance and cost of industrial halved cell PV modules are discussed.

  1. Field nonuniformity correction for quantitative analysis of digitized mammograms

    International Nuclear Information System (INIS)

    Pawluczyk, Olga; Yaffe, Martin J.

    2001-01-01

    Several factors, including the heel effect, variation in distance from the x-ray source to points in the image and path obliquity contribute to the signal nonuniformity of mammograms. To best use digitized mammograms for quantitative image analysis, these field non-uniformities must be corrected. An empirically based correction method, which uses a bowl-shaped calibration phantom, has been developed. Due to the annular spherical shape of the phantom, its attenuation is constant over the entire image. Remaining nonuniformities are due only to the heel and inverse square effects as well as the variable path through the beam filter, compression plate and image receptor. In logarithmic space, a normalized image of the phantom can be added to mammograms to correct for these effects. Then, an analytical correction for path obliquity in the breast can be applied to the images. It was found that the correction causes the errors associated with field nonuniformity to be reduced from 14% to 2% for a 4 cm block of material corresponding to a combination of 50% fibroglandular and 50% fatty breast tissue. A repeatability study has been conducted to show that in regions as far as 20 cm away from the chest wall, variations due to imaging conditions and phantom alignment contribute to <2% of overall corrected signal

  2. Full-Range Public Health Leadership, Part 1: Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Erik L. Carlton

    2015-04-01

    Full Text Available Background. Workforce and leadership development are central to the future of public health. However, public health has been slow to translate and apply leadership models from other professions and to incorporate local perspectives in understanding public health leadership. Purpose. This study utilized the full-range leadership model in order to examine public health leadership. Specifically, it sought to measure leadership styles among local health department directors and to understand the context of leadership local health departments.Methods. Leadership styles among local health department directors (n=13 were examined using survey methodology. Quantitative analysis methods included descriptive statistics, boxplots, and Pearson bivariate correlations using SPSS v18.0. Findings. Self-reported leadership styles were highly correlated to leadership outcomes at the organizational level. However, they were not related to county health rankings. Results suggest the preeminence of leader behaviors and providing individual consideration to staff as compared to idealized attributes of leaders, intellectual stimulation, or inspirational motivation. Implications. Holistic leadership assessment instruments, such as the Multifactor Leadership Questionnaire (MLQ can be useful in assessing public health leaders approaches and outcomes. Comprehensive, 360-degree reviews may be especially helpful. Further research is needed to examine the effectiveness of public health leadership development models, as well as the extent that public health leadership impacts public health outcomes.

  3. Quantitative analysis of dynamic association in live biological fluorescent samples.

    Directory of Open Access Journals (Sweden)

    Pekka Ruusuvuori

    Full Text Available Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed. Point-pattern matching provides a measure of correspondence between two point-sets under various changes between the sets. Thus, it can be used for robust quantitative analysis of vesicle association between image channels. Results for a large set of synthetic images shows that the novel association method based on point-pattern matching demonstrates robust capability to detect association of closely located vesicles in live cell-microscopy where traditional colocalization methods fail to produce results. In addition, the method outperforms compared Iterated Closest Points registration method. Results for fixed and live experimental data shows the association method to perform comparably to traditional methods in colocalization studies for fixed cells and to perform favorably in association studies for live cells.

  4. Qualitative and quantitative analysis of plutonium in solid waste drums

    International Nuclear Information System (INIS)

    Anno, Jacques; Escarieux, Emile

    1977-01-01

    An assessment of the results given by a study carried out for the development of qualitative and quantitative analysis, by γ spectrometry, of plutonium in solid waste drums is presented. After having reminded the standards and their incidence on the quantities of plutonium to be measured (application at industrial Pu: 20% of Pu 240 ) the equipment used is described. Measurement station provided with a mechanical system consisting of: a rail and a pulley block to bring the drums; a pit and a hydraulic jack with a rotating platform. The detection instrumentation consisting of: a high volume coaxial Ge(Li) detector with a γ ray resolution of 2 keV; an associated electronic; a processing of data by a 'Plurimat 20' minicomputer. Principles of the identification and measurements are specified and supported by experimental results. They are the following: determination of the quality of Pu by measuring the ratio between the γ ray intensities of the 239 Pu 129 keV and of the 241 Pu 148 keV; measurement of the 239 Pu mass by estimating the γ ray counting rate of the 375 keV from the calibrating curves given by plutonium samples varying from 32 mg to 80 g; correction of the results versus the source position into the drum and versus the filling in plastic materials into this drum. The experimental results obtained over 40 solid waste drums are presented along with the error estimates [fr

  5. A temperature-controlled photoelectrochemical cell for quantitative product analysis

    Science.gov (United States)

    Corson, Elizabeth R.; Creel, Erin B.; Kim, Youngsang; Urban, Jeffrey J.; Kostecki, Robert; McCloskey, Bryan D.

    2018-05-01

    In this study, we describe the design and operation of a temperature-controlled photoelectrochemical cell for analysis of gaseous and liquid products formed at an illuminated working electrode. This cell is specifically designed to quantitatively analyze photoelectrochemical processes that yield multiple gas and liquid products at low current densities and exhibit limiting reactant concentrations that prevent these processes from being studied in traditional single chamber electrolytic cells. The geometry of the cell presented in this paper enables front-illumination of the photoelectrode and maximizes the electrode surface area to electrolyte volume ratio to increase liquid product concentration and hence enhances ex situ spectroscopic sensitivity toward them. Gas is bubbled through the electrolyte in the working electrode chamber during operation to maintain a saturated reactant concentration and to continuously mix the electrolyte. Gaseous products are detected by an in-line gas chromatograph, and liquid products are analyzed ex situ by nuclear magnetic resonance. Cell performance was validated by examining carbon dioxide reduction on a silver foil electrode, showing comparable results both to those reported in the literature and identical experiments performed in a standard parallel-electrode electrochemical cell. To demonstrate a photoelectrochemical application of the cell, CO2 reduction experiments were carried out on a plasmonic nanostructured silver photocathode and showed different product distributions under dark and illuminated conditions.

  6. FFT transformed quantitative EEG analysis of short term memory load.

    Science.gov (United States)

    Singh, Yogesh; Singh, Jayvardhan; Sharma, Ratna; Talwar, Anjana

    2015-07-01

    The EEG is considered as building block of functional signaling in the brain. The role of EEG oscillations in human information processing has been intensively investigated. To study the quantitative EEG correlates of short term memory load as assessed through Sternberg memory test. The study was conducted on 34 healthy male student volunteers. The intervention consisted of Sternberg memory test, which runs on a version of the Sternberg memory scanning paradigm software on a computer. Electroencephalography (EEG) was recorded from 19 scalp locations according to 10-20 international system of electrode placement. EEG signals were analyzed offline. To overcome the problems of fixed band system, individual alpha frequency (IAF) based frequency band selection method was adopted. The outcome measures were FFT transformed absolute powers in the six bands at 19 electrode positions. Sternberg memory test served as model of short term memory load. Correlation analysis of EEG during memory task was reflected as decreased absolute power in Upper alpha band in nearly all the electrode positions; increased power in Theta band at Fronto-Temporal region and Lower 1 alpha band at Fronto-Central region. Lower 2 alpha, Beta and Gamma band power remained unchanged. Short term memory load has distinct electroencephalographic correlates resembling the mentally stressed state. This is evident from decreased power in Upper alpha band (corresponding to Alpha band of traditional EEG system) which is representative band of relaxed mental state. Fronto-temporal Theta power changes may reflect the encoding and execution of memory task.

  7. Quantitative risk analysis of the pipeline GASDUC III - solutions

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Edmilson P.; Bettoni, Izabel Cristina [PETROBRAS, Rio de Janeiro, RJ (Brazil)

    2009-07-01

    In this work the quantitative risks analysis to the external public of the Pipeline Cabiunas - REDUC (GASDUC III), with 180 km, linking the municipalities of Macae and Duque de Caxias - RJ was performed by the Companies PETROBRAS and ITSEMAP do Brasil. In addition to the large diameter of the pipeline 38 inches and high operation pressure 100 kgf/cm{sup 2} operating with natural gas through several densely populated areas. Initially, the individual risk contours were calculated without considering mitigating measures, obtaining as result the individual risk contour with frequencies of 1x10{sup -06} per year involving sensitive occupations and therefore considered unacceptable when compared with the INEA criterion. The societal risk was calculated for eight densely populated areas and their respective FN-curves situated below the advised limit established by INEA, except for two areas that required the proposal of additional mitigating measures to the reduction of societal risk. Regarding to societal risk, the FN-curve should be below the advised limit presented in the Technical Instruction of INEA. The individual and societal risk were reassessed incorporating some mitigating measures and the results situated below the advised limits established by INEA and PETROBRAS has obtained the license for installation of the pipeline. (author)

  8. Quantitative immunoelectrophoretic analysis of extract from cow hair and dander

    Energy Technology Data Exchange (ETDEWEB)

    Prahl, P; Weeke, B; Loewenstein, H [Rigshospitalet, Copenhagen (Denmark)

    1978-01-01

    Quantitative immunoelectrophoresis used for the analysis of a dialysed, centrifuged and freeze-dried extract from cow hair and dander revealed 17 antigens. Five of these were identified as serum proteins. Partial identity to antigens of serum and extract from hair and dander of goat, sheep, swine, horse, dog, cat, and guinea pig, and to antigens of house dust was demonstrated. Sera from 36 patients with manifest allergy to cow hair and dander selected on the basis of case history, RAST, skin and provocation test, were examined in crossed radioimmunoelectrophoresis (CRIE); sera from five persons with high serum IgE, but without allergy to cow hair and dander, and sera from five normal individuals were controls. 31/36 of the sera contained IgE with specific affinity for two of the antigens of the extract. Further, two major and six minor allergens were identified. The control sera showed no specific IgE binding. A significant positive correlation was found between RAST and CRIE for the first group of patients. The approximate molecular weights of the four major allergens obtained by means of gel chromatography were: 2.4 x 10/sup 4/, 2 x 10/sup 4/, 2 x 10/sup 5/ dalton, respectively. Using Con-A and Con-A Sepharose in crossed immunoaffinoelectrophoresis, eight of the antigens were revealed to contain groups with affinity for Con-A.

  9. Quantitative produced water analysis using mobile 1H NMR

    International Nuclear Information System (INIS)

    Wagner, Lisabeth; Fridjonsson, Einar O; May, Eric F; Stanwix, Paul L; Graham, Brendan F; Carroll, Matthew R J; Johns, Michael L; Kalli, Chris

    2016-01-01

    Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1 H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1 H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1 H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1–30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography. (paper)

  10. Photographers’ Nomenclature Units: A Structural and Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Margarita A. Mihailova

    2017-11-01

    Full Text Available Addressing the needs of cross and intercultural communication as well as the methodology of contrastive research, the paper presents the results of the complex analysis conducted to describe semantic and pragmatic parameters of nomenclature units denoting photography equipment in the modern Russian informal discourse of professional photographers. The research is exemplified by 34 original nomenclature units and their 34 Russian equivalents used in 6871 comments posted at “Клуб.Foto.ru” web-site in 2015. The structural and quantitative analyses of photographers’ nomenclature demonstrate the users’ morphological and graphic preferences and indirectly reflect their social and professional values. The corpus-based approach developed by Kast-Aigner (2009: 141 was applied in the study with the aim to identify the nomenclature units denoting photography equipment, validate and elaborate the data of the existing corpus. The research also throws light on the problems of professional language development and derivational processes. The perspective of the study lies in the research of the broader context of professional nomenclature.

  11. Quantitative immunoelectrophoretic analysis of extract from cow hair and dander

    International Nuclear Information System (INIS)

    Prahl, P.; Weeke, B.; Loewenstein, H.

    1978-01-01

    Quantitative immunoelectrophoresis used for the analysis of a dialysed, centrifuged and freeze-dried extract from cow hair and dander revealed 17 antigens. Five of these were identified as serum proteins. Partial identity to antigens of serum and extract from hair and dander of goat, sheep, swine, horse, dog, cat, and guinea pig, and to antigens of house dust was demonstrated. Sera from 36 patients with manifest allergy to cow hair and dander selected on the basis of case history, RAST, skin and provocation test, were examined in crossed radioimmunoelectrophoresis (CRIE); sera from five persons with high serum IgE, but without allergy to cow hair and dander, and sera from five normal individuals were controls. 31/36 of the sera contained IgE with specific affinity for two of the antigens of the extract. Further, two major and six minor allergens were identified. The control sera showed no specific IgE binding. A significant positive correlation was found between RAST and CRIE for the first group of patients. The approximate molecular weights of the four major allergens obtained by means of gel chromatography were: 2.4 x 10 4 , 2 x 10 4 , 2 x 10 5 dalton, respectively. Using Con-A and Con-A Sepharose in crossed immunoaffinoelectrophoresis, eight of the antigens were revealed to contain groups with affinity for Con-A. (author)

  12. Social media in epilepsy: A quantitative and qualitative analysis.

    Science.gov (United States)

    Meng, Ying; Elkaim, Lior; Wang, Justin; Liu, Jessica; Alotaibi, Naif M; Ibrahim, George M; Fallah, Aria; Weil, Alexander G; Valiante, Taufik A; Lozano, Andres M; Rutka, James T

    2017-06-01

    While the social burden of epilepsy has been extensively studied, an evaluation of social media related to epilepsy may provide novel insight into disease perception, patient needs and access to treatments. The objective of this study is to assess patterns in social media and online communication usage related to epilepsy and its associated topics. We searched two major social media platforms (Facebook and Twitter) for public accounts dedicated to epilepsy. Results were analyzed using qualitative and quantitative methodologies. The former involved thematic and word count analysis for online posts and tweets on these platforms, while the latter employed descriptive statistics and non-parametric tests. Facebook had a higher number of pages (840 accounts) and users (3 million) compared to Twitter (137 accounts and 274,663 users). Foundation and support groups comprised most of the accounts and users on both Facebook and Twitter. The number of accounts increased by 100% from 2012 to 2016. Among the 403 posts and tweets analyzed, "providing information" on medications or correcting common misconceptions in epilepsy was the most common theme (48%). Surgical interventions for epilepsy were only mentioned in 1% of all posts and tweets. The current study provides a comprehensive reference on the usage of social media in epilepsy. The number of online users interested in epilepsy is likely the highest among all neurological conditions. Surgery, as a method of treating refractory epilepsy, however, could be underrepresented on social media. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Phytochemical analysis and antimicrobial activity of baobab (Adansonia digitata leaves and stem bark extracts on Staphylococcus aureus and Escherichia coli

    Directory of Open Access Journals (Sweden)

    Mohammed Sani Sambo Datsugwai

    2017-05-01

    Full Text Available The phytochemical analysis and antibacterial activity of methanolic and ethanolic leaf and stem bark extracts of baobab tree on Escherichia coli and Staphylococcus aureus were carried out using agar well diffusion method. The clinical bacterial isolates of Escherichia coli and Staphylococcus aureus were obtained from Microbiology laboratory, Kaduna State University, Kaduna. The bacteria isolates were re-confirmed and identified based on their morphology, cultural characteristics and biochemical tests. The bacteria isolates were confirmed to be Escherichia coli and Staphylococcus aureus. The phytochemical analysis revealed the presence of Alkaloids, Saponins, Flavonoids, Tannins and Terpenoids. The methanolic leaf extract showed a wide range of activity on test isolates, with varying zones of inhibitions as 12 mm, 10 mm, 7 mm, and 4 mm against Staphylococcus aureus and 13 mm, 9 mm, 7 mm, and 3 mm against Escherichia coli at concentration of 1000 mg/ml, 500 mg/ml, 200 mg/ml and 100 mg/ml respectively. The ethanolic leaf extract also showed a wide range of activity on test isolates with varying zones of inhibitions, such as 11mm, 6mm, 5mm and 3mm against S. aureus and 8mm, 7mm, 5mm, and 4mm against E. coli at the concentration of 1000 mg/ml, 500mg/ml, 200 mg/ml and 100mg/ml for each respectively. The methanolic stem bark extract showed less antibacterial activity against the test isolates with the inhibition of 5mm and 4mm against S. aureus and 4mm and 3mm against E.coli at concentration of 1000 mg/ml and 500 mg/ml respectively with no zones of inhibition at concentration of 200 mg/ml and 100mg/ml. The ethanolic stem bark extract also showed no antibacterial activity with no zones of inhibition against the test isolates at concentration of 1000 mg/ml, 500 mg/ml, 200mg/ml and 100 mg/ml. The methanolic leaf extract inhibited the growth of S. aureus and E.coli at concentration of 100 mg/ml with minimum bactericidal concentration at 100 mg/ml. The

  14. B1 -sensitivity analysis of quantitative magnetization transfer imaging.

    Science.gov (United States)

    Boudreau, Mathieu; Stikov, Nikola; Pike, G Bruce

    2018-01-01

    To evaluate the sensitivity of quantitative magnetization transfer (qMT) fitted parameters to B 1 inaccuracies, focusing on the difference between two categories of T 1 mapping techniques: B 1 -independent and B 1 -dependent. The B 1 -sensitivity of qMT was investigated and compared using two T 1 measurement methods: inversion recovery (IR) (B 1 -independent) and variable flip angle (VFA), B 1 -dependent). The study was separated into four stages: 1) numerical simulations, 2) sensitivity analysis of the Z-spectra, 3) healthy subjects at 3T, and 4) comparison using three different B 1 imaging techniques. For typical B 1 variations in the brain at 3T (±30%), the simulations resulted in errors of the pool-size ratio (F) ranging from -3% to 7% for VFA, and -40% to > 100% for IR, agreeing with the Z-spectra sensitivity analysis. In healthy subjects, pooled whole-brain Pearson correlation coefficients for F (comparing measured double angle and nominal flip angle B 1 maps) were ρ = 0.97/0.81 for VFA/IR. This work describes the B 1 -sensitivity characteristics of qMT, demonstrating that it varies substantially on the B 1 -dependency of the T 1 mapping method. Particularly, the pool-size ratio is more robust against B 1 inaccuracies if VFA T 1 mapping is used, so much so that B 1 mapping could be omitted without substantially biasing F. Magn Reson Med 79:276-285, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  15. Quantitative Gait Analysis in Patients with Huntington’s Disease

    Directory of Open Access Journals (Sweden)

    Seon Jong Pyo

    2017-09-01

    Full Text Available Objective Gait disturbance is the main factor contributing to a negative impact on quality of life in patients with Huntington’s disease (HD. Understanding gait features in patients with HD is essential for planning a successful gait strategy. The aim of this study was to investigate temporospatial gait parameters in patients with HD compared with healthy controls. Methods We investigated 7 patients with HD. Diagnosis was confirmed by genetic analysis, and patients were evaluated with the Unified Huntington’s Disease Rating Scale (UHDRS. Gait features were assessed with a gait analyzer. We compared the results of patients with HD to those of 7 age- and sex-matched normal controls. Results Step length and stride length were decreased and base of support was increased in the HD group compared to the control group. In addition, coefficients of variability for step and stride length were increased in the HD group. The HD group showed slower walking velocity, an increased stance/swing phase in the gait cycle and a decreased proportion of single support time compared to the control group. Cadence did not differ significantly between groups. Among the UHDRS subscores, total motor score and total behavior score were positively correlated with step length, and total behavior score was positively correlated with walking velocity in patients with HD. Conclusion Increased variability in step and stride length, slower walking velocity, increased stance phase, and decreased swing phase and single support time with preserved cadence suggest that HD gait patterns are slow, ataxic and ineffective. This study suggests that quantitative gait analysis is needed to assess gait problems in HD.

  16. Quantitative analysis of LISA pathfinder test-mass noise

    International Nuclear Information System (INIS)

    Ferraioli, Luigi; Congedo, Giuseppe; Hueller, Mauro; Vitale, Stefano; Hewitson, Martin; Nofrarias, Miquel; Armano, Michele

    2011-01-01

    LISA Pathfinder (LPF) is a mission aiming to test the critical technology for the forthcoming space-based gravitational-wave detectors. The main scientific objective of the LPF mission is to demonstrate test masses free falling with residual accelerations below 3x10 -14 m s -2 /√(Hz) at 1 mHz. Reaching such an ambitious target will require a significant amount of system optimization and characterization, which will in turn require accurate and quantitative noise analysis procedures. In this paper, we discuss two main problems associated with the analysis of the data from LPF: i) excess noise detection and ii) noise parameter identification. The mission is focused on the low-frequency region ([0.1, 10] mHz) of the available signal spectrum. In such a region, the signal is dominated by the force noise acting on test masses. At the same time, the mission duration is limited to 90 days and typical data segments will be 24 hours in length. Considering those constraints, noise analysis is expected to deal with a limited amount of non-Gaussian data, since the spectrum statistics will be far from Gaussian and the lowest available frequency is limited by the data length. In this paper, we analyze the details of the expected statistics for spectral data and develop two suitable excess noise estimators. One is based on the statistical properties of the integrated spectrum, the other is based on the Kolmogorov-Smirnov test. The sensitivity of the estimators is discussed theoretically for independent data, then the algorithms are tested on LPF synthetic data. The test on realistic LPF data allows the effect of spectral data correlations on the efficiency of the different noise excess estimators to be highlighted. It also reveals the versatility of the Kolmogorov-Smirnov approach, which can be adapted to provide reasonable results on correlated data from a modified version of the standard equations for the inversion of the test statistic. Closely related to excess noise

  17. Qualitative and Quantitative Analysis for US Army Recruiting Input Allocation

    National Research Council Canada - National Science Library

    Brence, John

    2004-01-01

    .... An objective study of the quantitative and qualitative aspects of recruiting is necessary to meet the future needs of the Army, in light of strong possibilities of recruiting resource reduction...

  18. Quantitative analysis of psychological personality for NPP operators

    International Nuclear Information System (INIS)

    Gao Jia; Huang Xiangrui

    1998-01-01

    The author introduces the relevant personality quantitative psychological research work carried out by 'Prognoz' Laboratory and Taiwan, and presents the primary results of the research for Chinese Nuclear Power Plant (NPP) operator's psychological personality assessment, which based on the survey of MMPI, and presents the main contents for the personality quantitative psychological research in NPP of China. And emphasizes the need to carry out psychological selection and training in nuclear industry

  19. Hydrocarbons on Phoebe, Iapetus, and Hyperion: Quantitative Analysis

    Science.gov (United States)

    Cruikshank, Dale P.; MoreauDalleOre, Cristina; Pendleton, Yvonne J.; Clark, Roger Nelson

    2012-01-01

    We present a quantitative analysis of the hydrocarbon spectral bands measured on three of Saturn's satellites, Phoebe, Iaperus, and Hyperion. These bands, measured with the Cassini Visible-Infrared Mapping Spectrometer on close fly-by's of these satellites, are the C-H stretching modes of aromatic hydrocarbons at approximately 3.28 micrometers (approximately 3050 per centimeter), and the are four blended bands of aliphatic -CH2- and -CH3 in the range approximately 3.36-3.52 micrometers (approximately 2980- 2840 per centimeter) bably indicating the presence of polycyclic aromatic hydrocarbons (PAH), is unusually strong in comparison to the aliphatic bands, resulting in a unique signarure among Solar System bodies measured so far, and as such offers a means of comparison among the three satellites. The ratio of the C-H bands in aromatic molecules to those in aliphatic molecules in the surface materials of Phoebe, NAro:NAliph approximately 24; for Hyperion the value is approximately 12, while laperus shows an intermediate value. In view of the trend of the evolution (dehydrogenation by heat and radiation) of aliphatic complexes toward more compact molecules and eventually to aromatics, the relative abundances of aliphatic -CH2- and -CH3- is an indication of the lengths of the molecular chain structures, hence the degree of modification of the original material. We derive CH2:CH3 approximately 2.2 in the spectrum of low-albedo material on laperus; this value is the same within measurement errors to the ratio in the diffuse interstellar medium. The similarity in the spectral signatures of the three satellites, plus the apparent weak trend of aromatic/aliphatic abundance from Phoebe to Hyperion, is consistent with, and effectively confirms that the source of the hydrocarbon-bearing material is Phoebe, and that the appearance of that material on the other two satellites arises from the deposition of the inward-spiraling dust that populates the Phoebe ring.

  20. A qualitative and quantitative analysis of vegetable pricing in supermarket

    Science.gov (United States)

    Miranda, Suci

    2017-06-01

    The purpose of this study is to analyze the variables affecting the determination of the sale price of vegetable which is constant over time in a supermarket qualitatively and quantitavely. It focuses on the non-organic vegetable with a fixed selling price over time such as spinach, beet, and parsley. In qualitative analysis, the sale price determination is influenced by the vegetable characteristics: (1) vegetable segmentation (low to high daily consumed); (2) vegetable age (how long it can last related to freshness); which both characteristic relates to the inventory management and ultimately to the sale price in supermarket. While quantitatively, the vegetables are divided into two categories: the leaf vegetable group that the leaves are eaten as a vegetable with the aging product (a) = 0 and the shelf life (t) = 0, and the non-leafy vegetable group with the aging group (a) = a+1 and the shelf life (t) = t+1. The vegetable age (a) = 0 means they only last for one day when they are ordered then they have to terminate. Whereas a+1 is that they have a longer life for more than a day such as beet, white radish, and string beans. The shelf life refers to how long it will be placed in a shelf in supermarket in line with the vegetable age. According to the cost plus pricing method using full price costing approach, production costs, non-production costs, and markup are adjusted differently for each category. There is a holding cost added to the sale price of the non-leafy vegetable, yet it is assumed a 0 holding cost for the leafy vegetable category. The amount of expected margin of each category is correlated to the vegetable characteristics.

  1. High temperature in combination with UV irradiation enhances horizontal transfer of stx2 gene from E. coli O157:H7 to non-pathogenic E. coli.

    Directory of Open Access Journals (Sweden)

    Wan-Fu Yue

    Full Text Available Shiga toxin (stx genes have been transferred to numerous bacteria, one of which is E. coli O157:H7. It is a common belief that stx gene is transferred by bacteriophages, because stx genes are located on lambdoid prophages in the E. coli O157:H7 genome. Both E. coli O157:H7 and non-pathogenic E. coli are highly enriched in cattle feedlots. We hypothesized that strong UV radiation in combination with high temperature accelerates stx gene transfer into non-pathogenic E. coli in feedlots.E. coli O157:H7 EDL933 strain were subjected to different UV irradiation (0 or 0.5 kJ/m(2 combination with different temperature (22, 28, 30, 32, and 37 °C treatments, and the activation of lambdoid prophages was analyzed by plaque forming unit while induction of Stx2 prophages was quantified by quantitative real-time PCR. Data showed that lambdoid prophages in E. coli O157:H7, including phages carrying stx2, were activated under UV radiation, a process enhanced by elevated temperature. Consistently, western blotting analysis indicated that the production of Shiga toxin 2 was also dramatically increased by UV irradiation and high temperature. In situ colony hybridization screening indicated that these activated Stx2 prophages were capable of converting laboratory strain of E. coli K12 into new Shiga toxigenic E. coli, which were further confirmed by PCR and ELISA analysis.These data implicate that high environmental temperature in combination with UV irradiation accelerates the spread of stx genes through enhancing Stx prophage induction and Stx phage mediated gene transfer. Cattle feedlot sludge are teemed with E. coli O157:H7 and non-pathogenic E. coli, and is frequently exposed to UV radiation via sunlight, which may contribute to the rapid spread of stx gene to non-pathogenic E. coli and diversity of shiga toxin producing E. coli.

