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Sample records for multiple markers analyzed

  1. Multiple capillary biochemical analyzer

    DOEpatents

    Dovichi, Norman J.; Zhang, Jian Z.

    1995-01-01

    A multiple capillary analyzer allows detection of light from multiple capillaries with a reduced number of interfaces through which light must pass in detecting light emitted from a sample being analyzed, using a modified sheath flow cuvette. A linear or rectangular array of capillaries is introduced into a rectangular flow chamber. Sheath fluid draws individual sample streams through the cuvette. The capillaries are closely and evenly spaced and held by a transparent retainer in a fixed position in relation to an optical detection system. Collimated sample excitation radiation is applied simultaneously across the ends of the capillaries in the retainer. Light emitted from the excited sample is detected by the optical detection system. The retainer is provided by a transparent chamber having inward slanting end walls. The capillaries are wedged into the chamber. One sideways dimension of the chamber is equal to the diameter of the capillaries and one end to end dimension varies from, at the top of the chamber, slightly greater than the sum of the diameters of the capillaries to, at the bottom of the chamber, slightly smaller than the sum of the diameters of the capillaries. The optical system utilizes optic fibres to deliver light to individual photodetectors, one for each capillary tube. A filter or wavelength division demultiplexer may be used for isolating fluorescence at particular bands.

  2. Multiple capillary biochemical analyzer

    DOEpatents

    Dovichi, N.J.; Zhang, J.Z.

    1995-08-08

    A multiple capillary analyzer allows detection of light from multiple capillaries with a reduced number of interfaces through which light must pass in detecting light emitted from a sample being analyzed, using a modified sheath flow cuvette. A linear or rectangular array of capillaries is introduced into a rectangular flow chamber. Sheath fluid draws individual sample streams through the cuvette. The capillaries are closely and evenly spaced and held by a transparent retainer in a fixed position in relation to an optical detection system. Collimated sample excitation radiation is applied simultaneously across the ends of the capillaries in the retainer. Light emitted from the excited sample is detected by the optical detection system. The retainer is provided by a transparent chamber having inward slanting end walls. The capillaries are wedged into the chamber. One sideways dimension of the chamber is equal to the diameter of the capillaries and one end to end dimension varies from, at the top of the chamber, slightly greater than the sum of the diameters of the capillaries to, at the bottom of the chamber, slightly smaller than the sum of the diameters of the capillaries. The optical system utilizes optic fibers to deliver light to individual photodetectors, one for each capillary tube. A filter or wavelength division demultiplexer may be used for isolating fluorescence at particular bands. 21 figs.

  3. A statistical framework for analyzing hypothesized interactions between cells imaged using multispectral microscopy and multiple immunohistochemical markers

    PubMed Central

    Rose, Chris J.; Naidoo, Khimara; Clay, Vanessa; Linton, Kim; Radford, John A.; Byers, Richard J.

    2013-01-01

    Background: Multispectral microscopy and multiple staining can be used to identify cells with distinct immunohistochemical (IHC) characteristics. We present here a method called hypothesized interaction distribution (HID) analysis for characterizing the statistical distribution of pair-wise spatial relationships between cells with particular IHC characteristics and apply it to clinical data. Materials and Methods: We retrospectively analyzed data from a study of 26 follicular lymphoma patients in which sections were stained for CD20 and YY1. HID analysis, using leave-one-out validation, was used to assign patients to one of two groups. We tested the null hypothesis of no difference in Kaplan–Meier survival curves between the groups. Results: Shannon entropy of HIDs assigned patients to groups that had significantly different survival curves (median survival was 7.70 versus 110 months, P = 0.00750). Hypothesized interactions between pairs of cells positive for both CD20 and YY1 were associated with poor survival. Conclusions: HID analysis provides quantitative inferences about possible interactions between spatially proximal cells with particular IHC characteristics. In follicular lymphoma, HID analysis was able to distinguish between patients with poor versus good survival, and it may have diagnostic and prognostic utility in this and other diseases. PMID:23766940

  4. Multiple capillary biochemical analyzer with barrier member

    DOEpatents

    Dovichi, Norman J.; Zhang, Jian Z.

    1996-01-01

    A multiple capillary biochemical analyzer for sequencing DNA and performing other analyses, in which a set of capillaries extends from wells in a microtiter plate into a cuvette. In the cuvette the capillaries are held on fixed closely spaced centers by passing through a sandwich construction having a pair of metal shims which squeeze between them a rubber gasket, forming a leak proof seal for an interior chamber in which the capillary ends are positioned. Sheath fluid enters the chamber and entrains filament sample streams from the capillaries. The filament sample streams, and sheath fluid, flow through aligned holes in a barrier member spaced close to the capillary ends, into a collection chamber having a lower glass window. The filament streams are illuminated above the barrier member by a laser, causing them to fluoresce. The fluorescence is viewed end-on by a CCD camera chip located below the glass window. The arrangement ensures an equal optical path length from all fluorescing spots to the CCD chip and also blocks scattered fluorescence illumination, providing more uniform results and an improved signal to noise ratio.

  5. Multiple capillary biochemical analyzer with barrier member

    DOEpatents

    Dovichi, N.J.; Zhang, J.Z.

    1996-10-22

    A multiple capillary biochemical analyzer is disclosed for sequencing DNA and performing other analyses, in which a set of capillaries extends from wells in a microtiter plate into a cuvette. In the cuvette the capillaries are held on fixed closely spaced centers by passing through a sandwich construction having a pair of metal shims which squeeze between them a rubber gasket, forming a leak proof seal for an interior chamber in which the capillary ends are positioned. Sheath fluid enters the chamber and entrains filament sample streams from the capillaries. The filament sample streams, and sheath fluid, flow through aligned holes in a barrier member spaced close to the capillary ends, into a collection chamber having a lower glass window. The filament streams are illuminated above the barrier member by a laser, causing them to fluoresce. The fluorescence is viewed end-on by a CCD camera chip located below the glass window. The arrangement ensures an equal optical path length from all fluorescing spots to the CCD chip and also blocks scattered fluorescence illumination, providing more uniform results and an improved signal-to-noise ratio. 12 figs.

  6. Neurophysiological markers of multiple facets of impulsivity.

    PubMed

    Neal, Lauren B; Gable, Philip A

    2016-03-01

    Human behavior is influenced by three core personality systems: approach, avoidance, and supervisory control. The supervisory control system is inversely related to impulsivity. Although past research has related some aspects of impulsivity to frontal hemispheric asymmetry, impulsivity as a multi-faceted construct has not been studied in relation with frontal asymmetry. In addition, past work has potentially confounded impulsivity with approach-motivation. In the current study, greater relative left frontal activity was related to multiple facets of impulsivity: negative urgency, lack of premeditation, lack of perseverance, and positive urgency. Regressing both positive and negative urgency on frontal asymmetry revealed that approach-related positive urgency related to greater left frontal activity, but withdrawal-related negative urgency marginally related to greater right frontal activity. These results suggest that impulsivity, independent of affective valence, relates to greater left frontal activity. When controlling for trait approach motivation, the relationship between impulsivity and left frontal activity is unchanged.

  7. Analyzing Student Confidence in Classroom Voting with Multiple Choice Questions

    ERIC Educational Resources Information Center

    Stewart, Ann; Storm, Christopher; VonEpps, Lahna

    2013-01-01

    The purpose of this paper is to present results of a recent study in which students voted on multiple choice questions in mathematics courses of varying levels. Students used clickers to select the best answer among the choices given; in addition, they were also asked whether they were confident in their answer. In this paper we analyze data…

  8. An Alternative Method for Analyzing Active Multiplicity Data.

    SciTech Connect

    Pickrell, M. M.

    2005-01-01

    The authors have developed a novel method for analyzing active neutron multiplicity data. The conventional method was derived from the standard passive multiplicity equations known as the point model. The approach was to substitute a term consisting of the product of the interrogation source strength, the coupling coefficient, and the sample mass for the product term of the sample mass and the fission rate: I{kappa}{sub c}m {yields} F{sub 0}m, where I is the source strength, {kappa}{sub c} is the coupling coefficient, m is the sample mass and F is the fission rate. Note that the sample mass, m, refers to the fissile material (e.g. {sup 235}U) in the active case and fertile material (e.g. {sup 240}Pu{sub eff}) in the passive case. In addition, the spontaneous fission multiplicity coefficients, {nu}{sub s}, were replaced with the induced fission multiplicity coefficients, {nu}{sub i}. This model has several drawbacks. The most significant is that the coupling coefficient, {kappa}{sub c}, varies significantly with the multiplication. As a consequence, there is not a clear linear relationship between the doubles rate and the sample mass, nor is there a clear linear relationship between the multiplication-corrected doubles rate and the sample mass. This problem has limited the application of active neutron multiplicity counting. They propose here a novel approach to deriving the multiplicity equations. A different substitution is made in the point model equations. The value of alpha is replaced with a new term, alpha-prime: {alpha} {yields} {alpha}{prime} {triple_bond} {alpha} + {kappa}{sub p}I/Fm{sub 0}{nu}{sub s1}. There are several benefits to this approach, but most significant is that the new coupling coefficient, {kappa}{sub p}, remains constant. In this paper they will establish the general physics justification why this different substitution is appropriate. They will derive the new point model equations for active neutron multiplicity starting from the original

  9. Allele capture by selection for flanking markers: A new method for analyzing multigenic traits

    SciTech Connect

    Harrison, D.E.; Roderick, T.H.; Paigen, K.

    1995-12-31

    in complex living organisms like mammals, most important processes are controlled by sets of interacting genes organized in biological pathways. A vital area of research during the coming decades will be to identify the genes that regulate such pathways and to analyze their functions. We here outline a new procedure to accomplish this: allele capture using flanking markers. Here illustrated for mice, it should be useful for all organisms in which adequate numbers of marker genes are available. This procedure combines mankind`s oldest and best proven logical technique, selective breeding, with the modern technologies of molecular markers, linkage analyses and computer programs. 7 refs.

  10. Using Live-Cell Markers in Maize to Analyze Cell Division Orientation and Timing.

    PubMed

    Rasmussen, Carolyn G

    2016-01-01

    Recently developed live-cell markers provide an opportunity to explore the dynamics and localization of proteins in maize, an important crop and model for monocot development. A step-by-step method is outlined for observing and analyzing the process of division in maize cells. The steps include plant growth conditions, sample preparation, time-lapse setup, and calculation of division rates.

  11. Gold nanoparticle modified capacitive sensor platform for multiple marker detection.

    PubMed

    Altintas, Zeynep; Kallempudi, Sreenivasa Saravan; Gurbuz, Yasar

    2014-01-01

    The detection and quantification of cancer biomarkers in human blood is crucial to diagnose patients in the early stage of a disease. The recent advances in biosensor technology can improve detection by reducing the application time and cost without an invasive approach. In this study, a highly sensitive, novel nanoparticle-modified capacitive sensor was developed for the detection of cancer markers. The current work mainly focused on developing a surface modification protocol for achieving higher sensitivity using Au-NPs. An interdigitated electrode (IDE) transducer was modified using gold nanoparticles (Au-NPs) for signal enhancement, the platform was initially optimized with a small size IL-6 protein and the methodology was then applied for multiple marker detection with the aim of precise disease diagnostics. Carcinoembryonic antigen (CEA) and epidermal growth factor receptor (hEGFR) could be successfully detected in the concentration range of 20-1000 pg mL(-1) while cancer antigen 15-3 (CA15-3) was detected in the range of 10-200 U mL(-1). These results show an increase of sensitivity by five-fold with respect to those not modified, demonstrating a highly sensitive and specific capacitive immunoassay that has a great potential for the use of early diagnosis of cancer disease. PMID:24274298

  12. A traffic analyzer for multiple SpaceWire links

    NASA Astrophysics Data System (ADS)

    Liu, Scige J.; Giusi, Giovanni; Di Giorgio, Anna M.; Vertolli, Nello; Galli, Emanuele; Biondi, David; Farina, Maria; Pezzuto, Stefano; Spinoglio, Luigi

    2014-07-01

    Modern space missions are becoming increasingly complex: the interconnection of the units in a satellite is now a network of terminals linked together through routers, where devices with different level of automation and intelligence share the same data-network. The traceability of the network transactions is performed mostly at terminal level through log analysis and hence it is difficult to verify in real time the reliability of the interconnections and the interchange protocols. To improve and ease the traffic analysis in a SpaceWire network we implemented a low-level link analyzer, with the specific goal to simplify the integration and test phases in the development of space instrumentation. The traffic analyzer collects signals coming from pod probes connected in-series on the interested links between two SpaceWire terminals. With respect to the standard traffic analyzers, the design of this new tool includes the possibility to internally reshape the LVDS signal. This improvement increases the robustness of the analyzer towards environmental noise effects and guarantees a deterministic delay on all analyzed signals. The analyzer core is implemented on a Xilinx FPGA, programmed to decode the bidirectional LVDS signals at Link and Network level. Successively, the core packetizes protocol characters in homogeneous sets of time ordered events. The analyzer provides time-tagging functionality for each characters set, with a precision down to the FPGA Clock, i.e. about 20nsec in the adopted HW environment. The use of a common time reference for each character stream allows synchronous performance measurements. The collected information is then routed to an external computer for quick analysis: this is done via high-speed USB2 connection. With this analyzer it is possible to verify the link performances in terms of induced delays in the transmitted signals. A case study focused on the analysis of the Time-Code synchronization in presence of a SpaceWire Router is

  13. Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers.

    PubMed

    Mrinalini; Thorpe, Roger S; Creer, Simon; Lallias, Delphine; Dawnay, Louise; Stuart, Bryan L; Malhotra, Anita

    2015-11-01

    Using multiple markers and multiple analytical approaches is critical for establishing species boundaries reliably, especially so in the case of cryptic species. Despite development of new and powerful analytical methods, most studies continue to adopt a few, with the choice often being subjective. One such example is routine analysis of Amplified Fragment Length Polymorphism (AFLP) data using population genetic models despite disparity between method assumptions and data properties. The application of newly developed methods for analyzing this dominant marker may not be entirely clear in the context of species delimitation. In this study, we use AFLPs and mtDNA to investigate cryptic speciation in the Trimeresurus macrops complex that belongs to a taxonomically difficult lineage of Asian pitvipers. We analyze AFLPs using population genetic, phylogenetic, multivariate statistical, and Bayes Factor Delimitation methods. A gene tree from three mtDNA markers provided additional evidence. Our results show that the inferences about species boundaries that can be derived from population genetic analysis of AFLPs have certain limitations. In contrast, four multivariate statistical analyses produced clear clusters that are consistent with each other, as well as with Bayes Factor Delimitation results, and with mtDNA and total evidence phylogenies. Furthermore, our results concur with allopatric distributions and patterns of variation in individual morphological characters previously identified in the three proposed species: T. macrops sensu stricto, T. cardamomensis, and T. rubeus. Our study provides evidence for reproductive isolation and genetic distinctiveness that define these taxa as full species. In addition, we re-emphasize the importance of examining congruence of results from multiple methods of AFLP analysis for inferring species diversity. PMID:26162672

  14. Development of a Multiple-Stage Differential Mobility Analyzer (MDMA)

    SciTech Connect

    Chen, Da-Ren; Cheng, Mengdawn

    2007-01-01

    A new DMA column has been designed with the capability of simultaneously extracting monodisperse particles of different sizes in multiple stages. We call this design a multistage DMA, or MDMA. A prototype MDMA has been constructed and experimentally evaluated in this study. The new column enables the fast measurement of particles in a wide size range, while preserving the powerful particle classification function of a DMA. The prototype MDMA has three sampling stages, capable of classifying monodisperse particles of three different sizes simultaneously. The scanning voltage operation of a DMA can be applied to this new column. Each stage of MDMA column covers a fraction of the entire particle size range to be measured. The covered size fractions of two adjacent stages of the MDMA are designed somewhat overlapped. The arrangement leads to the reduction of scanning voltage range and thus the cycling time of the measurement. The modular sampling stage design of the MDMA allows the flexible configuration of desired particle classification lengths and variable number of stages in the MDMA. The design of our MDMA also permits operation at high sheath flow, enabling high-resolution particle size measurement and/or reduction of the lower sizing limit. Using the tandem DMA technique, the performance of the MDMA, i.e., sizing accuracy, resolution, and transmission efficiency, was evaluated at different ratios of aerosol and sheath flowrates. Two aerosol sampling schemes were investigated. One was to extract aerosol flows at an evenly partitioned flowrate at each stage, and the other was to extract aerosol at a rate the same as the polydisperse aerosol flowrate at each stage. We detail the prototype design of the MDMA and the evaluation result on the transfer functions of the MDMA at different particle sizes and operational conditions.

  15. Analyzing the multiple-target-multiple-agent scenario using optimal assignment algorithms

    SciTech Connect

    Kwok, K.S.; Driessen, B.J.; Phillips, C.A.; Tovey, C.A.

    1997-10-01

    This work considers the problem of maximum utilization of a set of mobile robots with limited sensor-range capabilities and limited travel distances. The robots are initially in random positions. A set of robots properly guards or covers a region if every point within the region is within the effective sensor range of at least one vehicle. The authors wish to move the vehicles into surveillance positions so as to guard or cover a region, while minimizing the maximum distance traveled by any vehicle. This problem can be formulated as an assignment problem, in which they must optimally decide which robot to assign to which slot of a desired matrix of grid points. The cost function is the maximum distance traveled by any robot. Assignment problems can be solved very efficiently. Solutions times for one hundred robots took only seconds on a Silicon Graphics Crimson workstation. The initial positions of all the robots can be sampled by a central base station and their newly assigned positions communicated back to the robots. Alternatively, the robots can establish their own coordinate system with the origin fixed at one of the robots and orientation determined by the compass bearing of another robot relative to this robot. This paper presents example solutions to the multiple-target-multiple-agent scenario using a matching algorithm. Two separate cases with one hundred agents in each were analyzed using this method. They have found these mobile robot problems to be a very interesting application of network optimization methods, and they expect this to be a fruitful area for future research.

  16. Genetic Biodiversity of Italian Olives (Olea europaea) Germplasm Analyzed by SSR Markers

    PubMed Central

    Vendramin, Giuseppe Giovanni; Chiappetta, Adriana

    2014-01-01

    The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l'Agricoltura, Centro di Ricerca per l'Olivicoltura e l'Industria Olearia (CRA-OLI), in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools. PMID:24723801

  17. Genetic markers in the blood of multiple sclerosis patients.

    PubMed

    Marković, S; Bozicević, D; Simić, D; Brzović, Z

    1991-01-01

    Poligenetically determined predisposition to multiple sclerosis (MS) defines the way of immunological reaction to environmental factors and leads to clinically manifest disease. Although the connection between MS and some loci of the HLA system has been established, the hereditary predisposition to MS remains to be elucidated. We determined the phenotypes of monogenic hereditary characteristics linked to the surface of red blood cells that were obtained from 45 MS patients and 458 healthy subjects. The antigens on the erythrocytic surface of the ABO, Rh, MN, Ss, Kell, Kidd, Duffy, P and Lewis system were analyzed. Our results demonstrate that the MS patients differ from the normal subjects with regard to the Rh, ABO and Lewis erythrocytic antigens. The Rh positive factor was present in 95.55% of the MS patients compared to 84.29% of the controls, whereas the Rh negative factor was found in only 4.45% of the MS patients and 15.71% of the healthy subjects. The blood group O was demonstrated in 22.22% of the MS patients compared to 40.42% of the healthy persons. The MS patients had the blood group A in 15.11% of the cases as opposed to 43.99% of the subjects in the control groups. The blood group B was found in 22.22% of the MS patients compared to 11.10% of the controls. The distribution of the Lewis system in the MS patients was also demonstrated to be different from that in the general population. The MS patients were found to have less frequently the Le a+b- phenotype (11.12%) and more frequently Le a- b- (13.33%) compared to the healthy subjects who had the Le a+b- phenotype in 12.00% of the cases and Le a- b- in 5.00%.

  18. [Cloning and analyzing of the female-specific marker in the dioecious species Asparagus officinalis L].

    PubMed

    Lu, Long Dou; Li, Rui Li; Gao, Wu Jun; Deng, Chuan Liang; Wang, Lian Jun

    2006-06-01

    Sex-linked molecular markers are being obtained, which would be essential to be used in the screening of different sex of dioecious plants at the seedling stage. Furthermore, it is important in cloning the gene related to the sex. In this study the random amplified polymorphic DNA (RAPD) technique was employed with the objective to find markers linked to sex determination in Asparagus. A total of 100 primers were tested with the same PCR cycling procedure. A female-associated fragment with a length of about 867bp was generated with S12 primer. The fragment was cloned and sequenced, showing it is abundant in AT and contains 2 shorter open reading frames. In order to convert the RAPD marker into SCAR (sequence characterized amplified regions) marker, 24bp specific primers were constructed and used for PCR amplifying. The female-linked dominant SCAR marker was obtained, which would be efficient to identify the different sex of Asparagus officinalis L. PMID:16944605

  19. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

    PubMed

    Bálint, Miklós; Bahram, Mohammad; Eren, A Murat; Faust, Karoline; Fuhrman, Jed A; Lindahl, Björn; O'Hara, Robert B; Öpik, Maarja; Sogin, Mitchell L; Unterseher, Martin; Tedersoo, Leho

    2016-09-01

    With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.

  20. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

    PubMed

    Bálint, Miklós; Bahram, Mohammad; Eren, A Murat; Faust, Karoline; Fuhrman, Jed A; Lindahl, Björn; O'Hara, Robert B; Öpik, Maarja; Sogin, Mitchell L; Unterseher, Martin; Tedersoo, Leho

    2016-09-01

    With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology. PMID:27358393

  1. Comparative usefulness of inflammatory markers to indicate bacterial infection-analyzed according to blood culture results and related clinical factors.

    PubMed

    Nishikawa, Hirokazu; Shirano, Michinori; Kasamatsu, Yu; Morimura, Ayumi; Iida, Ko; Kishi, Tomomi; Goto, Tetsushi; Okamoto, Saki; Ehara, Eiji

    2016-01-01

    To assess relationships of inflammatory markers and 2 related clinical factors with blood culture results, we retrospectively investigated inpatients' blood culture and blood chemistry findings that were recorded from January to December 2014 using electronic medical records and analyzed the data of 852 subjects (426 culture-positive and 426 culture-negative). Results suggested that the risk of positive blood culture statistically increased as inflammatory marker levels and the number of related factors increased. Concerning the effectiveness of inflammatory markers, when the outcome definition was also changed for C-reactive protein (CRP), the odds ratio had a similar value, whereas when the outcome definition of blood culture positivity was used for procalcitonin (PCT), the greatest effectiveness of that was detected. Therefore, the current results suggest that PCT is more useful than CRP as an auxiliary indication of bacterial infection.

  2. Cancers Screening in an Asymptomatic Population by Using Multiple Tumour Markers

    PubMed Central

    Wang, Hsin-Yao; Hsieh, Chia-Hsun; Wen, Chiao-Ni; Wen, Ying-Hao

    2016-01-01

    Background Analytic measurement of serum tumour markers is one of commonly used methods for cancer risk management in certain areas of the world (e.g. Taiwan). Recently, cancer screening based on multiple serum tumour markers has been frequently discussed. However, the risk–benefit outcomes appear to be unfavourable for patients because of the low sensitivity and specificity. In this study, cancer screening models based on multiple serum tumour markers were designed using machine learning methods, namely support vector machine (SVM), k-nearest neighbour (KNN), and logistic regression, to improve the screening performance for multiple cancers in a large asymptomatic population. Methods AFP, CEA, CA19-9, CYFRA21-1, and SCC were determined for 20 696 eligible individuals. PSA was measured in men and CA15-3 and CA125 in women. A variable selection process was applied to select robust variables from these serum tumour markers to design cancer detection models. The sensitivity, specificity, positive predictive value (PPV), negative predictive value, area under the curve, and Youden index of the models based on single tumour markers, combined test, and machine learning methods were compared. Moreover, relative risk reduction, absolute risk reduction (ARR), and absolute risk increase (ARI) were evaluated. Results To design cancer detection models using machine learning methods, CYFRA21-1 and SCC were selected for women, and all tumour markers were selected for men. SVM and KNN models significantly outperformed the single tumour markers and the combined test for men. All 3 studied machine learning methods outperformed single tumour markers and the combined test for women. For either men or women, the ARRs were between 0.003–0.008; the ARIs were between 0.119–0.306. Conclusion Machine learning methods outperformed the combined test in analysing multiple tumour markers for cancer detection. However, cancer screening based solely on the application of multiple tumour

  3. Statistical methods for analysis of coordination of chest wall motion using optical reflectance imaging of multiple markers

    NASA Astrophysics Data System (ADS)

    Kenyon, C. M.; Ghezzo, R. H.; Cala, S. J.; Ferrigno, Giancarlo; Pedotti, Antonio; Macklem, P. T.; Rochester, D. F.