  2. E. Coli

    Science.gov (United States)

    ... for the bacteria's medical name Escherichia coli . The strange thing about these bacteria — and lots of other ... In some cases, E. coli poisoning can cause life-threatening kidney problems. What Can Kids Do? Adults ...

  3. Quantitative PCR analysis of salivary pathogen burden in periodontitis

    Science.gov (United States)

    Salminen, Aino; Kopra, K. A. Elisa; Hyvärinen, Kati; Paju, Susanna; Mäntylä, Päivi; Buhlin, Kåre; Nieminen, Markku S.; Sinisalo, Juha; Pussinen, Pirkko J.

    2015-01-01

    Our aim was to investigate the value of salivary concentrations of four major periodontal pathogens and their combination in diagnostics of periodontitis. The Parogene study included 462 dentate subjects (mean age 62.9 ± 9.2 years) with coronary artery disease (CAD) diagnosis who underwent an extensive clinical and radiographic oral examination. Salivary levels of four major periodontal bacteria were measured by quantitative real-time PCR (qPCR). Median salivary concentrations of Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia, as well as the sum of the concentrations of the four bacteria, were higher in subjects with moderate to severe periodontitis compared to subjects with no to mild periodontitis. Median salivary Aggregatibacter actinomycetemcomitans concentrations did not differ significantly between the subjects with no to mild periodontitis and subjects with moderate to severe periodontitis. In logistic regression analysis adjusted for age, gender, diabetes, and the number of teeth and implants, high salivary concentrations of P. gingivalis, T. forsythia, and P. intermedia were significantly associated with moderate to severe periodontitis. When looking at different clinical and radiographic parameters of periodontitis, high concentrations of P. gingivalis and T. forsythia were significantly associated with the number of 4–5 mm periodontal pockets, ≥6 mm pockets, and alveolar bone loss (ABL). High level of T. forsythia was associated also with bleeding on probing (BOP). The combination of the four bacteria, i.e., the bacterial burden index, was associated with moderate to severe periodontitis with an odds ratio (OR) of 2.40 (95% CI 1.39–4.13). When A. actinomycetemcomitans was excluded from the combination of the bacteria, the OR was improved to 2.61 (95% CI 1.51–4.52). The highest OR 3.59 (95% CI 1.94–6.63) was achieved when P. intermedia was further excluded from the combination and only the levels of P. gingivalis and

  4. Flux Balance Analysis of Escherichia coli under Temperature and pH Stress Conditions

    KAUST Repository

    Xu, Xiaopeng

    2015-01-01

    important roles in specific conditions and are essential genes under those conditions. E. coli is a model organism, which is widely used. It can adapt to many stress conditions, including temperature, pH, osmotic, antibiotic, etc. Underlying mechanisms

  5. Quantitative transfer of Escherichia coli O157:H7 to equipment during small-scale production of fresh-cut leafy greens.

    Science.gov (United States)

    Buchholz, Annemarie L; Davidson, Gordon R; Marks, Bradley P; Todd, Ewen C D; Ryser, Elliot T

    2012-07-01

    Postharvest contamination and subsequent spread of Escherichia coli O157:H7 can occur during shredding, conveying, fluming, and dewatering of fresh-cut leafy greens. This study quantified E. coli O157:H7 transfer from leafy greens to equipment surfaces during simulated small-scale commercial processing. Three to five batches (22.7 kg) of baby spinach, iceberg lettuce, and romaine lettuce were dip inoculated with a four-strain cocktail of avirulent, green fluorescent protein-labeled, ampicillinresistant E. coli O157:H7 to contain ∼10(6), 10(4), and 10(2) CFU/g, and then were processed after 1 h of draining at ∼23°C or 24 h of storage at 4°C. Lettuce was shredded using an Urschel TransSlicer at two different blade and belt speeds to obtain normal (5 by 5 cm) and more finely shredded (0.5 by 5 cm) lettuce. Thereafter, the lettuce was step conveyed to a flume tank and was washed and then dried using a shaker table and centrifugal dryer. Product (25-g) and water (40-ml) samples were collected at various points during processing. After processing, product contact surfaces (100 cm(2)) on the shredder (n = 14), conveyer (n = 8), flume tank (n = 11), shaker table (n = 9), and centrifugal dryer (n = 8) were sampled using one-ply composite tissues. Sample homogenates diluted in phosphate or neutralizing buffer were plated, with or without prior 0.45- m m membrane filtration, on Trypticase soy agar containing 0.6% yeast extract supplemented with 100 ppm of ampicillin to quantify green fluorescent protein-labeled E. coli O157:H7 under UV light. During leafy green processing, ∼90% of the E. coli O157:H7 inoculum transferred to the wash water. After processing, E. coli O157:H7 populations were highest on the conveyor and shredder (Ptransfer.

  6. Quantitative resistance level (MIC) of Escherichia coli isolated from calves and pigs suffering from enteritis: national resistance monitoring by the BVL.

    Science.gov (United States)

    Schröer, Ulrike; Kaspar, Heike; Wallmann, Jürgen

    2007-01-01

    National Resistance Monitoring of the Federal Office of Consumer Protection and Food Safety (BVL), which was put into service in 2001, has made it possible to implement a valid and representative database on the basis of which the resistance situation, development and spread in animal pathogens can be evaluated. Escherichia coil (E. coli) strains originating from calves and pigs suffering from enteritis were first included in the investigations in the 2004/2005 study. A total of 258 bovine and 492 porcine E. coli strains were tested using the broth microdilution method to determine the in vitro susceptibility (minimum inhibitory concentration) to 23 (fattening pigs) and 28 (calves, piglets, weaners) different antimicrobial substances. Considerable prevalences of resistance were found for some antimicrobials. The strains originating from both animal species displayed high prevalences of resistance for tetracycline, trimethoprim, trimethoprim/sulfamethoxazole, doxycycline and ampicillin. Reduced susceptibility was detected particularly in the E. coli strains from calves. The data reveal that the resistance level of E. coli strains isolated from cases of enteric disease in calves and pigs is altogether higher than has so far been reported in pathogens causing different diseases and in other food-producing animal species. Based on the results presented, it is possible to assess the current resistance situation for E. coli strains in calves and pigs in Germany. This in turn helps to deduce the necessary management measures that can be taken in order to minimise resistance to antibiotics. Furthermore, the data help to decide on adequate therapy of E. coli infections of the intestinal tract in calves and pigs and encourage the responsible use of antibiotics in the interests of animal health and consumer protection.

  7. An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli.

    Science.gov (United States)

    Bohlin, Jon; Brynildsrud, Ola B; Sekse, Camilla; Snipen, Lars

    2014-10-09

    There are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation. Hierarchical clustering of dS and dN estimations from the E. coli core genome resulted in phylogenetic trees with topologies in agreement with known E. coli taxonomy and phylogroups. High values of dS, compared to dN, indicate that the E. coli core genome has been subjected to substantial purifying selection over time; significantly more than the non-core part of the genome (pcoli genome size correlated with estimated HGT size (pcoli are largely attained through HGT. No associations were found between selective pressures operating on the E. coli core genome, as estimated using relative entropy, and genome size (p~0.98). On a larger time frame, genome expansion in E. coli, which is significantly associated with the acquisition of virulence factors, appears to be independent of selective forces operating on the core genome.

  8. Analysis of Bacteriostatic Effect of Chinese Herbal Medicine Against E.coli

    OpenAIRE

    Ma, Li; Chen, Shuangjie; Yang, Yongguang

    2017-01-01

    To analyze the bacteriostatic effect of Chinese traditional herbal medicines on E. coli, total 35 different preparations (decoction, volatile oil and distillate) of Chinese traditional herbal medicines were tested using plate culture method. The results showed that 18 preparations of traditional Chinese herbal medicines have different inhibition effect on E. coli in vitro. The results also revealed that different process and combination affect the bacteriostatic effect and different medicines...

  9. Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.

    Science.gov (United States)

    Oshima, Taku; Aiba, Hirofumi; Masuda, Yasushi; Kanaya, Shigehiko; Sugiura, Masahito; Wanner, Barry L; Mori, Hirotada; Mizuno, Takeshi

    2002-10-01

    We have systematically examined the mRNA profiles of 36 two-component deletion mutants, which include all two-component regulatory systems of Escherichia coli, under a single growth condition. DNA microarray results revealed that the mutants belong to one of three groups based on their gene expression profiles in Luria-Bertani broth under aerobic conditions: (i) those with no or little change; (ii) those with significant changes; and (iii) those with drastic changes. Under these conditions, the anaeroresponsive ArcB/ArcA system, the osmoresponsive EnvZ/OmpR system and the response regulator UvrY showed the most drastic changes. Cellular functions such as flagellar synthesis and expression of the RpoS regulon were affected by multiple two-component systems. A high correlation coefficient of expression profile was found between several two-component mutants. Together, these results support the view that a network of functional interactions, such as cross-regulation, exists between different two-component systems. The compiled data are avail-able at our website (http://ecoli.aist-nara.ac.jp/xp_analysis/ 2_components).

  10. Quantitative analysis of real-time radiographic systems

    International Nuclear Information System (INIS)

    Barker, M.D.; Condon, P.E.; Barry, R.C.; Betz, R.A.; Klynn, L.M.

    1988-01-01

    A method was developed which yields quantitative information on the spatial resolution, contrast sensitivity, image noise, and focal spot size from real time radiographic images. The method uses simple image quality indicators and computer programs which make it possible to readily obtain quantitative performance measurements of single or multiple radiographic systems. It was used for x-ray and optical images to determine which component of the system was not operating up to standard. Focal spot size was monitored by imaging a bar pattern. This paper constitutes the second progress report on the development of the camera and radiation image quality indicators

  11. Budget analysis of Escherichia coli at a southern Lake Michigan Beach

    Science.gov (United States)

    Thupaki, P.; Phanikumar, M.S.; Beletsky, D.; Schwab, D.J.; Nevers, M.B.; Whitman, R.L.

    2010-01-01

    Escherichia coli (EC) concentrations at two beaches impacted by river plume dynamics in southern Lake Michigan were analyzed using three-dimensional hydrodynamic and transport models. The relative importance of various physical and biological processes influencing the fate and transport of EC were examined via budget analysis and a first-order sensitivity analysis of model parameters. The along-shore advective fluxofEC(CFU/m2·s)was found to be higher compared to its crossshore counterpart; however, the sum of diffusive and advective components was of a comparable magnitude in both directions showing the importance of cross-shore exchange in EC transport. Examination of individual terms in the EC mass balance equation showed that vertical turbulent mixing in the water column dominated the overall EC transport for the summer conditions simulated. Dilution due to advection and diffusion accounted for a large portion of the total EC budget in the nearshore, and the net EC loss rate within the water column (CFU/m3·s) was an order of magnitude smaller compared to the horizontal and vertical transport rates. This result has important implications for modeling EC at recreational beaches; however, the assessment of the magnitude of EC loss rate is complicated due to the strong coupling between vertical exchange and depth-dependent EC loss processes such as sunlight inactivation and settling. Sensitivity analysis indicated that solar inactivation has the greatest impact on EC loss rates. Although these results are site-specific, they clearly bring out the relative importance of various processes involved.

  12. Quantitative analysis of results for quality assurance in radiotherapy

    International Nuclear Information System (INIS)

    Passaro, Bruno Martins

    2011-01-01

    The linear accelerators represent the most important, practical and versatile source of ionizing radiation in radiotherapy. These functional characteristics influence the geometric and dosimetric accuracy of therapeutic doses applied to patients. The performance of this equipment may vary due to electronic defects, component failures or mechanical breakdowns, or may vary due to the deterioration and aging of components. Maintaining the quality of care depends on the stability of the accelerators and quality control of the institutions to monitor deviations in the parameters of the beam. The aim of this study is to assess and analyze the stability of the calibration factor of linear accelerators, as well as the other dosimetric parameters normally included in a program of quality control in radiotherapy. The average calibration factors of the accelerators for the period of approximately four years for the Clinac 600C and Clinac 6EX were (0,998 ± 0,012) and (0,996 ± 0,014), respectively. For the Clinac 2100CD 6 MV and 15 MV was (1,008 ± 0,009) and (1,006 ± 0,010), respectively, in a period of approximately four years. Statistical analysis of the three linear accelerators was found that the coefficient of variation of calibration factors had values below 2% which shows a consistency in the data. By calculating the normal distribution of calibration factors, we found that for the Clinac 600C and Clinac 2100CD, is an expected probability that more than 90% of cases the values are within acceptable limits according to the TG-142, while for the Clinac 6EX is expected around 85% since this had several exchanges of accelerator components. The values of TPR 20,10 of three accelerators are practically constant and within acceptable limits according to the TG-142. It can be concluded that a detailed study of data from the calibration factor of the accelerators and TPR20,10 from a quantitative point of view, is extremely useful in a quality assurance program. (author)

  13. A Quantitative Analysis of the Behavioral Checklist of the Movement ABC Motor Test

    Science.gov (United States)

    Ruiz, Luis Miguel; Gomez, Marta; Graupera, Jose Luis; Gutierrez, Melchor; Linaza, Jose Luis

    2007-01-01

    The fifth section of the Henderson and Sugden's Movement ABC Checklist is part of the general Checklist that accompanies The Movement ABC Battery. The authors maintain that the analysis of this section must be mainly qualitative instead of quantitative. The main objective of this study was to employ a quantitative analysis of this behavioural…

  14. Metabolic regulation analysis of an ethanologenic Escherichia coli strain based on RT-PCR and enzymatic activities

    Directory of Open Access Journals (Sweden)

    Martinez Alfredo

    2008-05-01

    Full Text Available Abstract Background A metabolic regulation study was performed, based upon measurements of enzymatic activities, fermentation performance, and RT-PCR analysis of pathways related to central carbon metabolism, in an ethanologenic Escherichia coli strain (CCE14 derived from lineage C. In comparison with previous engineered strains, this E coli derivative has a higher ethanol production rate in mineral medium, as a result of the elevated heterologous expression of the chromosomally integrated genes encoding PDCZm and ADHZm (pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas mobilis. It is suggested that this behavior might be due to lineage differences between E. coli W and C. Results This study demonstrated that the glycolytic flux is controlled, in this case, by reactions outside glycolysis, i.e., the fermentative pathways. Changes in ethanol production rate in this ethanologenic strain result in low organic acid production rates, and high glycolytic and ethanologenic fluxes, that correlate with enhanced transcription and enzymatic activity levels of PDCZm and ADHZm. Furthermore, a higher ethanol yield (90% of the theoretical in glucose-mineral media was obtained with CCE14 in comparison with previous engineered E. coli strains, such as KO11, that produces a 70% yield under the same conditions. Conclusion Results suggest that a higher ethanol formation rate, caused by ahigher PDCZm and ADHZm activities induces a metabolic state that cells compensate through enhanced glucose transport, ATP synthesis, and NAD-NADH+H turnover rates. These results show that glycolytic enzymatic activities, present in E. coli W and C under fermentative conditions, are sufficient to contend with increases in glucose consumption and product formation rates.

  15. Computer aided approach to qualitative and quantitative common cause failure analysis for complex systems

    International Nuclear Information System (INIS)

    Cate, C.L.; Wagner, D.P.; Fussell, J.B.

    1977-01-01

    Common cause failure analysis, also called common mode failure analysis, is an integral part of a complete system reliability analysis. Existing methods of computer aided common cause failure analysis are extended by allowing analysis of the complex systems often encountered in practice. The methods aid in identifying potential common cause failures and also address quantitative common cause failure analysis

  16. Quantitative analysis of soluble elements in environmental waters by PIXE

    International Nuclear Information System (INIS)

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

    1999-01-01

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

  17. Identification of Case Content with Quantitative Network Analysis

    DEFF Research Database (Denmark)

    Christensen, Martin Lolle; Olsen, Henrik Palmer; Tarissan, Fabian

    2016-01-01

    the relevant articles. In order to enhance information retrieval about case content, without relying on manual labor and subjective judgment, we propose in this paper a quantitative method that gives a better indication of case content in terms of which articles a given case is more closely associated with...

  18. Quantitative analysis of prediction models for hot cracking in ...

    Indian Academy of Sciences (India)

    A RodrМguez-Prieto

    2017-11-16

    Nov 16, 2017 ... enhancing safety margins and adding greater precision to quantitative accident prediction [45]. One deterministic methodology is the stringency level (SL) approach, which is recognized as a valuable decision tool in the selection of standardized materials specifications to prevent potential failures [3].

  19. Analysis association of milk fat and protein percent in quantitative ...

    African Journals Online (AJOL)

    SAM

    2014-05-14

    May 14, 2014 ... African Journal of Biotechnology. Full Length ... quantitative trait locus (QTLs) on chromosomes 1, 6, 7 and 20 in ... Protein and fat percent as content of milk are high-priority criteria for financial aims and selection of programs ...

  20. Teaching Quantitative Reasoning for Nonscience Majors through Carbon Footprint Analysis

    Science.gov (United States)

    Boose, David L.

    2014-01-01

    Quantitative reasoning is a key intellectual skill, applicable across disciplines and best taught in the context of authentic, relevant problems. Here, I describe and assess a laboratory exercise that has students calculate their "carbon footprint" and evaluate the impacts of various behavior choices on that footprint. Students gather…

  1. How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli

    Directory of Open Access Journals (Sweden)

    Barth Sandra

    2005-04-01

    Full Text Available Abstract Background In screening of libraries derived by expression cloning, expression of active proteins in E. coli can be limited by formation of inclusion bodies. In these cases it would be desirable to enrich gene libraries for coding sequences with soluble gene products in E. coli and thus to improve the efficiency of screening. Previously Wilkinson and Harrison showed that solubility can be predicted from amino acid composition (Biotechnology 1991, 9(5:443–448. We have applied this analysis to members of the alpha/beta hydrolase fold family to predict their solubility in E. coli. alpha/beta hydrolases are a highly diverse family with more than 1800 proteins which have been grouped into homologous families and superfamilies. Results The predicted solubility in E. coli depends on hydrolase size, phylogenetic origin of the host organism, the homologous family and the superfamily, to which the hydrolase belongs. In general small hydrolases are predicted to be more soluble than large hydrolases, and eukaryotic hydrolases are predicted to be less soluble in E. coli than prokaryotic ones. However, combining phylogenetic origin and size leads to more complex conclusions. Hydrolases from prokaryotic, fungal and metazoan origin are predicted to be most soluble if they are of small, medium and large size, respectively. We observed large variations of predicted solubility between hydrolases from different homologous families and from different taxa. Conclusion A comprehensive analysis of all alpha/beta hydrolase sequences allows more efficient screenings for new soluble alpha/beta hydrolases by the use of libraries which contain more soluble gene products. Screening of hydrolases from families whose members are hard to express as soluble proteins in E. coli should first be done in coding sequences of organisms from phylogenetic groups with the highest average of predicted solubility for proteins of this family. The tools developed here can be used

  2. Comparative evolutionary analysis of protein complexes in E. coli and yeast

    Directory of Open Access Journals (Sweden)

    Ranea Juan AG

    2010-02-01

    Full Text Available Abstract Background Proteins do not act in isolation; they frequently act together in protein complexes to carry out concerted cellular functions. The evolution of complexes is poorly understood, especially in organisms other than yeast, where little experimental data has been available. Results We generated accurate, high coverage datasets of protein complexes for E. coli and yeast in order to study differences in the evolution of complexes between these two species. We show that substantial differences exist in how complexes have evolved between these organisms. A previously proposed model of complex evolution identified complexes with cores of interacting homologues. We support findings of the relative importance of this mode of evolution in yeast, but find that it is much less common in E. coli. Additionally it is shown that those homologues which do cluster in complexes are involved in eukaryote-specific functions. Furthermore we identify correlated pairs of non-homologous domains which occur in multiple protein complexes. These were identified in both yeast and E. coli and we present evidence that these too may represent complex cores in yeast but not those of E. coli. Conclusions Our results suggest that there are differences in the way protein complexes have evolved in E. coli and yeast. Whereas some yeast complexes have evolved by recruiting paralogues, this is not apparent in E. coli. Furthermore, such complexes are involved in eukaryotic-specific functions. This implies that the increase in gene family sizes seen in eukaryotes in part reflects multiple family members being used within complexes. However, in general, in both E. coli and yeast, homologous domains are used in different complexes.

  3. On-Orbit Quantitative Real-Time Gene Expression Analysis Using the Wetlab-2 System

    Science.gov (United States)

    Parra, Macarena; Jung, Jimmy; Almeida, Eduardo; Boone, Travis; Tran, Luan; Schonfeld, Julie

    2015-01-01

    NASA Ames Research Center's WetLab-2 Project enables on-orbit quantitative Reverse Transcriptase PCR (qRT-PCR) analysis without the need for sample return. The WetLab-2 system is capable of processing sample types ranging from microbial cultures to animal tissues dissected on-orbit. The project developed a RNA preparation module that can lyse cells and extract RNA of sufficient quality and quantity for use as templates in qRT-PCR reactions. Our protocol has the advantage of using non-toxic chemicals and does not require alcohols or other organics. The resulting RNA is dispensed into reaction tubes that contain all lyophilized reagents needed to perform qRT-PCR reactions. System operations require simple and limited crew actions including syringe pushes, valve turns and pipette dispenses. The project selected the Cepheid SmartCycler (TradeMark), a Commercial-Off-The-Shelf (COTS) qRT-PCR unit, because of its advantages including rugged modular design, low power consumption, rapid thermal ramp times and four-color multiplex detection. Single tube multiplex assays can be used to normalize for RNA concentration and integrity, and to study multiple genes of interest in each module. The WetLab-2 system can downlink data from the ISS to the ground after a completed run and uplink new thermal cycling programs. The ability to conduct qRT-PCR and generate results on-orbit is an important step towards utilizing the ISS as a National Laboratory facility. Specifically, the ability to get on-orbit data will provide investigators with the opportunity to adjust experimental parameters in real time without the need for sample return and re-flight. On orbit gene expression analysis can also eliminate the confounding effects on gene expression of reentry stresses and shock acting on live cells and organisms or the concern of RNA degradation of fixed samples and provide on-orbit gene expression benchmarking prior to sample return. Finally, the system can also be used for analysis of

  4. Microchromatography of hemoglobins. VIII. A general qualitative and quantitative method in plastic drinking straws and the quantitative analysis of Hb-F.

    Science.gov (United States)

    Schroeder, W A; Pace, L A

    1978-03-01

    The microchromatographic procedure for the quantitative analysis of the hemoglobin components in a hemolysate uses columns of DEAE-cellulose in a plastic drinking straw with a glycine-KCN-NaCl developer. Not only may the method be used for the quantitative analysis of Hb-F but also for the analysis of the varied components in mixtures of hemoglobins.

  5. Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli

    Directory of Open Access Journals (Sweden)

    Maryam Iman

    2017-08-01

    Full Text Available Microbial remediation of nitroaromatic compounds (NACs is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT. Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E. coli to account for a curated version of major TNT transformation pathways known or evidently hypothesized to be active in E. coli in present of TNT. Using constraint-based analysis (CBA methods, we then performed several series of in silico experiments to elucidate the contribution of these pathways individually or in combination to the E. coli TNT transformation capacity. Results of our analyses were validated by replicating several experimentally observed TNT degradation phenotypes in E. coli cultures. We further used the extended model to explore the influence of process parameters, including aeration regime, TNT concentration, cell density, and carbon source on TNT degradation efficiency. We also conducted an in silico metabolic engineering study to design a series of E. coli mutants capable of degrading TNT at higher yield compared with the wild-type strain. Our study, therefore, extends the application of CBA to bioremediation of nitroaromatics and demonstrates the usefulness of this approach to inform bioremediation research.

  6. Frequency and risk-factors analysis of Escherichia coli O157:H7 in Bali-cattle.

    Science.gov (United States)

    Suardana, I Wayan; Widiasih, Dyah Ayu; Nugroho, Widagdo Sri; Wibowo, Michael Haryadi; Suyasa, I Nyoman

    2017-08-01

    Cattle are known as the main reservoir of zoonotic agents verocytotoxin-producing Escherichia coli. These bacteria are usually isolated from calves with diarrhea and/or mucus and blood. Tolerance of these agents to the environmental conditions will strengthen of their transmission among livestock. A total of 238 cattle fecal samples from four sub-districts in Badung, Bali were used in this study. Epidemiological data observed include cattle age, sex, cattle rearing system, the source of drinking water, weather, altitude, and type of cage floor, the cleanliness of cage floor, the slope of cage floor, and the level of cattle cleanliness. The study was initiated by culturing of samples onto eosin methylene blue agar, then Gram stained, and tested for indole, methyl-red, voges proskauer, and citrate, Potential E.coli isolates were then cultured onto sorbitol MacConkey agar, and further tested using O157 latex agglutination test and H7 antisera. Molecular identification was performed by analysis of the 16S rRNA gene, and epidemiological data was analyzed using STATA 12.0 software. The results showed, the prevalence of E. coli O157:H7 in cattle at Badung regency was 6.30% (15/238) covering four sub districts i.e. Petang, Abiansemal, Mengwi, and Kuta which their prevalence was 8.62%(5/58), 10%(6/60), 3.33%(2/60), and 3.33(2/60)%, respectively. The analysis of 16S rRNA gene confirmed of isolates as an E. coli O157:H7 strain with 99% similarities. Furthermore, the risk factors analysis showed that the slope of the cage floor has a highly significant effect (P<0.05) to the distribution of infection. Consequently, implementing this factor must be concerned in order to decrease of infection. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Quantitative chromatography in the analysis of labelled compounds 1. Quantitative paper chromotography of amino acids by A spot comparison technique

    International Nuclear Information System (INIS)

    Barakat, M.F.; Farag, A.N.; El-Gharbawy, A.A.

    1974-01-01

    For the determination of the specific activity of labelled compounds separated by paper sheet chromatography, it was found essential to perfect the quantitative aspect of the paper chromatographic technique. Actually, so far paper chromatography has been used as a separation tool mainly and its use in quantification of the separated materials is by far less studied. In the present work, the quantitative analysis of amino acids by paper sheet chromatography has been carried out by methods, depending on the use of the relative spot area values for correcting the experimental data obtained. The results obtained were good and reproducible. The main advantage of the proposed technique is its extreme simplicity. No complicated equipment of procedures are necessary

  8. Quantitative analysis of Moessbauer backscatter spectra from multilayer films

    International Nuclear Information System (INIS)

    Bainbridge, J.

    1975-01-01

    The quantitative interpretation of Moessbauer backscatter spectra with particular reference to internal conversion electrons has been treated assuming that electron attenuation in a surface film can be satisfactorily described by a simple exponential law. The theory of Krakowski and Miller has been extended to include multi-layer samples, and a relation between the Moessbauer spectrum area and an individual layer thickness derived. As an example, numerical results are obtained for a duplex oxide film grown on pure iron. (Auth.)

  9. Geometrical conditions at the quantitative neutronographic texture analysis

    International Nuclear Information System (INIS)

    Tobisch, J.; Kleinstueck, K.

    1975-10-01

    The beam geometry for measuring quantitative pole figures by a neutronographic texture diffractometer is explained for transmission and reflection arrangement of spherical samples and sheets. For given dimensions of counter aperture the maximum possible cross sections of the incident beam are calculated as a function of sample dimensions and the Bragg angle theta. Methods for the calculation of absorption factors and volume correction are given. Under special conditions advantages result in the transmission case for sample motion into the direction +α. (author)

  10. Quantitative analysis of strategic and tactical purchasing decisions

    OpenAIRE

    Heijboer, G.J.

    2003-01-01

    Purchasing management is a relatively new scientific research field, partly due to the fact that purchasing has only recently been recognized as a factor of strategic importance to an organization. In this thesis, the author focuses on a selection of strategic and tactical purchasing decision problems. New quantitative models are developed for these decision problems using a range of mathematical techniques, thereby contributing to the further development of purchasing theory and its appliati...

  11. Quantitative analysis of carbon radiation in edge plasmas of LHD

    International Nuclear Information System (INIS)

    Dong, C.F.; Morita, S.; Oishi, T.; Goto, M.; Murakami, I.; Wang, E.R.; Huang, X.L.

    2013-01-01

    It is of interest to compare the carbon radiation loss between LHD and tokamaks. Since the radiation from C"3"+ is much smaller than that from C"5"+, it is also interesting to examine the difference in the detached plasma. In addition, it is important to study quantitatively the radiation from each ionization stage of carbon which is uniquely the dominant impurity in most tokamaks and LHD. (J.P.N.)

  12. Pulmonary nodule characterization, including computer analysis and quantitative features.

    Science.gov (United States)

    Bartholmai, Brian J; Koo, Chi Wan; Johnson, Geoffrey B; White, Darin B; Raghunath, Sushravya M; Rajagopalan, Srinivasan; Moynagh, Michael R; Lindell, Rebecca M; Hartman, Thomas E

    2015-03-01

    Pulmonary nodules are commonly detected in computed tomography (CT) chest screening of a high-risk population. The specific visual or quantitative features on CT or other modalities can be used to characterize the likelihood that a nodule is benign or malignant. Visual features on CT such as size, attenuation, location, morphology, edge characteristics, and other distinctive "signs" can be highly suggestive of a specific diagnosis and, in general, be used to determine the probability that a specific nodule is benign or malignant. Change in size, attenuation, and morphology on serial follow-up CT, or features on other modalities such as nuclear medicine studies or MRI, can also contribute to the characterization of lung nodules. Imaging analytics can objectively and reproducibly quantify nodule features on CT, nuclear medicine, and magnetic resonance imaging. Some quantitative techniques show great promise in helping to differentiate benign from malignant lesions or to stratify the risk of aggressive versus indolent neoplasm. In this article, we (1) summarize the visual characteristics, descriptors, and signs that may be helpful in management of nodules identified on screening CT, (2) discuss current quantitative and multimodality techniques that aid in the differentiation of nodules, and (3) highlight the power, pitfalls, and limitations of these various techniques.

  13. Phenotypic analysis of antibiotic resistant E. coli recovered from urban aquatic environment in Banda Aceh, Indonesia

    Science.gov (United States)

    Suhartono, S.; Ismail, Y. S.; Yulvizar, C.; Nursanty, R.; Mahyuddin, M.; Jannah, M.

    2018-03-01

    Of aquatic environment, antibiotic resistant bacteria, including total coliforms and E. coli disseminate and emerge at an alarming rate. The study aims to determine enumerate, isolate,E. coliand determine their antibiotic resistance and compare between those which were recovered from residentials and home industries in Banda Aceh and its surrounding area. The bacterial density and antibiotic susceptibility of total coliforms and E. coli were determined using Standard Total Coliform Multiple-Tube (MPN) Fermentation method and the disk diffusion method, respectively. Despite there was no significant difference of total coliforms and E. coli population between residentials and home industries (P > 0.05) in this study, their density as well as prevalence remained high in the water sample. This might expose serious health risks since the resistance might be easily spread acquired through horizontal gene transfer within the aquatic environment.

  14. Quantitative phase analysis of a highly textured industrial sample using a Rietveld profile analysis

    International Nuclear Information System (INIS)

    Shin, Eunjoo; Huh, Moo-Young; Seong, Baek-Seok; Lee, Chang-Hee

    2001-01-01

    For the quantitative phase analysis on highly textured two-phase materials, samples with known weight fractions of zirconium and aluminum were prepared. Strong texture components prevailed in both zirconium and aluminum sheet. The diffraction patterns of samples were measured by the neutron and refined by the Rietveld method. The preferred orientation correction of diffraction patterns was carried out by means of recalculated pole figures from the ODF. The present Rietveld analysis of various samples with different weight fractions showed that the absolute error of the calculated weight fractions was less than 7.1%. (author)

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

    International Nuclear Information System (INIS)

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

    1985-01-01

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

  16. The Quantitative Analysis of a team game performance made by men basketball teams at OG 2008

    OpenAIRE

    Kocián, Michal

    2009-01-01

    Title: The quantitative analysis of e team game performance made by men basketball teams at Olympis games 2008 Aims: Find reason successes and failures of teams in Olympis game play-off using quantitative (numerical) observation of selected game statistics. Method: The thesis was made on the basic a quantitative (numerical) observation of videorecordings using KVANTÝM. Results: Obtained selected statistic desribed the most essentials events for team winning or loss. Keywords: basketball, team...

  17. Genomic Analysis Reveals Distinct Concentration-Dependent Evolutionary Trajectories for Antibiotic Resistance in Escherichia coli

    Science.gov (United States)

    Mogre, Aalap; Sengupta, Titas; Veetil, Reshma T.; Ravi, Preethi; Seshasayee, Aswin Sai Narain

    2014-01-01

    Evolution of bacteria under sublethal concentrations of antibiotics represents a trade-off between growth and resistance to the antibiotic. To understand this trade-off, we performed in vitro evolution of laboratory Escherichia coli under sublethal concentrations of the aminoglycoside kanamycin over short time durations. We report that fixation of less costly kanamycin-resistant mutants occurred earlier in populations growing at lower sublethal concentration of the antibiotic, compared with those growing at higher sublethal concentrations; in the latter, resistant mutants with a significant growth defect persisted longer. Using deep sequencing, we identified kanamycin resistance-conferring mutations, which were costly or not in terms of growth in the absence of the antibiotic. Multiple mutations in the C-terminal end of domain IV of the translation elongation factor EF-G provided low-cost resistance to kanamycin. Despite targeting the same or adjacent residues of the protein, these mutants differed from each other in the levels of resistance they provided. Analysis of one of these mutations showed that it has little defect in growth or in synthesis of green fluorescent protein (GFP) from an inducible plasmid in the absence of the antibiotic. A second class of mutations, recovered only during evolution in higher sublethal concentrations of the antibiotic, deleted the C-terminal end of the ATP synthase shaft. This mutation confers basal-level resistance to kanamycin while showing a strong growth defect in the absence of the antibiotic. In conclusion, the early dynamics of the development of resistance to an aminoglycoside antibiotic is dependent on the levels of stress (concentration) imposed by the antibiotic, with the evolution of less costly variants only a matter of time. PMID:25281544

  18. Whole-genome transcriptional analysis of Escherichia coli during heat inactivation processes related to industrial cooking.

    Science.gov (United States)

    Guernec, A; Robichaud-Rincon, P; Saucier, L

    2013-08-01

    Escherichia coli K-12 was grown to the stationary phase, for maximum physiological resistance, in brain heart infusion (BHI) broth at 37°C. Cells were then heated at 58°C or 60°C to reach a process lethality value \\[\\mathbf{\\left(}{{\\mathit{F}}^{\\mathit{o}}}_{\\mathbf{70}}^{\\mathbf{10}}\\mathbf{\\right)} \\] of 2 or 3 or to a core temperature of 71°C (control industrial cooking temperature). Growth recovery and cell membrane integrity were evaluated immediately after heating, and a global transcription analysis was performed using gene expression microarrays. Only cells heated at 58°C with F(o) = 2 were still able to grow on liquid or solid BHI broth after heat treatment. However, their transcriptome did not differ from that of bacteria heated at 58°C with F(o) = 3 (P value for the false discovery rate [P-FDR] > 0.01), where no growth recovery was observed posttreatment. Genome-wide transcriptomic data obtained at 71°C were distinct from those of the other treatments without growth recovery. Quantification of heat shock gene expression by real-time PCR revealed that dnaK and groEL mRNA levels decreased significantly above 60°C to reach levels similar to those of control cells at 37°C (P citE, glyS, oppB, and asd, whose expression was upregulated at 71°C, may be worth investigating as good biomarkers for accurately determining the efficiency of heat treatments, especially when cells are too injured to be enumerated using growth media.

  19. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling.

    Directory of Open Access Journals (Sweden)

    Donghyuk Kim

    Full Text Available Genome-wide transcription start site (TSS profiles of the enterobacteria Escherichia coli and Klebsiella pneumoniae were experimentally determined through modified 5' RACE followed by deep sequencing of intact primary mRNA. This identified 3,746 and 3,143 TSSs for E. coli and K. pneumoniae, respectively. Experimentally determined TSSs were then used to define promoter regions and 5' UTRs upstream of coding genes. Comparative analysis of these regulatory elements revealed the use of multiple TSSs, identical sequence motifs of promoter and Shine-Dalgarno sequence, reflecting conserved gene expression apparatuses between the two species. In both species, over 70% of primary transcripts were expressed from operons having orthologous genes during exponential growth. However, expressed orthologous genes in E. coli and K. pneumoniae showed a strikingly different organization of upstream regulatory regions with only 20% identical promoters with TSSs in both species. Over 40% of promoters had TSSs identified in only one species, despite conserved promoter sequences existing in the other species. 662 conserved promoters having TSSs in both species resulted in the same number of comparable 5' UTR pairs, and that regulatory element was found to be the most variant region in sequence among promoter, 5' UTR, and ORF. In K. pneumoniae, 48 sRNAs were predicted and 36 of them were expressed during exponential growth. Among them, 34 orthologous sRNAs between two species were analyzed in depth, and the analysis showed that many sRNAs of K. pneumoniae, including pleiotropic sRNAs such as rprA, arcZ, and sgrS, may work in the same way as in E. coli. These results reveal a new dimension of comparative genomics such that a comparison of two genomes needs to be comprehensive over all levels of genome organization.

  20. Phylogenetic analysis of Escherichia coli isolates from healthy and diarrhoeic calves in Mashhad, Iran

    Directory of Open Access Journals (Sweden)

    M. Barzan

    2017-03-01

    Full Text Available Escherichia coli is a normal inhabitant of the gastrointestinal tract of vertebrates. Certain Escherichia coli strains have been associated with neonatal diarrhoea in ruminants. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D. Several studies have shown the rela-tionship between phylogeny and pathogenicity of E. coli, a great deal can be obtained by determining the phylogroup of unknown E. coli strains. In this study, we aimed to evaluate the influence of diar-rhoea on the genetic composition of E. coli populations isolated from calves. A total of 80 Es-cherichia coli isolates were obtained from healthy and diarrhoeic calves. Phylogenetic grouping was done based on the Clermont triplex PCR method using primers targeted at three genetic markers, chuA, yjaA and TspE4.C2. According to our results, phylogenetic group A strains was the most prevalent in both healthy (37.5% and diarrhoeic calves (55%. Group B1 contained 27.5% of isolates in healthy calves, followed by group B2 (17.5%, and group D (7.5%. Also, four isolates from healthy calves were not included in the major phylogenetic groups or subgroups. A total of 14% and 4% of isolates from diarrhoeic calves beloned to phylogroups B2 and D respectively. Although no isolate from diarrhoeic calves was found to belong to group B1, there was no significant difference between healthy and diarrhoeic calves for other phylogroups. There was not a dramatic shift in E. coli phylogroup/subgroup due to occurrence of diarrhoea in calves, except for phylogroup B1 which was higher in healthy calves. This can be due to the difference in secretions of digestive system in diarrhoeic calves which can prevent the conditions for instability of Escherichia coli isolates of phy-logroup B1. The majority of isolates from both healthy and diarrhoeic calves belonged to non-pathogenic phylogentic group A and B1.

  1. Three-decade epidemiological analysis of Escherichia coli O15:K52:H1

    DEFF Research Database (Denmark)

    Olesen, Bente; Scheutz, Flemming; Menard, Megan

    2009-01-01

    The successful Escherichia coli O15:K52:H1 clonal group provides a case study for the emergence of multiresistant clonal groups of Enterobacteriaceae generally. Accordingly, we tested the hypotheses that, over time, the O15:K52:H1 clonal group has become increasingly (i) virulent and (ii) resistant...... to antibiotics. One hundred archived international E. coli O15:K52:[H1] clinical isolates from 100 unique patients (1975 to 2006) were characterized for diverse phenotypic and molecular traits. All 100 isolates derived from phylogenetic group D and, presumptively, sequence type ST393. They uniformly carried...

  2. A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis

    Directory of Open Access Journals (Sweden)

    Akira Ishikawa

    2017-11-01

    Full Text Available Large numbers of quantitative trait loci (QTL affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

  3. A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis.

    Science.gov (United States)

    Ishikawa, Akira

    2017-11-27

    Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

  4. Quantitative Analysis of Piezoelectric and Seismoelectric Anomalies in Subsurface Geophysics

    Science.gov (United States)

    Eppelbaum, Lev

    2017-04-01

    problem was the basis for an inverse problem, i.e. revealing depth of a body occurrence, its location in a space as well as determining physical properties. At the same time, this method has not received a wide practical application taking into account complexity of real geological media. Careful analysis piezo- and seismoelectric anomalies shows the possibility of application of quantitative analysis of these effects advanced methodologies developed in magnetic prospecting for complex physical-geological conditions (Eppelbaum et al., 2000, 2001, 2010; Eppelbaum, 2010; 2011, 2015). Employment of these methodologies (improved modifications of tangents, characteristic points areal methods) for obtaining quantitative characteristics of ore bodies, environmental features and archaeological targets (models of horizontal circular cylinder, sphere, thin bed, thick bed and thin horizontal plate were utilized) have demonstrated their effectiveness. Case study at the archaeological site Tel Kara Hadid Field piezoelectric observations were conducted at the ancient archaeological site Tel Kara Hadid with gold-quartz mineralization in southern Israel within the Precambrian terrain at the northern extension of the Arabian-Nubian Shield (Neishtadt et al., 2006). The area of the archaeological site is located eight kilometers north of the town of Eilat, in an area of strong industrial noise. Ancient river alluvial terraces (extremely heterogeneous at a local scale, varying from boulders to silt) cover the quartz veins and complicate their identification. Piezoelectric measurements conducted over a quartz vein covered by surface sediments (approximately of 0.4 m thickness) produced a sharp (500 μV ) piezoelectric anomaly. Values recorded over the host rocks (clays and shales of basic composition) were close to zero. The observed piezoelectric anomaly was successfully interpreted by the use of methodologies developed in magnetic prospecting. For effective integration of piezo- and

  5. Quantitative analysis of water heavy by NMR spectroscopy

    International Nuclear Information System (INIS)

    Gomez Gil, V.

    1975-01-01

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

  6. Quantitative analysis of a wind energy conversion model

    International Nuclear Information System (INIS)

    Zucker, Florian; Gräbner, Anna; Strunz, Andreas; Meyn, Jan-Peter

    2015-01-01

    A rotor of 12 cm diameter is attached to a precision electric motor, used as a generator, to make a model wind turbine. Output power of the generator is measured in a wind tunnel with up to 15 m s −1 air velocity. The maximum power is 3.4 W, the power conversion factor from kinetic to electric energy is c p = 0.15. The v 3 power law is confirmed. The model illustrates several technically important features of industrial wind turbines quantitatively. (paper)

  7. Risk management and analysis: risk assessment (qualitative and quantitative)

    OpenAIRE

    Valentin Mazareanu

    2007-01-01

    We use to define risk as the possibility of suffering a loss. Starting this, risk management is defined as a business process whose purpose is to ensure that the organization is protected against risks and their effects. In order to prioritize, to develop a response plan and after that to monitor the identified risks we need to asses them. But at this point a question is born: should I choose a qualitative approach or a quantitative one? This paper will make a short overview over the risk eva...

  8. Correlation of quantitative histopathological morphology and quantitative radiological analysis during aseptic loosening of hip endoprostheses.

    Science.gov (United States)

    Bertz, S; Kriegsmann, J; Eckardt, A; Delank, K-S; Drees, P; Hansen, T; Otto, M

    2006-01-01

    Aseptic hip prosthesis loosening is the most important long-term complication in total hip arthroplasty. Polyethylene (PE) wear is the dominant etiologic factor in aseptic loosening, which together with other factors induces mechanisms resulting in bone loss, and finally in implant loosening. The single-shot radiograph analysis (EBRA, abbreviation for the German term "Einzel-Bild-Röntgenanalyse") is a computerized method for early radiological prediction of aseptic loosening. In this study, EBRA parameters were correlated with histomorphological parameters of the periprosthetic membrane. Periprosthetic membranes obtained from 19 patients during revision surgery of loosened ABG I-type total hip pros-theses were analyzed histologically and morphometrically. The pre-existing EBRA parameters, the thickness of the PE debris lay-er and the dimension of inclination and anteversion, were compared with the density of macrophages and giant cells. Addi-tionally, the semiquantitatively determined density of lymphocytes, plasma cells, giant cells and the size of the necrotic areas were correlated with the EBRA results. All periprosthetic membranes were classified as debris-induced type membranes. We found a positive correlation between the number of giant cells and the thickness of the PE debris layer. There was no significant correlation between the number of macrophages or all semiquantitative parameters and EBRA parameters. The number of giant cells decreased with implant duration. The morphometrically measured number of foreign body giant cells more closely reflects the results of the EBRA. The semiquantitative estimation of giant cell density could not substitute for the morphometrical analysis. The density of macrophages, lymphocytes, plasma cells and the size of necrotic areas did not correlate with the EBRA parameters, indicating that there is no correlation with aseptic loosening.

  9. MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis.

    Science.gov (United States)

    Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

    2016-01-01

    Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Both Ki-67 and MCM-2 are markers of proliferation which are closely linked to grade. Therefore, they

  10. The usefulness of 3D quantitative analysis with using MRI for measuring osteonecrosis of the femoral head

    International Nuclear Information System (INIS)

    Hwang, Ji Young; Lee, Sun Wha; Park, Youn Soo

    2006-01-01

    We wanted to evaluate the usefulness of MRI 3D quantitative analysis for measuring osteonecrosis of the femoral head in comparison with MRI 2D quantitative analysis and quantitative analysis of the specimen. For 3 months at our hospital, 14 femoral head specimens with osteonecrosis were obtained after total hip arthroplasty. The patients preoperative MRIs were retrospectively reviewed for quantitative analysis of the size of the necrosis. Each necrotic fraction of the femoral head was measured by 2D quantitative analysis with using mid-coronal and mid-sagittal MRIs, and by 3D quantitative analysis with using serial continuous coronal MRIs and 3D reconstruction software. The necrotic fraction of the specimen was physically measured by the fluid displacement method. The necrotic fraction according to MRI 2D or 3D quantitative analysis was compared with that of the specimen by using Spearman's correlation test. On the correlative analysis, the necrotic fraction by MRI 2D quantitative analysis and quantitative analysis of the specimen showed moderate correlation (r = 0.657); on the other hand, the necrotic fraction by MRI 3D quantitative analysis and quantitative analysis of the specimen demonstrated a strong correlation (r = 0.952) (ρ < 0.05). MRI 3D quantitative analysis was more accurate than 2D quantitative analysis using MRI for measuring osteonecrosis of the femoral head. Therefore, it may be useful for predicting the clinical outcome and deciding the proper treatment option

  11. Micro-computer system for quantitative image analysis of damage microstructure

    International Nuclear Information System (INIS)

    Kohyama, A.; Kohno, Y.; Satoh, K.; Igata, N.

    1984-01-01

    Quantitative image analysis of radiation induced damage microstructure is very important in evaluating material behaviors in radiation environment. But, quite a few improvement have been seen in quantitative analysis of damage microstructure in these decades. The objective of this work is to develop new system for quantitative image analysis of damage microstructure which could improve accuracy and efficiency of data sampling and processing and could enable to get new information about mutual relations among dislocations, precipitates, cavities, grain boundaries, etc. In this system, data sampling is done with X-Y digitizer. The cavity microstructure in dual-ion irradiated 316 SS is analyzed and the effectiveness of this system is discussed. (orig.)

  12. Quantitative analysis of the secretion of the MCP family of chemokines by muscle cells

    DEFF Research Database (Denmark)

    Henningsen, Jeanette; Pedersen, Bente Klarlund; Kratchmarova, Irina

    2011-01-01

    by Amino acids in Cell culture (SILAC) method for quantitative analysis resulted in the identification and generation of quantitative profiles of 59 growth factors and cytokines, including 9 classical chemokines. The members of the CC chemokine family of proteins such as monocyte chemotactic proteins 1, 2...

  13. Quantitative analysis of target components by comprehensive two-dimensional gas chromatography

    NARCIS (Netherlands)

    Mispelaar, V.G. van; Tas, A.C.; Smilde, A.K.; Schoenmakers, P.J.; Asten, A.C. van

    2003-01-01

    Quantitative analysis using comprehensive two-dimensional (2D) gas chromatography (GC) is still rarely reported. This is largely due to a lack of suitable software. The objective of the present study is to generate quantitative results from a large GC x GC data set, consisting of 32 chromatograms.

  14. Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method

    OpenAIRE

    Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

    2014-01-01

    Objective: To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. Methods: TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Results: Both assays provided good linearity, accuracy, reproducibility and selectivity for dete...

  15. Chemical Fingerprint Analysis and Quantitative Analysis of Rosa rugosa by UPLC-DAD

    Directory of Open Access Journals (Sweden)

    Sanawar Mansur

    2016-12-01

    Full Text Available A method based on ultra performance liquid chromatography with a diode array detector (UPLC-DAD was developed for quantitative analysis of five active compounds and chemical fingerprint analysis of Rosa rugosa. Ten batches of R. rugosa collected from different plantations in the Xinjiang region of China were used to establish the fingerprint. The feasibility and advantages of the used UPLC fingerprint were verified for its similarity evaluation by systematically comparing chromatograms with professional analytical software recommended by State Food and Drug Administration (SFDA of China. In quantitative analysis, the five compounds showed good regression (R2 = 0.9995 within the test ranges, and the recovery of the method was in the range of 94.2%–103.8%. The similarities of liquid chromatography fingerprints of 10 batches of R. rugosa were more than 0.981. The developed UPLC fingerprint method is simple, reliable, and validated for the quality control and identification of R. rugosa. Additionally, simultaneous quantification of five major bioactive ingredients in the R. rugosa samples was conducted to interpret the consistency of the quality test. The results indicated that the UPLC fingerprint, as a characteristic distinguishing method combining similarity evaluation and quantification analysis, can be successfully used to assess the quality and to identify the authenticity of R. rugosa.

  16. Structural and functional analysis of the kid toxin protein from E. coli Plasmid R1

    NARCIS (Netherlands)

    Hargreaves, D.; Santos-Sierra, S.; Giraldo, R.; Sabariegos-Jareño, R.; de la Cueva-Méndez, G.; Boelens, R.|info:eu-repo/dai/nl/070151407; Díaz-Orejas, R.; Rafferty, J.B.

    2002-01-01

    We have determined the structure of Kid toxin protein from E. coli plasmid R1 involved in stable plasmid inheritance by postsegregational killing of plasmid-less daughter cells. Kid forms a two-component system with its antagonist, Kis antitoxin. Our 1.4 Å crystal structure of Kid reveals a 2-fold

  17. Mutational analysis of Glu272 in elongation factor 1A of E. coli

    DEFF Research Database (Denmark)

    Mansilla, Francisco; Knudsen, Charlotte Rohde; Clark, Brian F. C.

    1998-01-01

    In our previous work (Mansilla et al. (1997) Protein Eng. 10, 927-934) we showed that Arg7 of Escherichia coli elongation factor Tu (EF1A) plays an essential role in aminoacyl-tRNA (aa-tRNA) binding. Substitution of Arg7 by Ala or Glu lost this activity. We proposed that Arg7 forms a salt bridge...

  18. Analysis of gene essentiality in Escherichia coli across strains and growth conditions

    DEFF Research Database (Denmark)

    Bonde, Ida; Lennen, Rebecca; Cardoso, Joao

    are either essential or detrimental for growth in the test condition in question. In this study the TN-Seq method was used to investigate the differences in gene essentiality between four laboratory strains of E.coli subjected to four different growth conditions to investigate the reason for the differences...

  19. Mutational analysis of Glu272 in elongation factor 1A of E. coli

    DEFF Research Database (Denmark)

    Mansilla, Francisco; Knudsen, Charlotte Rohde; Clark, Brian F. C.

    1998-01-01

    In our previous work (Mansilla et al. (1997) Protein Eng. 10, 927-934) we showed that Arg7 of Escherichia coli elongation factor Tu (EF1A) plays an essential role in aminoacyl-tRNA (aa-tRNA) binding. Substitution of Arg7 by Ala or Glu lost this activity. We proposed that Arg7 forms a salt bridge ...

  20. Crystallization and preliminary X-ray diffraction analysis of the lytic transglycosylase MltE from Escherichia coli

    International Nuclear Information System (INIS)

    Artola-Recolons, Cecilia; Llarrull, Leticia I.; Lastochkin, Elena; Mobashery, Shahriar; Hermoso, Juan A.