    1994-07-01

    To analyze coordination of chest wall motion we have used principle component analysis (PCA) and multiple regression analysis (MRA) with respect to spirometry on the displacements of 93 optical reflective markers placed upon the chest wall (CW). Each marker is tracked at 10 Hz with an accuracy of 0.2 mm in each spatial dimension using the ELITE system (IEEE Trans. Biomed. Eng. 11:943-949, 1985). PCA enables the degree of linear coordination between all of the markers to be assessed using the eigenvectors and eigenvalues of the covariance of the matrix of marker displacements in each dimension against time. Thus the number of linear degrees of freedom (DOF) which contribute more than a particular amount to the total variance can be determined and analyzed. MRA with respect to spirometrically measured lung volume changes enables identification of the CW points whose movement correlates best with lung volume. We have used this analysis to compare a quiet breathing sequence with one where tidal volume was increased fourfold involuntarily and show that the number of DOF with eigenvalues accounting for >5% of the covariance increased from 2 to 3. Also the point whose movement correlated best with lung volume changed from halfway down the lower costal margin to a more lateral point at the level of the bottom of the sternum. This quantification of CW coordination may be useful in analysis and staging of many respiratory disorders and is applicable to any nonrigid body motion where points can be tracked.

  4. Genetic diversity and structure in Asian native goat analyzed by newly developed SNP markers.

    PubMed

    Lin, Bang Zhong; Kato, Taiki; Kaneda, Makoto; Matsumoto, Hirokazu; Sasazaki, Shinji; Mannen, Hideyuki

    2013-08-01

    In the current study, a total of 65 single nucleotide polymorphisms (SNPs) within the intron region were developed in goat (Capra hircus) by utilizing genomic information of cattle and sheep due to poor available genomic information on goat. Using these markers, we carried out genetic diversity and structure analyses for 10 Asian goat populations. The phylogenetic tree and principal components analysis showed good correspondence between clustered populations and their geographic locations. The STRUCTURE software analysis illustrated six divergent genetic structures among 10 populations. Myanmar and Cambodia populations showed high admixture patterns with different ancestry, suggesting genetic introgression into native goat populations. We also investigated the correlation between genetic diversity and geographic distance from a domestication center. This result showed a decreasing trend of genetic diversity according to the distance (P = 0.014). This result supported common consensus that western Asia is one of the centers of origin for modern Asian domestic goat.

  5. Markers

    ERIC Educational Resources Information Center

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  6. Lectin-based glycoproteomics to explore and analyze hepatocellular carcinoma-related glycoprotein markers.

    PubMed

    Dai, Zhi; Zhou, Jian; Qiu, Shuang-Jian; Liu, Yin-Kun; Fan, Jia

    2009-09-01

    More and more new diagnostic biomarkers of hepatocellular carcinoma (HCC) have been found in association with advances in the standardization of 2-DE coupled with MS analysis. However, the diagnosis of HCC is still detected in the late stages of the disease, when treatment options are limited and prognosis is poor. The glycosylation of proteins is known to change in tumor cells during the development of HCC as the result of alterations in the levels of glycosyltransferases, such as increased fucosylation of Golgi Protein 73 and alpha-fetoprotein. These structural changes can influence the function or physiochemical properties of a protein, resulting in abnormal cancer cell behavior. Therefore, identification of HCC-related glycoprotein markers and analysis of glycan structural alterations might assist in the early detection of HCC. Here, we summarize lectin-based glycoproteomic strategies for the discovery of relevant biomarkers of HCC. The carbohydrate-binding specificities of different lectins offer a biological affinity approach that complements existing MS capabilities. These strategies involve the enrichment of glycoproteins or glycopeptides by lectins, followed by releasing carbohydrates with peptide-N-glycosidase F or reductive beta-elimination. The obtained glycopeptides are then identified by automated MS/MS and structural analysis of glycans is performed through modern methods such as quadrupole IT-TOF, MALDI-TOF/TOF and lectin microarray. These strategies will lead to faster and more clinically adaptable tests with greater sensitivity and specificity.

  7. Generating Multiple Imputations for Matrix Sampling Data Analyzed with Item Response Models.

    ERIC Educational Resources Information Center

    Thomas, Neal; Gan, Nianci

    1997-01-01

    Describes and assesses missing data methods currently used to analyze data from matrix sampling designs implemented by the National Assessment of Educational Progress. Several improved methods are developed, and these models are evaluated using an EM algorithm to obtain maximum likelihood estimates followed by multiple imputation of complete data…

  8. Application of ISSR markers to analyze molecular relationships in Iranian jasmine (Jasminum spp.) accessions.

    PubMed

    Ghasemi Ghehsareh, Masood; Salehi, Hassan; Khosh-Khui, Morteza; Niazi, Ali

    2015-01-01

    There are many species of jasmines in different regions of Iran in natural or cultivated form, and there is no information about their genetic status. Therefore, inter-simple sequence repeat (ISSR) analysis was used to evaluate genetic variations of the 53 accessions representing eight species of Jasminum collected from different regions of Iran. A total of 21 ISSR primers were used which generated 981 bands of different sizes. Mean percentage of polymorphic bands was 90.64 %. Maximum resolving power, polymorphic information content average, and marker index values were 21.55, 0.35, and 14.42 for primers of 3, 4, and 3 respectively. The unweighted pair group method with arithmetic mean dendrogram based on Jaccard's coefficients indicated that 53 accessions were divided into two major clusters. The first major cluster was divided into two subclusters; the subcluster A included Jasminum grandiflorum L., J. officinale L., and J. azoricum L. and the subcluster B consisted of three forms of J. sambac L. (single, semi-double, and double flowers). The second major cluster was divided into two subclusters; the first subcluster (C) included J. humile L., J. primulinum Hemsl., J. nudiflorum Lindl. and the second subcluster (D) consisted of J. fruticans L. At the species level, the highest percentage of polymorphism (34.05 %), numbers of effective alleles (1.16), Shannon index (0.151), and Nei's genetic diversity (0.098) were observed in J. officinale. The lowest values of percentage polymorphism (0.011), number of effective alleles (1.009), Shannon index (0.007), and Nei's genetic diversity (0.005) were obtained for J. nudiflorum. Based on pairwise population matrix of Nei's unbiased genetic identity, the highest identity (0.85) was found between J.officinale and J. azoricum and the lowest identity (0.69) was between J. grandiflorum and J. perimulinum. Based on analysis of molecular variance, the amount of genetic variations among the eight populations was 83 %. This study

  9. A Study on Marker Overlapping Control for M2M-Based Augmented Reality Multiple Object Loading Using Bresenham Algorithm

    NASA Astrophysics Data System (ADS)

    Jung, Sungmo; Song, Jae-Gu; Kim, Seoksoo

    The problem of one marker one object loading only available in marker-based augmented reality technology can be solved by PPHT-based augmented reality multiple objects loading technology which detects the same marker in the image and copies at a desirable location. However, since the distance between markers will not be measured in the process of detecting and copying markers, markers can be overlapped and thus the objects would not be augmented. To solve this problem, a circle having the longest radius needs to be created from a focal point of a marker to be copied, so that no object is copied within the confines of the circle. Therefore, a marker overlapping control for M2M-based augmented reality multiple object loading has been studied using Bresenham algorithm.

  10. Cerebrospinal fluid inflammatory markers in patients with multiple sclerosis: a pilot study.

    PubMed

    Matejčíková, Z; Mareš, J; Přikrylová Vranová, H; Klosová, J; Sládková, V; Doláková, J; Zapletalová, J; Kaňovský, P

    2015-02-01

    Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system. Autoimmune inflammation is common in the early stages of MS. This stage is followed by the neurodegenerative process. The result of these changes is axon and myelin breakdown. Although MS is according to McDonald's revised diagnostic criteria primarily a clinical diagnosis, paraclinical investigation methods are an important part in the diagnosis of MS. In common practice, magnetic resonance imaging of the brain and spinal cord, examination of cerebrospinal fluid (CSF) and examination of visual evoked potentials are used. There are an increasing number of studies dealing with biomarkers in CSF and their role in the diagnosis and treatment of MS. We hypothesized that the levels of some markers could be changed in MS in comparison with controls. We studied five inflammatory markers [interleukin-6 (IL-6), interleukin-8, interleukin-10 (IL-10), beta-2-microglobulin, orosomucoid]. CSF and serum levels of inflammatory markers were assessed in 38 patients with newly diagnosed MS meeting McDonald's revised diagnostic criteria and in 28 subjects as a control group (CG). Levels of beta-2-microglobulin and interleukin-8 in CSF were found to be significantly higher in MS patients in comparison to CG (p < 0.001 resp. p = 0.007). No differences in other CSF markers (IL-6, IL-10 and orosomucoid) and serum levels of all markers between both groups were found. The levels of two studied inflammatory markers were found to be increased at the time of first clinical symptoms of MS. Research on the role of inflammatory and neurodegenerative markers in MS should continue. PMID:24894698

  11. Multiple marker screening test: identification of fetal cystic hygroma, hydrops, and sex chromosome aneuploidy.

    PubMed

    Wenstrom, K D; Boots, L R; Cosper, P C

    1996-01-01

    The goal of this study was to determine if the multiple marker screening test (maternal serum alpha-fetoprotein, unconjugated estriol, human chorionic gonadotrophin, and maternal age) detects fetal Turner syndrome or just cystic hygroma/hydrops. Multiple marker screening tests from 4 groups were compared: 1) Turner syndrome with hydrops/ hygroma group (n = 10) = fetuses with cystic hygroma/hydrops and a 45X karyotype, 2) Turner syndrome without hydrops/hygroma (n = 9) = sonographically unremarkable fetal Turner syndrome or Turner mosaic, 3) hydrops group (n = 8) = all cases of fetal cystic hygroma/hydrops excluding Turner syndrome, 4) sex chromosome aneuploidy group (n = 16) = other sonographically normal fetal sex chromosome aneuploidies. Positive screening tests (Down syndrome risk > or = 1:190 or MSAFP > or = 2.5 MOM) were found in 60% (6/10) of the Turner syndrome with hydrops/hygroma group, but only 11% (1/9) of the Turner syndrome without hydrops/hygroma group (P = .04). The incidence of positive screening tests in the Hydrops group was 75% (6/8), while it was only 12.5% (2/16) in the other sex chromosome aneuploidy group. We conclude that the multiple marker screening test identifies fetuses with cystic hygroma/hydrops, and may do so independently of the etiology of the hydrops. PMID:8796763

  12. Multiple mass analysis using an ion trap array (ITA) mass analyzer.

    PubMed

    Yu, Xiao; Chu, Yanqiu; Ling, Xing; Ding, Zhengzhi; Xu, Chongsheng; Ding, Li; Ding, Chuan-Fan

    2013-09-01

    A novel ion trap array (ITA) mass analyzer with six ion trapping and analyzing channels was investigated. It is capable of analyzing multiple samples simultaneously. The ITA was built with several planar electrodes made of stainless steel and 12 identical parallel zirconia ceramic substrates plated with conductive metal layers. Each two of the opposing ceramic electrode plates formed a boundary of an ion trap channel and six identical ion trapping and analyzing channels were placed in parallel without physical electrode between any two adjacent channels. The electric field distribution inside each channel was studied with simulation. The new design took the advantage of high precision machining attributable to the rigidity of ceramic, and the convenience of surface patterning technique. The ITA system was tested by using a two-channel electrospray ionization source, a multichannel simultaneous quadruple ion guide, and two detectors. The simultaneous analysis of two different samples with two adjacent ITA channels was achieved and independent mass spectra were obtained. For each channel, the mass resolution was tested. Additional ion trap functions such as mass-selected ion isolation and collision-induced dissociation (CID) were also tested. The results show that one ITA is well suited for multiple simultaneous mass analyses. PMID:23797864

  13. Multiple Mass Analysis Using an Ion Trap Array (ITA) Mass Analyzer

    NASA Astrophysics Data System (ADS)

    Xiao, Yu; Chu, Yanqiu; Ling, Xing; Ding, Zhengzhi; Xu, Chongsheng; Ding, Li; Ding, Chuan-Fan

    2013-09-01

    A novel ion trap array (ITA) mass analyzer with six ion trapping and analyzing channels was investigated. It is capable of analyzing multiple samples simultaneously. The ITA was built with several planar electrodes made of stainless steel and 12 identical parallel zirconia ceramic substrates plated with conductive metal layers. Each two of the opposing ceramic electrode plates formed a boundary of an ion trap channel and six identical ion trapping and analyzing channels were placed in parallel without physical electrode between any two adjacent channels. The electric field distribution inside each channel was studied with simulation. The new design took the advantage of high precision machining attributable to the rigidity of ceramic, and the convenience of surface patterning technique. The ITA system was tested by using a two-channel electrospray ionization source, a multichannel simultaneous quadruple ion guide, and two detectors. The simultaneous analysis of two different samples with two adjacent ITA channels was achieved and independent mass spectra were obtained. For each channel, the mass resolution was tested. Additional ion trap functions such as mass-selected ion isolation and collision-induced dissociation (CID) were also tested. The results show that one ITA is well suited for multiple simultaneous mass analyses.

  14. PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments

    PubMed Central

    Caffrey, Daniel R; Dana, Paul H; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E; Somaroo, Shyamal; Caffrey, Brian E; Potluri, Shobha; Huang, Enoch S

    2007-01-01

    Background By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Results Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. Conclusion PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function. PMID:17931421

  15. Multiple Small Supernumerary Marker Chromosomes Resulting from Maternal Meiosis I or II Errors

    PubMed Central

    Hochstenbach, Ron; Nowakowska, Beata; Volleth, Marianne; Ummels, Amber; Kutkowska-Kaźmierczak, Anna; Obersztyn, Ewa; Ziemkiewicz, Kamila; Gerloff, Claudia; Schanze, Denny; Zenker, Martin; Muschke, Petra; Schanze, Ina; Poot, Martin; Liehr, Thomas

    2016-01-01

    We present 2 cases with multiple de novo supernumerary marker chromosomes (sSMCs), each derived from a different chromosome. In a prenatal case, we found mosaicism for an sSMC(4), sSMC(6), sSMC(9), sSMC(14) and sSMC(22), while a postnatal case had an sSMC(4), sSMC(8) and an sSMC(11). SNP-marker segregation indicated that the sSMC(4) resulted from a maternal meiosis II error in the prenatal case. Segregation of short tandem repeat markers on the sSMC(8) was consistent with a maternal meiosis I error in the postnatal case. In the latter, a boy with developmental/psychomotor delay, autism, hyperactivity, speech delay, and hypotonia, the sSMC(8) was present at the highest frequency in blood. By comparison to other patients with a corresponding duplication, a minimal region of overlap for the phenotype was identified, with CHRNB3 and CHRNA6 as dosage-sensitive candidate genes. These genes encode subunits of nicotinic acetylcholine receptors (nAChRs). We propose that overproduction of these subunits leads to perturbed component stoichiometries with dominant negative effects on the function of nAChRs, as was shown by others in vitro. With the limitation that in each case only one sSMC could be studied, our findings demonstrate that different meiotic errors lead to multiple sSMCs. We relate our findings to age-related aneuploidy in female meiosis and propose that predivision sister-chromatid separation during meiosis I or II, or both, may generate multiple sSMCs. PMID:26997941

  16. Sum statistics for the joint detection of multiple disease loci in case-control association studies with SNP markers.

    PubMed

    Wille, Anja; Hoh, Josephine; Ott, Jurg

    2003-12-01

    In complex traits, multiple disease loci presumably interact to produce the disease. For this reason, even with high-resolution single nucleotide polymorphism (SNP) marker maps, it has been difficult to map susceptibility loci by conventional locus-by-locus methods. Fine mapping strategies are needed that allow for the simultaneous detection of interacting disease loci while handling large numbers of densely spaced markers. For this purpose, sum statistics were recently proposed as a first-stage analysis method for case-control association studies with SNPs. Via sums of single-marker statistics, information over multiple disease-associated markers is combined and, with a global significance value alpha, a small set of "interesting" markers is selected for further analysis. Here, the statistical properties of such approaches are examined by computer simulation. It is shown that sum statistics can often be successfully applied when marker-by-marker approaches fail to detect association. Compared with Bonferroni or False Discovery Rate (FDR) procedures, sum statistics have greater power, and more disease loci can be detected. However, in studies with tightly linked markers, simple sum statistics can be suboptimal, since the intermarker correlation is ignored. A method is presented that takes the correlation structure among marker loci into account when marker statistics are combined.

  17. Analyzing Multiple Informant Data from an Evaluation of the Health Disparities Collaboratives

    PubMed Central

    James O'Malley, A; Landon, Bruce E; Guadagnoli, Edward

    2007-01-01

    Objective To use multivariate regression methods to analyze simultaneously data obtained from multiple respondents or data sources (informants) at health centers. Data Source Surveys of executive directors, medical directors, and providers from 65 community health centers (176 informants) who participated in an evaluation of the Health Disparities Collaboratives. Study Design Cross-sectional survey of staff at the health centers during 2003–2004. Statistical Methods In order to illustrate this method, we analyze the association between informants' assessments of the culture of the center and participation in the collaborative, and the association between computer availability and the effort made by management to improve the quality of the care and services at their center. Multivariate regression models are used to pool information across informants while accounting for informant-specific effects and retaining informants in the analysis even if the data from some of them are missing. The results are compared with those obtained by traditional methods that use data from a single informant or average over informants' ratings. Findings In both the Collaborative participation and quality improvement efforts analyses, the multivariate regression multiple informants' analysis found significant effects and differences between informants that traditional methods failed to find. Participating centers emphasized developmental (entrepreneurship, innovation, risk-taking) and rational culture. The effect of hierarchical culture (stability and bureaucracy) on participation depended on the informant; executive directors and medical providers were the most discrepant. In centers that participated in the Collaborative, the availability of computers was positively associated with the effort that management made toward improving quality. Conclusions The multiple informants model provided the most precise estimates and alerts users to differential effects across informants. Because

  18. Analysis of multiple enteric viral targets as sewage markers in coral reefs

    USGS Publications Warehouse

    Lipp, Erin K.; Futch, J. Carrie; Griffin, Dale W.

    2007-01-01

    Water and coral mucus samples were collected from throughout the Florida Keys National Marine Sanctuary and the Dry Tortugas for three years and were analyzed for human enteric viruses (enteroviruses, noroviruses, hepatitis A virus and adenoviruses) as conservative markers of human sewage using molecular methods. Of the 100 coral and water samples collected, 40 contained genetic material from one or more human enteric viruses. DNA-based adenoviruses were detected widely, in 37.8% of samples and at 91% of stations, including ‘pristine’ reefs in the Dry Tortugas; however, the detection rate was ⩽12% for the RNA-based enteroviruses and noroviruses (hepatitis A virus was never detected). The disparity between the prevalence of RNA- and DNA-based viruses suggests the need for additional work to determine the utility of adenovirus as marker of human sewage.

  19. Asymmetric signal amplification for simultaneous SERS detection of multiple cancer markers with significantly different levels.

    PubMed

    Ye, Sujuan; Wu, Yanying; Zhai, Xiaomo; Tang, Bo

    2015-08-18

    Simultaneous detection of cancer biomarkers holds great promise for the early diagnosis of different cancers. However, in the presence of high-concentration biomarkers, the signals of lower-expression biomarkers are overlapped. Existing techniques are not suitable for simultaneously detecting multiple biomarkers at concentrations with significantly different orders of magnitude. Here, we propose an asymmetric signal amplification method for simultaneously detecting multiple biomarkers with significantly different levels. Using the bifunctional probe, a linear amplification mode responds to high-concentration markers, and quadratic amplification mode responds to low-concentration markers. With the combined biobarcode probe and hybridization chain reaction (HCR) amplification method, the detection limits of microRNA (miRNA) and ATP via surface-enhanced Raman scattering (SERS) detection are 0.15 fM and 20 nM, respectively, with a breakthrough of detection concentration difference over 11 orders of magnitude. Furthermore, successful determination of miRNA and ATP in cancer cells supports the practicability of the assay. This methodology promises to open an exciting new avenue for the detection of various types of biomolecules. PMID:26218034

  20. Twice-weighted multiple interval estimation of a marginal structural model to analyze cost-effectiveness.

    PubMed

    Goldfeld, K S

    2014-03-30

    Cost-effectiveness analysis is an important tool that can be applied to the evaluation of a health treatment or policy. When the observed costs and outcomes result from a nonrandomized treatment, making causal inference about the effects of the treatment requires special care. The challenges are compounded when the observation period is truncated for some of the study subjects. This paper presents a method of unbiased estimation of cost-effectiveness using observational study data that is not fully observed. The method-twice-weighted multiple interval estimation of a marginal structural model-was developed in order to analyze the cost-effectiveness of treatment protocols for advanced dementia residents living nursing homes when they become acutely ill. A key feature of this estimation approach is that it facilitates a sensitivity analysis that identifies the potential effects of unmeasured confounding on the conclusions concerning cost-effectiveness.

  1. IPAT: a freely accessible software tool for analyzing multiple patent documents with inbuilt landscape visualizer.

    PubMed

    Ajay, Dara; Gangwal, Rahul P; Sangamwar, Abhay T

    2015-01-01

    Intelligent Patent Analysis Tool (IPAT) is an online data retrieval tool, operated based on text mining algorithm to extract specific patent information in a predetermined pattern into an Excel sheet. The software is designed and developed to retrieve and analyze technology information from multiple patent documents and generate various patent landscape graphs and charts. The software is C# coded in visual studio 2010, which extracts the publicly available patent information from the web pages like Google Patent and simultaneously study the various technology trends based on user-defined parameters. In other words, IPAT combined with the manual categorization will act as an excellent technology assessment tool in competitive intelligence and due diligence for predicting the future R&D forecast.

  2. IPAT: a freely accessible software tool for analyzing multiple patent documents with inbuilt landscape visualizer.

    PubMed

    Ajay, Dara; Gangwal, Rahul P; Sangamwar, Abhay T

    2015-01-01

    Intelligent Patent Analysis Tool (IPAT) is an online data retrieval tool, operated based on text mining algorithm to extract specific patent information in a predetermined pattern into an Excel sheet. The software is designed and developed to retrieve and analyze technology information from multiple patent documents and generate various patent landscape graphs and charts. The software is C# coded in visual studio 2010, which extracts the publicly available patent information from the web pages like Google Patent and simultaneously study the various technology trends based on user-defined parameters. In other words, IPAT combined with the manual categorization will act as an excellent technology assessment tool in competitive intelligence and due diligence for predicting the future R&D forecast. PMID:26452016

  3. Cytogenetic abnormality in patients with multiple myeloma analyzed by fluorescent in situ hybridization

    PubMed Central

    Hu, Ying; Chen, Wenming; Chen, Shilun; Huang, Zhongxia

    2016-01-01

    Objective To analyze the fluorescent in situ hybridization (FISH) data and the association with clinical characteristics, therapy response, and survival time in patients with multiple myeloma. Method We performed a retrospective review of patients with multiple myeloma from November 2010 to April 2014. Results Cytogenetic abnormalities by FISH were detectable in 66% of patients. One cytogenetic abnormality, two cytogenetic abnormalities, and complex abnormalities were detectable in 21.2%, 51.5%, and 27.3% of cases, respectively. 1q21 amplification, t(4p16.3/14q32), and 17p deletion were observed in 69.7%, 30.3%, and 21.2% of cases, respectively. Total response rates (complete response [CR] + near CR + partial response) were 93.8% and 82.1%, respectively, in cytogenetic normality group and abnormality group. CR rates were 50% and 32.1%, respectively. Median overall survival (OS) time was 51 months and 24 months, respectively, in cytogenetic normality group and abnormality group (P<0.05). Median OS time was not significantly different between 1q21 amplification group and no 1q21 amplification group in patients with FISH abnormalities (P>0.05). Median OS time was not significantly different between t(4;14) group and no t(4;14) group in patients with FISH abnormalities (P>0.05). Seven patients of 17p deletion died in 2 years. Conclusion Multiple myeloma is characterized by a high occurrence of chromosomal aberrations. 1q21 amplification and t(4;14) are the most common abnormalities. Multiple cytogenetic abnormalities are frequently observed in the same one patient. The total response rate, CR rate, and OS time are worse in cytogenetic abnormal patients compared with cytogenetic normal patients. Patients with 17p deletion have a very poor prognosis. Future goals of therapy will be to achieve minimal residual disease, biomarkers, and genomic data, which might provide a better estimate of the depth of response to therapy and OS. PMID:27042105

  4. Multiple template-based fluoroscopic tracking of lung tumor mass without implanted fiducial markers

    NASA Astrophysics Data System (ADS)

    Cui, Ying; Dy, Jennifer G.; Sharp, Gregory C.; Alexander, Brian; Jiang, Steve B.