    2010-01-01

    Crystals of the lytic transglycosylase MltE from E. coli were grown using the microbatch method and diffracted to a resolution of 2.1 Å. MltE from Escherichia coli (193 amino acids, 21 380 Da) is a lytic transglycosylase that initiates the first step of cell-wall recycling. This enzyme is responsible for the cleavage of the cell-wall peptidoglycan at the β-1,4-glycosidic bond between the N-acetylglucosamine and N-acetylmuramic acid units. At the end this reaction generates a disaccharide that is internalized and initiates the recycling process. To obtain insights into the biological functions of MltE, crystallization trials were performed and crystals of MltE protein that were suitable for X-ray diffraction analysis were obtained. The MltE protein of E. coli was crystallized using the hanging-drop vapour-diffusion method at 291 K. Crystals grew from a mixture consisting of 28% polyethylene glycol 4000, 0.1 M Tris pH 8.4 and 0.2 M magnesium chloride. Further optimization was performed using the microbatch technique. Single crystals were obtained that belonged to the orthorhombic space group C222 1 , with unit-cell parameters a = 123.32, b = 183.93, c = 35.29 Å, and diffracted to a resolution of 2.1 Å

  1. Expression, crystallization and preliminary X-ray analysis of the periplasmic stress sensory protein RseB from Escherichia coli

    International Nuclear Information System (INIS)

    Wollmann, Petra; Zeth, Kornelius

    2006-01-01

    The periplasmic stress protein RseB from E. coli was cloned, expressed and crystallized. Crystallographic data are presented and structure solution using the multiple isomorphous replacement approach (MIR) is in progress. Sensing external stress in the bacterial periplasm and signal transduction to the cytoplasm are important functions of the CpxAR, Bae and σ E signalling pathways. In Escherichia coli, the σ E pathway can be activated through degradation of the antisigma factor RseA by DegS and YaeL. The periplasmic protein RseB plays an important role in this pathway by exerting a direct or indirect negative effect on YaeL cleavage efficiency. RseB from E. coli, missing the periplasmic signal sequence (RseB ΔN ), was cloned, expressed, purified and crystallized. Crystals were obtained in two different forms belonging to space group P42 1 2 (form I) and C222 1 (form II) and diffracted to 2.8 and 2.4 Å resolution, respectively. In crystal form I two copies of the protein were located in the asymmetric unit according to heavy-atom analysis, while crystal form II contained three copies

  2. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the regulator AcrR from Escherichia coli

    International Nuclear Information System (INIS)

    Li, Ming; Qiu, Xi; Su, Chih-Chia; Long, Feng; Gu, Ruoyu; McDermott, Gerry; Yu, Edward W.

    2006-01-01

    The transcriptional regulator AcrR from Escherichia coli has been cloned, overexpressed, purified and crystallized and X-ray diffraction data have been collected to a resolution of 2.5 Å. This paper describes the cloning, expression, purification and preliminary X-ray data analysis of the AcrR regulatory protein. The Escherichia coli AcrR is a member of the TetR family of transcriptional regulators. It regulates the expression of the AcrAB multidrug transporter. Recombinant AcrR with a 6×His tag at the C-terminus was expressed in E. coli and purified by metal-affinity chromatography. The protein was crystallized using hanging-drop vapor diffusion. X-ray diffraction data were collected from cryocooled crystals at a synchrotron light source. The best crystal diffracted to 2.5 Å. The space group was determined to be P3 2 , with unit-cell parameters a = b = 46.61, c = 166.16 Å

  3. Graphene-Based FET Detector for E. coli K12 Real-Time Monitoring and Its Theoretical Analysis

    Directory of Open Access Journals (Sweden)

    Jieyi Zhu

    2016-01-01

    Full Text Available This paper presents a theoretical analysis for a graphene-based FET real-time detector of the target bacteria E. coli K12. The motivation for this study is to design a sensor device for detection of bacteria in food and water in order to guarantee food safety. Graphene is chosen as our material for sensor design, which has outstanding electrical, physical, and optical performance. In our sensor structure, graphene-based solution gate field effect transistor (FET is the device model; fabrication and functionalization protocol are presented together in this paper. What is more, a real-time signal display system is the accompanied equipment for our designed biosensor device. In this system, the sensor bias current signal Ids would change obviously when the target bacteria are attached to the sensor surface. And the bias current Ids increases when the E. coli concentration increases. In the latter part, a theoretical interpretation of the sensor signal is to explain the bias current Ids increasing after the E. coli K12 attachment.

  4. Molecular Analysis of Asymptomatic Bacteriuria Escherichia coli Strain VR50 Reveals Adaptation to the Urinary Tract by Gene Acquisition

    DEFF Research Database (Denmark)

    Beatson, Scott A.; Ben Zakour, Nouri L.; Totsika, Makrina

    2015-01-01

    the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has...... a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50...... mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability...

  5. Glucose uptake regulation in E. coli by the small RNA SgrS: comparative analysis of E. coli K-12 (JM109 and MG1655 and E. coli B (BL21

    Directory of Open Access Journals (Sweden)

    Ng Weng-Ian

    2010-09-01

    Full Text Available Abstract Background The effect of high glucose concentration on the transcription levels of the small RNA SgrS and the messenger RNA ptsG, (encoding the glucose transporter IICBGlc, was studied in both E. coli K-12 (MG1655 and JM109 and E. coli B (BL21. It is known that the transcription level of sgrS increases when E. coli K-12 (MG1655 and JM109 is exposed to the non-metabolized glucose alpha methyl glucoside (αMG or when the bacteria with a defective glycolysis pathway is grown in presence of glucose. The increased level of sRNA SgrS reduces the level of the ptsG mRNA and consequently lowers the level of the glucose transporter IICBGlc. The suggested trigger for this action is the accumulation of the corresponding phospho-sugars. Results In the course of the described work, it was found that E. coli B (BL21 and E. coli K-12 (JM109 and MG1655 responded similarly to αMG: both strains increased SgrS transcription and reduced ptsG transcription. However, the two strains reacted differently to high glucose concentration (40 g/L. E. coli B (BL21 reacted by increasing sgrS transcription and reducing ptsG transcription while E. coli K-12 (JM109 and MG1655 did not respond to the high glucose concentration, and, therefore, transcription of sgrS was not detected and ptsG mRNA level was not affected. Conclusions The results suggest that E. coli B (BL21 tolerates high glucose concentration not only by its more efficient central carbon metabolism, but also by controlling the glucose transport into the cells regulated by the sRNA SgrS, which may suggest a way to control glucose consumption and increase its efficient utilization.

  6. Transportation and quantitative analysis of socio-economic development of relations

    Science.gov (United States)

    Chen, Yun

    2017-12-01

    Transportation has a close relationship with socio-economic. This article selects the indicators which can measure the development of transportation and socio-economic, using the method of correlation analysis, regression analysis, intensity of transportation analysis and transport elastic analysis, to analyze the relationship between them quantitatively, so that it has the fact guiding sense in the national development planning for the future.

  7. Toward best practices in data processing and analysis for intact biotherapeutics by MS in quantitative bioanalysis.

    Science.gov (United States)

    Kellie, John F; Kehler, Jonathan R; Karlinsey, Molly Z; Summerfield, Scott G

    2017-12-01

    Typically, quantitation of biotherapeutics from biological matrices by LC-MS is based on a surrogate peptide approach to determine molecule concentration. Recent efforts have focused on quantitation of the intact protein molecules or larger mass subunits of monoclonal antibodies. To date, there has been limited guidance for large or intact protein mass quantitation for quantitative bioanalysis. Intact- and subunit-level analyses of biotherapeutics from biological matrices are performed at 12-25 kDa mass range with quantitation data presented. Linearity, bias and other metrics are presented along with recommendations made on the viability of existing quantitation approaches. This communication is intended to start a discussion around intact protein data analysis and processing, recognizing that other published contributions will be required.

  8. Quantitative phosphoproteomic analysis of porcine muscle within 24 h postmortem

    DEFF Research Database (Denmark)

    Huang, Honggang; Larsen, Martin Røssel; Palmisano, Giuseppe

    2014-01-01

    in meat quality development, a quantitative mass spectrometry-based phosphoproteomic study was performed to analyze the porcine muscle within 24h PM using dimethyl labeling combined with the TiSH phosphopeptide enrichment strategy. In total 305 unique proteins were identified, including 160...... phosphorylation levels in muscle within 24 h PM. The high phosphorylation level of heat shock proteins (HSPs) in early PM may be an adaptive response to slaughter stress and protect muscle cell from apoptosis, as observed in the serine 84 of HSP27. This work indicated that PM muscle proteins underwent significant...... and rigor mortis development in PM muscle. BIOLOGICAL SIGNIFICANCE: The manuscript describes the characterization of postmortem (PM) porcine muscle within 24 h postmortem from the perspective of protein phosphorylation using advanced phosphoproteomic techniques. In the study, the authors employed...

  9. Quantitative analysis of distributed control paradigms of robot swarms

    DEFF Research Database (Denmark)

    Ngo, Trung Dung

    2010-01-01

    describe the physical and simulated robots, experiment scenario, and experiment setup. Third, we present our robot controllers based on behaviour based and neural network based paradigms. Fourth, we graphically show their experiment results and quantitatively analyse the results in comparison of the two......Given a task of designing controller for mobile robots in swarms, one might wonder which distributed control paradigms should be selected. Until now, paradigms of robot controllers have been within either behaviour based control or neural network based control, which have been recognized as two...... mainstreams of controller design for mobile robots. However, in swarm robotics, it is not clear how to determine control paradigms. In this paper we study the two control paradigms with various experiments of swarm aggregation. First, we introduce the two control paradigms for mobile robots. Second, we...

  10. Dynamic Quantitative Trait Locus Analysis of Plant Phenomic Data.

    Science.gov (United States)

    Li, Zitong; Sillanpää, Mikko J

    2015-12-01

    Advanced platforms have recently become available for automatic and systematic quantification of plant growth and development. These new techniques can efficiently produce multiple measurements of phenotypes over time, and introduce time as an extra dimension to quantitative trait locus (QTL) studies. Functional mapping utilizes a class of statistical models for identifying QTLs associated with the growth characteristics of interest. A major benefit of functional mapping is that it integrates information over multiple timepoints, and therefore could increase the statistical power for QTL detection. We review the current development of computationally efficient functional mapping methods which provide invaluable tools for analyzing large-scale timecourse data that are readily available in our post-genome era. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Quantitative Analysis of Matrine in Liquid Crystalline Nanoparticles by HPLC

    Directory of Open Access Journals (Sweden)

    Xinsheng Peng

    2014-01-01

    Full Text Available A reversed-phase high-performance liquid chromatographic method has been developed to quantitatively determine matrine in liquid crystal nanoparticles. The chromatographic method is carried out using an isocratic system. The mobile phase was composed of methanol-PBS(pH6.8-triethylamine (50 : 50 : 0.1% with a flow rate of 1 mL/min with SPD-20A UV/vis detector and the detection wavelength was at 220 nm. The linearity of matrine is in the range of 1.6 to 200.0 μg/mL. The regression equation is y=10706x-2959 (R2=1.0. The average recovery is 101.7%; RSD=2.22%  (n=9. This method provides a simple and accurate strategy to determine matrine in liquid crystalline nanoparticle.

  12. Quantitative Trait Loci Analysis of Allelopathy in Rice

    DEFF Research Database (Denmark)

    Jensen, L B; Courtois, B; Olofsdotter, M

    2008-01-01

    The allelopathic potential of rice (Oryza sativa L.) against Echinochloa crus-galli (L.) Beauv. was investigated under both laboratory and greenhouse conditions. A population of 150 recombinant inbred lines (RILs) was derived through single-seed descent from a cross between the indica cultivar AC...... the population phenotype was normally distributed. Two quantitative trait loci (QTLs) were located on chromosomes 4 and 7, explaining 20% of the phenotypic variation. A second relay seeding experiment was set up, this time including charcoal in the perlite. This screening showed that the allelopathic rice...... varieties did not have any effect on the weed species when grown with charcoal, the charcoal reversing the effect of any potential allelochemicals exuded from the rice roots. The second phenotypic experiment was conducted under greenhouse conditions in pots. Thirteen QTLs were detected for four different...

  13. Quantitative analysis on electric dipole energy in Rashba band splitting.

    Science.gov (United States)

    Hong, Jisook; Rhim, Jun-Won; Kim, Changyoung; Ryong Park, Seung; Hoon Shim, Ji

    2015-09-01

    We report on quantitative comparison between the electric dipole energy and the Rashba band splitting in model systems of Bi and Sb triangular monolayers under a perpendicular electric field. We used both first-principles and tight binding calculations on p-orbitals with spin-orbit coupling. First-principles calculation shows Rashba band splitting in both systems. It also shows asymmetric charge distributions in the Rashba split bands which are induced by the orbital angular momentum. We calculated the electric dipole energies from coupling of the asymmetric charge distribution and external electric field, and compared it to the Rashba splitting. Remarkably, the total split energy is found to come mostly from the difference in the electric dipole energy for both Bi and Sb systems. A perturbative approach for long wave length limit starting from tight binding calculation also supports that the Rashba band splitting originates mostly from the electric dipole energy difference in the strong atomic spin-orbit coupling regime.

  14. Integration of Qualitative and Quantitative Methods: Building and Interpreting Clusters from Grounded Theory and Discourse Analysis

    Directory of Open Access Journals (Sweden)

    Aldo Merlino

    2007-01-01

    Full Text Available Qualitative methods present a wide spectrum of application possibilities as well as opportunities for combining qualitative and quantitative methods. In the social sciences fruitful theoretical discussions and a great deal of empirical research have taken place. This article introduces an empirical investigation which demonstrates the logic of combining methodologies as well as the collection and interpretation, both sequential as simultaneous, of qualitative and quantitative data. Specifically, the investigation process will be described, beginning with a grounded theory methodology and its combination with the techniques of structural semiotics discourse analysis to generate—in a first phase—an instrument for quantitative measuring and to understand—in a second phase—clusters obtained by quantitative analysis. This work illustrates how qualitative methods allow for the comprehension of the discursive and behavioral elements under study, and how they function as support making sense of and giving meaning to quantitative data. URN: urn:nbn:de:0114-fqs0701219

  15. Application of non-quantitative modelling in the analysis of a network warfare environment

    CSIR Research Space (South Africa)

    Veerasamy, N

    2008-07-01

    Full Text Available based on the use of secular associations, chronological origins, linked concepts, categorizations and context specifications. This paper proposes the use of non-quantitative methods through a morphological analysis to better explore and define...

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

    National Research Council Canada - National Science Library

    Hansen, Eric C

    2005-01-01

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

  17. Quantitative analysis by microchip capillary electrophoresis – current limitations and problem-solving strategies

    NARCIS (Netherlands)

    Revermann, T.; Götz, S.; Künnemeyer, Jens; Karst, U.

    2008-01-01

    Obstacles and possible solutions for the application of microchip capillary electrophoresis in quantitative analysis are described and critically discussed. Differences between the phenomena occurring during conventional capillary electrophoresis and microchip-based capillary electrophoresis are

  18. Quantitative method of X-ray diffraction phase analysis of building materials

    International Nuclear Information System (INIS)

    Czuba, J.; Dziedzic, A.

    1978-01-01

    Quantitative method of X-ray diffraction phase analysis of building materials, with use of internal standard, has been presented. The errors committed by determining the content of particular phases have been also given. (author)

  19. Genome-wide analysis of E. coli cell-gene interactions.

    Science.gov (United States)

    Cardinale, S; Cambray, G

    2017-11-23

    The pursuit of standardization and reliability in synthetic biology has achieved, in recent years, a number of advances in the design of more predictable genetic parts for biological circuits. However, even with the development of high-throughput screening methods and whole-cell models, it is still not possible to predict reliably how a synthetic genetic construct interacts with all cellular endogenous systems. This study presents a genome-wide analysis of how the expression of synthetic genes is affected by systematic perturbations of cellular functions. We found that most perturbations modulate expression indirectly through an effect on cell size, putting forward the existence of a generic Size-Expression interaction in the model prokaryote Escherichia coli. The Size-Expression interaction was quantified by inserting a dual fluorescent reporter gene construct into each of the 3822 single-gene deletion strains comprised in the KEIO collection. Cellular size was measured for single cells via flow cytometry. Regression analyses were used to discriminate between expression-specific and gene-specific effects. Functions of the deleted genes broadly mapped onto three systems with distinct primary influence on the Size-Expression map. Perturbations in the Division and Biosynthesis (DB) system led to a large-cell and high-expression phenotype. In contrast, disruptions of the Membrane and Motility (MM) system caused small-cell and low-expression phenotypes. The Energy, Protein synthesis and Ribosome (EPR) system was predominantly associated with smaller cells and positive feedback on ribosome function. Feedback between cell growth and gene expression is widespread across cell systems. Even though most gene disruptions proximally affect one component of the Size-Expression interaction, the effect therefore ultimately propagates to both. More specifically, we describe the dual impact of growth on cell size and gene expression through cell division and ribosomal content

  20. [Antibiotic resistance patterns of Escherichia coli strains isolated from urine cultures in Turkey: a meta-analysis].

    Science.gov (United States)

    Aykan, Sadiye Berna; Ciftci, Ihsan Hakkı

    2013-10-01

    Escherichia coli is the most frequently isolated microorganism from both community-acquired and nosocomial urinary tract infections in Turkey. A large number of studies concerning antibiotic susceptibility of E.coli have been published from different centers throughout the country. The aim of this study was to evaluate the antibiotic resistance patterns of E.coli strains isolated from urine cultures by a meta-analysis in published medical literature between the years of 1996-2012 in Turkey. The study was planned and conducted in accordance with the declaration of PRISMA and describes the methods of literature search, the determining criteria for inclusion and evaluation of articles, data collection and statistical analysis. To find the published series Google Scholar and PubMed international databases were used to access published manuscripts evaluated according to the determined criteria for acceptance and rejection. For each study, general data and antibiotic resistance rates were collected as a common unit. Publications considered as lacking in appropriate content was eliminated from the study. Statistical analysis of the data obtained were 95% confidence intervals, and p≤ 0.05 value was considered as significant difference. A total of 228 articles were found to be published during 1996-2012 period, while 101 of them were included in the meta-analysis according to the eligibility criteria. The analyses indicated that nitrofurantoin and piperacillin resistance rates have been decreased, whereas ciprofloxacin, cefepime, co-trimoxazole and extended-spectrum beta-lactamase (ESBL) positivity rates have been increased during the study period. The increases in the rates of ciprofloxacin and cefepime resistance and and ESBL production were statistically-significant (pAntibiotic resistance rates, except for imipenem, in bacterial strains, isolated from hospitalized patients were found significantly higher in strains obtained from outpatients. The differences between

  1. Quantitative phosphoproteomic analysis of porcine muscle within 24 h postmortem.

    Science.gov (United States)

    Huang, Honggang; Larsen, Martin R; Palmisano, Giuseppe; Dai, Jie; Lametsch, René

    2014-06-25

    Protein phosphorylation can regulate most of the important processes in muscle, such as metabolism and contraction. The postmortem (PM) metabolism and rigor mortis have essential effects on meat quality. In order to identify and characterize the protein phosphorylation events involved in meat quality development, a quantitative mass spectrometry-based phosphoproteomic study was performed to analyze the porcine muscle within 24h PM using dimethyl labeling combined with the TiSH phosphopeptide enrichment strategy. In total 305 unique proteins were identified, including 160 phosphoproteins with 784 phosphorylation sites. Among these, 184 phosphorylation sites on 93 proteins had their phosphorylation levels significantly changed. The proteins involved in glucose metabolism and muscle contraction were the two largest clusters of phosphoproteins with significantly changed phosphorylation levels in muscle within 24 h PM. The high phosphorylation level of heat shock proteins (HSPs) in early PM may be an adaptive response to slaughter stress and protect muscle cell from apoptosis, as observed in the serine 84 of HSP27. This work indicated that PM muscle proteins underwent significant changes at the phosphorylation level but were relatively stable at the total protein level, suggesting that protein phosphorylation may have important roles in meat quality development through the regulation of proteins involved in glucose metabolism and muscle contraction, thereby affecting glycolysis and rigor mortis development in PM muscle. The manuscript describes the characterization of postmortem (PM) porcine muscle within 24 h postmortem from the perspective of protein phosphorylation using advanced phosphoproteomic techniques. In the study, the authors employed the dimethyl labeling combined with the TiSH phosphopeptide enrichment and LC-MS/MS strategy. This was the first high-throughput quantitative phosphoproteomic study in PM muscle of farm animals. In the work, both the proteome

  2. Quantitative analysis of agricultural land use change in China

    Science.gov (United States)

    Chou, Jieming; Dong, Wenjie; Wang, Shuyu; Fu, Yuqing

    This article reviews the potential impacts of climate change on land use change in China. Crop sown area is used as index to quantitatively analyze the temporal-spatial changes and the utilization of the agricultural land. A new concept is defined as potential multiple cropping index to reflect the potential sowing ability. The impacting mechanism, land use status and its surplus capacity are investigated as well. The main conclusions are as following; During 1949-2010, the agricultural land was the greatest in amount in the middle of China, followed by that in the country's eastern and western regions. The most rapid increase and decrease of agricultural land were observed in Xinjiang and North China respectively, Northwest China and South China is also changed rapid. The variation trend before 1980 differed significantly from that after 1980. Agricultural land was affected by both natural and social factors, such as regional climate and environmental changes, population growth, economic development, and implementation of policies. In this paper, the effects of temperature and urbanization on the coverage of agriculture land are evaluated, and the results show that the urbanization can greatly affects the amount of agriculture land in South China, Northeast China, Xinjiang and Southwest China. From 1980 to 2009, the extent of agricultural land use had increased as the surplus capacity had decreased. Still, large remaining potential space is available, but the future utilization of agricultural land should be carried out with scientific planning and management for the sustainable development.

  3. [Device for quantitative analysis of perception and pain sensation].

    Science.gov (United States)

    Arita, Hideko; Kato, Jitsu; Ogawa, Setsuro; Hanaoka, Kazuo

    2014-07-01

    The article describes an analysing device that measures the perception and intensity of pain quantitatively. While it is not necessarily true that psychological aspect is totally irrelevant to pain measurement, this device is remarkable in that it is capable of measuring the intensity of pain felt by the patient more objectively by using electric stimuli. The feature of this device is that it uses a non-pain heteresthesia for measuring the intensity of pain. The device is compact, light-weight, and portable. Unlike VAS that requires only a scale, the device requires a person to carry out the measurement. Nevertheless, as the National Health Insurance (NHI) coverage has been approved, introduction of the device may be facilitated in terms of budget for the purchase and labor. The device is useful to better understand not only the intensity of pain but also the pathological conditions, resulting in more appropriate treatment, by (1) comparing degree of pain or VAS values taken by a multicenter study with those of a patient; (2) using both degree of pain and VAS; and (3) multiple measurements of degree of pain and VAS in one case.

  4. Quantitative analysis of impact measurements using dynamic load cells

    Directory of Open Access Journals (Sweden)

    Brent J. Maranzano

    2016-03-01

    Full Text Available A mathematical model is used to estimate material properties from a short duration transient impact force measured by dropping spheres onto rectangular coupons fixed to a dynamic load cell. The contact stress between the dynamic load cell surface and the projectile are modeled using Hertzian contact mechanics. Due to the short impact time relative to the load cell dynamics, an additional Kelvin–Voigt element is included in the model to account for the finite response time of the piezoelectric crystal. Calculations with and without the Kelvin–Voigt element are compared to experimental data collected from combinations of polymeric spheres and polymeric and metallic surfaces. The results illustrate that the inclusion of the Kelvin–Voigt element qualitatively captures the post impact resonance and non-linear behavior of the load cell signal and quantitatively improves the estimation of the Young's elastic modulus and Poisson's ratio. Mathematically, the additional KV element couples one additional differential equation to the Hertzian spring-dashpot equation. The model can be numerically integrated in seconds using standard numerical techniques allowing for its use as a rapid technique for the estimation of material properties. Keywords: Young's modulus, Poisson's ratio, Dynamic load cell

  5. Quantitative risk analysis offshore-Human and organizational factors

    International Nuclear Information System (INIS)

    Espen Skogdalen, Jon; Vinnem, Jan Erik

    2011-01-01

    Quantitative Risk Analyses (QRAs) are one of the main tools for risk management within the Norwegian and UK oil and gas industry. Much criticism has been given to the limitations related to the QRA-models and that the QRAs do not include human and organizational factors (HOF-factors). Norway and UK offshore legislation and guidelines require that the HOF-factors are included in the QRAs. A study of 15 QRAs shows that the factors are to some extent included, and there are large differences between the QRAs. The QRAs are categorized into four levels according to the findings. Level 1 QRAs do not describe or comment on the HOF-factors at all. Relevant research projects have been conducted to fulfill the requirements of Level 3 analyses. At this level, there is a systematic collection of data related to HOF. The methods are systematic and documented, and the QRAs are adjusted. None of the QRAs fulfill the Level 4 requirements. Level 4 QRAs include the model and describe the HOF-factors as well as explain how the results should be followed up in the overall risk management. Safety audits by regulatory authorities are probably necessary to point out the direction for QRA and speed up the development.

  6. Quantitative analysis of cholesteatoma using high resolution computed tomography

    International Nuclear Information System (INIS)

    Kikuchi, Shigeru; Yamasoba, Tatsuya; Iinuma, Toshitaka.