    2007-10-01

    Precise lung tumor localization in real time is particularly important for some motion management techniques, such as respiratory gating or beam tracking with a dynamic multi-leaf collimator, due to the reduced clinical tumor volume (CTV) to planning target volume (PTV) margin and/or the escalated dose. There might be large uncertainties in deriving tumor position from external respiratory surrogates. While tracking implanted fiducial markers has sufficient accuracy, this procedure may not be widely accepted due to the risk of pneumothorax. Previously, we have developed a technique to generate gating signals from fluoroscopic images without implanted fiducial markers using a template matching method (Berbeco et al 2005 Phys. Med. Biol. 50 4481-90, Cui et al 2007 Phys. Med. Biol. 52 741-55). In this paper, we present an extension of this method to multiple-template matching for directly tracking the lung tumor mass in fluoroscopy video. The basic idea is as follows: (i) during the patient setup session, a pair of orthogonal fluoroscopic image sequences are taken and processed off-line to generate a set of reference templates that correspond to different breathing phases and tumor positions; (ii) during treatment delivery, fluoroscopic images are continuously acquired and processed; (iii) the similarity between each reference template and the processed incoming image is calculated; (iv) the tumor position in the incoming image is then estimated by combining the tumor centroid coordinates in reference templates with proper weights based on the measured similarities. With different handling of image processing and similarity calculation, two such multiple-template tracking techniques have been developed: one based on motion-enhanced templates and Pearson's correlation score while the other based on eigen templates and mean-squared error. The developed techniques have been tested on six sequences of fluoroscopic images from six lung cancer patients against the reference

  5. Multiple template-based fluoroscopic tracking of lung tumor mass without implanted fiducial markers.

    PubMed

    Cui, Ying; Dy, Jennifer G; Sharp, Gregory C; Alexander, Brian; Jiang, Steve B

    2007-10-21

    Precise lung tumor localization in real time is particularly important for some motion management techniques, such as respiratory gating or beam tracking with a dynamic multi-leaf collimator, due to the reduced clinical tumor volume (CTV) to planning target volume (PTV) margin and/or the escalated dose. There might be large uncertainties in deriving tumor position from external respiratory surrogates. While tracking implanted fiducial markers has sufficient accuracy, this procedure may not be widely accepted due to the risk of pneumothorax. Previously, we have developed a technique to generate gating signals from fluoroscopic images without implanted fiducial markers using a template matching method (Berbeco et al 2005 Phys. Med. Biol. 50 4481-90, Cui et al 2007 Phys. Med. Biol. 52 741-55). In this paper, we present an extension of this method to multiple-template matching for directly tracking the lung tumor mass in fluoroscopy video. The basic idea is as follows: (i) during the patient setup session, a pair of orthogonal fluoroscopic image sequences are taken and processed off-line to generate a set of reference templates that correspond to different breathing phases and tumor positions; (ii) during treatment delivery, fluoroscopic images are continuously acquired and processed; (iii) the similarity between each reference template and the processed incoming image is calculated; (iv) the tumor position in the incoming image is then estimated by combining the tumor centroid coordinates in reference templates with proper weights based on the measured similarities. With different handling of image processing and similarity calculation, two such multiple-template tracking techniques have been developed: one based on motion-enhanced templates and Pearson's correlation score while the other based on eigen templates and mean-squared error. The developed techniques have been tested on six sequences of fluoroscopic images from six lung cancer patients against the reference

  6. Fingolimod modulates multiple neuroinflammatory markers in a mouse model of Alzheimer’s disease

    PubMed Central

    Aytan, Nurgul; Choi, Ji-Kyung; Carreras, Isabel; Brinkmann, Volker; Kowall, Neil W.; Jenkins, Bruce G.; Dedeoglu, Alpaslan

    2016-01-01

    Sphingosine 1-phosphate (SP1) receptors may be attractive targets for modulation of inflammatory processes in neurodegenerative diseases. Recently fingolimod, a functional S1P1 receptor antagonist, was introduced for treatment of multiple sclerosis. We postulated that anti-inflammatory mechanisms of fingolimod might also be protective in Alzheimer’s disease (AD). Therefore, we treated a mouse model of AD, the 5xFAD model, with two doses of fingolimod (1 and 5 mg/kg/day) and measured the response of numerous markers of Aβ pathology as well as inflammatory markers and neurochemistry using biochemical, immunohistochemistry and high resolution magic angle spinning magnetic resonance spectroscopy (MRS). In mice at 3 months of age, we found that fingolimod decreased plaque density as well as soluble plus insoluble Aβ measured by ELISA. Fingolimod also decreased GFAP staining and the number of activated microglia. Taurine has been demonstrated to play a role as an endogenous anti-inflammatory molecule. Taurine levels, measured using MRS, showed a very strong inverse correlation with GFAP levels and ELISA measurements of Aβ, but not with plaque density or activated microglia levels. MRS also showed an effect of fingolimod on glutamate levels. Fingolimod at 1 mg/kg/day provided better neuroprotection than 5 mg/kg/day. Together, these data suggest a potential therapeutic role for fingolimod in AD. PMID:27117087

  7. A new scoring system using multiple immunohistochemical markers for diagnosis of uterine smooth muscle tumors

    PubMed Central

    Rath-Wolfson, Lea; Rosenblat, Yevgenia; Halpern, Marisa; Herbert, M; Hammel, I; Gal, Rivka; Leabu, M; Koren, Rumelia

    2006-01-01

    The diagnosis of uterine smooth muscle neoplasms by light microscopy is difficult. Multiple classification schemes have been proposed based on mitotic rate, nuclear atypia, and the presence or absence of necrosis. None of these classification systems has been entirely successful. This study was undertaken to evaluate the use of selected immunohistochemical and histochemical markers in differentiating these tumors, in addition to accepted morphologic criteria. Ten cases of each of the following: leiomyosarcomas (LMS), atypical leiomyomas (AL), cellular leiomyomas (CL) and usual leiomyomas (UL), were classically evaluated for histological diagnosis and were stained for Ki-67 (MIB-1), bcl-2 and p53 using monoclonal antibodies and the avidin-biotin peroxidase method, and argyrophilic nucleolar organizer region (AgNORs). The number of stained cells was counted in the most positively stained region in a 4 mm2 square cover glass mounted on each slide. The mean value was calculated for each group of tumors. The data for Ki-67 (MIB-1), bcl-2, p53 and AgNOR staining respectively, were significantly higher in LMS by comparison to UL, CL or AL. Because many singular cases had superimposed data being difficult to diagnose, a new scoring system for pathological evaluation was created. The results obtained by this scoring system suggest that immunohistochemical markers Ki-67 (MIB-1), bcl-2, p53 together with the AgNOR staining could be useful, by the scoring system, as an adjunct to the current accepted morphologic criteria in differentiating smooth muscle tumors of the uterus. PMID:16563231

  8. Investigation of oxidative balance in patients with dysmenorrhea by multiple serum markers

    PubMed Central

    Turhan, Nilgün; Çelik, Havva; Duvan, Candan İltemir; Onaran, Yüksel; Aydın, Murat; Armutcu, Ferah

    2012-01-01

    Objective: To investigate the level of oxidative stress in patients with dysmenorrhea by multiple serum markers including malondialdehyde (MDA), nitrotyrosine (3-NT), deoxyguanosine (8-OHdG) and superoxide dismutase (SOD). Material and Methods: Fifty-eight women, aged between 20 and 34, who had had regular menses for at least six previous cycles, were involved. The women were divided into two groups. The study group consisted of 33 patients with primary dysmenorrhea, and the control group consisted of 25 healthy women. Results: Demographic characteristics of patients were similar between the two groups. The serum MDA levels were 1.32±0.46 and 0.91±0.26 nmol/mL for the dysmenorrhea and control groups, respectively (p<0.001). The differences in plasma levels of 3-NT, SOD and serum 8-OhdG were similar in both groups (p>0.05). Also, no correlation was found between the severity of dysmenorrhea and the levels of oxidative markers. Conclusion: Oxidative stress is slightly aggravated in patients with dysmenorrhea. PMID:24592048

  9. A discrimination index for selecting markers of tumor growth dynamic across multiple cancer studies with a cure fraction.

    PubMed

    Rouam, Sigrid; Broët, Philippe

    2013-08-01

    To identify genomic markers with consistent effect on tumor dynamics across multiple cancer series, discrimination indices based on proportional hazards models can be used since they do not depend heavily on the sample size. However, the underlying assumption of proportionality of the hazards does not always hold, especially when the studied population is a mixture of cured and uncured patients, like in early-stage cancers. We propose a novel index that quantifies the capability of a genomic marker to separate uncured patients, according to their time-to-event outcomes. It allows to identify genomic markers characterizing tumor growth dynamic across multiple studies. Simulation results show that our index performs better than classical indices based on the Cox model. It is neither affected by the sample size nor the cure rate fraction. In a cross-study of early-stage breast cancers, the index allows to select genomic markers with a potential consistent effect on tumor growth dynamics.

  10. Reassessment of Blood Gene Expression Markers for the Prognosis of Relapsing-Remitting Multiple Sclerosis

    PubMed Central

    Hecker, Michael; Paap, Brigitte Katrin; Goertsches, Robert Hermann; Kandulski, Ole; Fatum, Christian; Koczan, Dirk; Hartung, Hans-Peter; Thiesen, Hans-Juergen; Zettl, Uwe Klaus

    2011-01-01

    Despite considerable advances in the treatment of multiple sclerosis, current drugs are only partially effective. Most patients show reduced disease activity with therapy, but still experience relapses, increasing disability, and new brain lesions. Since there are no reliable clinical or biological markers of disease progression, long-term prognosis is difficult to predict for individual patients. We identified 18 studies that suggested genes expressed in blood as predictive biomarkers. We validated the prognostic value of those genes with three different microarray data sets comprising 148 patients in total. Using these data, we tested whether the genes were significantly differentially expressed between patients with good and poor courses of the disease. Poor progression was defined by relapses and/or increase of disability during a two-year follow-up, independent of the administered therapy. Of 110 genes that have been proposed as predictive biomarkers, most could not be confirmed in our analysis. However, the G protein-coupled membrane receptor GPR3 was expressed at significantly lower levels in patients with poor disease progression in all data sets. GPR3 has therefore a high potential to be a biomarker for predicting future disease activity. In addition, we examined the IL17 cytokines and receptors in more detail and propose IL17RC as a new, promising, transcript-based biomarker candidate. Further studies are needed to better understand the roles of these receptors in multiple sclerosis and its treatment and to clarify the utility of GPR3 and IL17RC expression levels in the blood as markers of long-term prognosis. PMID:22216338

  11. Analyzing Multiple-Choice Questions by Model Analysis and Item Response Curves

    NASA Astrophysics Data System (ADS)

    Wattanakasiwich, P.; Ananta, S.

    2010-07-01

    In physics education research, the main goal is to improve physics teaching so that most students understand physics conceptually and be able to apply concepts in solving problems. Therefore many multiple-choice instruments were developed to probe students' conceptual understanding in various topics. Two techniques including model analysis and item response curves were used to analyze students' responses from Force and Motion Conceptual Evaluation (FMCE). For this study FMCE data from more than 1000 students at Chiang Mai University were collected over the past three years. With model analysis, we can obtain students' alternative knowledge and the probabilities for students to use such knowledge in a range of equivalent contexts. The model analysis consists of two algorithms—concentration factor and model estimation. This paper only presents results from using the model estimation algorithm to obtain a model plot. The plot helps to identify a class model state whether it is in the misconception region or not. Item response curve (IRC) derived from item response theory is a plot between percentages of students selecting a particular choice versus their total score. Pros and cons of both techniques are compared and discussed.

  12. 21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple...

  13. 21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple...

  14. 21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple...

  15. 21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple...

  16. 21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple...

  17. Comparison of gSSR and EST-SSR markers for analyzing genetic variability among tomato cultivars (Solanum lycopersicum L.).

    PubMed

    Zhou, R; Wu, Z; Jiang, F L; Liang, M

    2015-10-27

    In order to study genetic variability and develop better strategies for the utilization of 48 tomato cultivars from America, China, the Netherlands, and Portugal, genomic simple sequence repeat (gSSR) and EST-derived SSR (EST-SSR) markers were applied. In all, 15 of 82 gSSR and 18 of 115 EST-SSR markers showed polymorphic loci. There were 995 and 2072 clear fragments amplified by polymorphic gSSR and EST-SSR markers, respectively. The total and average number of alleles detected by EST-SSRs (75, 4.2) was more than gSSRs (54, 3.6) as a result of some multi-locus EST-SSRs. A lower polymorphism information content value was found in gSSRs (0.529) compared to EST-SSRs (0.620). Similarity coefficient matrixes of the 48 tomato cultivars were established based on the gSSRs and EST-SSRs, and UPGMA dendrograms were constructed from the gSSRs and EST-SSRs similarity coefficient matrixes. A high similarity was observed between the gSSRs and EST-SSRs dendrograms. Genetic variability of four tomato populations from different countries showed that the observed number of alleles and Nei's genetic diversity were highest in the American population, and the effective number of alleles was highest in the Dutch population. The estimated genetic structure showed some tomato cultivars from different countries shared a common genetic background, which might be related to gene flow. It was inferred that both gSSR and EST-SSR markers were effective to assess genetic variability of tomato cultivars, and the combination of both markers could be more effective for genetic diversity analysis in tomato.

  18. Effects of ivermectin on Danio rerio: a multiple endpoint approach: behaviour, weight and subcellular markers.

    PubMed

    Domingues, I; Oliveira, R; Soares, A M V M; Amorim, M J B

    2016-04-01

    Ivermectin (IVM) is a broad acting antihelmintic used in various veterinary pharmaceuticals. It has been shown that IVM enters the aquatic compartment and adversely affects organisms including fish. This study is based on the hypothesis that long term exposure to IVM affects fish and thus, the main objective was to assess the chronic effects of 0.25 and 25 µg IVM/L to zebrafish using multiple endpoints representative of several levels of biological organization: weight, behaviour (swimming and feeding) and subcellular markers including biomarkers for oestrogenicity (vitellogenin-VTG), oxidative stress (catalase-CAT and glutathione-S-transferase-GST) and neurotransmission (cholinesterase-ChE). Concentrations as low as 0.25 µg IVM/L disrupted the swimming behaviour, causing fish to spend more time at the bottom of aquaria. Such reduction of the swimming performance affected the feeding ability which is likely responsible for the weight loss. The effects on weight were gender differentiated, being more pronounced in males (0.25 µg IVM/L) than in females (25 µg IVM/L). Fish exposed to 25 µg/L exhibited darker coloration and mild curvature of the spine. No effects on VTG and AChE were observed, but a reduction on CAT and GST levels was observed in fish exposed to 25 µg IVM/L, although these alterations probably only reflect the general condition of the fish which was significantly compromised at this concentration. Despite that predicted environmental concentrations of IVM are below 0.25 µg/L, the behavioural effects may be translated into important ecological impacts, e.g. at predator-prey interactions where fish competitive advantage can be decreased. Future work should address the link between behaviour disruption and population fitness. The current study was based on a one experiment and multiple endpoint (anchored) approach, allowing the results to be integrated and linked towards a mechanistic understanding.

  19. [Cutaneous lesion associated with multiple endocrine neoplasms type 2A (Sipple's syndrome). An early clinical marker].

    PubMed

    Chabre, O; Labat-Moleur, F; Berthod, F; Tarel, V; Stoebner, P; Sobol, H; Bachelot, I

    1992-02-22

    We report the association of a cutaneous lesion with multiple endocrine neoplasia type 2A (MEN 2A) in three patients from a French family. These lesions are very similar to those previously described in an Italian and an American MEN 2A family and called cutaneous lichen amyloidosis. In all three families the patients presented with a pruritic and pigmented cutaneous lesion localized unilaterally on the upper back. However, in the French family the patients also complained of paroxysmal pain in the same area, in which we could elicit a touch hypoesthesia and pain hyperesthesia. Such an association of cutaneous and neurological features in the upper back is known as Notalgia Paresthetica (NP). NP is believed to represent a neuropathy of the posterior dorsal nerve rami. Unlike the two previously reported families, the histological, immunohistochemical and ultrastructural analysis of the skin biopsies of the French patients did not show any amyloid material. This suggests that the presence of amyloid may not be a constant feature of the cutaneous lesions associated with MEN 2A. We consider these lesions as a form of dorsal neuropathy rather than a cutaneous lichen amyloidosis. Whatever their origin, these cutaneous lesion usually precede the appearance of the neoplastic lesions of MEN 2A. They may act as an early clinical marker that must be searched for in each subject at risk for MEN 2A. In addition, all patients presenting with NP should be screened for MEN 2A. PMID:1348355

  20. Nonparametric Tests for Analyzing Interactions among Intra-Block Ranks in Multiple Group Repeated Measures Designs.

    ERIC Educational Resources Information Center

    Beasley, T. Mark

    2000-01-01

    Developed an extension of the Hollander and Sethuraman (M. Hollander and J. Sethuraman, 1978) statistic (B squared) for testing discordance among intra-block rankings of K elements for multiple groups of raters. Simulation results confirmed the usefulness of B squared as an omnibus test of interaction among intra-block ranks and demonstrated its…

  1. What Is Wrong with ANOVA and Multiple Regression? Analyzing Sentence Reading Times with Hierarchical Linear Models

    ERIC Educational Resources Information Center

    Richter, Tobias

    2006-01-01

    Most reading time studies using naturalistic texts yield data sets characterized by a multilevel structure: Sentences (sentence level) are nested within persons (person level). In contrast to analysis of variance and multiple regression techniques, hierarchical linear models take the multilevel structure of reading time data into account. They…

  2. Explorative Function in Williams Syndrome Analyzed through a Large-Scale Task with Multiple Rewards

    ERIC Educational Resources Information Center

    Foti, F.; Petrosini, L.; Cutuli, D.; Menghini, D.; Chiarotti, F.; Vicari, S.; Mandolesi, L.

    2011-01-01

    This study aimed to evaluate spatial function in subjects with Williams syndrome (WS) by using a large-scale task with multiple rewards and comparing the spatial abilities of WS subjects with those of mental age-matched control children. In the present spatial task, WS participants had to explore an open space to search nine rewards placed in…

  3. Combining versus Analyzing Multiple Causes: How Domain Assumptions and Task Context Affect Integration Rules

    ERIC Educational Resources Information Center

    Waldmann, Michael R.

    2007-01-01

    In everyday life, people typically observe fragments of causal networks. From this knowledge, people infer how novel combinations of causes they may never have observed together might behave. I report on 4 experiments that address the question of how people intuitively integrate multiple causes to predict a continuously varying effect. Most…

  4. Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology.

    PubMed

    Mramba, Lazarus K; Barber, Stuart; Hommola, Kerstin; Dyer, Lee A; Wilson, Joseph S; Forister, Matthew L; Gilks, Walter R

    2013-12-01

    There is a need for a reliable statistical test which is appropriate for assessing cospeciation of more than two phylogenies. We have developed an algorithm using a permutation method that can be used to test for and infer tri-trophic evolutionary relationships of organisms given both their phylogenies and pairwise interactions. An overall statistic has been developed based on the dominant eigenvalue of a covariance matrix, and compared to values of the statistic computed when tree labels are permuted. The resulting overall p-value is used to test for the presence or absence of cospeciation in a tri-trophic system. If cospeciation is detected, we propose new test statistics based on partial correlations to uncover more details about the relationships between multiple phylogenies. One of the strengths of our method is that it allows more parasites than hosts or more hosts than parasites, with multiple associations and more than one parasite attached to a host (or one parasite attached to multiple hosts). The new method does not require any parametric assumptions of the distribution of the data, and unlike the old methods, which utilize several pairwise steps, the overall statistic used is obtained in one step. We have applied our method to two published datasets where we obtained detailed information about the strength of associations among species with calculated partial p-values and one overall p-value from the dominant eigenvalue test statistic. Our permutation method produces reliable results with a clear procedure and statistics applied in an intuitive manner. Our algorithm is useful in testing evidence for three-way cospeciation in multiple phylogenies with tri-trophic associations and determining which phylogenies are involved in cospeciation. PMID:24114867

  5. Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies.

    PubMed

    Gallagher, William M; Bergin, Orla E; Rafferty, Mairin; Kelly, Zoë D; Nolan, Ilse-Maria; Fox, Edward J P; Culhane, Aedin C; McArdle, Linda; Fraga, Mario F; Hughes, Linda; Currid, Caroline A; O'Mahony, Fiona; Byrne, Aileen; Murphy, Alison A; Moss, Catherine; McDonnell, Susan; Stallings, Raymond L; Plumb, Jane A; Esteller, Manel; Brown, Robert; Dervan, Peter A; Easty, David J

    2005-11-01

    The incidence of melanoma is increasing rapidly, with advanced lesions generally failing to respond to conventional chemotherapy. Here, we utilized DNA microarray-based gene expression profiling techniques to identify molecular determinants of melanoma progression within a unique panel of isogenic human melanoma cell lines. When a poorly tumorigenic cell line, derived from an early melanoma, was compared with two increasingly aggressive derivative cell lines, the expression of 66 genes was significantly changed. A similar pattern of differential gene expression was found with an independently derived metastatic cell line. We further examined these melanoma progression-associated genes via use of a tailored TaqMan Low Density Array (LDA), representing the majority of genes within our cohort of interest. Considerable concordance was seen between the transcriptomic profiles determined by DNA microarray and TaqMan LDA approaches. A range of novel markers were identified that correlated here with melanoma progression. Most notable was TSPY, a Y chromosome-specific gene that displayed extensive down-regulation in expression between the parental and derivative cell lines. Examination of a putative CpG island within the TSPY gene demonstrated that this region was hypermethylated in the derivative cell lines, as well as metastatic melanomas from male patients. Moreover, treatment of the derivative cell lines with the DNA methyltransferase inhibitor, 2'-deoxy-5-azacytidine (DAC), restored expression of the TSPY gene to levels comparable with that found in the parental cells. Additional DNA microarray studies uncovered a subset of 13 genes from the above-mentioned 66 gene cohort that displayed re-activation of expression following DAC treatment, including TSPY, CYBA and MT2A. DAC suppressed tumor cell growth in vitro. Moreover, systemic treatment of mice with DAC attenuated growth of melanoma xenografts, with consequent re-expression of TSPY mRNA. Overall, our data support

  6. PL1 fusion gene: a novel visual selectable marker gene that confers tolerance to multiple abiotic stresses in transgenic tomato.

    PubMed

    Jin, Feng; Li, Shu; Dang, Lijie; Chai, Wenting; Li, Pengli; Wang, Ning Ning

    2012-10-01

    Visual selectable markers, including the purple color caused by the accumulation of anthocyanins, have been proposed for use as antibiotic-free alternatives. However, the excessive accumulation of anthocyanins seriously inhibits the growth and development of transgenic plants. In our study, the AtDWF4 promoter from Arabidopsis and the tomato LeANT1 gene, encoding a MYB transcription factor, were used to construct the PL1 fusion gene to test whether it could be used as a visual selectable marker gene for tomato transformation. All the PL1 transgenic shoots exhibited intense purple color on shoot induction medium. In the transgenic tomato plants, PL1 was highly expressed in the cotyledons, but expressed only slightly in the true leaves and other organs. The expression of PL1 had no significantly adverse effects on the growth or development of the transgenic tomato plants, and conferred tolerance to multiple abiotic stresses in them. With the “cut off green shoots” method, multiple independent 35S::GFP transgenic tomato lines were successfully obtained using PL1 as the selectable marker gene. These results suggest that PL1 has potential application of visual selectable marker gene for tomato transformation.

  7. Analyzing Statistical Mediation with Multiple Informants: A New Approach with an Application in Clinical Psychology.

    PubMed

    Papa, Lesther A; Litson, Kaylee; Lockhart, Ginger; Chassin, Laurie; Geiser, Christian

    2015-01-01

    Testing mediation models is critical for identifying potential variables that need to be targeted to effectively change one or more outcome variables. In addition, it is now common practice for clinicians to use multiple informant (MI) data in studies of statistical mediation. By coupling the use of MI data with statistical mediation analysis, clinical researchers can combine the benefits of both techniques. Integrating the information from MIs into a statistical mediation model creates various methodological and practical challenges. The authors review prior methodological approaches to MI mediation analysis in clinical research and propose a new latent variable approach that overcomes some limitations of prior approaches. An application of the new approach to mother, father, and child reports of impulsivity, frustration tolerance, and externalizing problems (N = 454) is presented. The results showed that frustration tolerance mediated the relationship between impulsivity and externalizing problems. The new approach allows for a more comprehensive and effective use of MI data when testing mediation models. PMID:26617536

  8. Balancing Precision and Risk: Should Multiple Detection Methods Be Analyzed Separately in N-Mixture Models?

    PubMed Central

    Graves, Tabitha A.; Royle, J. Andrew; Kendall, Katherine C.; Beier, Paul; Stetz, Jeffrey B.; Macleod, Amy C.

    2012-01-01

    Using multiple detection methods can increase the number, kind, and distribution of individuals sampled, which may increase accuracy and precision and reduce cost of population abundance estimates. However, when variables influencing abundance are of interest, if individuals detected via different methods are influenced by the landscape differently, separate analysis of multiple detection methods may be more appropriate. We evaluated the effects of combining two detection methods on the identification of variables important to local abundance using detections of grizzly bears with hair traps (systematic) and bear rubs (opportunistic). We used hierarchical abundance models (N-mixture models) with separate model components for each detection method. If both methods sample the same population, the use of either data set alone should (1) lead to the selection of the same variables as important and (2) provide similar estimates of relative local abundance. We hypothesized that the inclusion of 2 detection methods versus either method alone should (3) yield more support for variables identified in single method analyses (i.e. fewer variables and models with greater weight), and (4) improve precision of covariate estimates for variables selected in both separate and combined analyses because sample size is larger. As expected, joint analysis of both methods increased precision as well as certainty in variable and model selection. However, the single-method analyses identified different variables and the resulting predicted abundances had different spatial distributions. We recommend comparing single-method and jointly modeled results to identify the presence of individual heterogeneity between detection methods in N-mixture models, along with consideration of detection probabilities, correlations among variables, and tolerance to risk of failing to identify variables important to a subset of the population. The benefits of increased precision should be weighed against

  9. Balancing precision and risk: should multiple detection methods be analyzed separately in N-mixture models?

    USGS Publications Warehouse

    Graves, Tabitha A.; Royle, J. Andrew; Kendall, Katherine C.; Beier, Paul; Stetz, Jeffrey B.; Macleod, Amy C.

    2012-01-01

    Using multiple detection methods can increase the number, kind, and distribution of individuals sampled, which may increase accuracy and precision and reduce cost of population abundance estimates. However, when variables influencing abundance are of interest, if individuals detected via different methods are influenced by the landscape differently, separate analysis of multiple detection methods may be more appropriate. We evaluated the effects of combining two detection methods on the identification of variables important to local abundance using detections of grizzly bears with hair traps (systematic) and bear rubs (opportunistic). We used hierarchical abundance models (N-mixture models) with separate model components for each detection method. If both methods sample the same population, the use of either data set alone should (1) lead to the selection of the same variables as important and (2) provide similar estimates of relative local abundance. We hypothesized that the inclusion of 2 detection methods versus either method alone should (3) yield more support for variables identified in single method analyses (i.e. fewer variables and models with greater weight), and (4) improve precision of covariate estimates for variables selected in both separate and combined analyses because sample size is larger. As expected, joint analysis of both methods increased precision as well as certainty in variable and model selection. However, the single-method analyses identified different variables and the resulting predicted abundances had different spatial distributions. We recommend comparing single-method and jointly modeled results to identify the presence of individual heterogeneity between detection methods in N-mixture models, along with consideration of detection probabilities, correlations among variables, and tolerance to risk of failing to identify variables important to a subset of the population. The benefits of increased precision should be weighed against

  10. Balancing precision and risk: should multiple detection methods be analyzed separately in N-mixture models?

    PubMed

    Graves, Tabitha A; Royle, J Andrew; Kendall, Katherine C; Beier, Paul; Stetz, Jeffrey B; Macleod, Amy C

    2012-01-01

    Using multiple detection methods can increase the number, kind, and distribution of individuals sampled, which may increase accuracy and precision and reduce cost of population abundance estimates. However, when variables influencing abundance are of interest, if individuals detected via different methods are influenced by the landscape differently, separate analysis of multiple detection methods may be more appropriate. We evaluated the effects of combining two detection methods on the identification of variables important to local abundance using detections of grizzly bears with hair traps (systematic) and bear rubs (opportunistic). We used hierarchical abundance models (N-mixture models) with separate model components for each detection method. If both methods sample the same population, the use of either data set alone should (1) lead to the selection of the same variables as important and (2) provide similar estimates of relative local abundance. We hypothesized that the inclusion of 2 detection methods versus either method alone should (3) yield more support for variables identified in single method analyses (i.e. fewer variables and models with greater weight), and (4) improve precision of covariate estimates for variables selected in both separate and combined analyses because sample size is larger. As expected, joint analysis of both methods increased precision as well as certainty in variable and model selection. However, the single-method analyses identified different variables and the resulting predicted abundances had different spatial distributions. We recommend comparing single-method and jointly modeled results to identify the presence of individual heterogeneity between detection methods in N-mixture models, along with consideration of detection probabilities, correlations among variables, and tolerance to risk of failing to identify variables important to a subset of the population. The benefits of increased precision should be weighed against

  11. The influence of multiple interviews on the verbal markers of children's deception.

    PubMed

    Saykaly, Christine; Talwar, Victoria; Lindsay, R C L; Bala, Nicholas C; Lee, Kang

    2013-06-01

    This study investigated different verbal expressive markers of children recounting both true and false events. Seventy-eight children (M age = 7.58 years) interacted with a research assistant on 3 consecutive days. All children played a game that included a touching component in which the research assistant placed stickers on the child's body. Parents were then asked to coach their children to lie during subsequent interviews occurring 1 week later. Children were interviewed over 3 consecutive days. Results indicated that verbal expressive markers (e.g., cognitive operations, spontaneous corrections, admissions of lack of knowledge, temporal markers) of true and intentionally false reports were different in the first interview. However, these differences disappeared over subsequent interviews. Results of the current study highlight the importance of recording the first interview in which children disclose, particularly when using verbal markers as indicators of deception.

  12. Detecting and Analyzing Multiple Moving Objects in Crowded Environments with Coherent Motion Regions

    SciTech Connect

    Cheriyadat, Anil M.

    2013-01-04

    Understanding the world around us from large-scale video data requires vision systems that can perform automatic interpretation. While human eyes can unconsciously perceive independent objects in crowded scenes and other challenging operating environments, automated systems have difficulty detecting, counting, and understanding their behavior in similar scenes. Computer scientists at ORNL have a developed a technology termed as "Coherent Motion Region Detection" that invloves identifying multiple indepedent moving objects in crowded scenes by aggregating low-level motion cues extracted from moving objects. Humans and other species exploit such low-level motion cues seamlessely to perform perceptual grouping for visual understanding. The algorithm detects and tracks feature points on moving objects resulting in partial trajectories that span coherent 3D region in the space-time volume defined by the video. In the case of multi-object motion, many possible coherent motion regions can be constructed around the set of trajectories. The unique approach in the algorithm is to identify all possible coherent motion regions, then extract a subset of motion regions based on an innovative measure to automatically locate moving objects in crowded environments.The software reports snapshot of the object, count, and derived statistics ( count over time) from input video streams. The software can directly process videos streamed over the internet or directly from a hardware device (camera).

  13. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes

    SciTech Connect

    Gupta, Nitin; Benhamida, Jamal; Bhargava, Vipul; Goodman, Daniel; Kain , Elisabeth; Kerman, Ian; Nguyen , Ngan; Ollikainen, Noah; Rodriguez, Jesse; Wang, J.; Lipton, Mary S.; Romine, Margaret F.; Bafna, Vineet; Smith, Richard D.; Pevzner, Pavel A.

    2008-07-30

    While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages and cleavage of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.

  14. Detecting and Analyzing Multiple Moving Objects in Crowded Environments with Coherent Motion Regions

    2013-01-04

    Understanding the world around us from large-scale video data requires vision systems that can perform automatic interpretation. While human eyes can unconsciously perceive independent objects in crowded scenes and other challenging operating environments, automated systems have difficulty detecting, counting, and understanding their behavior in similar scenes. Computer scientists at ORNL have a developed a technology termed as "Coherent Motion Region Detection" that invloves identifying multiple indepedent moving objects in crowded scenes by aggregating low-level motionmore » cues extracted from moving objects. Humans and other species exploit such low-level motion cues seamlessely to perform perceptual grouping for visual understanding. The algorithm detects and tracks feature points on moving objects resulting in partial trajectories that span coherent 3D region in the space-time volume defined by the video. In the case of multi-object motion, many possible coherent motion regions can be constructed around the set of trajectories. The unique approach in the algorithm is to identify all possible coherent motion regions, then extract a subset of motion regions based on an innovative measure to automatically locate moving objects in crowded environments.The software reports snapshot of the object, count, and derived statistics ( count over time) from input video streams. The software can directly process videos streamed over the internet or directly from a hardware device (camera).« less

  15. Method of analyzing multiple sample simultaneously by detecting absorption and systems for use in such a method

    DOEpatents

    Yeung, Edward S.; Gong, Xiaoyi

    2004-09-07

    The present invention provides a method of analyzing multiple samples simultaneously by absorption detection. The method comprises: (i) providing a planar array of multiple containers, each of which contains a sample comprising at least one absorbing species, (ii) irradiating the planar array of multiple containers with a light source and (iii) detecting absorption of light with a detetion means that is in line with the light source at a distance of at leaat about 10 times a cross-sectional distance of a container in the planar array of multiple containers. The absorption of light by a sample indicates the presence of an absorbing species in it. The method can further comprise: (iv) measuring the amount of absorption of light detected in (iii) indicating the amount of the absorbing species in the sample. Also provided by the present invention is a system for use in the abov metho.The system comprises; (i) a light source comrnpising or consisting essentially of at leaat one wavelength of light, the absorption of which is to be detected, (ii) a planar array of multiple containers, and (iii) a detection means that is in line with the light source and is positioned in line with and parallel to the planar array of multiple contiainers at a distance of at least about 10 times a cross-sectional distance of a container.

  16. A dynamic factor modeling framework for analyzing multiple groundwater head series simultaneously

    NASA Astrophysics Data System (ADS)

    Berendrecht, W. L.; van Geer, F. C.

    2016-05-01

    In this paper we present an approach in which we combine a dynamic factor model (DFM) and predefined response functions to analyze a set of groundwater head series simultaneously. Each groundwater head series is decomposed into: (a) one or more deterministic components as a response to known driving forces, (b) one or more common dynamic factors, representing spatial patterns not related to any of the input series and (c) one specific dynamic factor for each groundwater head series, describing unique variation for that series. The approach reduces the degrees of freedom for each response function, enables the application to irregular observed data, and exploits the correlation between residual series of a set of groundwater head series. The common dynamic factors may be interpreted as spatial patterns due to e.g. limitations in the model specification or concept, spatially correlated errors in input variables, or driving forces which have not been included in the model. In the latter case the model can be applied in the context of an alarming system, e.g. to monitor regional trends. The specific dynamic factor depicts the variation of a particular groundwater head series that cannot be related to any other time series of the set nor to any input series. Therefore the specific dynamic factor is suitable for analyzing local variations and detecting incidental measurement errors, for example in a quality control procedure. The DFM framework is illustrated with a set of 8 groundwater head series and applied for filling gaps in time series, reconstructing high-frequency data, and detecting outliers.

  17. Development of an In-Situ Data Logging System for Multiple Trace Gas Analyzers

    SciTech Connect

    Mioduszewski, John R.; Yu, Xiao-Ying

    2008-09-01

    A field deployable in-situ data logging system was developed at Pacific Northwest National Laboratory for trace gases including carbon monoxide (CO), ozone (O3), sulfur dioxide (SO2), and nitrogen oxides including nitric oxide, nitrogen dioxide, and odd nitrogens (NO/NO2/NOx). On-line data acquisition and calibration are essential to analysis of observables and data integrity. As such, a program was written to control the communication between the data logger and each analyzer in Logger Net, a program used to communicate with the data logger. Analog outputs were collected by a CR-23X Campbell data logger between July 2, 2007 and August 7, 2007 in Richland, Washington, with data being averaged every minute. A dynamic calibrator was used to calibrate the instruments using a gas standard with NIST-certified concentration. The National Oceanic and Atmospheric Administration’s HYSPLIT model was used to create a backward and forward trajectory of air during an episode of peak O3 to determine pollutant sources and sinks. Data collected through the duration of the sampling period revealed several observations. Concentrations of all trace gases were low, due in part to the scarcity of pollutant sources in the region. The average SO2 reading was less than 0.05 ppb over the period, whereas mixing ratios of 1-20 ppb are more common in rural-suburban environments. NO, NO2, and NOx averaged 0.3, 12.2, and 12.8 ppb, respectively, while the average CO was 228.5 ppb. Typical O3 in similar environments peaks at 80-150 ppb, but the highest mixing ratio of O3 observed was less than 45 ppb. HYSPLIT offered no apparent source for additional pollutants during the high O3 episode, but increased photochemistry due to high temperatures would explain the increase in O3. Both SO2 and NO readings registered near the detection limit of the instruments, and displayed a trend similar to background noise. The development of the data logging and display system for key trace gas species is an

  18. Multiple congenital abnormalities in a newborn with two supernumerary marker chromosomes derived from chromosome 14.

    PubMed

    Faas, B H W; Van Der Deure, J; Wunderink, M I; Merkx, G; Brunner, H G

    2006-01-01

    Pure partial duplication or triplication of the proximal part of chromosome 14 has been reported in only 4 patients. Other individuals with a duplication or triplication of this region have additional chromosome imbalances. We present a new case with a supernumerary marker chromosome in all blood cells and in 35% of the cells an additional smaller marker chromosome. Both markers appeared to be derived from chromosome 14 (del(14)(q21.2) in all cells and del(14)(q11.2) in 35% of the cells). This results in a partial duplication of the proximal region of chromosome 14, combined with a mosaic partial triplication of a smaller segment of the same region. In this paper, we compare the clinical features of this case to those of cases from the literature. Although most of the patients from literature were unbalanced translocation carriers, their clinical features were comparable, except from renal abnormalities.

  19. MYC amplification in multiple marker chromosomes and EZH2 microdeletion in a man with acute myeloid leukemia.

    PubMed

    Xiang, Zhifu; Abdallah, Al-Ola; Govindarajan, Rangaswamy; Mehta, Paulette; Emanuel, Peter D; Papenhausen, Peter; Schichman, Steven A

    2015-03-01

    The role of MYC and EZH2 in acute myeloid leukemia (AML) pathogenesis is poorly understood. Herein we present a case of AML with MYC amplification in marker chromosomes and a microdeletion of chromosome 7 below cytogenetic resolution. The karyotype of the patient's bone marrow aspirate showed three to five marker chromosomes in all dividing cells without other structural or numerical chromosomal abnormalities. Analysis by fluorescence in situ hybridization (FISH) with a probe specific for the human MYC gene revealed amplification of the oncogene localized to the marker chromosomes. Using whole genome single nucleotide polymorphism (SNP) microarray analysis, an approximately 4.4 Mb amplicon containing the MYC gene was identified with an estimated amplification of about 30 copies per leukemic cell and, thus, an average of about 8 copies per marker chromosome. A 6.4 Mb hemizygous microdeletion of chromosome 7 within band q36.1 was also found by SNP microarray analysis in a cellular-equivalent dosage of 50%. The microdeletion spans multiple genes, including EZH2, a gene with well-known cancer association. No mutation was found in the remaining EZH2 allele by next generation gene sequencing. The combination of MYC amplification and EZH2 deletion, which has not been described previously in AML, may suggest a synergistic role of the two oncogenes in the pathogenesis of the patient's acute leukemia.

  20. Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers.

    PubMed

    McBenedict, Billy; Chimwamurombe, Percy; Kwembeya, Ezekeil; Maggs-Kölling, Gillian

    2016-01-01

    Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia. PMID:27433479

  1. Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers.

    PubMed

    McBenedict, Billy; Chimwamurombe, Percy; Kwembeya, Ezekeil; Maggs-Kölling, Gillian

    2016-01-01

    Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia.

  2. Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers

    PubMed Central

    McBenedict, Billy; Chimwamurombe, Percy; Kwembeya, Ezekeil; Maggs-Kölling, Gillian

    2016-01-01

    Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia. PMID:27433479

  3. Simultaneous quantitative detection of multiple tumor markers with a rapid and sensitive multicolor quantum dots based immunochromatographic test strip.

    PubMed

    Wang, Chunying; Hou, Fei; Ma, Yicai

    2015-06-15

    A novel multicolor quantum dots (QDs) based immunochromatographic test strip (ICTS) was developed for simultaneous quantitative detection of multiple tumor markers, by utilizing alpha fetoprotein (AFP) and carcinoembryonic antigen (CEA) as models. The immunosensor could realize simultaneous quantitative detection of tumor markers with only one test line and one control line on the nitrocellulose membrane (NC membrane) due to the introduction of multicolor QDs. In this method, a mixture of mouse anti-AFP McAb and mouse anti-CEA McAb was coated on NC membrane as test line and goat anti-mouse IgG antibody was coated as control line. Anti-AFP McAb-QDs546 conjugates and anti-CEA McAb-QDs620 conjugates were mixed and applied to the conjugate pad. Simultaneous quantitative detection of multiple tumor markers was achieved by detecting the fluorescence intensity of captured QDs labels on test line and control line using a test strip reader. Under the optimum conditions, AFP and CEA could be detected as low as 3 ng/mL and 2 ng/mL in 15 min with a sample volume of 80 μL, and no obvious cross-reactivity was observed. The immunosensor was validated with 130 clinical samples and in which it exhibited high sensitivity (93% for AFP and 87% for CEA) and specificity (94% for AFP and 97% for CEA). The immunosensor also demonstrated high recoveries (87.5-113% for AFP and 90-97.3% for CEA) and low relative standard deviations (RSDs) (2.8-6.2% for AFP and 4.9-9.6% for CEA) when testing spiked human serum. This novel multicolor QDs based ICTS provides an easy and rapid, simultaneous quantitative detecting strategy for point-of-care testing of tumor markers. PMID:25562743

  4. Multiple endocrine neoplasia type I (MEN1): Identification of informative polymorphic markers and candidate genes

    SciTech Connect

    Taggart, R.T.; Qian, C.; An, Y.

    1994-09-01

    Linkage and tumor deletion studies have mapped this autosomal dominant disease to 11q12{yields}13. The MEN1 gene product is suspected to be a growth suppressor or regulator. We report here isolation of polymorphic PCR markers used to narrow the nonrecombinant region and localization of genomic clones encoding expressed sequences within this region. 552 genomic clones were isolated from a radiation hybrid (RH) cell line containing a 5-10 Mb region flanking the gene. We screened the RH cell line with 17 markers flanking the MEN1 region to confirm its integrity. The representation of the markers in the panel of genomic clones derived from the RH cell line indicated a 1- to 4-fold representation of the region. A set of radiation hybrids was used to sublocalized genomic and cDNA clones of interest to 3 regions: centromeric, telomeric and a 1.2 Mb nonrecombinant region. Highly polymorphic PCR markers were developed by hybridization of the clones with tetra- and trinucleotide probes 3 of 7 PCR markers (heterozygosity .46-.92) were nonrecombinant with MEN1. The PCR markers were utilized for definition of the critical region and also proved useful for presymptomatic diagnosis. Genomic clones mapped to the 1.2 Mb nonrecombinant region were used to identify expressed sequences corresponding to 5 different genes. One cDNA clone corresponded to a ubiquitously expressed gene sequence located near PYGM. Two major (3.4, 2.5 kb) and one minor transcript (1.8 kb) were found in pancreas, kidney, brain, lung, heart, skeletal muscle, and liver. DNA analysis matched with 2 anonymous cDNA clones in GenBank. The genomic and cDNA clones were used to screen Southern and Northern blots for MEN1 associated rearrangements before attempting SSCP analysis to detect point mutations. The genomic fragment used to identify the corresponding cDNA clones did not detect alterations in MEN1 patients on Southern blots, however additional fragments were identified in one MEN1 patient with the cDNA clones.

  5. Multiple RT-PCR markers for the detection of circulating tumour cells of metastatic canine mammary tumours.

    PubMed

    da Costa, A; Kohn, B; Gruber, A D; Klopfleisch, R

    2013-04-01

    In humans, detection of circulating tumour cells (CTCs) using nucleic acid-based methods such as reverse transcription polymerase chain reaction (RT-PCR) has proven to be of prognostic relevance. However, similar procedures are still lacking in veterinary oncology. To assess the correlation of CTC markers with the metastatic potential of canine mammary tumours, 120 peripheral blood samples from bitches with mammary carcinomas with (group 1) and without (group 2) histological evidence of vascular invasion and/or presence of lymph node metastases and mammary adenomas (group 3) were analyzed. Blood samples were collected in EDTA tubes and RNA was extracted within 48 h. Subsequently, the samples were tested by RT-PCR for a panel of seven CTC mRNA markers. CRYAB was the most sensitive single marker with a sensitivity of 35% and also the most specific marker with a specificity of 100% to detect group 1 blood samples. A multimarker assay combining four genes enhanced the sensitivity up to 77.5%, but decreased the specificity to 80%. CRYAB appeared to be highly specific but only moderately sensitive at detecting blood samples from dogs with metastatic tumours and detection significantly correlated with vascular invasion of primary mammary tumours. However, a multimarker assay of four genes significantly enhanced the sensitivity of the assay and is therefore preferable for CTC detection. PMID:23036177

  6. The genetic variance for multiple linked quantitative trait loci conditional on marker information in a crossed population.

    PubMed

    Matsuda, H; Iwaisaki, H

    2002-01-01

    In the prediction of genetic values and quantitative trait loci (QTLs) mapping via the mixed model method incorporating marker information in animal populations, it is important to model the genetic variance for individuals with an arbitrary pedigree structure. In this study, for a crossed population originated from different genetic groups such as breeds or outbred strains, the variance of additive genetic values for multiple linked QTLs that are contained in a chromosome segment, especially the segregation variance, is investigated assuming the use of marker data. The variance for a finite number of QTLs in one chromosomal segment is first examined for the crossed population with the general pedigree. Then, applying the concept of the expectation of identity-by-descent proportion, an approximation to the mean of the conditional probabilities for the linked QTLs over all loci is obtained, and using it an expression for the variance in the case of an infinite number of linked QTLs marked by flanking markers is derived. It appears that the approach presented can be useful in the segment mapping using, and in the genetic evaluation of, crosses with general pedigrees in the population of concern. The calculation of the segregation variance through the current approach is illustrated numerically, using a small data-set.