    1992-01-01

    Seventy-three cases of adult cholesteatoma, including 52 cases of pars flaccida type cholesteatoma and 21 of pars tensa type cholesteatoma, were examined using high resolution computed tomography, in both axial (lateral semicircular canal plane) and coronal sections (cochlear, vestibular and antral plane). These cases were classified into two subtypes according to the presence of extension of cholesteatoma into the antrum. Sixty cases of chronic otitis media with central perforation (COM) were also examined as controls. Various locations of the middle ear cavity were measured in terms of size in comparison with pars flaccida type cholesteatoma, pars tensa type cholesteatoma and COM. The width of the attic was significantly larger in both pars flaccida type and pars tensa type cholesteatoma than in COM. With pars flaccida type cholesteatoma there was a significantly larger distance between the malleus and lateral wall of the attic than with COM. In contrast, the distance between the malleus and medial wall of the attic was significantly larger with pars tensa type cholesteatoma than with COM. With cholesteatoma extending into the antrum, regardless of the type of cholesteatoma, there were significantly larger distances than with COM at the following sites: the width and height of the aditus ad antrum, and the width, height and anterior-posterior diameter of the antrum. However, these distances were not significantly different between cholesteatoma without extension into the antrum and COM. The hitherto demonstrated qualitative impressions of bone destruction in cholesteatoma were quantitatively verified in detail using high resolution computed tomography. (author)

  7. Quantitative XRD analysis of {110} twin density in biotic aragonites.

    Science.gov (United States)

    Suzuki, Michio; Kim, Hyejin; Mukai, Hiroki; Nagasawa, Hiromichi; Kogure, Toshihiro

    2012-12-01

    {110} Twin densities in biotic aragonite have been estimated quantitatively from the peak widths of specific reflections in powder X-ray diffraction (XRD) patterns, as well as direct confirmation of the twins using transmission electron microscopy (TEM). Influence of the twin density on the peak widths in the XRD pattern was simulated using DIFFaX program, regarding (110) twin as interstratification of two types of aragonite unit layers with mirrored relationship. The simulation suggested that the twin density can be estimated from the difference of the peak widths between 111 and 021, or between 221 and 211 reflections. Biotic aragonite in the crossed-lamellar microstructure (three species) and nacreous microstructure (four species) of molluscan shells, fish otoliths (two species), and a coral were investigated. The XRD analyses indicated that aragonite crystals in the crossed-lamellar microstructure of the three species contain high density of the twins, which is consistent with the TEM examination. On the other hand, aragonite in the nacre of the four species showed almost no difference of the peak widths between the paired reflections, indicating low twin densities. The results for the fish otoliths were varied between the species. Such variation of the twin density in biotic aragonites may reflect different schemes of crystal growth in biomineralization. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. Quantitative Analysis and Efficient Surface Modification of Silica Nanoparticles

    Directory of Open Access Journals (Sweden)

    Hak-Sung Jung

    2012-01-01

    Full Text Available Aminofunctional trialkoxysilanes such as aminopropyltrimethoxysilane (APTMS and (3-trimethoxysilylpropyldiethylenetriamine (DETAS were employed as a surface modification molecule for generating monolayer modification on the surface of silica (SiO2 nanoparticles. We were able to quantitatively analyze the number of amine functional groups on the modified SiO2 nanoparticles by acid-base back titration method and determine the effective number of amine functional groups for the successive chemical reaction by absorption measurements after treating with fluorescent rhodamine B isothiocyanate (RITC molecules. The numbers of amine sites measured by back titration were 2.7 and 7.7 ea/nm2 for SiO2-APTMS and SiO2-DETAS, respectively, while the numbers of effective amine sites measured by absorption calibration were about one fifth of the total amine sites, namely, 0.44 and 1.3 ea/nm2 for SiO2-APTMS(RITC and SiO2-DETAS(RITC, respectively. Furthermore, it was confirmed that the reactivity of amino groups on the surface-modified silica nanoparticles could be maintained in ethanol for more than 1.5 months without showing any significant differences in the reactivity.

  9. Quantitative analysis of TALE-DNA interactions suggests polarity effects.

    Science.gov (United States)

    Meckler, Joshua F; Bhakta, Mital S; Kim, Moon-Soo; Ovadia, Robert; Habrian, Chris H; Zykovich, Artem; Yu, Abigail; Lockwood, Sarah H; Morbitzer, Robert; Elsäesser, Janett; Lahaye, Thomas; Segal, David J; Baldwin, Enoch P

    2013-04-01

    Transcription activator-like effectors (TALEs) have revolutionized the field of genome engineering. We present here a systematic assessment of TALE DNA recognition, using quantitative electrophoretic mobility shift assays and reporter gene activation assays. Within TALE proteins, tandem 34-amino acid repeats recognize one base pair each and direct sequence-specific DNA binding through repeat variable di-residues (RVDs). We found that RVD choice can affect affinity by four orders of magnitude, with the relative RVD contribution in the order NG > HD ≈ NN > NI > NK. The NN repeat preferred the base G over A, whereas the NK repeat bound G with 10(3)-fold lower affinity. We compared AvrBs3, a naturally occurring TALE that recognizes its target using some atypical RVD-base combinations, with a designed TALE that precisely matches 'standard' RVDs with the target bases. This comparison revealed unexpected differences in sensitivity to substitutions of the invariant 5'-T. Another surprising observation was that base mismatches at the 5' end of the target site had more disruptive effects on affinity than those at the 3' end, particularly in designed TALEs. These results provide evidence that TALE-DNA recognition exhibits a hitherto un-described polarity effect, in which the N-terminal repeats contribute more to affinity than C-terminal ones.

  10. Quantitative analysis of the thermal damping of coherent axion oscillations

    International Nuclear Information System (INIS)

    Turner, M.S.

    1985-01-01

    Unruh and Wald have recently discussed a new mechanism for damping coherent axion oscillations, ''thermal damping,'' which occurs due to the temperature dependence of the axion mass and neutrino viscosity. We investigate the effect quantitatively and find that the present energy density in axions can be written as rho/sub a/ = rho/sub a0//(1+J/sub UW/), where rho/sub a/0 is what the axion energy density would be in the absence of the thermal-damping effect and J/sub UW/ is an integral whose integrand depends upon (dm/sub a//dT) 2 . As a function of f(equivalentPeccei-Quinn symmetry-breaking scale) J/sub UW/ achieves its maximum value for f/sub PQ/approx. =3 x 10 12 GeV; unless the axion mass turn-on is very sudden, Vertical Bar(T/m/sub a/)(dm/sub a//dT)Vertical Bar>>1, J/sub UW/ is <<1, implying that this damping mechanism is not significant

  11. Quantitative analysis of minerals by X-ray diffraction

    International Nuclear Information System (INIS)

    Pietroluongo, L.R.V.; Veiga, M.M. da

    1982-01-01

    Considerations about the X-ray diffraction technique for quantitative analyses are made; some experiments carried out at CETEM - Centro de Tecnologia Mineral (Rio de Janeiro, Brazil) with synthetic samples and real samples of diatomites (from northeastern region of Brazil) are described. Quartz quantification has been a problem for analytical chemists and is of great importance to the industries which use this raw material. Comments are made about the main factors influencing the intensity of diffracted X-rays, such as: the crystallinity of the mineral phase; the granulometry, the preferential orientation; sample preparation and pressing, the chemical composition of standards and experimental analytical conditions. Several analytical methods used are described: direct measurement of the height or area of a peak resulting from a particular reflection and comparison with a pre-calibrated curve; method of sequential addition of the mineral of interest in the sample and extrapolation of results for ZERO addition; methods of external and internal standards. (C.L.B.) [pt

  12. Quantitative analysis of complexes in electron irradiated CZ silicon

    International Nuclear Information System (INIS)

    Inoue, N.; Ohyama, H.; Goto, Y.; Sugiyama, T.

    2007-01-01

    Complexes in helium or electron irradiated silicon are quantitatively analyzed by highly sensitive and accurate infrared (IR) absorption spectroscopy. Carbon concentration (1x10 15 -1x10 17 cm -3 ) and helium dose (5x10 12 -5x10 13 cm -2 ) or electron dose (1x10 15 -1x10 17 cm -2 ) are changed by two orders of magnitude in relatively low regime compared to the previous works. It is demonstrated that the carbon-related complex in low carbon concentration silicon of commercial grade with low electron dose can be detected clearly. Concentration of these complexes is estimated. It is clarified that the complex configuration and thermal behavior in low carbon and low dose samples is simple and almost confined within the individual complex family compared to those in high concentration and high dose samples. Well-established complex behavior in electron-irradiated sample is compared to that in He-irradiated samples, obtained by deep level transient spectroscopy (DLTS) or cathodoluminescence (CL), which had close relation to the Si power device performance

  13. Quantitative analysis of task selection for brain-computer interfaces

    Science.gov (United States)

    Llera, Alberto; Gómez, Vicenç; Kappen, Hilbert J.

    2014-10-01

    Objective. To assess quantitatively the impact of task selection in the performance of brain-computer interfaces (BCI). Approach. We consider the task-pairs derived from multi-class BCI imagery movement tasks in three different datasets. We analyze for the first time the benefits of task selection on a large-scale basis (109 users) and evaluate the possibility of transferring task-pair information across days for a given subject. Main results. Selecting the subject-dependent optimal task-pair among three different imagery movement tasks results in approximately 20% potential increase in the number of users that can be expected to control a binary BCI. The improvement is observed with respect to the best task-pair fixed across subjects. The best task-pair selected for each subject individually during a first day of recordings is generally a good task-pair in subsequent days. In general, task learning from the user side has a positive influence in the generalization of the optimal task-pair, but special attention should be given to inexperienced subjects. Significance. These results add significant evidence to existing literature that advocates task selection as a necessary step towards usable BCIs. This contribution motivates further research focused on deriving adaptive methods for task selection on larger sets of mental tasks in practical online scenarios.

  14. Quantitative Performance Analysis of the SPEC OMPM2001 Benchmarks

    Directory of Open Access Journals (Sweden)

    Vishal Aslot

    2003-01-01

    Full Text Available The state of modern computer systems has evolved to allow easy access to multiprocessor systems by supporting multiple processors on a single physical package. As the multiprocessor hardware evolves, new ways of programming it are also developed. Some inventions may merely be adopting and standardizing the older paradigms. One such evolving standard for programming shared-memory parallel computers is the OpenMP API. The Standard Performance Evaluation Corporation (SPEC has created a suite of parallel programs called SPEC OMP to compare and evaluate modern shared-memory multiprocessor systems using the OpenMP standard. We have studied these benchmarks in detail to understand their performance on a modern architecture. In this paper, we present detailed measurements of the benchmarks. We organize, summarize, and display our measurements using a Quantitative Model. We present a detailed discussion and derivation of the model. Also, we discuss the important loops in the SPEC OMPM2001 benchmarks and the reasons for less than ideal speedup on our platform.

  15. A CGE analysis for quantitative evaluation of electricity market changes

    International Nuclear Information System (INIS)

    Hwang, Won-Sik; Lee, Jeong-Dong

    2015-01-01

    Risk and uncertainty entailed by electricity industry privatization impose a heavy burden on the political determination. In this sense, ex ante analyses are important in order to investigate the economic effects of privatization or liberalization in the electricity industry. For the purpose of fulfilling these quantitative analyses, a novel approach is developed, incorporating a top-down and bottom-up model that takes into account economic effects and technological constraints simultaneously. This study also examines various counterfactual scenarios after Korean electricity industry reform through the integrated framework. Simulation results imply that authorities should prepare an improved regulatory system and policy measures such as forward contracts for industry reform, in order to promote competition in the distribution sector as well as the generation sector. -- Highlights: •A novel approach is proposed for incorporating a top-down and bottom-up model. •This study examines various counterfactual scenarios after Korean electricity industry reform. •An improved regulatory system and policy measures are required before the reform

  16. An iterative approach to case study analysis: insights from qualitative analysis of quantitative inconsistencies

    Directory of Open Access Journals (Sweden)

    Allain J Barnett

    2016-09-01

    Full Text Available Large-N comparative studies have helped common pool resource scholars gain general insights into the factors that influence collective action and governance outcomes. However, these studies are often limited by missing data, and suffer from the methodological limitation that important information is lost when we reduce textual information to quantitative data. This study was motivated by nine case studies that appeared to be inconsistent with the expectation that the presence of Ostrom’s Design Principles increases the likelihood of successful common pool resource governance. These cases highlight the limitations of coding and analysing Large-N case studies. We examine two issues: 1 the challenge of missing data and 2 potential approaches that rely on context (which is often lost in the coding process to address inconsistencies between empirical observations theoretical predictions.  For the latter, we conduct a post-hoc qualitative analysis of a large-N comparative study to explore 2 types of inconsistencies: 1 cases where evidence for nearly all design principles was found, but available evidence led to the assessment that the CPR system was unsuccessful and 2 cases where the CPR system was deemed successful despite finding limited or no evidence for design principles.  We describe inherent challenges to large-N comparative analysis to coding complex and dynamically changing common pool resource systems for the presence or absence of design principles and the determination of “success”.  Finally, we illustrate how, in some cases, our qualitative analysis revealed that the identity of absent design principles explained inconsistencies hence de-facto reconciling such apparent inconsistencies with theoretical predictions.  This analysis demonstrates the value of combining quantitative and qualitative analysis, and using mixed-methods approaches iteratively to build comprehensive methodological and theoretical approaches to understanding

  17. Structure-function analysis of the self-recognizing Antigen 43 autotransporter protein from Escherichia coli

    DEFF Research Database (Denmark)

    Klemm, Per; Hjerrild, L.; Gjermansen, Morten

    2004-01-01

    Antigen 43 (Ag43) is a self-recognizing surface adhesin found in most Escherichia coli strains. Expression of Ag43 confers aggregation and fluffing of cells, promotes biofilm formation and is associated with enhanced resistance to antimicrobial agents. Ag43 is an autotransporter protein and consi......Antigen 43 (Ag43) is a self-recognizing surface adhesin found in most Escherichia coli strains. Expression of Ag43 confers aggregation and fluffing of cells, promotes biofilm formation and is associated with enhanced resistance to antimicrobial agents. Ag43 is an autotransporter protein......-clumping variants, we have pinpointed the region of the protein responsible for autoaggregation to be located within the N-terminal one-third of the passenger domain. Our data suggest that ionic interactions between charged residues residing in interacting pairs of Ag43(alpha) domains may be important for the self...

  18. Cloning, purification, crystallization and preliminary crystallographic analysis of LsrR from Escherichia coli

    International Nuclear Information System (INIS)

    Liu, Xiaotian; Wu, Minhao; Sun, Demeng; Zang, Jianye

    2010-01-01

    The E. coli transcription repressor LsrR has been overexpressed, purified and crystallized. Diffraction data were collected to about 3 Å resolution. In Escherichia coli, the lsr operon is composed of six genes lsrACDBFG which regulate uptake and modification of the signalling molecule AI-2. LsrR is a repressor of the lsr operon and itself, which can bind phospho-AI-2 and be released from the promoter region of the operon and thus activate gene expression. LsrR fused with an HHHHHH sequence at the C-terminus was expressed, purified and crystallized in order to determine its structure and elucidate the molecular mechanism of repression. The crystal belonged to space group I222, with unit-cell parameters a = 79.84, b = 116.65, c = 186.04 Å, and was estimated to contain two protein molecules per asymmetric unit

  19. Genetic Analysis of Diaminopimelic Acid- and Lysine-Requiring Mutants of Escherichia coli1

    Science.gov (United States)

    Bukhari, Ahmad I.; Taylor, Austin L.

    1971-01-01

    Several diaminopimelic acid (DAP)- and lysine-requiring mutants of Escherichia coli were isolated and studied by genetic, physiological, and biochemical means. The genes concerned with DAP-lysine synthesis map at several different sites on the E. coli chromosome and, therefore, do not constitute a single operon. Three separate loci affecting DAP synthesis are located in the 0 to 2.5 min region of the genetic map. The order of the loci in this region is thr-dapB-pyrA-ara-leu-pan-dapC-tonA-dapD. Two additional DAP genes map in the region between min 47 and 48, with the gene order being gua-dapA-dapE-ctr. The lys locus at min 55 determines the synthesis of the enzyme DAP decarboxylase, which catalyzes the conversion of DAP into lysine. The order of the genes in this region is serA-lysA-thyA. PMID:4926684

  20. Genetic analysis of diaminopimelic acid- and lysine-requiring mutants of Escherichia coli.

    Science.gov (United States)

    Bukhari, A I; Taylor, A L

    1971-03-01

    Several diaminopimelic acid (DAP)- and lysine-requiring mutants of Escherichia coli were isolated and studied by genetic, physiological, and biochemical means. The genes concerned with DAP-lysine synthesis map at several different sites on the E. coli chromosome and, therefore, do not constitute a single operon. Three separate loci affecting DAP synthesis are located in the 0 to 2.5 min region of the genetic map. The order of the loci in this region is thr-dapB-pyrA-ara-leu-pan-dapC-tonA-dapD. Two additional DAP genes map in the region between min 47 and 48, with the gene order being gua-dapA-dapE-ctr. The lys locus at min 55 determines the synthesis of the enzyme DAP decarboxylase, which catalyzes the conversion of DAP into lysine. The order of the genes in this region is serA-lysA-thyA.

  1. A Comparative Analysis of Recombinant Expression and Solubility Screening of Two Phytases in E. coli

    Directory of Open Access Journals (Sweden)

    Ashok Pandey

    2011-01-01

    Full Text Available Microbial phytases, especially from fungal and bacterial sources, have received much attention as food additives in human nutrition and as feed supplements for monogastric animals. An effective expression screening method for recombinant production of this enzyme on a small scale is industrially desirable. An effort has been made in this work to clone and express phytase genes from Aspergillus sp. and Escherichia coli with the selected host, vector and inducer combination. Albeit the formation of insoluble inclusion bodies by fungal phytase, recombinant E. coli appA was effectively expressed in a cost-effective manner in the periplasm of BL21plysS using an inducer concentration of 0.01 mM in 4 h of growth. Enzyme was purified in three consecutive steps and functional studies were carried out.

  2. [Quantitative spectrum analysis of characteristic gases of spontaneous combustion coal].

    Science.gov (United States)

    Liang, Yun-Tao; Tang, Xiao-Jun; Luo, Hai-Zhu; Sun, Yong

    2011-09-01

    Aimed at the characteristics of spontaneous combustion gas such as a variety of gases, lou limit of detection, and critical requirement of safety, Fourier transform infrared (FTIR) spectral analysis is presented to analyze characteristic gases of spontaneous combustion In this paper, analysis method is introduced at first by combing characteristics of absorption spectra of analyte and analysis requirement. Parameter setting method, sample preparation, feature variable abstract and analysis model building are taken into consideration. The methods of sample preparation, feature abstraction and analysis model are introduced in detail. And then, eleven kinds of gases were tested with Tensor 27 spectrometer. CH4, C2H6, C3H8, iC4H10, nC4H10, C2 H4, C3 H6, C3 H2, SF6, CO and CO2 were included. The optical path length was 10 cm while the spectra resolution was set as 1 cm(-1). The testing results show that the detection limit of all analytes is less than 2 x 10(-6). All the detection limits fit the measurement requirement of spontaneous combustion gas, which means that FTIR may be an ideal instrument and the analysis method used in this paper is competent for spontaneous combustion gas measurement on line.

  3. Development of a Rapid and Sensitive Method Combining a Cellulose Ester Microfilter and a Real-Time Quantitative PCR Assay To Detect Campylobacter jejuni and Campylobacter coli in 20 Liters of Drinking Water or Low-Turbidity Waters

    Science.gov (United States)

    Tissier, Adeline; Denis, Martine; Hartemann, Philippe

    2012-01-01

    Investigations of Campylobacter jejuni and Campylobacter coli in samples of drinking water suspected of being at the origin of an outbreak very often lead to negative results. One of the reasons for this failure is the small volume of water typically used for detecting these pathogens (10 to 1,000 ml). The efficiencies of three microfilters and different elution procedures were determined using real-time quantitative PCR to propose a procedure allowing detection of Campylobacter in 20 liters of drinking water or low-turbidity water samples. The results showed that more than 80% of the bacteria inoculated in 1 liter of drinking water were retained on each microfilter. An elution with a solution containing 3% beef extract, 0.05 M glycine at pH 9, combined with direct extraction of the bacterial genomes retained on the cellulose ester microfilter, allowed recovery of 87.3% (±22% [standard deviation]) of Campylobacter per 1 liter of tap water. Recoveries obtained from 20-liter volumes of tap water spiked with a C. coli strain were 69.5% (±10.3%) and 78.5% (±15.1%) for 91 CFU and 36 CFU, respectively. Finally, tests performed on eight samples of 20 liters of groundwater collected from an alluvial well used for the production of drinking water revealed the presence of C. jejuni and C. coli genomes, whereas no bacteria were detected with the normative culture method in volumes ranging from 10 to 1,000 ml. In the absence of available epidemiological data and information on bacterial viability, these last results indicate only that the water resource is not protected from contamination by Campylobacter. PMID:22138985

  4. Mutational Analysis of the RecJ Exonuclease of Escherichia coli: Identification of Phosphoesterase Motifs

    OpenAIRE

    Sutera, Vincent A.; Han, Eugene S.; Rajman, Luis A.; Lovett, Susan T.

    1999-01-01

    The recJ gene, identified in Escherichia coli, encodes a Mg+2-dependent 5′-to-3′ exonuclease with high specificity for single-strand DNA. Genetic and biochemical experiments implicate RecJ exonuclease in homologous recombination, base excision, and methyl-directed mismatch repair. Genes encoding proteins with strong similarities to RecJ have been found in every eubacterial genome sequenced to date, with the exception of Mycoplasma and Mycobacterium tuberculosis. Multiple genes encoding protei...

  5. An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli

    OpenAIRE

    Bohlin, Jon; Brynildsrud, Ola B; Sekse, Camilla; Snipen, Lars

    2014-01-01

    Background There are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence fa...

  6. Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli

    DEFF Research Database (Denmark)

    George, Kevin W; Thompson, Mitchell; Kim, Joonhoon

    2018-01-01

    evidence that IPP can be transported by E. coli, findings that might be broadly relevant for the study of isoprenoid biosynthesis. Finally, we discover that IPP accumulation leads to the formation of ApppI, a nucleotide analog of IPP that may contribute to observed toxicity phenotypes. This comprehensive...... assessment of IPP stress suggests potential strategies for the alleviation of prenyl diphosphate toxicity and highlights possible engineering targets for improved IPP flux and high titer isoprenoid production....

  7. Construction and analysis of the model of energy metabolism in E. coli.

    Directory of Open Access Journals (Sweden)

    Zixiang Xu

    Full Text Available Genome-scale models of metabolism have only been analyzed with the constraint-based modelling philosophy and there have been several genome-scale gene-protein-reaction models. But research on the modelling for energy metabolism of organisms just began in recent years and research on metabolic weighted complex network are rare in literature. We have made three research based on the complete model of E. coli's energy metabolism. We first constructed a metabolic weighted network using the rates of free energy consumption within metabolic reactions as the weights. We then analyzed some structural characters of the metabolic weighted network that we constructed. We found that the distribution of the weight values was uneven, that most of the weight values were zero while reactions with abstract large weight values were rare and that the relationship between w (weight values and v (flux values was not of linear correlation. At last, we have done some research on the equilibrium of free energy for the energy metabolism system of E. coli. We found that E(out (free energy rate input from the environment can meet the demand of E(ch(in (free energy rate dissipated by chemical process and that chemical process plays a great role in the dissipation of free energy in cells. By these research and to a certain extend, we can understand more about the energy metabolism of E. coli.

  8. In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli-mastitis

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Rontved, Christine M.; Edwards, Stefan McKinnon

    2011-01-01

    Background Bovine mastitis is one of the most costly and prevalent diseases affecting dairy cows worldwide. In order to develop new strategies to prevent Escherichia coli-induced mastitis, a detailed understanding of the molecular mechanisms underlying the host immune response to an E. coli.......i. to represent the acute phase response (APR) and chronic stage, respectively. Differentially expressed (DE) genes for each stage were analyzed and the DE genes detected at T=24h were also compared to data collected from two previous E. coli mastitis studies that were carried out on post mortem tissue. Results...... of the up-regulated transcripts were associated with tissue healing processes. Comparison of T=24h DE genes detected in the three E. coli mastitis studies revealed 248 were common and mainly involved immune response functions. KEGG pathway analysis indicated these genes were involved in 12 pathways related...

  9. Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis

    DEFF Research Database (Denmark)

    Leon, Ileana R; Schwämmle, Veit; Jensen, Ole N

    2013-01-01

    a combination of qualitative and quantitative LC-MS/MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein...... conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents prior to analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative LC-MS/MS workflow quantified over 3700 distinct peptides with 96% completeness between all...... protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows...

  10. Stable Isotope Quantitative N-Glycan Analysis by Liquid Separation Techniques and Mass Spectrometry.

    Science.gov (United States)

    Mittermayr, Stefan; Albrecht, Simone; Váradi, Csaba; Millán-Martín, Silvia; Bones, Jonathan

    2017-01-01

    Liquid phase separation analysis and subsequent quantitation remains a challenging task for protein-derived oligosaccharides due to their inherent structural complexity and diversity. Incomplete resolution or co-detection of multiple glycan species complicates peak area-based quantitation and associated statistical analysis when optical detection methods are used. The approach outlined herein describes the utilization of stable isotope variants of commonly used fluorescent tags that allow for mass-based glycan identification and relative quantitation following separation by liquid chromatography (LC) or capillary electrophoresis (CE). Comparability assessment of glycoprotein-derived oligosaccharides is performed by derivatization with commercially available isotope variants of 2-aminobenzoic acid or aniline and analysis by LC- and CE-mass spectrometry. Quantitative information is attained from the extracted ion chromatogram/electropherogram ratios generated from the light and heavy isotope clusters.

  11. Quantitative analysis of some volatile components in Mimusops elengi L.

    Directory of Open Access Journals (Sweden)

    Chantana Aromdee

    2009-08-01

    Full Text Available Dried pikul flower (Mimusops elengi L., Sapotaceae is used in many recipes of Thai traditional medicine i.e. cardiotonic and stomachic. In this study, fresh and dried pikul flowers were investigated. The odour of pikul flower, even when it was dried, is very strong and characteristic. The constituents of volatile oils in fresh and dried pikul flowers extracted by ether were analysed by gas chromatography-mass spectrometry. 2-Phenylethanol, 4-hydroxybenzenemethanol and cinnamyl alcohol were mainly found in fresh flower, 10.49, 8.69 and 6.17%, respectively. Whereas those mainly found in dried flowers were long chain carboxylic acid ester and (Z-9-octadecenoic acid, 5.37 and 4.71% of ether extract, respectively.An analytical method simultaneously determining benzyl alcohol, 2-phenylethanol and methyl paraben was developed by using the GC-FID method. The percent recoveries were 91.66, 104.59 and 105.28%, respectively. The intraday variations(% RSD were 7.22, 6.67 and 1.86%; and the interday variation were 3.12, 2.52 and 3.55%, respectively. Detection limits were 0.005, 0.014 and 0.001 ppm, and quantitation limits were 0.015, 0.048 and 0.003 ppm, respectively. Benzyl alcohol, 2-phenylethanol and methyl paraben content of dried flowers (9 samples from various drug stores in Thailand and one sample from China were 6.40-13.46, 17.57-196.57 and 27.35-355.53 ppm, respectively.