  7. Sodium imaging as a marker of tissue injury in patients with multiple sclerosis.

    PubMed

    Inglese, M; Oesingmann, N; Zaaraoui, W; Ranjeva, J P; Fleysher, L

    2013-10-01

    Recent studies have suggested that intra-axonal sodium accumulation contribute to axonal degeneration in patients with MS. Advances in MRI hardware and software allow acquisition of brain sodium signal in vivo. This review begins with a summary of the experimental evidence for impairment of sodium homeostasis in MS. Then, MRI methods for sodium acquisition are reviewed and the application of the techniques in patients with MS is discussed. Sodium imaging and ultra-high field MRI have the potential to provide tissue-specific markers of neurodegeneration in MS.

  8. Discovery of Novel Disease-specific and Membrane-associated Candidate Markers in a Mouse Model of Multiple Sclerosis*

    PubMed Central

    Dagley, Laura F.; Croft, Nathan P.; Isserlin, Ruth; Olsen, Jonathan B.; Fong, Vincent; Emili, Andrew; Purcell, Anthony W.

    2014-01-01

    Multiple sclerosis is a chronic demyelinating disorder characterized by the infiltration of auto-reactive immune cells from the periphery into the central nervous system resulting in axonal injury and neuronal cell death. Experimental autoimmune encephalomyelitis represents the best characterized animal model as common clinical, histological, and immunological features are recapitulated. A label-free mass spectrometric proteomics approach was used to detect differences in protein abundance within specific fractions of disease-affected tissues including the soluble lysate derived from the spinal cord and membrane protein-enriched peripheral blood mononuclear cells. Tissues were harvested from actively induced experimental autoimmune encephalomyelitis mice and sham-induced (“vehicle” control) counterparts at the disease peak followed by subsequent analysis by nanoflow liquid chromatography tandem mass spectrometry. Relative protein quantitation was performed using both intensity- and fragmentation-based approaches. After statistical evaluation of the data, over 500 and 250 differentially abundant proteins were identified in the spinal cord and peripheral blood mononuclear cell data sets, respectively. More than half of these observations have not previously been linked to the disease. The biological significance of all candidate disease markers has been elucidated through rigorous literature searches, pathway analysis, and validation studies. Results from comprehensive targeted mass spectrometry analyses have confirmed the differential abundance of ∼200 candidate markers (≥twofold dysregulated expression) at a 70% success rate. This study is, to our knowledge, the first to examine the cell-surface proteome of peripheral blood mononuclear cells in experimental autoimmune encephalomyelitis. These data provide a unique mechanistic insight into the dynamics of peripheral immune cell infiltration into CNS-privileged sites at a molecular level and has identified

  9. Endovascular treatment of chronic cerebro spinal venous insufficiency in patients with multiple sclerosis modifies circulating markers of endothelial dysfunction and coagulation activation: a prospective study.

    PubMed

    Napolitano, Mariasanta; Bruno, Aldo; Mastrangelo, Diego; De Vizia, Marcella; Bernardo, Benedetto; Rosa, Buonagura; De Lucia, Domenico

    2014-10-01

    We performed a monocentric observational prospective study to evaluate coagulation activation and endothelial dysfunction parameters in patients with multiple sclerosis undergoing endovascular treatment for cerebro-spinal-venous insufficiency. Between February 2011 and July 2012, 144 endovascular procedures in 110 patients with multiple sclerosis and chronical cerebro-spinal venous insufficiency were performed and they were prospectively analyzed. Each patient was included in the study according to previously published criteria, assessed by the investigators before enrollment. Endothelial dysfunction and coagulation activation parameters were determined before the procedure and during follow-up at 1, 3, 6, 9, 12, 15 and 18 months after treatment, respectively. After the endovascular procedure, patients were treated with standard therapies, with the addition of mesoglycan. Fifty-five percent of patients experienced a favorable outcome of multiple sclerosis within 1 month after treatment, 25% regressed in the following 3 months, 24.9% did not experience any benefit. In only 0.1% patients, acute recurrence was observed and it was treated with high-dose immunosuppressive therapy. No major complications were observed. Coagulation activation and endothelial dysfunction parameters were shown to be reduced at 1 month and stable up to 12-month follow-up, and they were furthermore associated with a good clinical outcome. Endovascular procedures performed by a qualified staff are well tolerated; they can be associated with other currently adopted treatments. Correlations between inflammation, coagulation activation and neurodegenerative disorders are here supported by the observed variations in plasma levels of markers of coagulation activation and endothelial dysfunction.

  10. Multiples in dermatology: markers for special considerations in diagnosis, therapy, and prognosis.

    PubMed

    Trevino, Julian; Grosshandler, Josh; Chen, Amy Y-Y; Chiang, Charles; Serrao, Rocco; Dohil, Magdalene

    2012-07-01

    Multiples of certain cutaneous lesions should alert the clinician to a wider differential diagnosis and possible systemic associations although the individual skin lesion is often benign in nature and banal in appearance. This article focuses on such findings in selected multiple cutaneous lesions that may be classified according to the primary cutaneous feature as vascular, pigmentary, nevoid hamartomas, and tumors/neoplastic conditions. The clinical presentation of each entity and its significance, appropriate diagnostic evaluation, therapeutic and prognostic considerations and pertinent differential diagnoses will be reviewed.

  11. Multiple markers of cortical morphology reveal evidence of supragranular thinning in schizophrenia

    PubMed Central

    Wagstyl, K; Ronan, L; Whitaker, K J; Goodyer, I M; Roberts, N; Crow, T J; Fletcher, P C

    2016-01-01

    In vivo structural neuroimaging can reliably identify changes to cortical morphology and its regional variation but cannot yet relate these changes to specific cortical layers. We propose, however, that by synthesizing principles of cortical organization, including relative contributions of different layers to sulcal and gyral thickness, regional patterns of variation in thickness of different layers across the cortical sheet and profiles of layer variation across functional hierarchies, it is possible to develop indirect morphological measures as markers of more specific cytoarchitectural changes. We developed four indirect measures sensitive to changes specifically occurring in supragranular cortical layers, and applied these to test the hypothesis that supragranular layers are disproportionately affected in schizophrenia. Our findings from the four different measures converge to indicate a predominance of supragranular thinning in schizophrenia, independent of medication and illness duration. We propose that these indirect measures offer novel ways of identifying layer-specific cortical changes, offering complementary in vivo observations to existing post-mortem studies. PMID:27070408

  12. Multiple markers of cortical morphology reveal evidence of supragranular thinning in schizophrenia.

    PubMed

    Wagstyl, K; Ronan, L; Whitaker, K J; Goodyer, I M; Roberts, N; Crow, T J; Fletcher, P C

    2016-01-01

    In vivo structural neuroimaging can reliably identify changes to cortical morphology and its regional variation but cannot yet relate these changes to specific cortical layers. We propose, however, that by synthesizing principles of cortical organization, including relative contributions of different layers to sulcal and gyral thickness, regional patterns of variation in thickness of different layers across the cortical sheet and profiles of layer variation across functional hierarchies, it is possible to develop indirect morphological measures as markers of more specific cytoarchitectural changes. We developed four indirect measures sensitive to changes specifically occurring in supragranular cortical layers, and applied these to test the hypothesis that supragranular layers are disproportionately affected in schizophrenia. Our findings from the four different measures converge to indicate a predominance of supragranular thinning in schizophrenia, independent of medication and illness duration. We propose that these indirect measures offer novel ways of identifying layer-specific cortical changes, offering complementary in vivo observations to existing post-mortem studies. PMID:27070408

  13. Minimal SNP overlap among multiple panels of ancestry informative markers argues for more international collaboration.

    PubMed

    Soundararajan, Usha; Yun, Libing; Shi, Meisen; Kidd, Kenneth K

    2016-07-01

    The century-old use of genetic markers to determine population relationships has morphed in modern forensics into use of markers to determine the ancestry of an individual from a DNA sample. Researchers have identified sets of SNPs that have frequency differences among populations and many sets of SNPs have been published for the purpose of inferring ancestry. Such inference also requires reference datasets for the particular set of SNPs selected. We have identified 21 largely independent published panels of ancestry informative SNPs (AISNPs) and examined their union of 1397 SNPs. No SNP occurs in more than 6 panels. The 1397 SNPs in 21 panels yield a largely empty matrix that is inhibiting progress on more refined ability to infer ancestry for a forensic sample. The most common set of reference populations is the HGDP set of 52 small population samples totaling a thousand individuals. Only 46 (3%) of the 1397 SNPs occur in three or more panels. We assembled a new dataset for 44 of those SNPs involving 4,559 individuals from 73 populations. Analyses of this dataset provided clear differentiation of only five biogeographic regions: sub-Saharan Africa, Europe and SW Asia, South Asia, East Asia, and the Americas. This is an inadequate level of biogeographic resolution already exceeded by other panels. We conclude that more such AISNP panels are not needed and that the forensic community must collaborate to develop a common set of highly differentiating AISNPs typed on a very large number of population samples. How that can be accomplished will be the subject of future discussion. PMID:26977931

  14. Phylogenetic Analysis of Multiple FISH Markers in Oral Tongue Squamous Cell Carcinoma Suggests that a Diverse Distribution of Copy Number Changes Is Associated with Poor Prognosis

    PubMed Central

    Wangsa, Darawalee; Chowdhury, Salim Akhter; Ryott, Michael; Gertz, E. Michael; Elmberger, Göran; Auer, Gert; Lundqvist, Elisabeth Åvall; Küffer, Stefan; Ströbel, Philipp; Schäffer, Alejandro A.; Schwartz, Russell; Munck-Wikland, Eva; Ried, Thomas; Heselmeyer-Haddad, Kerstin

    2016-01-01

    Oral tongue squamous cell carcinoma (OTSCC) is associated with poor prognosis. To improve prognostication, we analyzed four gene probes (TERC, CCND1, EGFR, and TP53) and the centromere probe CEP4 as a marker of chromosomal instability, using fluorescence in situ hybridization (FISH) in single cells from the tumors of sixty-five OTSCC patients (Stage I, n=15; Stage II, n=30; Stage III, n=7; Stage IV, n=13). Unsupervised hierarchical clustering of the FISH data distinguished three clusters related to smoking status. Copy number increases of all five markers were found to be correlated to non-smoking habits, while smokers in this cohort had low-level copy number gains. Using the phylogenetic modeling software FISHtrees, we constructed models of tumor progression for each patient based on the four gene probes. Then, we derived test statistics on the models that are significant predictors of disease-free and overall survival, independent of tumor stage and smoking status in multivariate analysis. The patients whose tumors were modeled as progressing by a more diverse distribution of copy number changes across the four genes have poorer prognosis. This is consistent with the view that multiple genetic pathways need to become deregulated in order for cancer to progress. PMID:26175310

  15. The Longue Durée of genetic ancestry: multiple genetic marker systems and Celtic origins on the Atlantic facade of Europe.

    PubMed

    McEvoy, Brian; Richards, Martin; Forster, Peter; Bradley, Daniel G

    2004-10-01

    Celtic languages are now spoken only on the Atlantic facade of Europe, mainly in Britain and Ireland, but were spoken more widely in western and central Europe until the collapse of the Roman Empire in the first millennium a.d. It has been common to couple archaeological evidence for the expansion of Iron Age elites in central Europe with the dispersal of these languages and of Celtic ethnicity and to posit a central European "homeland" for the Celtic peoples. More recently, however, archaeologists have questioned this "migrationist" view of Celtic ethnogenesis. The proposition of a central European ancestry should be testable by examining the distribution of genetic markers; however, although Y-chromosome patterns in Atlantic Europe show little evidence of central European influence, there has hitherto been insufficient data to confirm this by use of mitochondrial DNA (mtDNA). Here, we present both new mtDNA data from Ireland and a novel analysis of a greatly enlarged European mtDNA database. We show that mtDNA lineages, when analyzed in sufficiently large numbers, display patterns significantly similar to a large fraction of both Y-chromosome and autosomal variation. These multiple genetic marker systems indicate a shared ancestry throughout the Atlantic zone, from northern Iberia to western Scandinavia, that dates back to the end of the last Ice Age.

  16. Evidence of multiple paternity in Morelet's Crocodile (Crocodylus moreletii) in Belize, CA, inferred from microsatellite markers.

    PubMed

    McVay, John D; Rodriguez, David; Rainwater, Thomas R; Dever, Jennifer A; Platt, Steven G; McMurry, Scott T; Forstner, Michael R J; Densmore, Llewellyn D

    2008-12-01

    Microsatellite data were generated from hatchlings collected from ten nests of Morelet's Crocodile (Crocodylus moreletii) from New River Lagoon and Gold Button Lagoon in Belize to test for evidence of multiple paternity. Nine microsatellite loci were genotyped for 188 individuals from the 10 nests, alongside 42 nonhatchlings from Gold Button Lagoon. Then mitochondrial control region sequences were generated for the nonhatchlings and for one individual from each nest to test for presence of C. acutus-like haplotypes. Analyses of five of the nine microsatellite loci revealed evidence that progeny from five of the ten nests were sired by at least two males. These data suggest the presence of multiple paternity as a mating strategy in the true crocodiles. This information may be useful in the application of conservation and management techniques to the 12 species in this genus, most of which are threatened or endangered. PMID:18831002

  17. Development of Multiple Polymorphic Microsatellite Markers for Ceratina calcarata (Hymenoptera: Apidae) Using Genome-Wide Analysis

    PubMed Central

    Shell, Wyatt A.; Rehan, Sandra M.

    2016-01-01

    The small carpenter bee, Ceratina calcarata (Robertson), is a widespread native pollinator across eastern North America. The behavioral ecology and nesting biology of C. calcarata has been relatively well-studied and the species is emerging as a model organism for both native pollinator and social evolution research. C. calcarata is subsocial: reproductively mature females provide extended maternal care to their brood. As such, studies of C. calcarata may also reveal patterns of relatedness and demography unique to primitively social Hymenoptera. Here, we present 21 microsatellite loci, isolated from the recently completed C. calcarata genome. Screening in 39 individuals across their distribution revealed that no loci were in linkage disequilibrium, nor did any deviate significantly from Hardy-Weinberg following sequential Bonferroni correction. Allele count ranged from 2 to 14, and observed and expected heterozygosities ranged from 0.08 to 0.82 (mean 0.47) and 0.26 to 0.88 (mean 0.56), respectively. These markers will enable studies of population-wide genetic structuring across C. calcarata’s distribution. Such tools will also allow for exploration of between and within-colony relatedness in this subsocial native pollinator. PMID:27324584

  18. Development of Multiple Polymorphic Microsatellite Markers for Ceratina calcarata (Hymenoptera: Apidae) Using Genome-Wide Analysis.

    PubMed

    Shell, Wyatt A; Rehan, Sandra M

    2016-01-01

    The small carpenter bee, Ceratina calcarata (Robertson), is a widespread native pollinator across eastern North America. The behavioral ecology and nesting biology of C. calcarata has been relatively well-studied and the species is emerging as a model organism for both native pollinator and social evolution research. C. calcarata is subsocial: reproductively mature females provide extended maternal care to their brood. As such, studies of C. calcarata may also reveal patterns of relatedness and demography unique to primitively social Hymenoptera. Here, we present 21 microsatellite loci, isolated from the recently completed C. calcarata genome. Screening in 39 individuals across their distribution revealed that no loci were in linkage disequilibrium, nor did any deviate significantly from Hardy-Weinberg following sequential Bonferroni correction. Allele count ranged from 2 to 14, and observed and expected heterozygosities ranged from 0.08 to 0.82 (mean 0.47) and 0.26 to 0.88 (mean 0.56), respectively. These markers will enable studies of population-wide genetic structuring across C. calcarata's distribution. Such tools will also allow for exploration of between and within-colony relatedness in this subsocial native pollinator. PMID:27324584

  19. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations.

    PubMed

    Frantz, A C; McDevitt, A D; Pope, L C; Kochan, J; Davison, J; Clements, C F; Elmeros, M; Molina-Vacas, G; Ruiz-Gonzalez, A; Balestrieri, A; Van Den Berge, K; Breyne, P; Do Linh San, E; Agren, E O; Suchentrunk, F; Schley, L; Kowalczyk, R; Kostka, B I; Cirović, D; Sprem, N; Colyn, M; Ghirardi, M; Racheva, V; Braun, C; Oliveira, R; Lanszki, J; Stubbe, A; Stubbe, M; Stier, N; Burke, T

    2014-11-01

    Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events. PMID:24781805

  20. The haplotype analyses using multiple markers of the apolipoprotein B gene in patients with coronary artery disease.

    PubMed Central

    Hong, S. H.; Song, J.; Kim, J. Q.

    2001-01-01

    The high level of low density lipoprotein (LDL) is a risk factor for cardiovascular disease. Apolipoprotein (apo) B is a major protein component of LDL and plays an important role in the maintenance of cholesterol homeostasis. In this study, six polymorphic sites of the apoB gene were anlaysed in 235 patients with coronary artery disease (CAD) and 216 normal control subjects. There were no significant differences in the allele frequencies of apoB polymorphisms between the control and patient groups. However, haplotype frequencies were significantly different between the CAD patients and control (p<0.05). In addition, the allelic distributions of both EcoRI and MspI polymorphisms in Koreans were similar to those in Chinese but significantly different from those in Caucasians. ApoB polymorphisms showed no association with plasma lipid levels. In conclusion, haplotype analysis of the apoB gene using multiple diallelic markers might be a useful marker for Korean CAD patients. PMID:11748351

  1. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

    PubMed Central

    Frantz, A C; McDevitt, A D; Pope, L C; Kochan, J; Davison, J; Clements, C F; Elmeros, M; Molina-Vacas, G; Ruiz-Gonzalez, A; Balestrieri, A; Van Den Berge, K; Breyne, P; Do Linh San, E; Ågren, E O; Suchentrunk, F; Schley, L; Kowalczyk, R; Kostka, B I; Ćirović, D; Šprem, N; Colyn, M; Ghirardi, M; Racheva, V; Braun, C; Oliveira, R; Lanszki, J; Stubbe, A; Stubbe, M; Stier, N; Burke, T

    2014-01-01

    Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events. PMID:24781805

  2. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations.

    PubMed

    Frantz, A C; McDevitt, A D; Pope, L C; Kochan, J; Davison, J; Clements, C F; Elmeros, M; Molina-Vacas, G; Ruiz-Gonzalez, A; Balestrieri, A; Van Den Berge, K; Breyne, P; Do Linh San, E; Agren, E O; Suchentrunk, F; Schley, L; Kowalczyk, R; Kostka, B I; Cirović, D; Sprem, N; Colyn, M; Ghirardi, M; Racheva, V; Braun, C; Oliveira, R; Lanszki, J; Stubbe, A; Stubbe, M; Stier, N; Burke, T

    2014-11-01

    Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.

  3. Multiple immune deviations predictive for IVF failure as possible markers for IVIG therapy.

    PubMed

    Chernyshov, Viktor P; Dons'koi, Boris V; Sudoma, Iryna O; Goncharova, Yana O

    2016-08-01

    Recently we have shown that immune deviations (ID) may predict IVF failure. Benefit from IVIG therapy was observed in 115 women with repeated IVF failure according to proposed multiple ID that appeared unfavorable for implantation and live birth. Group of 123 women with repeated IVF failure without IVIG therapy was compared with former group. Immune phenotype and NK activity of peripheral blood lymphocytes were studied by flow cytometry. Potentially predictive for IVF failure ID included elevated expression of CD56, CD158a in T lymphocytes, decreased levels of CD4T lymphocytes, up-regulated expression of HLA DR in CD8+ T cells and NK cells, elevated number of NK cells and increased NK cytotoxicity, increased or decreased expression of CD158a and CD8 in NK cells. Three or more ID may predict implantation failure to a greater degree than one or two ID. In women receiving IVIG in subgroups with 0-1 and 2 ID, there was no increase in implantation rate (IR) and live birth rate (LBR) after IVIG in comparison with patients with the same number of ID but without IVIG correction. After IVIG therapy decreased IR and LBR were restored in women with three or more immune deviations. Multiple immune deviations indicate IVF patients who may benefit from IVIG therapy. IVIG seems to convert "unfavorable" immune phenotype to "favorable" one.

  4. Cognitive impairment as marker of diffuse brain abnormalities in early relapsing remitting multiple sclerosis

    PubMed Central

    Deloire, M; Salort, E; Bonnet, M; Arimone, Y; Boudineau, M; Amieva, H; Barroso, B; Ouallet, J; Pachai, C; Galliaud, E; Petry, K; Dousset, V; Fabrigoule, C; Brochet, B

    2005-01-01

    Objectives: To establish the frequency of cognitive impairment in a population based sample of patients with recently diagnosed relapsing-remitting multiple sclerosis (RRMS), and to determine the relation between cognitive abnormalities and the extent of macroscopic and microscopic tissue damage revealed by magnetic resonance imaging (MRI) and magnetisation transfer (MT) imaging. Methods: 58 patients with RRMS consecutively diagnosed in the previous six months in Aquitaine and 70 healthy controls underwent a battery of neuropsychological tests. Lesion load and atrophy indices (brain parenchymal fraction and ventricular fraction) were measured on brain MRI. MT ratio (MTR) histograms were obtained from lesions, normal appearing white matter (NAWM), and normal appearing grey matter (NAGM). Gadolinium enhanced lesions were counted. Results: 44 RRMS patients could be individually matched with healthy controls for age, sex, and education. Patients performed worse in tests of verbal and spatial memory, attention, information processing speed, inhibition, and conceptualisation. Measures of attention and information processing speed were correlated with lesion load, mean NAWM MTR, and the peak location of the NAGM MTR histogram in the patients. Multivariate regression analysis showed that lesion load and mean NAWM MTR were among the MR indices that were most significantly associated with impairment of attention and information processing speed in these early RRMS cases. Conclusions: Cognitive impairment appears to be common in the early stages of RRMS, mainly affecting attention, information processing speed, memory, inhibition, and conceptualisation. The severity of these deficits reflects the extent of the lesions and the severity of tissue disorganisation outside lesions. PMID:15774439

  5. Adaptive marker-free registration using a multiple point strategy for real-time and robust endoscope electromagnetic navigation.

    PubMed

    Luo, Xiongbiao; Wan, Ying; He, Xiangjian; Mori, Kensaku

    2015-02-01

    Registration of pre-clinical images to physical space is indispensable for computer-assisted endoscopic interventions in operating rooms. Electromagnetically navigated endoscopic interventions are increasingly performed at current diagnoses and treatments. Such interventions use an electromagnetic tracker with a miniature sensor that is usually attached at an endoscope distal tip to real time track endoscope movements in a pre-clinical image space. Spatial alignment between the electromagnetic tracker (or sensor) and pre-clinical images must be performed to navigate the endoscope to target regions. This paper proposes an adaptive marker-free registration method that uses a multiple point selection strategy. This method seeks to address an assumption that the endoscope is operated along the centerline of an intraluminal organ which is easily violated during interventions. We introduce an adaptive strategy that generates multiple points in terms of sensor measurements and endoscope tip center calibration. From these generated points, we adaptively choose the optimal point, which is the closest to its assigned the centerline of the hollow organ, to perform registration. The experimental results demonstrate that our proposed adaptive strategy significantly reduced the target registration error from 5.32 to 2.59 mm in static phantoms validation, as well as from at least 7.58 mm to 4.71 mm in dynamic phantom validation compared to current available methods.

  6. Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds

    PubMed Central

    Yang, Yuzhan; Zhan, Aibin; Meng, Fanjuan; Xu, Wenbin

    2016-01-01

    Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to

  7. Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds.