  12. Quantitative genetic analysis of anxiety trait in bipolar disorder.

    Science.gov (United States)

    Contreras, J; Hare, E; Chavarría, G; Raventós, H

    2018-01-01

    Bipolar disorder type I (BPI) affects approximately 1% of the world population. Although genetic influences on bipolar disorder are well established, identification of genes that predispose to the illness has been difficult. Most genetic studies are based on categorical diagnosis. One strategy to overcome this obstacle is the use of quantitative endophenotypes, as has been done for other medical disorders. We studied 619 individuals, 568 participants from 61 extended families and 51 unrelated healthy controls. The sample was 55% female and had a mean age of 43.25 (SD 13.90; range 18-78). Heritability and genetic correlation of the trait scale from the Anxiety State and Trait Inventory (STAI) was computed by using the general linear model (SOLAR package software). we observed that anxiety trait meets the following criteria for an endophenotype of bipolar disorder type I (BPI): 1) association with BPI (individuals with BPI showed the highest trait score (F = 15.20 [5,24], p = 0.009), 2) state-independence confirmed after conducting a test-retest in 321 subjects, 3) co-segregation within families 4) heritability of 0.70 (SE: 0.060), p = 2.33 × 10 -14 and 5) genetic correlation with BPI was 0.20, (SE = 0.17, p = 3.12 × 10 -5 ). Confounding factors such as comorbid disorders and pharmacological treatment could affect the clinical relationship between BPI and anxiety trait. Further research is needed to evaluate if anxiety traits are specially related to BPI in comparison with other traits such as anger, attention or response inhibition deficit, pathological impulsivity or low self-directedness. Anxiety trait is a heritable phenotype that follows a normal distribution when measured not only in subjects with BPI but also in unrelated healthy controls. It could be used as an endophenotype in BPI for the identification of genomic regions with susceptibility genes for this disorder. Published by Elsevier B.V.

  13. Synchrotron radiation microprobe quantitative analysis method for biomedical specimens

    International Nuclear Information System (INIS)

    Xu Qing; Shao Hanru

    1994-01-01

    Relative changes of trace elemental content in biomedical specimens are obtained easily by means of synchrotron radiation X-ray fluorescence microprobe analysis (SXRFM). However, the accurate assignment of concentration on a g/g basis is difficult. Because it is necessary to know both the trace elemental content and the specimen mass in the irradiated volume simultaneously. the specimen mass is a function of the spatial position and can not be weighed. It is possible to measure the specimen mass indirectly by measuring the intensity of Compton scattered peak for normal XRF analysis using a X-ray tube with Mo anode, if the matrix was consisted of light elements and the specimen was a thin sample. The Compton peak is not presented in fluorescence spectrum for white light SXRFM analysis. The continuous background in the spectrum was resulted from the Compton scattering with a linear polarization X-ray source. Biomedical specimens for SXRFM analysis, for example biological section and human hair, are always a thin sample for high energy X-ray, and they consist of H,C,N and O etc. light elements, which implies a linear relationship between the specimen mass and the Compton scattering background in the high energy region of spectrum. By this way , it is possible to carry out measurement of concentration for SXRFM analysis

  14. ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

    Science.gov (United States)

    Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

    2011-08-01

    Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

  15. Quantitative spectroscopy for the analysis of GOME data

    Science.gov (United States)

    Chance, K.

    1997-01-01

    Accurate analysis of the global ozone monitoring experiment (GOME) data to obtain atmospheric constituents requires reliable, traceable spectroscopic parameters for atmospheric absorption and scattering. Results are summarized for research that includes: the re-determination of Rayleigh scattering cross sections and phase functions for the 200 nm to 1000 nm range; the analysis of solar spectra to obtain a high-resolution reference spectrum with excellent absolute vacuum wavelength calibration; Ring effect cross sections and phase functions determined directly from accurate molecular parameters of N2 and O2; O2 A band line intensities and pressure broadening coefficients; and the analysis of absolute accuracies for ultraviolet and visible absorption cross sections of O3 and other trace species measurable by GOME.

  16. Quantitative risk assessment using the capacity-demand analysis

    International Nuclear Information System (INIS)

    Morgenroth, M.; Donnelly, C.R.; Westermann, G.D.; Huang, J.H.S.; Lam, T.M.

    1999-01-01

    The hydroelectric industry's recognition of the importance of avoiding unexpected failure, or forced outages, led to the development of probabilistic, or risk-based, methods in order to attempt to quantify exposures. Traditionally, such analysis has been carried out by qualitative assessments, relying on experience and sound engineering judgment to determine the optimum time to maintain, repair or replace a part or system. Depending on the nature of the problem, however, and the level of experience of those included in the decision making process, it is difficult to find a balance between acting proactively and accepting some amount of risk. The development of a practical means for establishing the probability of failure of any part or system, based on the determination of the statistical distribution of engineering properties such as acting stresses, is discussed. The capacity-demand analysis methodology, coupled with probablistic, risk-based analysis, permits all the factors associated with a decision to rehabilitate or replace a part, including the risks associated with the timing of the decision, to be assessed in a transparent and defendable manner. The methodology does not eliminate judgment altogether, but does move it from the level of estimating the risk of failure to the lower level of estimating variability in material properties, uncertainty in loading, and the uncertainties inherent in any engineering analysis. The method was successfully used in 1998 to carry out a comprehensive, economic risk analysis for the entire water conveyance system of a 90 year old hydropower station. The analysis included a number of diverse parts ranging from rock slopes and aging steel and concrete conduits, and the method allowed a rational assessment of the risks associated with reach of these varied parts to be determined, permitting the essential remedial works to be prioritized. 14 refs., 4 figs

  17. Quantitative Safety and Security Analysis from a Communication Perspective

    DEFF Research Database (Denmark)

    Malinowsky, Boris; Schwefel, Hans-Peter; Jung, Oliver

    2014-01-01

    This paper introduces and exemplifies a trade-off analysis of safety and security properties in distributed systems. The aim is to support analysis for real-time communication and authentication building blocks in a wireless communication scenario. By embedding an authentication scheme into a real...... at handover situations in a IEEE 802.11 wireless setup between mobile nodes and access points. The trade-offs involve application-layer data goodput, probability of completed handovers, and effect on usable protocol slots, to quantify the impact of security from a lower-layer communication perspective...

  18. Quantitative Immunofluorescence Analysis of Nucleolus-Associated Chromatin.

    Science.gov (United States)

    Dillinger, Stefan; Németh, Attila

    2016-01-01

    The nuclear distribution of eu- and heterochromatin is nonrandom, heterogeneous, and dynamic, which is mirrored by specific spatiotemporal arrangements of histone posttranslational modifications (PTMs). Here we describe a semiautomated method for the analysis of histone PTM localization patterns within the mammalian nucleus using confocal laser scanning microscope images of fixed, immunofluorescence stained cells as data source. The ImageJ-based process includes the segmentation of the nucleus, furthermore measurements of total fluorescence intensities, the heterogeneity of the staining, and the frequency of the brightest pixels in the region of interest (ROI). In the presented image analysis pipeline, the perinucleolar chromatin is selected as primary ROI, and the nuclear periphery as secondary ROI.

  19. Quantitative analysis of natural resource management options at different scales

    NARCIS (Netherlands)

    Keulen, van H.

    2007-01-01

    Natural capital (land, water, air) consists of many resources, each with its own quality, dynamics and renewability, but with strong interactions. The increasing competition for the natural resources, especially land and water, calls for a basic redirection in the analysis of land use. In this

  20. A quantitative method for Failure Mode and Effects Analysis

    NARCIS (Netherlands)

    Braaksma, Anne Johannes Jan; Meesters, A.J.; Klingenberg, W.; Hicks, C.

    2012-01-01

    Failure Mode and Effects Analysis (FMEA) is commonly used for designing maintenance routines by analysing potential failures, predicting their effect and facilitating preventive action. It is used to make decisions on operational and capital expenditure. The literature has reported that despite its

  1. [Evaluation of dental plaque by quantitative digital image analysis system].

    Science.gov (United States)

    Huang, Z; Luan, Q X

    2016-04-18

    To analyze the plaque staining image by using image analysis software, to verify the maneuverability, practicability and repeatability of this technique, and to evaluate the influence of different plaque stains. In the study, 30 volunteers were enrolled from the new dental students of Peking University Health Science Center in accordance with the inclusion criteria. The digital images of the anterior teeth were acquired after plaque stained according to filming standardization.The image analysis was performed using Image Pro Plus 7.0, and the Quigley-Hein plaque indexes of the anterior teeth were evaluated. The plaque stain area percentage and the corresponding dental plaque index were highly correlated,and the Spearman correlation coefficient was 0.776 (Pchart showed only a few spots outside the 95% consistency boundaries. The different plaque stains image analysis results showed that the difference of the tooth area measurements was not significant, while the difference of the plaque area measurements significant (P<0.01). This method is easy in operation and control,highly related to the calculated percentage of plaque area and traditional plaque index, and has good reproducibility.The different plaque staining method has little effect on image segmentation results.The sensitive plaque stain for image analysis is suggested.

  2. Quantitative analysis of prediction models for hot cracking in ...

    Indian Academy of Sciences (India)

    A RodrМguez-Prieto

    2017-11-16

    Nov 16, 2017 ... In this paper, a systematic analysis of different methods of d-ferrite estimation is carried out based ... Keywords. d-Ferrite; hot cracking; prediction methods; stringency levels; decision tool. 1. .... prediction of d-ferrite content using a system of multi- ..... support the selection of some materials according to their.

  3. Quantitative electron microscope autoradiography: application of multiple linear regression analysis

    International Nuclear Information System (INIS)

    Markov, D.V.

    1986-01-01

    A new method for the analysis of high resolution EM autoradiographs is described. It identifies labelled cell organelle profiles in sections on a strictly statistical basis and provides accurate estimates for their radioactivity without the need to make any assumptions about their size, shape and spatial arrangement. (author)

  4. Towards automatic quantitative analysis of cardiac MR perfusion images

    NARCIS (Netherlands)

    Breeuwer, M.; Quist, M.; Spreeuwers, Lieuwe Jan; Paetsch, I.; Al-Saadi, N.; Nagel, E.

    2001-01-01

    Magnetic Resonance Imaging (MRI) is a powerful technique for imaging cardiovascular diseases. The introduction of cardiovascular MRI into clinical practice is however hampered by the lack of efficient and reliable automatic image analysis methods. This paper focuses on the automatic evaluation of

  5. From POOSL to UPPAAL : transformation and quantitative analysis

    NARCIS (Netherlands)

    Xing, J.; Theelen, B.D.; Langerak, R.; Pol, van de J.C.; Tretmans, J.; Voeten, J.P.M.

    2010-01-01

    POOSL (Parallel Object-Oriented Specification Language) is a powerful general purpose system-level modeling language. In research on design space exploration of motion control systems, POOSL has been used to construct models for performance analysis. The considered motion control algorithms are

  6. Mass spectrometry for real-time quantitative breath analysis

    Czech Academy of Sciences Publication Activity Database

    Smith, D.; Španěl, Patrik; Herbig, J.; Beauchamp, J.

    2014-01-01

    Roč. 8, č. 2 (2014), 027101 ISSN 1752-7155 Institutional support: RVO:61388955 Keywords : breath analysis * proton transfer reaction mass spectrometry * selected ion flow tube mass spectrometry Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.631, year: 2014

  7. Quantitative analysis of night skyglow amplification under cloudy conditions

    Science.gov (United States)

    Kocifaj, Miroslav; Solano Lamphar, Héctor Antonio

    2014-10-01

    The radiance produced by artificial light is a major source of nighttime over-illumination. It can, however, be treated experimentally using ground-based and satellite data. These two types of data complement each other and together have a high information content. For instance, the satellite data enable upward light emissions to be normalized, and this in turn allows skyglow levels at the ground to be modelled under cloudy or overcast conditions. Excessive night lighting imposes an unacceptable burden on nature, humans and professional astronomy. For this reason, there is a pressing need to determine the total amount of downwelling diffuse radiation. Undoubtedly, cloudy periods can cause a significant increase in skyglow as a result of amplification owing to diffuse reflection from clouds. While it is recognized that the amplification factor (AF) varies with cloud cover, the effects of different types of clouds, of atmospheric turbidity and of the geometrical relationships between the positions of an individual observer, the cloud layer, and the light source are in general poorly known. In this paper the AF is quantitatively analysed considering different aerosol optical depths (AODs), urban layout sizes and cloud types with specific albedos and altitudes. The computational results show that the AF peaks near the edges of a city rather than at its centre. In addition, the AF appears to be a decreasing function of AOD, which is particularly important when modelling the skyglow in regions with apparent temporal or seasonal variability of atmospheric turbidity. The findings in this paper will be useful to those designing engineering applications or modelling light pollution, as well as to astronomers and environmental scientists who aim to predict the amplification of skyglow caused by clouds. In addition, the semi-analytical formulae can be used to estimate the AF levels, especially in densely populated metropolitan regions for which detailed computations may be CPU

  8. Quantitative analysis of intraoperative communication in open and laparoscopic surgery.

    Science.gov (United States)

    Sevdalis, Nick; Wong, Helen W L; Arora, Sonal; Nagpal, Kamal; Healey, Andrew; Hanna, George B; Vincent, Charles A

    2012-10-01

    Communication is important for patient safety in the operating room (OR). Several studies have assessed OR communications qualitatively or have focused on communication in crisis situations. This study used prospective, quantitative observation based on well-established communication theory to assess similarities and differences in communication patterns between open and laparoscopic surgery. Based on communication theory, a standardized proforma was developed for assessment in the OR via real-time observation of communication types, their purpose, their content, and their initiators/recipients. Data were collected prospectively in real time in the OR for 20 open and 20 laparoscopic inguinal hernia repairs. Assessors were trained and calibrated, and their reliability was established statistically. During 1,884 min of operative time, 4,227 communications were observed and analyzed (2,043 laparoscopic vs 2,184 open communications). The mean operative duration (laparoscopic, 48 min vs open, 47 min), mean communication frequency (laparoscopic, 102 communications/procedure vs open, 109 communications/procedure), and mean communication rate (laparoscopic, 2.13 communications/min vs open, 2.23 communications/min) did not differ significantly across laparoscopic and open procedures. Communications were most likely to be initiated by surgeons (80-81 %), to be received by either other surgeons (46-50%) or OR nurses (38-40 %), to be associated with equipment/procedural issues (39-47 %), and to provide direction for the OR team (38-46%) in open and laparoscopic cases. Moreover, communications in laparoscopic cases were significantly more equipment related (laparoscopic, 47 % vs open, 39 %) and aimed significantly more at providing direction (laparoscopic, 46 % vs open, 38 %) and at consulting (laparoscopic, 17 % vs open, 12 %) than at sharing information (laparoscopic, 17 % vs open, 31 %) (P communications were found in both laparoscopic and open cases during a relatively low

  9. Gene Expression Analysis of Escherichia Coli Grown in Miniaturized Bioreactor Platforms for High-Throughput Analysis of Growth and genomic Data

    DEFF Research Database (Denmark)

    Boccazzi, P.; Zanzotto, A.; Szita, Nicolas

    2005-01-01

    Combining high-throughput growth physiology and global gene expression data analysis is of significant value for integrating metabolism and genomics. We compared global gene expression using 500 ng of total RNA from Escherichia coli cultures grown in rich or defined minimal media in a miniaturize...... cultures using just 500 ng of total RNA indicate that high-throughput integration of growth physiology and genomics will be possible with novel biochemical platforms and improved detection technologies....

  10. Quantitative data analysis with SPSS release 8 for Windows a guide for social scientists

    CERN Document Server

    Bryman, Alan

    2002-01-01

    The latest edition of this best-selling introduction to Quantitative Data Analysis through the use of a computer package has been completely updated to accommodate the needs of users of SPSS Release 8 for Windows. Like its predecessor, it provides a non-technical approach to quantitative data analysis and a user-friendly introduction to the widely used SPSS for Windows. It assumes no previous familiarity with either statistics or computing but takes the reader step-by-step through the techniques, reinforced by exercises for further practice. Techniques explained in Quantitative Data Analysis with SPSS Release 8 for Windows include: * correlation * simple and multiple regression * multivariate analysis of variance and covariance * factor analysis The book also covers issues such as sampling, statistical significance, conceptualization and measurement and the selection of appropriate tests. For further information or to download the book's datasets, please visit the webstite: http://www.routledge.com/textbooks/...

  11. Integrated quantitative fractal polarimetric analysis of monolayer lung cancer cells

    Science.gov (United States)

    Shrestha, Suman; Zhang, Lin; Quang, Tri; Farrahi, Tannaz; Narayan, Chaya; Deshpande, Aditi; Na, Ying; Blinzler, Adam; Ma, Junyu; Liu, Bo; Giakos, George C.

    2014-05-01

    Digital diagnostic pathology has become one of the most valuable and convenient advancements in technology over the past years. It allows us to acquire, store and analyze pathological information from the images of histological and immunohistochemical glass slides which are scanned to create digital slides. In this study, efficient fractal, wavelet-based polarimetric techniques for histological analysis of monolayer lung cancer cells will be introduced and different monolayer cancer lines will be studied. The outcome of this study indicates that application of fractal, wavelet polarimetric principles towards the analysis of squamous carcinoma and adenocarcinoma cancer cell lines may be proved extremely useful in discriminating among healthy and lung cancer cells as well as differentiating among different lung cancer cells.

  12. Quantitative Safety and Security Analysis from a Communication Perspective

    Directory of Open Access Journals (Sweden)

    Boris Malinowsky

    2015-12-01

    Full Text Available This paper introduces and exemplifies a trade-off analysis of safety and security properties in distributed systems. The aim is to support analysis for real-time communication and authentication building blocks in a wireless communication scenario. By embedding an authentication scheme into a real-time communication protocol for safety-critical scenarios, we can rely on the protocol’s individual safety and security properties. The resulting communication protocol satisfies selected safety and security properties for deployment in safety-critical use-case scenarios with security requirements. We look at handover situations in a IEEE 802.11 wireless setup between mobile nodes and access points. The trade-offs involve application-layer data goodput, probability of completed handovers, and effect on usable protocol slots, to quantify the impact of security from a lower-layer communication perspective on the communication protocols. The results are obtained using the network simulator ns-3.

  13. Quantitative analysis of allantoin in Iranian corn silk

    OpenAIRE

    E. Khanpour*; M. Modarresi

    2017-01-01

    Background and objectives: Zea mays is cultivated in different parts of Iran and corn silk is used in traditional medicine. Allantoin is one of the major compounds in corn silk. The purpose of this research was the quantitatve analysis of allantoin in corn silks belonging to several regions of Iran. Methods: The samples of corn silk were prepared from three provinces of Iran (Kermanshah, Fars and Razavi Khorasan). The dried plant materials were infused in boiling distilled water with a temper...

  14. African Primary Care Research: Quantitative analysis and presentation of results

    Science.gov (United States)

    Ogunbanjo, Gboyega A.

    2014-01-01

    Abstract This article is part of a series on Primary Care Research Methods. The article describes types of continuous and categorical data, how to capture data in a spreadsheet, how to use descriptive and inferential statistics and, finally, gives advice on how to present the results in text, figures and tables. The article intends to help Master's level students with writing the data analysis section of their research proposal and presenting their results in their final research report. PMID:26245435

  15. Quantitative analysis of the renal aging in rats. Stereological study

    OpenAIRE

    Melchioretto, Eduardo Felippe; Zeni, Marcelo; Veronez, Djanira Aparecida da Luz; Martins Filho, Eduardo Lopes; Fraga, Rogério de

    2016-01-01

    ABSTRACT PURPOSE: To evaluate the renal function and the renal histological alterations through the stereology and morphometrics in rats submitted to the natural process of aging. METHODS: Seventy two Wistar rats, divided in six groups. Each group was sacrificed in a different age: 3, 6, 9, 12, 18 and 24 months. It was performed right nephrectomy, stereological and morphometric analysis of the renal tissue (renal volume and weight, density of volume (Vv[glom]) and numerical density (Nv[glo...

  16. Watershed Planning within a Quantitative Scenario Analysis Framework.

    Science.gov (United States)

    Merriam, Eric R; Petty, J Todd; Strager, Michael P

    2016-07-24

    There is a critical need for tools and methodologies capable of managing aquatic systems within heavily impacted watersheds. Current efforts often fall short as a result of an inability to quantify and predict complex cumulative effects of current and future land use scenarios at relevant spatial scales. The goal of this manuscript is to provide methods for conducting a targeted watershed assessment that enables resource managers to produce landscape-based cumulative effects models for use within a scenario analysis management framework. Sites are first selected for inclusion within the watershed assessment by identifying sites that fall along independent gradients and combinations of known stressors. Field and laboratory techniques are then used to obtain data on the physical, chemical, and biological effects of multiple land use activities. Multiple linear regression analysis is then used to produce landscape-based cumulative effects models for predicting aquatic conditions. Lastly, methods for incorporating cumulative effects models within a scenario analysis framework for guiding management and regulatory decisions (e.g., permitting and mitigation) within actively developing watersheds are discussed and demonstrated for 2 sub-watersheds within the mountaintop mining region of central Appalachia. The watershed assessment and management approach provided herein enables resource managers to facilitate economic and development activity while protecting aquatic resources and producing opportunity for net ecological benefits through targeted remediation.

  17. A Quantitative Accident Sequence Analysis for a VHTR

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jintae; Lee, Joeun; Jae, Moosung [Hanyang University, Seoul (Korea, Republic of)

    2016-05-15

    In Korea, the basic design features of VHTR are currently discussed in the various design concepts. Probabilistic risk assessment (PRA) offers a logical and structured method to assess risks of a large and complex engineered system, such as a nuclear power plant. It will be introduced at an early stage in the design, and will be upgraded at various design and licensing stages as the design matures and the design details are defined. Risk insights to be developed from the PRA are viewed as essential to developing a design that is optimized in meeting safety objectives and in interpreting the applicability of the existing demands to the safety design approach of the VHTR. In this study, initiating events which may occur in VHTRs were selected through MLD method. The initiating events were then grouped into four categories for the accident sequence analysis. Initiating events frequency and safety systems failure rate were calculated by using reliability data obtained from the available sources and fault tree analysis. After quantification, uncertainty analysis was conducted. The SR and LR frequency are calculated respectively 7.52E- 10/RY and 7.91E-16/RY, which are relatively less than the core damage frequency of LWRs.

  18. Comparative study of standard space and real space analysis of quantitative MR brain data.

    Science.gov (United States)

    Aribisala, Benjamin S; He, Jiabao; Blamire, Andrew M

    2011-06-01

    To compare the robustness of region of interest (ROI) analysis of magnetic resonance imaging (MRI) brain data in real space with analysis in standard space and to test the hypothesis that standard space image analysis introduces more partial volume effect errors compared to analysis of the same dataset in real space. Twenty healthy adults with no history or evidence of neurological diseases were recruited; high-resolution T(1)-weighted, quantitative T(1), and B(0) field-map measurements were collected. Algorithms were implemented to perform analysis in real and standard space and used to apply a simple standard ROI template to quantitative T(1) datasets. Regional relaxation values and histograms for both gray and white matter tissues classes were then extracted and compared. Regional mean T(1) values for both gray and white matter were significantly lower using real space compared to standard space analysis. Additionally, regional T(1) histograms were more compact in real space, with smaller right-sided tails indicating lower partial volume errors compared to standard space analysis. Standard space analysis of quantitative MRI brain data introduces more partial volume effect errors biasing the analysis of quantitative data compared to analysis of the same dataset in real space. Copyright © 2011 Wiley-Liss, Inc.

  19. Method of quantitative x-ray diffractometric analysis of Ta-Ta2C system

    International Nuclear Information System (INIS)

    Gavrish, A.A.; Glazunov, M.P.; Korolev, Yu.M.; Spitsyn, V.I.; Fedoseev, G.K.

    1976-01-01

    The syste86 Ta-Ta 2 C has beemonsidered because of specific features of diffraction patterns of the components, namely, overlapping of the most intensive reflexes of both phases. The method of standard binary system has been used for quantitative analysis. Because of overlapping of the intensive reflexes dsub(1/01)=2.36(Ta 2 C) and dsub(110)=2.33(Ta), the other, most intensive, reflexes have been used for quantitative determination of Ta 2 C and Ta: dsub(103)=1.404 A for tantalum subcarbide and dsub(211)=1.35A for tantalum. Besides, the TaTa 2 C phases have been determined quantitatively with the use of another pair of reflexes: dsub(102)=1.82 A for Ta 2 C and dsub(200)=1.65 A for tantalum. The agreement between the results obtained while performing the quantitative phase analysis is good. To increase reliability and accuracy of the quantitative determination of Ta and Ta 2 C, it is expedient to carry out the analysis with the use of two above-mentioned pairs of reflexes located in different regions of the diffraction spectrum. Thus, the procedure of quantitative analysis of Ta and Ta 2 C in different ratios has been developed taking into account the specific features of the diffraction patterns of these components as well as the ability of Ta 2 C to texture in the process of preparation

  20. Quantitative analysis of light elements in thick samples by PIGE

    International Nuclear Information System (INIS)

    Mateus, R.; Jesus, A.P.; Ribeiro, J.P.

    2004-01-01

    PIGE analysis of thick and intermediate samples is usually performed with the help of standards, but this method gives only good results when the standard is very similar to the sample to be analysed. In this work, we present an alternative method for PIGE analysis of light elements in thick samples. This method is based on a code that integrates the nuclear reaction excitation function along the depth of the sample. For the integration procedure the sample is divided in sublayers, defined by the energy steps that were used to measure accurately the excitation function. This function is used as input. Within each sublayer the stopping power cross-sections may be assumed as constant. With these two conditions the calculus of the contribution of each sublayer for the total yield becomes an easy task. This work presents results for the analysis of lithium, boron, fluorine and sodium in thick samples. For this purpose, excitation functions of the reactions 7 Li(p,p ' γ) 7 Li, 19 F(p,p ' γ) 19 F, 10 B(p,αγ) 7 Be and 23 Na(p,p ' γ) 23 Na were employed. Calculated γ-ray yields were compared, at several proton energy values, with experimental yields for thick samples made of inorganic compounds of the referred elements. The agreement is better than 7.5%. Taking into consideration the experimental uncertainty of the measured yields and the errors related to the stopping power values used, this agreement shows that effects as the beam energy straggling, ignored in the calculation, seem to play a minor role

  1. The quantitative analysis of 163Ho source by PIXE

    International Nuclear Information System (INIS)

    Sera, K.; Ishii, K.; Fujioka, M.; Izawa, G.; Omori, T.

    1984-01-01

    We have been studying the electron-capture in 163 Ho as a method for determining the mass of electron neutrino. The 163 Ho sources were produced with the 164 Dy(p,2n) reaction by means of a method of internal irradiation 2 ). We applied the PIXE method to determine the total number of 163 Ho atoms in the source. Proton beams of 3 MeV and a method of ''external standard'' were employed for nondestructive analysis of the 163 Ho source as well as an additional method of ''internal standard''. (author)

  2. Interleukin-2 signaling pathway analysis by quantitative phosphoproteomics

    DEFF Research Database (Denmark)

    Osinalde, Nerea; Moss, Helle; Arrizabalaga, Onetsine

    2011-01-01

    among which 79 were found with increased abundance in the tyrosine-phosphorylated complexes, including several previously not reported IL-2 downstream effectors. Combinatorial site-specific phosphoproteomic analysis resulted in identification of 99 phosphorylated sites mapping to the identified proteins...... with increased abundance in the tyrosine-phosphorylated complexes, of which 34 were not previously described. In addition, chemical inhibition of the identified IL-2-mediated JAK, PI3K and MAPK signaling pathways, resulted in distinct alteration on the IL-2 dependent proliferation....