    PubMed

    Yang, Yuzhan; Zhan, Aibin; Cao, Lei; Meng, Fanjuan; Xu, Wenbin

    2016-01-01

    Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to

  8. Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds

    PubMed Central

    Yang, Yuzhan; Zhan, Aibin; Meng, Fanjuan; Xu, Wenbin

    2016-01-01

    Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to

  9. Systems biology: building a useful model from multiple markers and profiles.

    PubMed

    Mayer, Paul; Mayer, Bernd; Mayer, Gert

    2012-11-01

    The pathophysiology of diabetic nephropathy (DN) is driven by a complex, multi-facetted interplay of numerous molecular processes (protective as well as damaging) and the balance between these, rather than the activity of a single pathway, determines clinical presentation and outcome. We present a concept for deriving a biomarker panel aimed to represent the relevant processes involved. Our approach rests on a hybrid gene/protein interaction network that holds ample information on molecular features (nodes) and their relations (edges), as a result providing a basic structure to navigate in molecular content and context being identified as relevant in DN. Extensive literature search on omics studies in DN provided a molecular feature list mapping to a total of 2175 unique protein-coding genes [13 from single nucleotide polymorphisms (SNPs), 12 as targets from relevant miRNAs, 1583 from transcriptomics, 5 from proteomics and 53 from metabolomics via linking to enzymes; 509 features were identified from multiple sources]. Two hundred and eighty-seven further human protein-coding genes associated with DN were derived from searching NCBI Pubmed (utilizing MeSH and gene-to-pubmed). Text mining of patents and clinical trial descriptors in the context of DN further added about 1,000 features. These data were used to label the respective nodes in the interaction network, as a result obtaining a DN-specific subgraph. Application of a segmentation algorithm on this subgraph allowed the identification of DN-specific molecular units, each characterizing a cluster of genes/proteins with a high internal functional association. We interpret each such unit as a functionally relevant molecular process contributing to the presentation of DN, and the total set of such units as a molecular model of DN. We propose that selecting appropriate biomarkers from each unit might allow the description of a patient's specific 'type' of DN, ultimately leading to a better stratification of

  10. Pigmentary Markers in Danes – Associations with Quantitative Skin Colour, Nevi Count, Familial Atypical Multiple-Mole, and Melanoma Syndrome

    PubMed Central

    Johansen, Peter; Andersen, Jeppe Dyrberg; Madsen, Linnea Nørgård; Ullum, Henrik; Glud, Martin; Børsting, Claus; Gniadecki, Robert; Morling, Niels

    2016-01-01

    To investigate whether pigmentation genes involved in the melanogenic pathway (melanogenesis) contributed to melanoma predisposition, we compared pigmentary genetics with quantitative skin pigmentation measurements, the number of atypical nevi, the total nevus count, and the familial atypical multiple mole and melanoma (FAMMM) syndrome. We typed 32 pigmentary SNP markers and sequenced MC1R in 246 healthy individuals and 116 individuals attending periodic control for malignant melanoma development, 50 of which were diagnosed with FAMMM. It was observed that individuals with any two grouped MC1R variants (missense, NM_002386:c. 456C > A (p.TYR152*), or NM_002386:c.83_84insA (p.Asn29Glnfs*14) had significantly (p<0.001) lighter skin pigmentation of the upper-inner arm than those with none or one MC1R variant. We did not observe any significant association of the MC1R variants with constitutive pigmentation measured on the buttock area. We hypothesize that the effect of MC1R variants on arm pigmentation is primarily reflecting the inability to tan when subjected to UVR. A gender specific effect on skin pigmentation was also observed, and it was found that the skin pigmentation of females on average were darker than that of males (p<0.01). We conclude that MC1R variants are associated with quantitative skin colour in a lightly pigmented Danish population. We did not observe any association between any pigmentary marker and the FAMMM syndrome. We suggest that the genetics of FAMMM is not related to the genetics of the pigmentary pathway. PMID:26938746

  11. A study of promoter and intronic markers of ApoI/Fas gene and the interaction with Fas ligand in relapsing multiple sclerosis.

    PubMed

    Lucas, Miguel; Zayas, María D; De Costa, Alzenira F; Solano, Francisca; Chadli, Amal; Dinca, Luminita; Izquierdo, Guillermo

    2004-01-01

    We studied the association between multiple sclerosis (MS) and a novel single nucleotide polymorphism (SNP), A/T(735)G/C, localized in intron IV of the ApoI/Fas gene, which is recognized by the restrictase MaeI. Fas-MaeI genotypes were screened in chromosomes of 215 healthy individuals and 312 relapsing MS patients of Spanish extraction. We also analyzed the interaction of this new intragenic marker with others previously associated with MS: class II HLA-DRB1*1501, Fas-MvaI and Fas ligand. The distribution of Fas-MaeI genotypes was in equilibrium in the control cohort, while a significant disequilibrium was observed in the patient group (chi(2) = 16; p = 0.0003). Fas-MaeI genotypes were statistically different in the MS and control groups, but the allele frequencies were not. Sharing of MvaI/MaeI genotypes of the promoter/intron IV region did not differ between patients and controls. We failed to find different frequencies of ApoI/Fas genotypes in the population of MS carriers of the class II HLA-DRB1*1501 allele. The case/control comparative study showed a relative risk (OR close to 1.6) of MS in individuals harboring the T and A alleles of Fas- MaeI and Fas ligand, respectively. In conclusion, our findings suggest a weak association between the intronic marker Fas-MaeI and MS and a relative interaction with Fas ligand in an MS cohort of South Spanish extraction.

  12. Impact of glatiramer acetate on paraclinical markers of neuroprotection in multiple sclerosis: A prospective observational clinical trial.

    PubMed

    Ehling, Rainer; Di Pauli, Franziska; Lackner, Peter; Rainer, Carolyn; Kraus, Viktoria; Hegen, Harald; Lutterotti, Andreas; Kuenz, Bettina; De Zordo, Tobias; Schocke, Michael; Glatzl, Susanne; Löscher, Wolfgang N; Deisenhammer, Florian; Reindl, Markus; Berger, Thomas

    2015-10-15

    Data from in vitro and animal studies support a neuroprotective role of glatiramer acetate (GA) in multiple sclerosis (MS). We investigated prospectively whether treatment with GA leads to clinical and paraclinical changes associated with neuroprotection in patients with relapsing-remitting (RR) MS. Primary aim of this clinical study was to determine serum BDNF levels in RR-MS patients who were started on GA as compared to patients who remained therapy-naive throughout 24 months. Secondary outcomes included relapses and EDSS, cognition, quality of life, fatigue and depression, BDNF expression levels on peripheral immune cells (FACS, RT-PCR), serum anti-myelin basic peptide (MBP) antibody status, evoked potential and cerebral MRI studies. While GA treatment did not alter serum levels or expression levels on peripheral immune cells of BDNF over time it resulted in a transient increase of serum IgG antibody response to MBP, mainly due to subtype IgG1 (p<0.05), after 3 months. However, no significant differences were found between GA treated and therapy-naive patients with regard to serum BDNF and intracellular BDNF expression levels, nerve conduction (including median and tibial nerve somatosensory, pattern-shift visual and upper and lower limb motor evoked potentials) or MRI (including volume of hyperintense lesions, volume of hypointense lesions after CE, mean diffusivity and fractional anisotropy) outcome parameters. In conclusion, our findings do not support a major impact of GA treatment on paraclinical markers of neuroprotection in human RR-MS.

  13. Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs.

    PubMed Central

    Knott, S A; Marklund, L; Haley, C S; Andersson, K; Davies, W; Ellegren, H; Fredholm, M; Hansson, I; Hoyheim, B; Lundström, K; Moller, M; Andersson, L

    1998-01-01

    A quantitative trait locus (QTL) analysis of growth and fatness data from a three generation pig experiment is presented. The population of 199 F2 animals was derived from a cross between wild boar and Large White pigs. Animals were typed for 240 markers spanning 23 Morgans of 18 autosomes and the X chromosome. A series of analyses are presented within a least squares framework. First, these identify chromosomes containing loci controlling trait variation and subsequently attempt to map QTLs to locations within chromosomes. This population gives evidence for a large QTL affecting back fat and another for abdominal fat segregating on chromosome 4. The best locations for these QTLs are within 4 cM of each other and, hence, this is likely to be a single QTL affecting both traits. The allele inherited from the wild boar causes an increase in fat deposition. A QTL for intestinal length was also located in the same region on chromosome 4 and could be the same QTL with pleiotropic effects. Significant effects, owing to multiple QTLs, for intestinal length were identified on chromosomes 3 and 5. A single QTL affecting growth rate to 30 kg was located on chromosome 13 such that the Large White allele increased early growth rate, another QTL on chromosome 10 affected growth rate from 30 to 70 kg and another on chromosome 4 affected growth rate to 70 kg. PMID:9611214

  14. Analyzing CRISM Data from mound B in Juventae Chasma, Mars, with the Multiple-Endmember Linear Spectral Unmixing Model MELSUM

    NASA Astrophysics Data System (ADS)

    Wendt, L.; Gross, C.; McGuire, P. C.; Combe, J.-P.; Neukum, G.

    2009-04-01

    Juventae Chasma, just north of Valles Marineris on Mars, contains several light-toned deposits (LTD), one of which is labelled mound B. Based on IR data from the imaging spectrometer OMEGA on Mars Express,[1] suggested kieserite for the lower part and gypsum for the upper part of the mound. In this study, we analyzed NIR data from the Compact Reconnaissance Imaging Spectrometer CRISM on MRO with the Multiple-Endmember Linear Spectral Unmixing Model MELSUM developed by Combe et al.[2]. We used CRISM data product FRT00009C0A from 1 to 2.6 µm. A novel, time-dependent volcano-scan technique [3] was applied to remove absorption bands related to CO2 much more effectively than the volcano-scan technique [4] that has been applied to CRISM and OMEGA data so far. In the classic SMA, a solution for the measured spectrum is calculated by a linear combination of all input spectra (which may come from a spectral library or from the image itself) at once. This can lead to negative coefficients, which have no physical meaning. MELSUM avoids this by calculating a solution for each possible combination of a subset of the reference spectra, with the maximum number of library spectra in the subset defined by the user. The solution with the lowest residual to the input spectrum is returned. We used MELSUM in a first step as similarity measure within the image by using averaged spectra from the image itself as input to MELSUM. This showed that three spectral units are enough to describe the variability in the data to first order: A lower, light-toned unit, an upper light-toned unit and a dark-toned unit. We then chose 34 laboratory spectra of sulfates, mafic minerals and iron oxides plus a spectrum for H2O ice as reference spectra for the unmixing of averaged spectra for each of these spectral regions. The best fit for the dark material was a combination of olivine, pyroxene and ice (present as cloud in the atmosphere and not on the surface). In agreement with [5], The lower unit was

  15. Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methods

    PubMed Central

    2015-01-01

    Background Computer-aided drug design has a long history of being applied to discover new molecules to treat various cancers, but it has always been focused on single targets. The development of systems biology has let scientists reveal more hidden mechanisms of cancers, but attempts to apply systems biology to cancer therapies remain at preliminary stages. Our lab has successfully developed various systems biology models for several cancers. Based on these achievements, we present the first attempt to combine multiple-target therapy with systems biology. Methods In our previous study, we identified 28 significant proteins--i.e., common core network markers--of four types of cancers as house-keeping proteins of these cancers. In this study, we ranked these proteins by summing their carcinogenesis relevance values (CRVs) across the four cancers, and then performed docking and pharmacophore modeling to do virtual screening on the NCI database for anti-cancer drugs. We also performed pathway analysis on these proteins using Panther and MetaCore to reveal more mechanisms of these cancer house-keeping proteins. Results We designed several approaches to discover targets for multiple-target cocktail therapies. In the first one, we identified the top 20 drugs for each of the 28 cancer house-keeping proteins, and analyzed the docking pose to further understand the interaction mechanisms of these drugs. After screening for duplicates, we found that 13 of these drugs could target 11 proteins simultaneously. In the second approach, we chose the top 5 proteins with the highest summed CRVs and used them as the drug targets. We built a pharmacophore and applied it to do virtual screening against the Life-Chemical library for anti-cancer drugs. Based on these results, wet-lab bio-scientists could freely investigate combinations of these drugs for multiple-target therapy for cancers, in contrast to the traditional single target therapy. Conclusions Combination of systems biology

  16. Vitamin D status and effect of interferon-β1a treatment on MRI activity and serum inflammation markers in relapsing-remitting multiple sclerosis.

    PubMed

    Røsjø, Egil; Myhr, Kjell-Morten; Løken-Amsrud, Kristin I; Bakke, Søren J; Beiske, Antonie G; Bjerve, Kristian S; Hovdal, Harald; Lilleås, Finn; Midgard, Rune; Pedersen, Tom; Šaltytė Benth, Jūratė; Torkildsen, Øivind; Wergeland, Stig; Michelsen, Annika E; Aukrust, Pål; Ueland, Thor; Holmøy, Trygve

    2015-03-15

    To explore if vitamin D modulates interferon-β1a treatment effects in relapsing-remitting multiple sclerosis, we examined relationships between serum vitamin D and magnetic resonance imaging (MRI) activity and ten systemic inflammation markers in 88 patients, before and during treatment. Odds ratios for all MRI parameters were negatively associated with vitamin D levels before therapy, but converged to equally low values irrespective of vitamin D status during treatment. During therapy, similar alterations of MRI activity and inflammation markers were found across patients categorized by mean vitamin D values. This suggests that vitamin D status has no major influence on interferon-β1a treatment effects.

  17. Analyzing Multiple Informant Data on Child and Adolescent Behavior Problems: Predictive Validity and Comparison of Aggregation Procedures

    ERIC Educational Resources Information Center

    van Dulmen, Manfred H. M.; Egeland, Byron

    2011-01-01

    We compared the predictive validity of five aggregation methods for multiple informant data on child and adolescent behavior problems. In addition, we compared the predictive validity of these aggregation methods with single informant scores. Data were derived from the Minnesota Longitudinal Study of Parents and Children (N = 175). Maternal and…

  18. Multiple Origins of Mutations in the mdr1 Gene—A Putative Marker of Chloroquine Resistance in P. vivax

    PubMed Central

    Schousboe, Mette L.; Ranjitkar, Samir; Rajakaruna, Rupika S.; Amerasinghe, Priyanie H.; Morales, Francisco; Pearce, Richard; Ord, Rosalyn; Leslie, Toby; Rowland, Mark; Gadalla, Nahla B.; Konradsen, Flemming; Bygbjerg, Ib C.; Roper, Cally; Alifrangis, Michael

    2015-01-01

    Background Chloroquine combined with primaquine has been the recommended antimalarial treatment of Plasmodium vivax malaria infections for six decades but the efficacy of this treatment regimen is threatened by chloroquine resistance (CQR). Single nucleotide polymorphisms (SNPs) in the multidrug resistance gene, Pvmdr1 are putative determinants of CQR but the extent of their emergence at population level remains to be explored. Objective In this study we describe the prevalence of SNPs in the Pvmdr1 among samples collected in seven P. vivax endemic countries and we looked for molecular evidence of drug selection by characterising polymorphism at microsatellite (MS) loci flanking the Pvmdr1 gene. Methods We examined the prevalence of SNPs in the Pvmdr1 gene among 267 samples collected from Pakistan, Afghanistan, Sri Lanka, Nepal, Sudan, São Tomé and Ecuador. We measured and diversity in four microsatellite (MS) markers flanking the Pvmdr1 gene to look evidence of selection on mutant alleles. Results SNP polymorphism in the Pvmdr1 gene was largely confined to codons T958M, Y976F and F1076L. Only 2.4% of samples were wildtype at all three codons (TYF, n = 5), 13.3% (n = 28) of the samples were single mutant MYF, 63.0% of samples (n = 133) were double mutant MYL, and 21.3% (n = 45) were triple mutant MFL. Clear geographic differences in the prevalence of these Pvmdr mutation combinations were observed. Significant linkage disequilibrium (LD) between Pvmdr1 and MS alleles was found in populations sampled in Ecuador, Nepal and Sri Lanka, while significant LD between Pvmdr1 and the combined 4 MS locus haplotype was only seen in Ecuador and Sri Lanka. When combining the 5 loci, high level diversity, measured as expected heterozygosity (He), was seen in the complete sample set (He = 0.99), while He estimates for individual loci ranged from 0.00–0.93. Although Pvmdr1 haplotypes were not consistently associated with specific flanking MS alleles, there was significant

  19. Acquisition of the Korean Imperfective Aspect Markers "-ko iss-" and "-a iss-" by Japanese Learners: A Multiple-Factor Account

    ERIC Educational Resources Information Center

    Ryu, Ju-Yeon; Horie, Kaoru; Shirai, Yasuhiro

    2015-01-01

    Although cross-linguistic research on second language tense-aspect acquisition has uncovered universal tendencies concerning the association between verbal semantics and tense-aspect markers, it is still unclear what mechanisms underlie this link. This study investigates the acquisition of two imperfective aspect markers ("-ko iss-" and…

  20. A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check

    PubMed Central

    Blenda, Anna; Fang, David D.; Rami, Jean-François; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

    2012-01-01

    A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. PMID:23029214

  1. DIFFERENTIAL ANALYZER

    DOEpatents

    Sorensen, E.G.; Gordon, C.M.

    1959-02-10

    Improvements in analog eomputing machines of the class capable of evaluating differential equations, commonly termed differential analyzers, are described. In general form, the analyzer embodies a plurality of basic computer mechanisms for performing integration, multiplication, and addition, and means for directing the result of any one operation to another computer mechanism performing a further operation. In the device, numerical quantities are represented by the rotation of shafts, or the electrical equivalent of shafts.

  2. Brain-Specific Cytoskeletal Damage Markers in Cerebrospinal Fluid: Is There a Common Pattern between Amyotrophic Lateral Sclerosis and Primary Progressive Multiple Sclerosis?

    PubMed

    Abdelhak, Ahmed; Junker, Andreas; Brettschneider, Johannes; Kassubek, Jan; Ludolph, Albert C; Otto, Markus; Tumani, Hayrettin

    2015-01-01

    Many neurodegenerative disorders share a common pathophysiological pathway involving axonal degeneration despite different etiological triggers. Analysis of cytoskeletal markers such as neurofilaments, protein tau and tubulin in cerebrospinal fluid (CSF) may be a useful approach to detect the process of axonal damage and its severity during disease course. In this article, we review the published literature regarding brain-specific CSF markers for cytoskeletal damage in primary progressive multiple sclerosis and amyotrophic lateral sclerosis in order to evaluate their utility as a biomarker for disease progression in conjunction with imaging and histological markers which might also be useful in other neurodegenerative diseases associated with affection of the upper motor neurons. A long-term benefit of such an approach could be facilitating early diagnostic and prognostic tools and assessment of treatment efficacy of disease modifying drugs. PMID:26263977

  3. Brain-Specific Cytoskeletal Damage Markers in Cerebrospinal Fluid: Is There a Common Pattern between Amyotrophic Lateral Sclerosis and Primary Progressive Multiple Sclerosis?

    PubMed

    Abdelhak, Ahmed; Junker, Andreas; Brettschneider, Johannes; Kassubek, Jan; Ludolph, Albert C; Otto, Markus; Tumani, Hayrettin

    2015-07-31

    Many neurodegenerative disorders share a common pathophysiological pathway involving axonal degeneration despite different etiological triggers. Analysis of cytoskeletal markers such as neurofilaments, protein tau and tubulin in cerebrospinal fluid (CSF) may be a useful approach to detect the process of axonal damage and its severity during disease course. In this article, we review the published literature regarding brain-specific CSF markers for cytoskeletal damage in primary progressive multiple sclerosis and amyotrophic lateral sclerosis in order to evaluate their utility as a biomarker for disease progression in conjunction with imaging and histological markers which might also be useful in other neurodegenerative diseases associated with affection of the upper motor neurons. A long-term benefit of such an approach could be facilitating early diagnostic and prognostic tools and assessment of treatment efficacy of disease modifying drugs.

  4. The Use of Multiple Regression and Path Analysis in Analyzing Success in Journalism at Iowa State University.

    ERIC Educational Resources Information Center

    Byerly, Richard Lee

    The general objectives of this study were to develop, investigate, and analyze the academic patterns of Iowa State journalism graduates from 1965-1970 and, with the use of multivariate statistical techniques, attempt to ascertain and determine possible inferences regarding their academic success. Grade point averages were considered as…

  5. Analyzing the trade-off between multiple memory controllers and memory channels on multi-core processor performance

    SciTech Connect

    Sancho Pitarch, Jose Carlos; Kerbyson, Darren; Lang, Mike

    2010-01-01

    Increasing the core-count on current and future processors is posing critical challenges to the memory subsystem to efficiently handle concurrent memory requests. The current trend to cope with this challenge is to increase the number of memory channels available to the processor's memory controller. In this paper we investigate the effectiveness of this approach on the performance of parallel scientific applications. Specifically, we explore the trade-off between employing multiple memory channels per memory controller and the use of multiple memory controllers. Experiments conducted on two current state-of-the-art multicore processors, a 6-core AMD Istanbul and a 4-core Intel Nehalem-EP, for a wide range of production applications shows that there is a diminishing return when increasing the number of memory channels per memory controller. In addition, we show that this performance degradation can be efficiently addressed by increasing the ratio of memory controllers to channels while keeping the number of memory channels constant. Significant performance improvements can be achieved in this scheme, up to 28%, in the case of using two memory controllers with each with one channel compared with one controller with two memory channels.

  6. Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data.

    PubMed

    Sand, Olivier; Thomas-Chollier, Morgane; Vervisch, Eric; van Helden, Jacques

    2008-01-01

    This protocol shows how to access the Regulatory Sequence Analysis Tools (RSAT) via a programmatic interface in order to automate the analysis of multiple data sets. We describe the steps for writing a Perl client that connects to the RSAT Web services and implements a workflow to discover putative cis-acting elements in promoters of gene clusters. In the presented example, we apply this workflow to lists of transcription factor target genes resulting from ChIP-chip experiments. For each factor, the protocol predicts the binding motifs by detecting significantly overrepresented hexanucleotides in the target promoters and generates a feature map that displays the positions of putative binding sites along the promoter sequences. This protocol is addressed to bioinformaticians and biologists with programming skills (notions of Perl). Running time is approximately 6 min on the example data set.

  7. Identification of QTLs of resistance to white mold in common bean from multiple markers by using Bayesian analysis.

    PubMed

    Lara, L A C; Santos, J B; Balestre, M; Lima, I A; Pamplona, A K A; Veloso, J S; Silva, P H

    2015-02-06

    In this study, we identified simple sequence repeat, ampli-fied fragment length polymorphism, and sequence-related amplified poly-morphism markers linked to quantitative trait loci (QTLs) for resistance to white mold disease in common bean progenies derived from a cross between lines CNFC 9506 and RP-2, evaluated using the oxalic acid test and using Bayesian analysis. DNA was extracted from 186 F₂ plants and their parental lines for molecular analysis. Fifteen experiments were car-ried out for phenotypic analysis, which included 186 F₂:₄ progenies, the F₁ generation, the F₂ generation, and the lines CNFC 9506, RP-2, and G122 as common treatments. A completely randomized experimental design with 3 replications was used in controlled environments. The adjusted means for the F₂:₄ generation were to identify QTLs by Bayesian shrink-age analysis. Significant differences were observed among the progenies for the reaction to white mold. The moving away method under the Bayes-ian approach was effective for identifying QTLs when it was not possible to obtain a genetic map because of low marker density. Using the Wald test, 25 markers identified QTLs for resistance to white mold, as well as 16 simple sequence repeats, 7 amplified fragment length polymorphisms, and 2 sequence-related amplified polymorphisms. The markers BM184, BM211, and PV-gaat001 showed low distances from QTLs related white mold resistance. In addition, these markers showed, signal effects with increasing resistance to white mold and high heritability in the analysis with oxalic acid, and thus, are promising for marker-assisted selection.

  8. Development of an inexact-variance hydrological modeling system for analyzing interactive effects of multiple uncertain parameters

    NASA Astrophysics Data System (ADS)

    Wang, C. X.; Li, Y. P.; Zhang, J. L.; Huang, G. H.

    2015-09-01

    Uncertainty assessment of hydrological model parameters has become one of the main topics due to their significant effects on prediction in arid and semi-arid river basins. Incorporation of uncertainty assessment within hydrological models can facilitate the calibration process and improve the degree of credibility to the subsequent prediction. In this study, an inexact-variance hydrological modeling system (IVHMS) is developed for assessing parameter uncertainty on modeling outputs in the Kaidu River Basin, China. Through incorporating the techniques of type-2 fuzzy analysis (T2FA) and analysis of variance (ANOVA) within the semi-distributed land use based runoff processes (SLURP) model, IVHMS can quantitatively evaluate the individual and interactive effects of multiple uncertain parameters expressed as type-2 fuzzy sets in the hydrological modeling system. The modeling outputs indicate a good performance of SLURP model in describing the daily streamflow at the Dashankou hydrological station. Uncertainty analysis is conducted through sampling from fuzzy membership functions under different α-cut levels. The results show that, under a lower degree of plausibility (i.e. a lower α-cut level), intervals for peak and average flows are both wider; while intervals of peak and average flows become narrower under a higher degree of plausibility. Results based on ANOVA reveal that (i) precipitation factor (PF), one of main factors dominating the runoff processes, should be paid more attention in order to enhance the model performance; (ii) retention constant for fast store (RS) controls the amount and timing of the outflow from saturated zone and has a highly nonlinear effect on the average flow; (iii) the interaction between retention constant for fast store (RF) and maximum capacity for fast store (MF) has statistically significant (p < 0.05) effect on modeling outputs through affecting the maximum water holding capacity and the soil infiltration rate. The findings can

  9. A SPR biosensor based on signal amplification using antibody-QD conjugates for quantitative determination of multiple tumor markers

    PubMed Central

    Wang, Huan; Wang, Xiaomei; Wang, Jue; Fu, Weiling; Yao, Chunyan

    2016-01-01

    The detection of tumor markers is very important in early cancer diagnosis; however, tumor markers are usually present at very low concentrations, especially in the early stages of tumor development. Surface plasmon resonance (SPR) is widely used to detect biomolecular interactions; it has inherent advantages of being high-throughput, real-time, and label-free technique. However, its sensitivity needs essential improvement for practical applications. In this study, we developed a signal amplification strategy using antibody-quantum dot (QD) conjugates for the sensitive and quantitative detection of α-fetoprotein (AFP), carcinoembryonic antigen (CEA) and cytokeratin fragment 21-1 (CYFRA 21-1) in clinical samples. The use of a dual signal amplification strategy using AuNP-antibody and antibody-QD conjugates increased the signal amplification by 50-folds. The constructed SPR biosensor showed a detection limit as low as 0.1 ng/mL for AFP, CEA, and CYFRA 21-1. Moreover, the results obtained using this SPR biosensor were consistent with those obtained using the electrochemiluminescence method. Thus, the constructed SPR biosensor provides a highly sensitive and specific approach for the detection of tumor markers. This SPR biosensor can be expected to be readily applied for the detection of other tumor markers and can offer a potentially powerful solution for tumor screening. PMID:27615417

  10. A SPR biosensor based on signal amplification using antibody-QD conjugates for quantitative determination of multiple tumor markers.

    PubMed

    Wang, Huan; Wang, Xiaomei; Wang, Jue; Fu, Weiling; Yao, Chunyan

    2016-01-01

    The detection of tumor markers is very important in early cancer diagnosis; however, tumor markers are usually present at very low concentrations, especially in the early stages of tumor development. Surface plasmon resonance (SPR) is widely used to detect biomolecular interactions; it has inherent advantages of being high-throughput, real-time, and label-free technique. However, its sensitivity needs essential improvement for practical applications. In this study, we developed a signal amplification strategy using antibody-quantum dot (QD) conjugates for the sensitive and quantitative detection of α-fetoprotein (AFP), carcinoembryonic antigen (CEA) and cytokeratin fragment 21-1 (CYFRA 21-1) in clinical samples. The use of a dual signal amplification strategy using AuNP-antibody and antibody-QD conjugates increased the signal amplification by 50-folds. The constructed SPR biosensor showed a detection limit as low as 0.1 ng/mL for AFP, CEA, and CYFRA 21-1. Moreover, the results obtained using this SPR biosensor were consistent with those obtained using the electrochemiluminescence method. Thus, the constructed SPR biosensor provides a highly sensitive and specific approach for the detection of tumor markers. This SPR biosensor can be expected to be readily applied for the detection of other tumor markers and can offer a potentially powerful solution for tumor screening. PMID:27615417

  11. Organic pollutant levels in an agricultural watershed: the importance of analyzing multiple matrices for assessing stream water pollution.

    PubMed

    Gonzalez, Mariana; Miglioranza, Karina S B; Grondona, Sebastían I; Silva Barni, Maria Florencia; Martinez, Daniel E; Peña, Aránzazu

    2013-04-01

    This study is aimed at analyzing the occurrence and transport of organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in the Quequén Grande river basin, as representative of a catchment under diffuse pollution sources. Pollutant levels in soils, river bottom sediments (RBS), streamwater (Sw), suspended particle materials (SPMs), macrophytes and muscle of silverside were determined by GC-ECD. Soil K(d) values for the current-used insecticides, endosulfans and cypermethrin, were established. Total levels (ng g(-1) dry weight) in soil ranged between 0.07–0.9 for OCPs, 0.03–0.37 for PCBs and 0.01–0.05 for PBDEs. Endosulfan insecticide (α- + b- + sulfate metabolite) represented up to 72.5% of OCPs. The low soil retention for α-endosulfan (K(d): 77) and endosulfan sulfate (K(d): 100) allows their transport to Sw, SPM and RBS. Levels of endosulfan in Sw in some cases exceeded the value postulated by international guidelines for aquatic biota protection (3 ng L(-1)). PCB and PBDE pollution was related to harbour, dumping sites and pile tire burning. Tri and hexa PCB congeners predominated in all matrices and exceeded the quality guideline value of 0.04 ng L(-1) in Sw. Considering levels in silverside muscle, none of the oral reference doses were exceeded, however, PCBs accounted for 18.6% of the total daily allowed ingest for a 70 kg individual. Although the levels of PCBs and OCPs in soil and RBS were low and did not go beyond quality guidelines, these compounds could still represent a risk to aquatic biota and humanbeings, and thus actions towards preventing this situation should be undertaken. PMID:23653907

  12. Organic pollutant levels in an agricultural watershed: the importance of analyzing multiple matrices for assessing stream water pollution.

    PubMed

    Gonzalez, Mariana; Miglioranza, Karina S B; Grondona, Sebastían I; Silva Barni, Maria Florencia; Martinez, Daniel E; Peña, Aránzazu

    2013-04-01

    This study is aimed at analyzing the occurrence and transport of organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in the Quequén Grande river basin, as representative of a catchment under diffuse pollution sources. Pollutant levels in soils, river bottom sediments (RBS), streamwater (Sw), suspended particle materials (SPMs), macrophytes and muscle of silverside were determined by GC-ECD. Soil K(d) values for the current-used insecticides, endosulfans and cypermethrin, were established. Total levels (ng g(-1) dry weight) in soil ranged between 0.07–0.9 for OCPs, 0.03–0.37 for PCBs and 0.01–0.05 for PBDEs. Endosulfan insecticide (α- + b- + sulfate metabolite) represented up to 72.5% of OCPs. The low soil retention for α-endosulfan (K(d): 77) and endosulfan sulfate (K(d): 100) allows their transport to Sw, SPM and RBS. Levels of endosulfan in Sw in some cases exceeded the value postulated by international guidelines for aquatic biota protection (3 ng L(-1)). PCB and PBDE pollution was related to harbour, dumping sites and pile tire burning. Tri and hexa PCB congeners predominated in all matrices and exceeded the quality guideline value of 0.04 ng L(-1) in Sw. Considering levels in silverside muscle, none of the oral reference doses were exceeded, however, PCBs accounted for 18.6% of the total daily allowed ingest for a 70 kg individual. Although the levels of PCBs and OCPs in soil and RBS were low and did not go beyond quality guidelines, these compounds could still represent a risk to aquatic biota and humanbeings, and thus actions towards preventing this situation should be undertaken.

  13. A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts.

    PubMed

    Moon, Hye Yun; Lee, Dong Wook; Sim, Gyu Hun; Kim, Hong-Jin; Hwang, Jee Youn; Kwon, Mun-Gyeong; Kang, Bo-Kyu; Kim, Jong Man; Kang, Hyun Ah

    2016-09-10

    The traditional yeast Saccharomyces cerevisiae has been widely used as a host system to produce recombinant proteins and metabolites of great commercial value. To engineer recombinant yeast that stably maintains expression cassettes without an antibiotic resistance gene, we developed new multiple integration cassettes by exploiting the non-transcribed spacer (NTS) of ribosomal DNA (rDNA) in combination with defective selection markers. The 5' and 3'-fragments of rDNA-NTS2 were used as flanking sequences for the expression cassettes carrying a set of URA3, LEU2, HIS3, and TRP1 selection markers with truncated promoters of different lengths. The integration numbers of NTS-based expression cassettes, ranging from one to ∼30 copies, showed a proportional increase with the extent of decreased expression of the auxotrophic markers. The NTS-based cassettes were used to construct yeast strains expressing the capsid protein of red-spotted grouper necrosis virus (RG-NNVCP) in a copy number-dependent manner. Oral administration of the recombinant yeast, harboring ∼30 copies of the integrated RG-NNVCP cassettes, provoked efficient immune responses in mice. In contrast, for the NTS cassettes expressing a truncated 3-hydroxyl-3-methylglutaryl-CoA reductase, the integrant carrying only 4 copies was screened as the highest producer of squalene, showing a 150-fold increase compared to that of the wild-type strain. The multiple integrated cassettes were stably retained under prolonged nonselective conditions. Altogether, our results strongly support that rDNA-NTS integrative cassettes are useful tools to construct recombinant yeasts carrying optimal copies of a desired expression cassette without an antibiotic marker gene, which are suitable as oral vaccines or feed additives for animal and human consumption. PMID:27411901

  14. A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts.

    PubMed

    Moon, Hye Yun; Lee, Dong Wook; Sim, Gyu Hun; Kim, Hong-Jin; Hwang, Jee Youn; Kwon, Mun-Gyeong; Kang, Bo-Kyu; Kim, Jong Man; Kang, Hyun Ah

    2016-09-10

    The traditional yeast Saccharomyces cerevisiae has been widely used as a host system to produce recombinant proteins and metabolites of great commercial value. To engineer recombinant yeast that stably maintains expression cassettes without an antibiotic resistance gene, we developed new multiple integration cassettes by exploiting the non-transcribed spacer (NTS) of ribosomal DNA (rDNA) in combination with defective selection markers. The 5' and 3'-fragments of rDNA-NTS2 were used as flanking sequences for the expression cassettes carrying a set of URA3, LEU2, HIS3, and TRP1 selection markers with truncated promoters of different lengths. The integration numbers of NTS-based expression cassettes, ranging from one to ∼30 copies, showed a proportional increase with the extent of decreased expression of the auxotrophic markers. The NTS-based cassettes were used to construct yeast strains expressing the capsid protein of red-spotted grouper necrosis virus (RG-NNVCP) in a copy number-dependent manner. Oral administration of the recombinant yeast, harboring ∼30 copies of the integrated RG-NNVCP cassettes, provoked efficient immune responses in mice. In contrast, for the NTS cassettes expressing a truncated 3-hydroxyl-3-methylglutaryl-CoA reductase, the integrant carrying only 4 copies was screened as the highest producer of squalene, showing a 150-fold increase compared to that of the wild-type strain. The multiple integrated cassettes were stably retained under prolonged nonselective conditions. Altogether, our results strongly support that rDNA-NTS integrative cassettes are useful tools to construct recombinant yeasts carrying optimal copies of a desired expression cassette without an antibiotic marker gene, which are suitable as oral vaccines or feed additives for animal and human consumption.

  15. Microsatellite markers in plants and insects part II: Databases and in silico tools for microsatellite mining and analyzing population genetic stratification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nucleotide sequence information available in searchable sequence databases and the free in silico software with which to extract and analyze microsatellite data continues to grow at a rapid rate across eukaryote taxa. The sheer amount of information available means that a comprehensive or exhaustive...

  16. Altered expression of oligodendrocyte and neuronal marker genes predicts the clinical onset of autoimmune encephalomyelitis and indicates the effectiveness of multiple sclerosis-directed therapeutics.

    PubMed

    Evangelidou, Maria; Karamita, Maria; Vamvakas, Sotiris-Spyros; Szymkowski, David E; Probert, Lesley

    2014-05-01

    Experimental autoimmune encephalomyelitis (EAE) is a valuable model for studying immunopathology in multiple sclerosis (MS) and for exploring the interface between autoimmune responses and CNS tissue that ultimately leads to lesion development. In this study, we measured gene expression in mouse spinal cord during myelin oligodendrocyte gp35-55 peptide-induced EAE, using quantitative RT-PCR, to identify gene markers that monitor individual hallmark pathological processes. We defined a small panel of genes whose longitudinal expression patterns provided insight into the timing, interrelationships, and mechanisms of individual disease processes and the efficacy of therapeutics for the treatment of MS. Earliest transcriptional changes were upregulation of Il17a and sharp downregulation of neuronal and oligodendrocyte marker genes preceding clinical disease onset, whereas neuroinflammatory markers progressively increased as symptoms and tissue lesions developed. EAE-induced gene-expression changes were not altered in mice deficient in IKKβ in cells of the myeloid lineage compared with controls, but the administration of a selective inhibitor of soluble TNF to mice from the day of immunization delayed changes in the expression of innate inflammation, myelin, and neuron markers from the presymptomatic phase. Proof of principle that the gene panel shows drug screening potential was obtained using a well-established MS therapeutic, glatiramer acetate. Prophylactic treatment of mice with glatiramer acetate normalized gene marker expression, and this correlated with the level of therapeutic success. These results show that neurons and oligodendrocytes are highly sensitive to CNS-directed autoimmunity before the development of clinical symptoms and immunopathology and reveal a role for soluble TNF in mediating the earliest changes in gene expression.

  17. E-cadherin in non-tumor epithelium adjacent to oral cancer as risk marker for the development of multiple tumors.

    PubMed

    González-Moles, M A; Bravo, M; Ruiz-Avila, I; Gil-Montoya, J A; Acebal, F; Esteban, F

    2013-03-01

    Our aim was to find out whether the loss of E-cadherin is a risk factor for the development of multiple tumours in the oral cavity and whether it could serve as a diagnostic marker for oral premalignant fields. We studied 77 oral squamous cell carcinomas (SCC) with associated non-tumour epithelia from 61 patients. Immunohistochemical studies (antibody NHC-38) were used to investigate E-cadherin expression, which was completely lost in basal (48% of cases) and parabasal (43%) layers of non-tumour epithelia close to the tumour and in basal (47%) and parabasal (38%) layers of non-tumour epithelia distant from the tumour. In multiple tumours E-cadherin expression was significantly lower than in single tumours in the basal, parabasal layers, and the middle third of close (p=0.002, <0.001, <0.001) and distant (p=0.041, p<0.001, p=0.005) non-tumour epithelia, respectively. Downregulation of E-cadherin may be valuable as a risk marker for the development of multiple tumours in the oral cavity and for the diagnosis of premalignant fields.

  18. Genetic diversity of wild and domesticated stocks of Thai abalone, Haliotis asinina (Haliotidae), analyzed by single-strand conformational polymorphism of AFLP-derived markers.

    PubMed

    Praipue, P; Klinbunga, S; Jarayabhand, P

    2010-01-01

    Amplified fragment length polymorphism (AFLP) analysis was carried out on representative individuals of wild Haliotis asinina using 64 primer combinations. Nine polymorphic AFLPs were cloned and sequenced. Sequence-specific primers were designed from six AFLP-derived fragments. Three sequence-characterized amplified region (SCAR) markers (HaSCAR(320), HaSCAR(295), HaSCAR(327)) were selected for genotyping of 8-month-old domesticated stocks of H. asinina cultured separately at Sichang Marine Science Research and Training Station (N = 95) and at a hatchery in Trang province (N = 40) using single-strand conformational polymorphism analysis. Genotypes of wild abalone originating from Talibong Island (N = 25), Cambodia (N = 22), and the P(0) progeny established from Samet Island founders (N = 20) were also investigated. Significant genetic differentiation (P<0.0001 for the exact test and F(ST) = 0.8759-0.8919, P<0.001) between abalone from the Gulf of Thailand (Cambodia and Samet Island--east) and the Andaman Sea (Talibong Island--west) were observed. This demonstrated the strong biogeographic structure of H. asinina in Thai waters. Non-overlapping composite genotypes for wild abalone from different coastal regions allow us to determine founder contributions in domesticated abalone stocks. Almost all Sichang Marine Science Research and Training Station and the Trang province hatchery stocks exhibited the east coast genotypes (97% of the 135 samples). We suggest that abalone from the east coast population have better survival rates under cultivated conditions than those from the west coast population.

  19. Concept and simulation study of a novel localization method for robotic endoscopic capsules using multiple positron emission markers

    SciTech Connect

    Than, Trung Duc Alici, Gursel Zhou, Hao Li, Weihua; Harvey, Steven

    2014-07-15

    Purpose: Over the last decade, wireless capsule endoscope has been the tool of choice for noninvasive inspection of the gastrointestinal tract, especially in the small intestine. However, the latest clinical products have not been equipped with a sufficiently accurate localization system which makes it difficult to determine the location of intestinal abnormalities, and to apply follow-up interventions such as biopsy or drug delivery. In this paper, the authors present a novel localization method based on tracking three positron emission markers embedded inside an endoscopic capsule. Methods: Three spherical {sup 22}Na markers with diameters of less than 1 mm are embedded in the cover of the capsule. Gamma ray detectors are arranged around a patient body to detect coincidence gamma rays emitted from the three markers. The position of each marker can then be estimated using the collected data by the authors’ tracking algorithm which consists of four consecutive steps: a method to remove corrupted data, an initialization method, a clustering method based on the Fuzzy C-means clustering algorithm, and a failure prediction method. Results: The tracking algorithm has been implemented inMATLAB utilizing simulation data generated from the Geant4 Application for Emission Tomography toolkit. The results show that this localization method can achieve real-time tracking with an average position error of less than 0.4 mm and an average orientation error of less than 2°. Conclusions: The authors conclude that this study has proven the feasibility and potential of the proposed technique in effectively determining the position and orientation of a robotic endoscopic capsule.

  20. Multiple-tracer gas analyzer

    SciTech Connect

    Uhl, J.E.

    1982-01-01

    A multi-gas tracer system has been designed, built, and used on an explosively fractured oil shale rubble bed. This paper deals exclusively with the hardware, software, and overall operation of the tracer system. This system is a field portable, self-contained unit, which utilizes a mass spectrometer for gas analysis. The unit has a 20 channel sample port capability and is controlled by a desk top computer. The system is configured to provide a dynamic sensitivity range of up to six orders of magnitude. A roots blower is manifolded to the unit to provide continuous flow in all sample lines. The continuous flow process allows representative samples as well as decreasing the time between each measurement. Typical multiplex cycle time to evaluate four unique gases is approximately 12 seconds.

  1. Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease-digested DNA: identification of markers tightly linked to the supernodulation locus in soybean.

    PubMed

    Caetano-Anollés, G; Bassam, B J; Gresshoff, P M

    1993-10-01

    Multiple endonuclease digestion of template DNA or amplification products can increase significantly the detection of polymorphic DNA in fingerprints generated by multiple arbitrary amplicon profiling (MAAP). This coupling of endonuclease cleavage and amplification of arbitrary stretches of DNA, directed by short oligonucleotide primers, readily allowed distinction of closely related fungal and bacterial isolates and plant cultivars. MAAP analysis of cleaved template DNA enabled the identification of molecular markers linked to a developmental locus of soybean (Glycine max L. Merrill). Ethyl methane sulfonate (EMS)-induced supernodulating, near-isogenic lines altered in the nts locus, which controls nodule formation, could be distinguished from each other and from the parent cultivar by amplification of template pre-digested with 2-3 restriction enzymes. A total of 42 DNA polymorphisms were detected using only 19 octamer primers. In the absence of digestion, 25 primers failed to differentiate these soybean genotypes. Several polymorphic products co-segregated tightly with the nts locus in F2 families from crosses between the allelic mutants nts382 and nts1007 and the ancestral G. soja Sieb. & Succ. PI468.397. Our results suggest that EMS is capable of inducing extensive DNA alterations, probably around discrete mutational hot-spots. EMS-induced DNA polymorphisms may constitute sequence-tagged markers diagnostic of specific genomic regions.

  2. Comprehensive peptide marker identification for the detection of multiple nut allergens using a non-targeted LC-HRMS multi-method.

    PubMed

    Korte, Robin; Lepski, Silke; Brockmeyer, Jens

    2016-05-01

    Food allergies have emerged as a global problem over the last few decades; therefore, reliable and sensitive analytical methods to ensure food safety for allergic consumers are required. The application of mass spectrometry is of growing interest in this field and several procedures based on low resolution tandem mass spectrometry using single tryptic peptides as analytical targets have recently been described. However, a comprehensive survey of marker peptides for the development of multi-methods is still missing, as is a consensus guide to marker identification. In this study, we therefore report a consistent approach to the development of liquid chromatography-mass spectrometry (LC-MS) multi-screening methods for the detection of allergens in food matrices. Proteotypic peptides were identified by a shotgun proteomics approach and verified through a thorough investigation of specificity and sensitivity. On the basis of this procedure, we identified 44 suitable tryptic marker peptides from six allergenic nut species and developed the first analytical LC-MS method for the detection of trace nut contaminations in processed foods using high resolution mass spectrometry (HRMS). The analysis of spiked matrix samples gave limits of detection (LODs) below 10 μg/g for several nuts; these LODs are comparable with routinely used methods such as ELISA and PCR. Notably, the HRMS approach can be used in an untargeted fashion to identify multiple allergens also retrospectively. In conclusion, we present here the so far largest consensus set of analytical markers from nut allergens and to the best of our knowledge the first multi-allergen method based on LC-HRMS.

  3. Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

    PubMed Central

    2011-01-01

    Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for

  4. Using multiple markers to elucidate the ancient, historical and modern relationships among North American Arctic dog breeds.

    PubMed

    Brown, S K; Darwent, C M; Wictum, E J; Sacks, B N

    2015-12-01

    Throughout most of the Americas, post-colonial dogs largely erased the genetic signatures of pre-historical dogs. However, the North American Arctic harbors dogs that are potentially descended from pre-historical ancestors, as well as those affected by post-colonial translocations and admixtures. In particular, Inuit dogs from Canada and Greenland are thought to descend from dogs associated with Thule peoples, who relied on them for transportation ca. 1000 years ago. Whether Thule dogs reflected an earlier colonization by Paleoeskimo dogs ca. 4500 years ago is unknown. During the Alaskan Gold Rush, additional sled dogs, possibly of post-colonial derivation, the Alaskan Husky, Malamute and Siberian Husky, were used in the Arctic. The genealogical relationships among and origins of these breeds are unknown. Here we use autosomal, paternal and maternal DNA markers to (1) test the hypothesis that Inuit dogs have retained their indigenous ancestry, (2) characterize their relationship to one another and to other Arctic breeds, and (3) estimate the age of North American indigenous matrilines and patrilines. On the basis of the agreement of all three markers we determined that Inuit dogs have maintained their indigenous nature, and that they likely derive from Thule dogs. In addition, we provide support for previous research that the Inuit dogs from Canada and Greenland dog should not be distinguished as two breeds. The Alaskan Husky displayed evidence of European introgression, in contrast to the Malamute and Siberian Husky, which appear to have maintained most of their ancient Siberian ancestry.