  3. Quantitation of Surface Coating on Nanoparticles Using Thermogravimetric Analysis.

    Science.gov (United States)

    Dongargaonkar, Alpana A; Clogston, Jeffrey D

    2018-01-01

    Nanoparticles are critical components in nanomedicine and nanotherapeutic applications. Some nanoparticles, such as metallic nanoparticles, consist of a surface coating or surface modification to aid in its dispersion and stability. This surface coating may affect the behavior of nanoparticles in a biological environment, thus it is important to measure. Thermogravimetric analysis (TGA) can be used to determine the amount of coating on the surface of the nanoparticle. TGA experiments run under inert atmosphere can also be used to determine residual metal content present in the sample. In this chapter, the TGA technique and experimental method are described.

  4. Quantitative analysis of overlapping XPS peaks by spectrum reconstruction

    DEFF Research Database (Denmark)

    Graat, Peter C.J.; Somers, Marcel A. J.

    1998-01-01

    parameters. The values obtained for the oxide film thickness were compared with thickness values determined from the intensity of the corresponding O 1s spectra and with thickness values resulting from ellipsometric analysis. The sensitivity of the reconstruction procedure with regard to film thickness...... contributions in the spectra owing to inelastic scattering of signal electrons were calculated from the depth distributions of these constituents and their reference spectra. In the reconstruction procedure the film thickness and the concentrations of Fe/sup 2+/ and Fe/sup 3+/ in the oxide film were used as fit...

  5. Experimental design and quantitative analysis of microbial community multiomics.

    Science.gov (United States)

    Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis

    2017-11-30

    Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.

  6. Quantitative risk analysis in two pipelines operated by TRANSPETRO

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, Claudio B. [PETROBRAS Transporte S/A (TRANSPETRO), Rio de Janeiro, RJ (Brazil); Pinho, Edson [Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropedica, RJ (Brazil); Bittencourt, Euclides [Centro Universitario FIB, Salvador , BA (Brazil)

    2009-07-01

    Transportation risk analysis techniques were used to study two pipelines operated by TRANSPETRO. The Pipeline A is for the simultaneous transportation of diesel, gasoline and LPG and comprises three parts, all of them crossing rural areas. The Pipeline B is for oil transportation and one of its ends is located in an area of a high density population. Both pipelines had their risk studied using the PHAST RISK{sup R} software and the individual risk measures, the only considered measures for license purposes for this type of studies, presented level far below the maximum tolerable levels considered. (author)

  7. Occurrence and molecular analysis of Balantidium coli in mountain gorilla (Gorilla beringei beringei) in the Volcanoes National Park, Rwanda.

    Science.gov (United States)

    Hassell, James M; Blake, Damer P; Cranfield, Michael R; Ramer, Jan; Hogan, Jennifer N; Noheli, Jean Bosco; Waters, Michael; Hermosilla, Carlos

    2013-10-01

    Cysts morphologically resembling Balantidium coli were identified in the feces of a mountain gorilla (Gorilla beringei beringei). Confirmatory PCR and sequencing revealed two distinct B. coli-specific sequences (ITS-1, sub-types A0 and B1). This represents the first report of B. coli in this species, raising the possibility of infection from a reservoir host.

  8. Escherichia coli tRNAArg acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis

    International Nuclear Information System (INIS)

    Eichert, André; Schreiber, Angela; Fürste, Jens P.; Perbandt, Markus; Betzel, Christian; Erdmann, Volker A.; Förster, Charlotte

    2009-01-01

    Various E. coli tRNA Arg acceptor-stem microhelix isoacceptors have been crystallized and investigated by high-resolution X-ray diffraction analysis. The aminoacylation of tRNA is a crucial step in cellular protein biosynthesis. Recognition of the cognate tRNA by the correct aminoacyl-tRNA synthetase is ensured by tRNA identity elements. In tRNA Arg , the identity elements consist of the anticodon, parts of the D-loop and the discriminator base. The minor groove of the aminoacyl stem interacts with the arginyl-tRNA synthetase. As a consequence of the redundancy of the genetic code, six tRNA Arg isoacceptors exist. In the present work, three different Escherichia coli tRNA Arg acceptor-stem helices were crystallized. Two of them, the tRNA Arg microhelices RR-1660 and RR-1662, were examined by X-ray diffraction analysis and diffracted to 1.7 and 1.8 Å resolution, respectively. The tRNA Arg RR-1660 helix crystallized in space group P1, with unit-cell parameters a = 26.28, b = 28.92, c = 29.00 Å, α = 105.74, β = 99.01, γ = 97.44°, whereas the tRNA Arg RR-1662 helix crystallized in space group C2, with unit-cell parameters a = 33.18, b = 46.16, c = 26.04 Å, β = 101.50°

  9. Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential.

    Science.gov (United States)

    Asplund-Samuelsson, Johannes; Janasch, Markus; Hudson, Elton P

    2018-01-01

    Introducing biosynthetic pathways into an organism is both reliant on and challenged by endogenous biochemistry. Here we compared the expansion potential of the metabolic network in the photoautotroph Synechocystis with that of the heterotroph E. coli using the novel workflow POPPY (Prospecting Optimal Pathways with PYthon). First, E. coli and Synechocystis metabolomic and fluxomic data were combined with metabolic models to identify thermodynamic constraints on metabolite concentrations (NET analysis). Then, thousands of automatically constructed pathways were placed within each network and subjected to a network-embedded variant of the max-min driving force analysis (NEM). We found that the networks had different capabilities for imparting thermodynamic driving forces toward certain compounds. Key metabolites were constrained differently in Synechocystis due to opposing flux directions in glycolysis and carbon fixation, the forked tri-carboxylic acid cycle, and photorespiration. Furthermore, the lysine biosynthesis pathway in Synechocystis was identified as thermodynamically constrained, impacting both endogenous and heterologous reactions through low 2-oxoglutarate levels. Our study also identified important yet poorly covered areas in existing metabolomics data and provides a reference for future thermodynamics-based engineering in Synechocystis and beyond. The POPPY methodology represents a step in making optimal pathway-host matches, which is likely to become important as the practical range of host organisms is diversified. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  10. Quantitative analysis of the renal aging in rats. Stereological study.

    Science.gov (United States)

    Melchioretto, Eduardo Felippe; Zeni, Marcelo; Veronez, Djanira Aparecida da Luz; Martins, Eduardo Lopes; Fraga, Rogério de

    2016-05-01

    To evaluate the renal function and the renal histological alterations through the stereology and morphometrics in rats submitted to the natural process of aging. Seventy two Wistar rats, divided in six groups. Each group was sacrificed in a different age: 3, 6, 9, 12, 18 and 24 months. It was performed right nephrectomy, stereological and morphometric analysis of the renal tissue (renal volume and weight, density of volume (Vv[glom]) and numerical density (Nv[glom]) of the renal glomeruli and average glomerular volume (Vol[glom])) and also it was evaluated the renal function for the dosage of serum creatinine and urea. There was significant decrease of the renal function in the oldest rats. The renal volume presented gradual increase during the development of the rats with the biggest values registered in the group of animals at 12 months of age and significant progressive decrease in older animals. Vv[glom] presented statistically significant gradual reduction between the groups and the Nv[glom] also decreased significantly. The renal function proved to be inferior in senile rats when compared to the young rats. The morphometric and stereological analysis evidenced renal atrophy, gradual reduction of the volume density and numerical density of the renal glomeruli associated to the aging process.

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

    OpenAIRE

    Schipper, Danny; Spekkink, Wouter

    2015-01-01

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

  12. Quantitative Myocardial Perfusion Imaging Versus Visual Analysis in Diagnosing Myocardial Ischemia: A CE-MARC Substudy.

    Science.gov (United States)

    Biglands, John D; Ibraheem, Montasir; Magee, Derek R; Radjenovic, Aleksandra; Plein, Sven; Greenwood, John P

    2018-05-01

    This study sought to compare the diagnostic accuracy of visual and quantitative analyses of myocardial perfusion cardiovascular magnetic resonance against a reference standard of quantitative coronary angiography. Visual analysis of perfusion cardiovascular magnetic resonance studies for assessing myocardial perfusion has been shown to have high diagnostic accuracy for coronary artery disease. However, only a few small studies have assessed the diagnostic accuracy of quantitative myocardial perfusion. This retrospective study included 128 patients randomly selected from the CE-MARC (Clinical Evaluation of Magnetic Resonance Imaging in Coronary Heart Disease) study population such that the distribution of risk factors and disease status was proportionate to the full population. Visual analysis results of cardiovascular magnetic resonance perfusion images, by consensus of 2 expert readers, were taken from the original study reports. Quantitative myocardial blood flow estimates were obtained using Fermi-constrained deconvolution. The reference standard for myocardial ischemia was a quantitative coronary x-ray angiogram stenosis severity of ≥70% diameter in any coronary artery of >2 mm diameter, or ≥50% in the left main stem. Diagnostic performance was calculated using receiver-operating characteristic curve analysis. The area under the curve for visual analysis was 0.88 (95% confidence interval: 0.81 to 0.95) with a sensitivity of 81.0% (95% confidence interval: 69.1% to 92.8%) and specificity of 86.0% (95% confidence interval: 78.7% to 93.4%). For quantitative stress myocardial blood flow the area under the curve was 0.89 (95% confidence interval: 0.83 to 0.96) with a sensitivity of 87.5% (95% confidence interval: 77.3% to 97.7%) and specificity of 84.5% (95% confidence interval: 76.8% to 92.3%). There was no statistically significant difference between the diagnostic performance of quantitative and visual analyses (p = 0.72). Incorporating rest myocardial

  13. Quantitative radiographic analysis of fiber reinforced polymer composites.

    Science.gov (United States)

    Baidya, K P; Ramakrishna, S; Rahman, M; Ritchie, A

    2001-01-01

    X-ray radiographic examination of the bone fracture healing process is a widely used method in the treatment and management of patients. Medical devices made of metallic alloys reportedly produce considerable artifacts that make the interpretation of radiographs difficult. Fiber reinforced polymer composite materials have been proposed to replace metallic alloys in certain medical devices because of their radiolucency, light weight, and tailorable mechanical properties. The primary objective of this paper is to provide a comparable radiographic analysis of different fiber reinforced polymer composites that are considered suitable for biomedical applications. Composite materials investigated consist of glass, aramid (Kevlar-29), and carbon reinforcement fibers, and epoxy and polyether-ether-ketone (PEEK) matrices. The total mass attenuation coefficient of each material was measured using clinical X-rays (50 kev). The carbon fiber reinforced composites were found to be more radiolucent than the glass and kevlar fiber reinforced composites.

  14. QUANTITATIVE ANALYSIS OF BANDED STRUCTURES IN DUAL-PHASE STEELS

    Directory of Open Access Journals (Sweden)

    Benoit Krebs

    2011-05-01

    Full Text Available Dual-Phase (DP steels are composed of martensite islands dispersed in a ductile ferrite matrix, which provides a good balance between strength and ductility. Current processing conditions (continuous casting followed by hot and cold rolling generate 'banded structures' i.e., irregular, parallel and alternating bands of ferrite and martensite, which are detrimental to mechanical properties and especially for in-use properties. We present an original and simple method to quantify the intensity and wavelength of these bands. This method, based on the analysis of covariance function of binary images, is firstly tested on model images. It is compared with ASTM E-1268 standard and appears to be more robust. Then it is applied on real DP steel microstructures and proves to be sufficiently sensitive to discriminate samples resulting from different thermo-mechanical routes.

  15. Global tractography with embedded anatomical priors for quantitative connectivity analysis

    Directory of Open Access Journals (Sweden)

    Alia eLemkaddem

    2014-11-01

    Full Text Available The main assumption of fiber-tracking algorithms is that fiber trajectories are represented by paths of highest diffusion, which is usually accomplished by following the principal diffusion directions estimated in every voxel from the measured diffusion MRI data. The state-of-the-art approaches, known as global tractography, reconstruct all the fiber tracts of the whole brain simultaneously by solving a global energy minimization problem. The tractograms obtained with these algorithms outperform any previous technique but, unfortunately, the price to pay is an increased computational cost which is not suitable in many practical settings, both in terms of time and memory requirements. Furthermore, existing global tractography algorithms suffer from an important shortcoming that is crucial in the context of brain connectivity analyses. As no anatomical priors are used during in the reconstruction process, the recovered fiber tracts are not guaranteed to connect cortical regions and, as a matter of fact, most of them stop prematurely in the white matter. This does not only unnecessarily slow down the estimation procedure and potentially biases any subsequent analysis but also, most importantly, prevents the de facto quantification of brain connectivity. In this work, we propose a novel approach for global tractography that is specifically designed for connectivity analysis applications by explicitly enforcing anatomical priors of the tracts in the optimization and considering the effective contribution of each of them, i.e. volume, to the acquired diffusion MRI image. We evaluated our approach on both a realistic diffusion MRI phantom and in-vivo data, and also compared its performance to existing tractography aloprithms.

  16. Quantitative analysis of a fault tree with priority AND gates

    International Nuclear Information System (INIS)

    Yuge, T.; Yanagi, S.

    2008-01-01

    A method for calculating the exact top event probability of a fault tree with priority AND gates and repeated basic events is proposed when the minimal cut sets are given. A priority AND gate is an AND gate where the input events must occur in a prescribed order for the occurrence of the output event. It is known that the top event probability of such a dynamic fault tree is obtained by converting the tree into an equivalent Markov model. However, this method is not realistic for a complex system model because the number of states which should be considered in the Markov analysis increases explosively as the number of basic events increases. To overcome the shortcomings of the Markov model, we propose an alternative method to obtain the top event probability in this paper. We assume that the basic events occur independently, exponentially distributed, and the component whose failure corresponds to the occurrence of the basic event is non-repairable. First, we obtain the probability of occurrence of the output event of a single priority AND gate by Markov analysis. Then, the top event probability is given by a cut set approach and the inclusion-exclusion formula. An efficient procedure to obtain the probabilities corresponding to logical products in the inclusion-exclusion formula is proposed. The logical product which is composed of two or more priority AND gates having at least one common basic event as their inputs is transformed into the sum of disjoint events which are equivalent to a priority AND gate in the procedure. Numerical examples show that our method works well for complex systems

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  18. Quantitative X ray analysis system. User's manual and guide to X ray fluorescence technique

    International Nuclear Information System (INIS)

    2009-01-01

    This guide covers trimmed and re-arranged version 3.6 of the Quantitative X ray Analysis System (QXAS) software package that includes the most frequently used methods of quantitative analysis. QXAS is a comprehensive quantitative analysis package that has been developed by the IAEA through research and technical contracts. Additional development has also been carried out in the IAEA Laboratories in Seibersdorf where QXAS was extensively tested. New in this version of the manual are the descriptions of the Voigt-profile peak fitting, the backscatter fundamental parameters' and emission-transmission methods of chemical composition analysis, an expanded chapter on the X ray fluorescence physics, and completely revised and increased number of practical examples of utilization of the QXAS software package. The analytical data accompanying this manual were collected in the IAEA Seibersdorf Laboratories in the years 2006/2007

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

    International Nuclear Information System (INIS)

    Michalska, J; Chmiela, B

    2014-01-01

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

  20. Potential Application of Quantitative Prostate-specific Antigen Analysis in Forensic Examination of Seminal Stains

    Directory of Open Access Journals (Sweden)

    Zhenping Liu

    2015-01-01

    Full Text Available The aims of this study are to use quantitative analysis of the prostate-specific antigen (PSA in the seminal stain examination and to explore the practical value of this analysis in forensic science. For a comprehensive analysis, vaginal swabs from 48 rape cases were tested both by a PSA fluorescence analyzer (i-CHROMA Reader and by a conventional PSA strip test. To confirm the results of these PSA tests, seminal DNA was tested following differential extraction. Compared to the PSA strip test, the PSA rapid quantitative fluorescence analyzer provided the more accurate and sensitive results. More importantly, individualized schemes based on quantitative PSA results of samples can be developed to improve the quality and procedural efficiency in the forensic seminal inspection of samples prior to DNA analysis.

  1. Quantitative proteomic analysis of post-translational modifications of human histones

    DEFF Research Database (Denmark)

    Beck, Hans Christian; Nielsen, Eva C; Matthiesen, Rune

    2006-01-01

    , and H4 in a site-specific and dose-dependent manner. This unbiased analysis revealed that a relative increase in acetylated peptide from the histone variants H2A, H2B, and H4 was accompanied by a relative decrease of dimethylated Lys(57) from histone H2B. The dose-response results obtained...... by quantitative proteomics of histones from HDACi-treated cells were consistent with Western blot analysis of histone acetylation, cytotoxicity, and dose-dependent expression profiles of p21 and cyclin A2. This demonstrates that mass spectrometry-based quantitative proteomic analysis of post-translational...

  2. Quantitative analysis of fission products by {gamma} spectrography; Analyse quantitative des produits de fission par spectrographie {gamma}

    Energy Technology Data Exchange (ETDEWEB)

    Malet, G

    1962-07-01

    The activity of the fission products present in treated solutions of irradiated fuels is given as a function of the time of cooling and of the irradiation time. The variation of the ratio ({sup 144}Ce + {sup 144}Pr activity/{sup 137}Cs activity) as a function of these same parameters is also given. From these results a method is deduced giving the 'age' of the solution analyzed. By {gamma}-scintillation spectrography it was possible to estimate the following elements individually: {sup 141}Ce, {sup 144}Ce + {sup 144}Pr, {sup 103}Ru, {sup 106}Ru + {sup 106}Rh, {sup 137}Cs, {sup 95}Zr + {sup 95}Nb. Yield curves are given for the case of a single emitter. Of the various existing methods, that of the least squares was used for the quantitative analysis of the afore-mentioned fission products. The accuracy attained varies from 3 to 10%. (author) [French] L'activite des produits de fission presents dans les solutions de traitement de combustibles irradies est donnee en fonction du temps de refroidissement et du temps d'irradiation. On etudie de plus la variation du rapport Activite du {sup 144}Ce + {sup 144}Pr /Activite du {sup 137}Cs en fonction de ces memes parametres. De ces resultats, on deduit une methode donnant l'age de la solution analysee. La spectrographie {gamma} a scintillation a permis le dosage individuel des produits suivants: {sup 141}Ce, {sup 144}Ce + {sup 144}Pr, {sup 103}Ru, {sup 106}Ru + {sup 106}Rh, {sup 137}Cs, {sup 95}Zr + {sup 95}Nb. Des courbes de rendement sont donnees dans le cas d'un emetteur unique. Des differentes methodes existantes, la methode des moindres carres a ete employee pour l'analyse quantitative des produits de fission precites. La precision obtenue varie entre 3 et 10 pour cent. (auteur)

  3. A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.

    Science.gov (United States)

    Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li

    2013-01-21

    A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments.

  4. A Quantitative Analysis of the Extrinsic and Intrinsic Turnover Factors of Relational Database Support Professionals

    Science.gov (United States)

    Takusi, Gabriel Samuto

    2010-01-01

    This quantitative analysis explored the intrinsic and extrinsic turnover factors of relational database support specialists. Two hundred and nine relational database support specialists were surveyed for this research. The research was conducted based on Hackman and Oldham's (1980) Job Diagnostic Survey. Regression analysis and a univariate ANOVA…

  5. [Quantitative image analysis in pulmonary pathology - digitalization of preneoplastic lesions in human bronchial epithelium (author's transl)].

    Science.gov (United States)

    Steinbach, T; Müller, K M; Kämper, H

    1979-01-01

    The report concerns the first phase of a quantitative study of normal and abnormal bronchial epithelium with the objective of establishing the digitalization of histologic patterns. Preparative methods, data collecting and handling, and further mathematical analysis are described. In cluster and discriminatory analysis the digitalized histologic features can be used to separate and classify the individual cases into the respective diagnostic groups.

  6. Three-way methods for the analysis of qualitative and quantitative two-way data.

    NARCIS (Netherlands)

    Kiers, Hendrik Albert Lambertus

    1989-01-01

    A problem often occurring in exploratory data analysis is how to summarize large numbers of variables in terms of a smaller number of dimensions. When the variables are quantitative, one may resort to Principal Components Analysis (PCA). When qualitative (categorical) variables are involved, one may

  7. Verbal Rehearsal and Memory in Children with Closed Head Injury: A Quantitative and Qualitative Analysis.

    Science.gov (United States)

    Harris, Jessica R.

    1996-01-01

    Nine closed head injured (CHI) children (mean age 11 years) with post-onset intervals of 7 months to 8 years were given an overt free recall task. Quantitative analysis suggested inefficient passive rehearsal strategy by severely injured subjects. Qualitative analysis revealed differences between CHI children and controls in rehearsal strategies,…

  8. A suite of models to support the quantitative assessment of spread in pest risk analysis

    NARCIS (Netherlands)

    Robinet, C.; Kehlenbeck, H.; Werf, van der W.

    2012-01-01

    In the frame of the EU project PRATIQUE (KBBE-2007-212459 Enhancements of pest risk analysis techniques) a suite of models was developed to support the quantitative assessment of spread in pest risk analysis. This dataset contains the model codes (R language) for the four models in the suite. Three

  9. Limitations for qualitative and quantitative neutron activation analysis using reactor neutrons

    International Nuclear Information System (INIS)

    El-Abbady, W.H.; El-Tanahy, Z.H.; El-Hagg, A.A.; Hassan, A.M.

    1999-01-01

    In this work, the most important limitations for qualitative and quantitative analysis using reactor neutrons for activation are reviewed. Each limitation is discussed using different examples of activated samples. Photopeak estimation, nuclear reactions interference and neutron flux measurements are taken into consideration. Solutions for high accuracy evaluation in neutron activation analysis applications are given. (author)

  10. Preliminary results of standard quantitative analysis by ED-XRF

    Energy Technology Data Exchange (ETDEWEB)

    Lara, Alessandro L. de; Franca, Alana C.; Neto, Manoel R.M.; Paschuk, Sergei A., E-mail: alellara@hotmail.com [Universidade Tecnologica Federal do Parana (UTFPR), Curitiba, PR (Brazil). Dept. de Fisica; Denyak, Valeriy, E-mail: denyak@gmail.com [Instituto de Pesquisa Pele Pequeno Principe (IPPP), Curitiba, PR (Brazil)

    2013-07-01

    A comparison between the results of elemental concentration proposed by XRS-FP software , using data obtained by EDXRF technique with those obtained by stoichiometric calculation was performed. For this purpose, five standard samples of known compounds were produced: two lead- oxide, magnesium chloride and iodine in controlled amounts. The compounds were subsequently mixed and compressed to form tablets. The samples were irradiated in three endpoints, according to an orientation. The measurements were performed at the Laboratory for Radiological UTFPR using X-123SDD the Amptek detector and X-ray tube with silver target from the same manufacturer. The operating conditions tube were 05μA current to a 40 kV voltage. Finally, the 15 spectra analyzed with the software to determine the concentration of chlorine, iodine and lead. Data from this analysis were compared with results expected in stoichiometric calculations. The data provided by the program, a convergence of results, indicating homogeneity of the samples was found. Compared to the stoichiometric calculation, a considerable discrepancy that may be the result of a misconfiguration or contamination of the sample was found. At the end, we created a proposal for continuation of the work using an auxiliary calculation should be developed in the next step.

  11. Quantitative analysis of gait in the visually impaired.

    Science.gov (United States)

    Nakamura, T

    1997-05-01

    In this comparative study concerning characteristics of independent walking by visually impaired persons, we used a motion analyser system to perform gait analysis of 15 late blind (age 36-54, mean 44.3 years), 15 congenitally blind (age 39-48, mean 43.8 years) and 15 sighted persons (age 40-50, mean 44.4 years) while walking a 10-m walkway. All subjects were male. Compared to the sighted, late blind and congenitally blind persons had a significantly slower walking speed, shorter stride length and longer time in the stance phase of gait. However, the relationships between gait parameters in the late and congenitally blind groups were maintained, as in the sighted group. In addition, the gait of the late blind showed a tendency to approximate the gait patterns of the congenitally blind as the duration of visual loss progressed. Based on these results we concluded that the gait of visually impaired persons, through its active use of non-visual sensory input, represents an attempt to adapt to various environmental conditions in order to maintain a more stable posture and to effect safe walking.

  12. Quantitative Analysis of Criteria in University Building Maintenance in Malaysia

    Directory of Open Access Journals (Sweden)

    Olanrewaju Ashola Abdul-Lateef

    2010-10-01

    Full Text Available University buildings are a significant part of university assets and considerable resources are committed to their design, construction and maintenance. The core of maintenance management is to optimize productivity and user satisfaction with optimum resources. An important segment in the maintenance management system is the analysis of criteria that influence building maintenance. Therefore, this paper aims to identify quantify, rank and discuss the criteria that influence maintenance costs, maintenance backlogs, productivity and user satisfaction in Malaysian university buildings. The paper reviews the related literature and presents the outcomes of a questionnaire survey. Questionnaires were administered on 50 university maintenance organizations. Thirty-one criteria were addressed to the university maintenance organizations to evaluate the degree to which each of the criteria influences building maintenance management. With a 66% response rate, it was concluded that the consideration of the criteria is critical to the university building maintenance management system. The quality of components and materials, budget constraints and the age of the building were found to be the most influential criteria but information on user performance satisfaction, problems associated with in-house workforce and shortage of materials and components were the least influential criteria. The paper also outlined that maintenance management is a strategic function in university administration.

  13. Magnetic resonance cholangiopancreatography findings of pancreatic diseases: quantitative analysis

    International Nuclear Information System (INIS)

    Xu Jun; Lu Jianping; Wang Jian; Wang Fei; Liu Qi; Wang Li; Gong Jianguo; Jin Aiguo; Zeng Hao

    2004-01-01

    Objective: To study the MR cholangiopancreatography (MRCP) characteristics of different pancreatic diseases, and to identify the diagnostic value of MRCP for pancreatic diseases. Methods: One hundred and eleven patients with suspected pancreatic diseases underwent MRCP examination. The MRCP sequences included thick-slice turbo spin echo (TSE) and thin-slice half-Fourier acquisition single shot turbo spin echo (HASTE) sequences. The pancreatic diseases included pancreatic carcinoma (n=46), chronic pancreatitis (n=39), peri-ampullar carcinoma (n=23), and choledocholith (n=3). Results: (1) The abnormal manifestation of pancreatic duct was observed in 37 cases of pancreatic carcinoma, 24 cases of chronic pancreatitis, and 12 cases of peri-ampullar carcinoma. Dilated pancreatic duct with smooth and regular caliber was observed in 33 cases of pancreatic carcinoma, 0 case of chronic pancreatitis, and 12 cases of peri-ampullar carcinoma, and statistical analysis showed significant difference (χ 2 =57.911, P 2 =60.343, P 2 =61.217, P 2 =34.654, P 2 =54.593, P<0.01). Conclusion: Different MRI characteristics were observed in various pancreatic diseases respectively. MRCP can show the subtle differences among the pancreatic diseases, and is very helpful in the diagnosis and differential diagnosis of pancreatic diseases

  14. Quantitative analysis of the individual dynamics of Psychology theses

    Directory of Open Access Journals (Sweden)

    Robles, Jaime R.

    2009-12-01

    Full Text Available Three cohorts of undergraduate psychology theses (n = 57 performed by last year undergraduate psychology students from Universidad Católica Andrés Bello, were monitored using 5 longitudinal measurements of progression. A Generalized Additive Model, to predict the completion time of the theses, is tested against two completion times: early and delayed. Effect size measures favor a multiple dimension model over a global progress model. The trajectory of the indicators through the 5 measurements allows the differentiation between early and delayed completion. The completion probabilities estimated by the dimensional model allow the identification of differential oscillation levels for the distinct completion times. The initial progression indicators allow the prediction of early completion with a 71% success rate, while the final measurement shows a success rate of 89%. The results support the effectiveness of the supervisory system and the analysis of the progression dynamics of the theses from a task-delay model, focused on the relationship between the amount of task completion and the deadlines

  15. Quantitative analysis of DNA methylation in chronic lymphocytic leukemia patients.

    Science.gov (United States)

    Lyko, Frank; Stach, Dirk; Brenner, Axel; Stilgenbauer, Stephan; Döhner, Hartmut; Wirtz, Michaela; Wiessler, Manfred; Schmitz, Oliver J

    2004-06-01

    Changes in the genomic DNA methylation level have been found to be closely associated with tumorigenesis. In order to analyze the relation of aberrant DNA methylation to clinical and biological risk factors, we have determined the cytosine methylation level of 81 patients diagnosed with chronic lymphocytic leukemia (CLL). The analysis was based on DNA hydrolysis followed by derivatization of the 2'-desoxyribonucleoside-3'-monophosphates with BODIPY FL EDA. Derivatives were separated by micellar electrokinetic chromatography, and laser-induced fluorescence was used for detection. We analyzed potential correlations between DNA methylation levels and numerous patient parameters, including clinical observations and biological data. As a result, we observed a significant correlation with the immunoglobulin variable heavy chain gene (VH) mutation status. This factor has been repeatedly proposed as a reliable prognostic marker for CLL, which suggests that the methylation level might be a valuable factor in determining the prognostic outcome of CLL. We are now in the process of refining our method to broaden its application potential. In this context, we show here that the oxidation of the fluorescence marker in the samples and the evaporation of methanol in the electrolytes can be prevented by a film of paraffin oil. In summary, our results thus establish capillary electrophoresis as a valuable tool for analyzing the DNA methylation status of clinical samples.

  16. Direct Quantitative Analysis of Arsenic in Coal Fly Ash

    Directory of Open Access Journals (Sweden)

    Sri Hartuti

    2012-01-01

    Full Text Available A rapid, simple method based on graphite furnace atomic absorption spectrometry is described for the direct determination of arsenic in coal fly ash. Solid samples were directly introduced into the atomizer without preliminary treatment. The direct analysis method was not always free of spectral matrix interference, but the stabilization of arsenic by adding palladium nitrate (chemical modifier and the optimization of the parameters in the furnace program (temperature, rate of temperature increase, hold time, and argon gas flow gave good results for the total arsenic determination. The optimal furnace program was determined by analyzing different concentrations of a reference material (NIST1633b, which showed the best linearity for calibration. The optimized parameters for the furnace programs for the ashing and atomization steps were as follows: temperatures of 500–1200 and 2150°C, heating rates of 100 and 500°C s−1, hold times of 90 and 7 s, and medium then maximum and medium argon gas flows, respectively. The calibration plots were linear with a correlation coefficient of 0.9699. This method was validated using arsenic-containing raw coal samples in accordance with the requirements of the mass balance calculation; the distribution rate of As in the fly ashes ranged from 101 to 119%.

  17. Preliminary results of standard quantitative analysis by ED-XRF

    International Nuclear Information System (INIS)

    Lara, Alessandro L. de; Franca, Alana C.; Neto, Manoel R.M.; Paschuk, Sergei A.

    2013-01-01

    A comparison between the results of elemental concentration proposed by XRS-FP software , using data obtained by EDXRF technique with those obtained by stoichiometric calculation was performed. For this purpose, five standard samples of known compounds were produced: two lead- oxide, magnesium chloride and iodine in controlled amounts. The compounds were subsequently mixed and compressed to form tablets. The samples were irradiated in three endpoints, according to an orientation. The measurements were performed at the Laboratory for Radiological UTFPR using X-123SDD the Amptek detector and X-ray tube with silver target from the same manufacturer. The operating conditions tube were 05μA current to a 40 kV voltage. Finally, the 15 spectra analyzed with the software to determine the concentration of chlorine, iodine and lead. Data from this analysis were compared with results expected in stoichiometric calculations. The data provided by the program, a convergence of results, indicating homogeneity of the samples was found. Compared to the stoichiometric calculation, a considerable discrepancy that may be the result of a misconfiguration or contamination of the sample was found. At the end, we created a proposal for continuation of the work using an auxiliary calculation should be developed in the next step

  18. Quantitative analysis of soil chromatography. I. Water and radionuclide transport

    Energy Technology Data Exchange (ETDEWEB)

    Reeves, M.; Francis, C.W.; Duguid, J.O.

    1977-12-01

    Soil chromatography has been used successfully to evaluate relative mobilities of pesticides and nuclides in soils. Its major advantage over the commonly used suspension technique is that it more accurately simulates field conditions. Under such conditions the number of potential exchange sites is limited both by the structure of the soil matrix and by the manner in which the carrier fluid moves through this structure. The major limitation of the chromatographic method, however, has been its qualitative nature. This document represents an effort to counter this objection. A theoretical basis is specified for the transport both of the carrier eluting fluid and of the dissolved constituent. A computer program based on this theory is developed which optimizes the fit of theoretical data to experimental data by automatically adjusting the transport parameters, one of which is the distribution coefficient k/sub d/. This analysis procedure thus constitutes an integral part of the soil chromatographic method, by means of which mobilities of nuclides and other dissolved constituents in soils may be quantified.

  19. Quantitative analysis of soil chromatography. I. Water and radionuclide transport

    International Nuclear Information System (INIS)

    Reeves, M.; Francis, C.W.; Duguid, J.O.

    1977-12-01

    Soil chromatography has been used successfully to evaluate relative mobilities of pesticides and nuclides in soils. Its major advantage over the commonly used suspension technique is that it more accurately simulates field conditions. Under such conditions the number of potential exchange sites is limited both by the structure of the soil matrix and by the manner in which the carrier fluid moves through this structure. The major limitation of the chromatographic method, however, has been its qualitative nature. This document represents an effort to counter this objection. A theoretical basis is specified for the transport both of the carrier eluting fluid and of the dissolved constituent. A computer program based on this theory is developed which optimizes the fit of theoretical data to experimental data by automatically adjusting the transport parameters, one of which is the distribution coefficient k/sub d/. This analysis procedure thus constitutes an integral part of the soil chromatographic method, by means of which mobilities of nuclides and other dissolved constituents in soils may be quantified

  20. Quantitative analysis of bloggers' collective behavior powered by emotions

    Science.gov (United States)

    Mitrović, Marija; Paltoglou, Georgios; Tadić, Bosiljka

    2011-02-01

    Large-scale data resulting from users' online interactions provide the ultimate source of information to study emergent social phenomena on the Web. From individual actions of users to observable collective behaviors, different mechanisms involving emotions expressed in the posted text play a role. Here we combine approaches of statistical physics with machine-learning methods of text analysis to study the emergence of emotional behavior among Web users. Mapping the high-resolution data from digg.com onto bipartite networks of users and their comments onto posted stories, we identify user communities centered around certain popular posts and determine emotional contents of the related comments by the emotion classifier developed for this type of text. Applied over different time periods, this framework reveals strong correlations between the excess of negative emotions and the evolution of communities. We observe avalanches of emotional comments exhibiting significant self-organized critical behavior and temporal correlations. To explore the robustness of these critical states, we design a network-automaton model on realistic network connections and several control parameters, which can be inferred from the dataset. Dissemination of emotions by a small fraction of very active users appears to critically tune the collective states.

  1. Leukoaraiosis is associated with arterial wall thickness: a quantitative analysis.

    Science.gov (United States)

    Auriel, Eitan; Csiba, Laszlo; Berenyi, Ervin; Varkonyi, Ildiko; Mehes, Gabor; Kardos, Laszlo; Karni, Arnon; Bornstein, Natan M

    2012-06-01

    Leukoaraiosis refers to an age-related, abnormal appearance of the brain white matter on neuroimaging. The association between leukoaraiosis and cerebrovascular disease suggests that ischemia may be an important contributing factor; however, the pathogenesis of the condition remains controversial. We hypothesized that physical abnormalities of blood vessels might be culpable and compared the external and internal measurements of blood vessel walls between brains that demonstrated leukoaraiosis on imaging and normal control brains. Fourteen brains of individuals who had been diagnosed as having severe leukoaraiosis and five non-leukoaraiosis control brains were studied. Arterial cross-sections were evaluated by length measurements with an image analysis device. Arterial wall thickness and the ratio of the outer and inner diameters of the vessel were measured. We measured a total of 108 vessels in the leukoaraiosis group and 95 vessels in the control group. The vessel walls of the leukoaraiosis patients were an average of 5.5 µm thicker than the walls of control vessels of the same inside diameter (P = 0.0000, 95% CI 3.01-8.08) and an average of 2.3 µm thicker than walls of control vessels of the same outside diameter (P = 0.016, 95% CI 0.48-4.17). Our data provide evidence that leukoaraiosis is associated with vessel wall thickening in an additive fashion and indicate that structural vascular abnormalities are associated with leukoaraiosis. © 2011 Japanese Society of Neuropathology.

  2. Quantitative analysis of allantoin in Iranian corn silk

    Directory of Open Access Journals (Sweden)

    E. Khanpour*

    2017-11-01

    Full Text Available Background and objectives: Zea mays is cultivated in different parts of Iran and corn silk is used in traditional medicine. Allantoin is one of the major compounds in corn silk. The purpose of this research was the quantitatve analysis of allantoin in corn silks belonging to several regions of Iran. Methods: The samples of corn silk were prepared from three provinces of Iran (Kermanshah, Fars and Razavi Khorasan. The dried plant materials were infused in boiling distilled water with a temperature of 90-95 °C on magnetic stirrer for 30 min. The levels of allantoin in aqueous extracts were determined by HPLC. Quantification was achieved using an C18 column (250×4.6 mm, 5 µm under isocratic conditions and phosphate buffer solution (pH 3.0 as the mobile phase at a flow rate of 0.5 mL/min. Column effluent was monitored at 210 nm. The calibration curve of allantoin standard was plotted with concentrations from 6.25 to 100 µg/mL. Results: The calibration curve of standard was linear over the concentration range used (R2=0.9999. The results showed that the amount of allantoin in samples was between 205 and 374 mg/100g of dry plant material. The corn silk samples of Razavi Khorasan and Fars provinces showed the lowest and highest amount of allantoin, respectively. Conclusion: The levels of allantoin obtained in this study were higher than the values reported in other studies; therefore, the researchers of this project are investigating the wound healing effect of corn silk.

  3. Quantitative analysis of thymus lymphoid cells during murine radioleukemogenesis

    International Nuclear Information System (INIS)

    Boniver, J.; Simar, L.J.; Courtoy, R.; Betz, E.H.

    1978-01-01

    Fractionated irradiation by four doses of 150 R leads to the development of lymphoma in the thymus of C57BL mice, after a long latent period (4 to 12 months) during which thymic subcapsular blast cells undergo neoplastic transformation. Electron microscope studies on this blast cell population have revealed several types that are distinguishable on the basis of nuclear ultrastructure and activity in the cell cycle. These blast cells are lymphoblasts, ring-shaped nucleolus cells, and x-cells. A stereological analysis demonstrates that the result of the irradiations is not an increase of the thymic blast cell number during the preleukemic period, as generally thought before, but important modifications in the relative proportion of the three cell types forming the blastic population. X-cells, which essentially appear in S phase, are more numerous after the third and fourth doses of radiation. They might be more ''sensitive'' to the action of the leukemogenic virus and facilitate the leukemogenic process. In contrast, in the preleukemic atrophic thymus just before the appearance of the lymphoma, x-cells are scarce, and ring-shaped nucleolus cells are more frequent than in the controls, suggesting important changes in thymus cell kinetics. The only modification detected in the blast cells at any time after irradiation concerns the surface of Golgi membranes, which decreases in x-cells and ring-shaped nucleolus cells of the atrophic thymus. Because the same change is observed later on in the lymphomatous cells, it is suggested that the change might be related to the transformation of the thymic blast cells into cancerous cells

  4. Quantitative flux analysis reveals folate-dependent NADPH production

    Science.gov (United States)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  5. Mutational analysis of the RecJ exonuclease of Escherichia coli: identification of phosphoesterase motifs.

    Science.gov (United States)

    Sutera, V A; Han, E S; Rajman, L A; Lovett, S T

    1999-10-01

    The recJ gene, identified in Escherichia coli, encodes a Mg(+2)-dependent 5'-to-3' exonuclease with high specificity for single-strand DNA. Genetic and biochemical experiments implicate RecJ exonuclease in homologous recombination, base excision, and methyl-directed mismatch repair. Genes encoding proteins with strong similarities to RecJ have been found in every eubacterial genome sequenced to date, with the exception of Mycoplasma and Mycobacterium tuberculosis. Multiple genes encoding proteins similar to RecJ are found in some eubacteria, including Bacillus and Helicobacter, and in the archaea. Among this divergent set of sequences, seven conserved motifs emerge. We demonstrate here that amino acids within six of these motifs are essential for both the biochemical and genetic functions of E. coli RecJ. These motifs may define interactions with Mg(2+) ions or substrate DNA. A large family of proteins more distantly related to RecJ is present in archaea, eubacteria, and eukaryotes, including a hypothetical protein in the MgPa adhesin operon of Mycoplasma, a domain of putative polyA polymerases in Synechocystis and Aquifex, PRUNE of Drosophila, and an exopolyphosphatase (PPX1) of Saccharomyces cereviseae. Because these six RecJ motifs are shared between exonucleases and exopolyphosphatases, they may constitute an ancient phosphoesterase domain now found in all kingdoms of life.

  6. Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli

    International Nuclear Information System (INIS)

    Alexopoulos, Eftichia; Kanjee, Usheer; Snider, Jamie; Houry, Walid A.; Pai, Emil F.

    2008-01-01

    The structure of the decameric inducible lysine decarboxylase from E. coli was determined by SIRAS using a hexatantalum dodecabromide (Ta 6 Br 12 2+ ) derivative. Model building and refinement are under way. The decameric inducible lysine decarboxylase (LdcI) from Escherichia coli has been crystallized in space groups C2 and C222 1 ; the Ta 6 Br 12 2+ cluster was used to derivatize the C2 crystals. The method of single isomorphous replacement with anomalous scattering (SIRAS) as implemented in SHELXD was used to solve the Ta 6 Br 12 2+ -derivatized structure to 5 Å resolution. Many of the Ta 6 Br 12 2+ -binding sites had twofold and fivefold noncrystallographic symmetry. Taking advantage of this feature, phase modification was performed in DM. The electron-density map of LdcI displays many features in agreement with the low-resolution negative-stain electron-density map [Snider et al. (2006 ▶), J. Biol. Chem.281, 1532–1546

  7. Analysis of Escherichia coli nicotinate mononucleotide adenylyltransferase mutants in vivo and in vitro

    Directory of Open Access Journals (Sweden)

    Rydén-Aulin Monica

    2005-09-01

    Full Text Available Abstract Background Adenylation of nicotinate mononucleotide to nicotinate adenine dinucleotide is the penultimate step in NAD+ synthesis. In Escherichia coli, the enzyme nicotinate mononucleotide adenylyltransferase is encoded by the nadD gene. We have earlier made an initial characterization in vivo of two mutant enzymes, NadD72 and NadD74. Strains with either mutation have decreased intracellular levels of NAD+, especially for one of the alleles, nadD72. Results In this study these two mutant proteins have been further characterized together with ten new mutant variants. Of the, in total, twelve mutations four are in a conserved motif in the C-terminus and eight are in the active site. We have tested the activity of the enzymes in vitro and their effect on the growth phenotype in vivo. There is a very good correlation between the two data sets. Conclusion The mutations in the C-terminus did not reveal any function for the conserved motif. On the other hand, our data has lead us to assign amino acid residues His-19, Arg-46 and Asp-109 to the active site. We have also shown that the nadD gene is essential for growth in E. coli.

  8. A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Olin K Silander

    2012-01-01

    Full Text Available Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as "phenotypic noise." In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alone.

  9. Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation.

    Science.gov (United States)

    Meadows, Adam L; Karnik, Rahi; Lam, Harry; Forestell, Sean; Snedecor, Brad

    2010-03-01

    We have developed a reactor-scale model of Escherichia coli metabolism and growth in a 1000 L process for the production of a recombinant therapeutic protein. The model consists of two distinct parts: (1) a dynamic, process specific portion that describes the time evolution of 37 process variables of relevance and (2) a flux balance based, 123-reaction metabolic model of E. coli metabolism. This model combines several previously reported modeling approaches including a growth rate-dependent biomass composition, maximum growth rate objective function, and dynamic flux balancing. In addition, we introduce concentration-dependent boundary conditions of transport fluxes, dynamic maintenance demands, and a state-dependent cellular objective. This formulation was able to describe specific runs with high-fidelity over process conditions including rich media, simultaneous acetate and glucose consumption, glucose minimal media, and phosphate depleted media. Furthermore, the model accurately describes the effect of process perturbations--such as glucose overbatching and insufficient aeration--on growth, metabolism, and titer. (c) 2009 Elsevier Inc. All rights reserved.

  10. A Quantitative Analysis of Dressing Dynamics for Robotic Dressing Assistance

    Directory of Open Access Journals (Sweden)

    Greg Chance

    2017-05-01

    Full Text Available Assistive robots have a great potential to address issues related to an aging population and an increased demand for caregiving. Successful deployment of robots working in close proximity with people requires consideration of both safety and human–robot interaction (HRI. One of the established activities of daily living where robots could play an assistive role is dressing. Using the correct force profile for robot control will be essential in this application of HRI requiring careful exploration of factors related to the user’s pose and the type of garments involved. In this paper, a Baxter robot was used to dress a jacket onto a mannequin and human participants considering several combinations of user pose and clothing type (base layers, while recording dynamic data from the robot, a load cell, and an IMU. We also report on suitability of these sensors for identifying dressing errors, e.g., fabric snagging. Data were analyzed by comparing the overlap of confidence intervals to determine sensitivity to dressing. We expand the analysis to include classification techniques such as decision tree and support vector machines using k-fold cross-validation. The 6-axis load cell successfully discriminated between clothing types with predictive model accuracies between 72 and 97%. Used independently, the IMU and Baxter sensors were insufficient to discriminate garment types with the IMU showing 40–72% accuracy, but when used in combination this pair of sensors achieved an accuracy similar to the more expensive load cell (98%. When observing dressing errors (snagging, Baxter’s sensors and the IMU data demonstrated poor sensitivity but applying machine learning methods resulted in model with high predicative accuracy and low false negative rates (≤5%. The results show that the load cell could be used independently for this application with good accuracy but a combination of the lower cost sensors could also be used without a significant loss in

  11. Evaluation of breast lesions by contrast enhanced ultrasound: Qualitative and quantitative analysis

    International Nuclear Information System (INIS)

    Wan Caifeng; Du Jing; Fang Hua; Li Fenghua; Wang Lin

    2012-01-01

    Objective: To evaluate and compare the diagnostic performance of qualitative, quantitative and combined analysis for characterization of breast lesions in contrast enhanced ultrasound (CEUS), with histological results used as the reference standard. Methods: Ninety-one patients with 91 breast lesions BI-RADS 3–5 at US or mammography underwent CEUS. All lesions underwent qualitative and quantitative enhancement evaluation. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic performance of different analytical method for discrimination between benign and malignant breast lesions. Results: Histopathologic analysis of the 91 lesions revealed 44 benign and 47 malignant. For qualitative analysis, benign and malignant lesions differ significantly in enhancement patterns (p z1 ), 0.768 (A z2 ) and 0.926(A z3 ) respectively. The values of A z1 and A z3 were significantly higher than that for A z2 (p = 0.024 and p = 0.008, respectively). But there was no significant difference between the values of A z1 and A z3 (p = 0.625). Conclusions: The diagnostic performance of qualitative and combined analysis was significantly higher than that for quantitative analysis. Although quantitative analysis has the potential to differentiate benign from malignant lesions, it has not yet improved the final diagnostic accuracy.

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

    Science.gov (United States)

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

    2012-04-01

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

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

    Science.gov (United States)

    Gao, Yi; Bouix, Sylvain

    2016-05-01

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

  14. Development and accuracy of quantitative real-time polymerase chain reaction assays for detection and quantification of enterotoxigenic Escherichia coli (ETEC) heat labile and heat stable toxin genes in travelers' diarrhea samples.

    Science.gov (United States)

    Youmans, Bonnie P; Ajami, Nadim J; Jiang, Zhi-Dong; Petrosino, Joseph F; DuPont, Herbert L; Highlander, Sarah K

    2014-01-01

    Enterotoxigenic Escherichia coli (ETEC), the leading bacterial pathogen of travelers' diarrhea, is routinely detected by an established DNA hybridization protocol that is neither sensitive nor quantitative. Quantitative real-time polymerase chain reaction (qPCR) assays that detect the ETEC toxin genes eltA, sta1, and sta2 in clinical stool samples were developed and tested using donor stool inoculated with known quantities of ETEC bacteria. The sensitivity of the qPCR assays is 89%, compared with 22% for the DNA hybridization assay, and the limits of detection are 10,000-fold lower than the DNA hybridization assays performed in parallel. Ninety-three clinical stool samples, previously characterized by DNA hybridization, were tested using the new ETEC qPCR assays. Discordant toxin profiles were observed for 22 samples, notably, four samples originally typed as ETEC negative were ETEC positive. The qPCR assays are unique in their sensitivity and ability to quantify the three toxin genes in clinical stool samples.

  15. Analysis of archaeological ceramics by total-reflection X-ray fluorescence: Quantitative approaches

    International Nuclear Information System (INIS)

    Fernandez-Ruiz, R.; Garcia-Heras, M.

    2008-01-01

    This paper reports the quantitative methodologies developed for the compositional characterization of archaeological ceramics by total-reflection X-ray fluorescence at two levels. A first quantitative level which comprises an acid leaching procedure, and a second selective level, which seeks to increase the number of detectable elements by eliminating the iron present in the acid leaching procedure. Total-reflection X-ray fluorescence spectrometry has been compared, at a quantitative level, with Instrumental Neutron Activation Analysis in order to test its applicability to the study of this kind of materials. The combination of a solid chemical homogenization procedure previously reported with the quantitative methodologies here presented allows the total-reflection X-ray fluorescence to analyze 29 elements with acceptable analytical recoveries and accuracies

  16. Analysis of archaeological ceramics by total-reflection X-ray fluorescence: Quantitative approaches

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Ruiz, R. [Servicio Interdepartamental de Investigacion, Facultad de Ciencias, Universidad Autonoma de Madrid, Modulo C-9, Laboratorio de TXRF, Crta. Colmenar, Km 15, Cantoblanco, E-28049, Madrid (Spain)], E-mail: ramon.fernandez@uam.es; Garcia-Heras, M. [Grupo de Arqueometria de Vidrios y Materiales Ceramicos, Instituto de Historia, Centro de Ciencias Humanas y Sociales, CSIC, C/ Albasanz, 26-28, 28037 Madrid (Spain)

    2008-09-15

    This paper reports the quantitative methodologies developed for the compositional characterization of archaeological ceramics by total-reflection X-ray fluorescence at two levels. A first quantitative level which comprises an acid leaching procedure, and a second selective level, which seeks to increase the number of detectable elements by eliminating the iron present in the acid leaching procedure. Total-reflection X-ray fluorescence spectrometry has been compared, at a quantitative level, with Instrumental Neutron Activation Analysis in order to test its applicability to the study of this kind of materials. The combination of a solid chemical homogenization procedure previously reported with the quantitative methodologies here presented allows the total-reflection X-ray fluorescence to analyze 29 elements with acceptable analytical recoveries and accuracies.

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

    International Nuclear Information System (INIS)

    Zhang Wei; Xiang Bingren; Wu Yanwei; Shang Erxin

    2005-01-01

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

  18. A critical appraisal of semi-quantitative analysis of 2-deoxyglucose autoradiograms

    International Nuclear Information System (INIS)

    Kelly, P.T.; McCulloch, J.

    1983-01-01

    Semi-quantitative analysis (e.g. optical density ratios) of [ 14 C]2-deoxyglucose autoradiograms is widely used in neuroscience research. The authors demonstrate that a fixed ratio of 14 C-concentrations in the CNS does not yield a constant optical density ratio but is dependent upon the exposure time in the preparation of the autoradiograms and the absolute amounts of 14 C from which the concentration ratio is derived. The failure of a fixed glucose utilization ratio to result in a constant optical density ratio represents a major interpretative difficulty in investigations where only semi-quantitative analysis of [ 14 C]2-deoxyglucose autoradiograms is undertaken. (Auth.)

  19. Critical appraisal of semi-quantitative analysis of 2-deoxyglucose autoradiograms

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, P T; McCulloch, J [Glasgow Univ. (UK)

    1983-06-13

    Semi-quantitative analysis (e.g. optical density ratios) of (/sup 14/C)2-deoxyglucose autoradiograms is widely used in neuroscience research. The authors demonstrate that a fixed ratio of /sup 14/C-concentrations in the CNS does not yield a constant optical density ratio but is dependent upon the exposure time in the preparation of the autoradiograms and the absolute amounts of /sup 14/C from which the concentration ratio is derived. The failure of a fixed glucose utilization ratio to result in a constant optical density ratio represents a major interpretative difficulty in investigations where only semi-quantitative analysis of (/sup 14/C)2-deoxyglucose autoradiograms is undertaken.

  20. Towards quantitative laser-induced breakdown spectroscopy analysis of soil samples

    International Nuclear Information System (INIS)

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

    2007-01-01

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