  5. DNA isolation from teeth by organic extraction and identification of sex of the individual by analyzing the AMEL gene marker using PCR

    PubMed Central

    Praveen Kumar, Subramanian Thangaraj; Aswath, Nalini

    2016-01-01

    Background: To identify the sex of the deceased individual from dental hard tissue such as enamel and dentine. Objective: To isolate the DNA from dental hard tissue (enamel and dentin) from teeth extracted for prophylactic purpose, to assess the quality and purity of DNA and to identify the sex using polymerized chain reactor (PCR). Materials and Methods: DNA was extracted following phenol/chloroform (organic) extraction from 20 male and 20 female teeth. The samples that contain the amelogenin gene (amel) were amplified by PCR. The products of the PCR were run on agarose gel with ethidium bromide staining on gel documentation system. Results: The results on the gel showed the presence of X-specific bands at 212 bp and Y-specific bands at 218 bp. Males were distinguished from females by the presence of two bands whereas female samples showed only one, that is, X-specific band on the gel. The gender from the known samples was determined with complete accuracy, and the results were analyzed statistically by the Chi-square test. Conclusion: In our study, the PCR-based method showed 100% specificity and sensitivity. PMID:27051218

  6. Insights into the phylogeny of sporadotrichid ciliates (Protozoa, Ciliophora: Hypotricha) based on genealogical analyses of multiple molecular markers

    NASA Astrophysics Data System (ADS)

    Hu, Xiaoyan; Hu, Xiaozhong; Al-Rasheid, Khaled A. S.; Al-Farraj, Saleh A.; Song, Weibo

    2011-01-01

    The sporadotrichid ciliates are an especially diverse group. A number of investigators have studied the morphological, morphogenetic, and molecular relationships among members of this group. Despite this, a consistent classification is still lacking and several important questions about the phylogenetic relationships within this group remain unsolved. To improve our understanding of these relationships, we constructed phylogenetic trees using the nucleotide sequences of the small-subunit rRNA (SSrRNA) gene and amino acid sequences of actin I and α-tubulin. Analyses of SSrRNA gene sequences indicated that: 1) the Sporadotrichida sensu Lynn (2008) and the Oxytrichidae are polyphyletic; 2) the Uroleptus species, which are classified to urostylids, formed a sister group with the oxytrichids; 3) Halteria grandinella, which is grouped morphologically with oligotrich species, clustered within the oxytrichids. These results are congruent with previous studies based on SSrRNA gene sequences. However, the amino acid sequences of actin I and α-tubulin yielded different topologies. The main results are: 1) in all phylogenetic trees, the genus Oxytricha was paraphyletic; 2) Uroleptus was sister to a subset of Urostyla and Holosticha, albeit with low supporting values; 3) Halteria grandinella was separated distantly from the Oxytrichidae in trees inferred from actin I amino acid sequences but clustered with oligotrichids in the α-tubulin analysis. The inconsistency among the trees inferred from these different molecular markers may be caused by rapidly accumulated genetic characterizations of ciliates. Further studies with additional molecular markers and sampling of more taxa are expected to better address the relationships among sporadotrichids.

  7. Objective markers for sleep propensity: comparison between the Multiple Sleep Latency Test and the Vigilance Algorithm Leipzig.

    PubMed

    Olbrich, Sebastian; Fischer, Marie M; Sander, Christian; Hegerl, Ulrich; Wirtz, Hubert; Bosse-Henck, Andrea

    2015-08-01

    The regulation of wakefulness is important for high-order organisms. Its dysregulation is involved in the pathomechanism of several psychiatric disorders. Thus, a tool for its objective but little time-consuming assessment would be of importance. The Vigilance Algorithm Leipzig allows the objective measurement of sleep propensity, based on a single resting state electroencephalogram. To compare the Vigilance Algorithm Leipzig with the standard for objective assessment of excessive daytime sleepiness, a four-trial Multiple Sleep Latency Test in 25 healthy subjects was conducted. Between the first two trials, a 15-min, 25-channel resting electroencephalogram was recorded, and Vigilance Algorithm Leipzig was used to classify the sleep propensity (i.e., type of vigilance regulation) of each subject. The results of both methods showed significant correlations with the Epworth Sleepiness Scale (ρ = -0.70; ρ = 0.45, respectively) and correlated with each other (ρ = -0.54). Subjects with a stable electroencephalogram-vigilance regulation yielded significant increased sleep latencies compared with an unstable regulation (multiple sleep latency 898.5 s versus 549.9 s; P = 0.03). Further, Vigilance Algorithm Leipzig classifications allowed the identification of subjects with average sleep latencies <6 min with a sensitivity of 100% and a specificity of 77%. Thus, Vigilance Algorithm Leipzig provides similar information on wakefulness regulation in comparison to the much more cost- and time-consuming Multiple Sleep Latency Test. Due to its high sensitivity and specificity for large sleep propensity, Vigilance Algorithm Leipzig could be an effective and reliable alternative to the Multiple Sleep Latency Test, for example for screening purposes in large cohorts, where objective information about wakefulness regulation is needed.

  8. A tale of two siblings: multiple paternity in big brown bats (Eptesicus fuscus) demonstrated using microsatellite markers.

    PubMed

    Vonhof, M J; Barber, D; Fenton, M B; Strobeck, C

    2006-01-01

    In many bat species, the opportunity for sperm competition or other mechanisms of post-copulatory paternity biasing is thought to be great, due to the long delay between copulation and fertilization, demonstrated sperm storage capabilities, and observed promiscuity. We present the results of the first study to assess whether litters of big brown bats (Eptesicus fuscus) containing dizygotic twins share the same father. We sampled 26 mother-offspring triads from three colonies in Indiana and Illinois, as well as 299 additional adults (237 females and 62 males) from these colonies and six other maternity colonies in the same area in 1997-1998. All individuals were genotyped at nine highly variable autosomal microsatellite loci and one X-linked locus. We assessed multiple paternity using autosomal and X-linked locus exclusions, and using maximum-likelihood methods. All methods confirmed multiple paternity within litters, and the maximum-likelihood analyses indicated that almost half of the sampled litters were composed of maternal half-siblings rather than full-siblings. Our results highlight the potential importance of post-copulatory mechanisms of paternity determination in the mating system of big brown bats, and have important implications for gene flow and population structuring in this species. PMID:16367843

  9. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    PubMed

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  10. Phylogenetic Reconstruction and DNA Barcoding for Closely Related Pine Moth Species (Dendrolimus) in China with Multiple Gene Markers

    PubMed Central

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), “best close match” (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10–97.40%, while ITS1 and ITS2 obtained a success rate of 64.70–81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition

  11. Lateral Ventricular Cerebrospinal Fluid Diffusivity as a Potential Neuroimaging Marker of Brain Temperature in Multiple Sclerosis: A Hypothesis and Implications

    PubMed Central

    Hasan, Khader M.; Lincoln, John A.; Nelson, Flavia M.; Wolinsky, Jerry S.; Narayana, Ponnada A.

    2014-01-01

    In this retrospective study we tested the hypothesis that the net effect of impaired electrical conduction and therefore increased heat dissipation in multiple sclerosis (MS) results in elevated lateral ventricular (LV) cerebrospinal fluid (CSF) diffusivity as a measure of brain temperature estimated in vivo using diffusion tensor imaging (DTI). We used validated DTI-based segmentation methods to obtain normalized LV-CSF volume and its corresponding CSF diffusivity in 108 MS patients and 103 healthy controls in the age range of 21-63 years. The LV CSF diffusivity was ~2% higher in MS compared to controls that corresponds to a temperature rise of ~1 °C that could not be explained by changes in the CSF viscosity due to altered CSF protein content in MS. The LV diffusivity decreased with age in healthy controls (r=−0.29; p=0.003), but not in MS (r=0.15; p=0.11), possibly related to MS pathology. Age-adjusted LV diffusivity increased with lesion load (r=0.518; p=1x10−8). Our data suggest that the total brain lesion load is the primary contributor to the increase in LV CSF diffusivity in MS. These findings suggest that LV diffusivity is a potential in vivo biomarker of the mismatch between heat generation and dissipation in MS. We also discuss limitations and possible confounders. PMID:25485790

  12. Lateral ventricular cerebrospinal fluid diffusivity as a potential neuroimaging marker of brain temperature in multiple sclerosis: a hypothesis and implications.

    PubMed

    Hasan, Khader M; Lincoln, John A; Nelson, Flavia M; Wolinsky, Jerry S; Narayana, Ponnada A

    2015-04-01

    In this retrospective study we tested the hypothesis that the net effect of impaired electrical conduction and therefore increased heat dissipation in multiple sclerosis (MS) results in elevated lateral ventricular (LV) cerebrospinal fluid (CSF) diffusivity as a measure of brain temperature estimated in vivo using diffusion tensor imaging (DTI). We used validated DTI-based segmentation methods to obtain normalized LV-CSF volume and its corresponding CSF diffusivity in 108 MS patients and 103 healthy controls in the age range of 21-63 years. The LV CSF diffusivity was ~2% higher in MS compared to controls that correspond to a temperature rise of ~1°C that could not be explained by changes in the CSF viscosity due to altered CSF protein content in MS. The LV diffusivity decreased with age in healthy controls (r=-0.29; p=0.003), but not in MS (r=0.15; p=0.11), possibly related to MS pathology. Age-adjusted LV diffusivity increased with lesion load (r=0.518; p=1×10(-8)). Our data suggest that the total brain lesion load is the primary contributor to the increase in LV CSF diffusivity in MS. These findings suggest that LV diffusivity is a potential in vivo biomarker of the mismatch between heat generation and dissipation in MS. We also discuss limitations and possible confounders. PMID:25485790

  13. Phylogenetic analysis with multiple markers indicates repeated loss of the adult medusa stage in Campanulariidae (Hydrozoa, Cnidaria).

    PubMed

    Govindarajan, Annette F; Boero, Ferdinando; Halanych, Kenneth M

    2006-03-01

    The Campanulariidae is a group of leptomedusan hydroids (Hydrozoa, Cnidaria) that exhibit a diverse array of life cycles ranging from species with a free medusa stage to those with a reduced or absent medusa stage. Perhaps the best-known member of the taxon is Obelia which is often used as a textbook model of hydrozoan life history. However, Obelia medusae have several unique features leading to a hypothesis that Obelia arose, in a saltational fashion, from an ancestor that lacked a medusa, possibly representing an example of a rare evolutionary reversal. To address the evolution of adult sexual stages in Campanulariidae, a molecular phylogenetic approach was employed using two nuclear (18S rDNA and calmodulin) and two mitochondrial (16S rDNA and cytochrome c oxidase subunit I) genes. Prior to the main analysis, we conducted a preliminary analysis of leptomedusan taxa which suggests that Campanulariidae as presently considered needs to be redefined. Campanulariid analyses are consistent with morphological understanding in that three major clades are recovered. However, several recognized genera are not monophyletic calling into question some "diagnostic" features. Furthermore, ancestral states were reconstructed using parsimony, and a sensitivity analysis was conducted to investigate possible evolutionary transitions in life-history stages. The results indicate that life-cycle transitions have occurred multiple times, and that Obelia might be derived from an ancestor with Clytia-like features.

  14. Efficacy of Fish Oil on Serum of TNFα, IL-1β, and IL-6 Oxidative Stress Markers in Multiple Sclerosis Treated with Interferon Beta-1b

    PubMed Central

    Ramirez-Ramirez, V.; Macias-Islas, M. A.; Ortiz, G. G.; Pacheco-Moises, F.; Torres-Sanchez, E. D.; Sorto-Gomez, T. E.; Cruz-Ramos, J. A.; Orozco-Aviña, G.; Celis de la Rosa, A. J.

    2013-01-01

    Multiple sclerosis (MS) is a chronic inflammatory disease, which leads to focal plaques of demyelination and tissue injury in the central nervous system. Oxidative stress is also thought to promote tissue damage in multiple sclerosis. Current research findings suggest that omega-3 polyunsaturated fatty acids (PUFAs) such as eicosapenta-enoic acid (EPA) and docosahexaenoic acid (DHA) contained in fish oil may have anti-inflammatory, antioxidant, and neuroprotective effects. The aim of the present work was to evaluate the efficacy of fish oil supplementation on serum proinflammatory cytokine levels, oxidative stress markers, and disease progression in MS. 50 patients with relapsing-remitting MS were enrolled. The experimental group received orally 4 g/day of fish oil for 12 months. The primary outcome was serum TNFα levels; secondary outcomes were IL-1β 1b, IL-6, nitric oxide catabolites, lipoperoxides, progression on the expanded disability status scale (EDSS), and annualized relapses rate (ARR). Fish oil treatment decreased the serum levels of TNFα, IL-1β, IL-6, and nitric oxide metabolites compared with placebo group (P ≤ 0.001). There was no significant difference in serum lipoperoxide levels during the study. No differences in EDSS and ARR were found. Conclusion. Fish oil supplementation is highly effective in reducing the levels of cytokines and nitric oxide catabolites in patients with relapsing-remitting MS. PMID:23861993

  15. Simultaneous time course analysis of multiple markers based on DNA microarray in incised wound in skeletal muscle for wound aging.

    PubMed

    Hassan Gaballah, Mohammed; Fukuta, Mamiko; Maeno, Yoshitaka; Seko-Nakamura, Yoshimi; Monma-Ohtaki, Jun; Shibata, Yuka; Kato, Hideaki; Aoki, Yasuhiro; Takamiya, Masataka

    2016-09-01

    Assessment of incised wound age in skeletal muscles is important because fatal injuries are often complicated with muscle involvement. Transcriptome of injured skeletal muscle along with histopathological and immunohistochemistry staining, were analyzed to explore the biological effect of incised injuries using a mouse incised injury model. An incisional wound was made at the biceps femoris muscle of anesthetized mice, and the muscles were sampled at 6, 12, 24, 36 and 48h post-injury. DNA microarray analysis using RNA extracted from the muscle samples of 12h post-injury identified 3,655 upregulated and 3,583 downregulated genes. Referring to the results of the gene ontology and gene expression pathway analysis, time course expression of five cytokines, namely chemokine (C-C motif) ligand 4 (CCL4), chemokine (C-X-C motif) ligand 5 (CXCL5), interleukin-1 beta (IL-1β), interleukin- 6 (IL-6) and interleukin-7 (IL-7), were analyzed by quantative reverse transcription PCR (qRT-PCR). CXCL5 was the most upregulated gene throughout the post-injury period with higher expression from 6 through 36h post injury. Upregulation of CCL4 and IL-1β was also persisted until 36h post injury. IL-6 mRNA was highly and rapidly expressed at 6h post-injury followed by significant decrease at 12h. Unlike other four cytokines, IL-7 showed slow and steady increasing over time until 48h post-injury. Immunohistochemical staining of post-injury samples showed gradual mild increase of staining intensity proportional to increasing time points especially around the wound edges. The present study highlights the unique dynamics of each cytokine and reflects their roles in the process of muscle wound healing, and suggests the potential of them as a tool for forensic wound age estimation.

  16. NFKB1 -94ins/delATTG polymorphism is a novel prognostic marker in first line-treated multiple myeloma.

    PubMed

    Varga, Gergely; Mikala, Gábor; Andrikovics, Hajnalka; Koszarska, Magdalena; Balassa, Katalin; Ádám, Emma; Kozma, András; Tordai, Attila; Masszi, Tamás

    2015-03-01

    Nuclear factor kappa B (NFKB) plays an important role in multiple myeloma (MM), and bortezomib affects this pathway. We retrospectively analysed the effect of the NFKB1 -94ins/delATTG polymorphism on the survival of 295 MM patients treated at a single centre. The median progression-free survival (PFS) was 790 (659-921) d in patients with NFKB1 homozygous insertion genotype (I/I, n = 99) and 624 (515-733) d in deletion-carriers (I/D&D/D, n = 196, P = 0·013). In multivariate analysis, I/I carriers showed a favourable PFS compared to I/D&D/D with a hazard ratio of 0·622 (0·457-0·847), P = 0·003, in addition to international staging system (ISS) score, fluorescence in situ hybridization (FISH) risk score, age and bortezomib treatment. I/I patients benefited more from bortezomib treatment [PFS 902 (703-1101) and 580 (343-817), P = 0·008] than I/D&D/D patients [PFS 659 (487-831) and 488 (323-653), P = 0·531]; in addition the beneficial effect of low ISS score was not observed in the I/D&D/D group [PFS 639 (454-824) and 650 (458-842), P = 0·226], while it was clear in I/I patients [PFS 1140 (803-1477) and 580 (408-752), P < 0·001]. We conclude that homozygous carriers of the insertion allele of the NFKB1 -94ins/delATTG polymorphism have a better prognosis and probably benefit more from bortezomib treatment than MM patients carrying the deletion allele.

  17. Managing Multiple Mandates: A System of Systems Model to Analyze Strategies for Producing Cellulosic Ethanol and Reducing Riverine Nitrate Loads in the Upper Mississippi River Basin.

    PubMed

    Housh, Mashor; Yaeger, Mary A; Cai, Ximing; McIsaac, Gregory F; Khanna, Madhu; Sivapalan, Murugesu; Ouyang, Yanfeng; Al-Qadi, Imad; Jain, Atul K

    2015-10-01

    Implementing public policies often involves navigating an array of choices that have economic and environmental consequences that are difficult to quantify due to the complexity of multiple system interactions. Implementing the mandate for cellulosic biofuel production in the Renewable Fuel Standard (RFS) and reducing hypoxia in the northern Gulf of Mexico by reducing riverine nitrate-N loads represent two such cases that overlap in the Mississippi River Basin. To quantify the consequences of these interactions, a system of systems (SoS) model was developed that incorporates interdependencies among the various subsystems, including biofuel refineries, transportation, agriculture, water resources and crop/ethanol markets. The model allows examination of the impact of imposing riverine nitrate-N load limits on the biofuel production system as a whole, including land use change and infrastructure needs. The synergies of crop choice (first versus second generation biofuel crops), infrastructure development, and environmental impacts (streamflow and nitrate-N load) were analyzed to determine the complementarities and trade-offs between environmental protection and biofuel development objectives. For example, the results show that meeting the cellulosic biofuel target in the RFS using Miscanthus x giganteus reduces system profits by 8% and reduces nitrate-N loads by 12% compared to the scenario without a mandate. However, greater water consumption by Miscanthus is likely to reduce streamflow with potentially adverse environmental consequences that need to be considered in future decision making.

  18. Managing Multiple Mandates: A System of Systems Model to Analyze Strategies for Producing Cellulosic Ethanol and Reducing Riverine Nitrate Loads in the Upper Mississippi River Basin.

    PubMed

    Housh, Mashor; Yaeger, Mary A; Cai, Ximing; McIsaac, Gregory F; Khanna, Madhu; Sivapalan, Murugesu; Ouyang, Yanfeng; Al-Qadi, Imad; Jain, Atul K

    2015-10-01

    Implementing public policies often involves navigating an array of choices that have economic and environmental consequences that are difficult to quantify due to the complexity of multiple system interactions. Implementing the mandate for cellulosic biofuel production in the Renewable Fuel Standard (RFS) and reducing hypoxia in the northern Gulf of Mexico by reducing riverine nitrate-N loads represent two such cases that overlap in the Mississippi River Basin. To quantify the consequences of these interactions, a system of systems (SoS) model was developed that incorporates interdependencies among the various subsystems, including biofuel refineries, transportation, agriculture, water resources and crop/ethanol markets. The model allows examination of the impact of imposing riverine nitrate-N load limits on the biofuel production system as a whole, including land use change and infrastructure needs. The synergies of crop choice (first versus second generation biofuel crops), infrastructure development, and environmental impacts (streamflow and nitrate-N load) were analyzed to determine the complementarities and trade-offs between environmental protection and biofuel development objectives. For example, the results show that meeting the cellulosic biofuel target in the RFS using Miscanthus x giganteus reduces system profits by 8% and reduces nitrate-N loads by 12% compared to the scenario without a mandate. However, greater water consumption by Miscanthus is likely to reduce streamflow with potentially adverse environmental consequences that need to be considered in future decision making. PMID:26348783

  19. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    PubMed

    Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

    2015-01-01

    The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus. PMID:26068192

  20. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    PubMed

    Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

    2015-01-01

    The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  1. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus

    PubMed Central

    Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

    2015-01-01

    The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus. PMID:26068192

  2. Initial Sequential Organ Failure Assessment score versus Simplified Acute Physiology score to analyze multiple organ dysfunction in infectious diseases in Intensive Care Unit

    PubMed Central

    Nair, Remyasri; Bhandary, Nithish M.; D’Souza, Ashton D.

    2016-01-01

    Aims: To investigate initial Sequential Organ Failure Assessment (SOFA) score of patients in Intensive Care Unit (ICU), who were diagnosed with infectious disease, as an indicator of multiple organ dysfunction and to examine if initial SOFA score is a better mortality predictor compared to Simplified Acute Physiology Score (SAPS). Materials and Methods: Hospital-based study done in medical ICU, from June to September 2014 with a sample size of 48. Patients aged 18 years and above, diagnosed with infectious disease were included. Patients with history of chronic illness (renal/hepatic/pulmonary/  cardiovascular), diabetes, hypertension, chronic obstructive pulmonary disease, heart disease, those on immunosuppressive therapy/chemoradiotherapy for malignancy and patients in immunocompromised state were excluded. Blood investigations were obtained. Six organ dysfunctions were assessed using initial SOFA score and graded from 0 to 4. SAPS was calculated as the sum of points assigned to each of the 17 variables (12 physiological, age, type of admission, and three underlying diseases). The outcome measure was survival status at ICU discharge. Results: We categorized infectious diseases into dengue fever, leptospirosis, malaria, respiratory tract infections, and others which included undiagnosed febrile illness, meningitis, urinary tract infection and gastroenteritis. Initial SOFA score was both sensitive and specific; SAPS lacked sensitivity. We found no significant association between age and survival status. Both SAPS and initial SOFA score were found to be statistically significant as mortality predictors. There is significant association of initial SOFA score in analyzing organ dysfunction in infectious diseases (P < 0.001). SAPS showed no statistical significance. There was statistically significant (P = 0.015) percentage of nonsurvivors with moderate and severe dysfunction, based on SOFA score. Nonsurvivors had higher SAPS but was not statistically significant (P

  3. Marker development

    SciTech Connect

    Adams, M.R.

    1987-05-01

    This report is to discuss the marker development for radioactive waste disposal sites. The markers must be designed to last 10,000 years, and place no undue burdens on the future generations. Barriers cannot be constructed that preclude human intrusion. Design specifications for surface markers will be discussed, also marker pictograms will also be covered.

  4. Multiple sclerosis risk markers in HLA-DRA, HLA-C, and IFNG genes are associated with sex-specific childhood leukemia risk.

    PubMed

    Morrison, Brittany A; Ucisik-Akkaya, Esma; Flores, Hilario; Alaez, Carmen; Gorodezky, Clara; Dorak, M Tevfik

    2010-12-01

    Previous epidemiologic studies showed four times increased risk of acute lymphoblastic leukemia (ALL) in children of women with multiple sclerosis (MS). MS shows a risk association with Human leukocyte antigens (HLA)-DRA single nucleotide polymorphism (SNP) rs3135388, which is a proxy marker for DRB1*1501. We examined the relevance of rs3135388 in childhood ALL risk along with two other HLA-DRA SNPs in two case-control groups: 114 cases and 388 controls from South Wales (UK) and 100 Mexican Mestizo cases and 253 controls. We first confirmed the correlation between rs3135388 and DRB1*1501 in HLA-typed reference cell lines. We noted a female-specific risk association in childhood ALL (pooled odds ratio (OR) = 2.6, 95% confidence interval (CI) = 1.5-4.5, Mantel-Haenszel P = 0.0009) similar to the stronger association of DRB1*1501 in females with MS. Examination of an HLA-C 5' flanking region SNP rs9264942, known to correlate with HLA-C expression, showed a protective association in girls (OR = 0.4, 95% CI = 0.2-0.7, Mantel-Haenszel P = 0.0003) similar to the protective HLA-Cw*05 association in MS. In a reference cell line panel, HLA-Cw5 homozygous samples (n = 8) were also homozygous for the minor allele of the SNP. Likewise, the male-specific protective association of interferon-gamma (IFNG) SNP rs2069727 in MS was replicated with the same sex specificity in childhood ALL (OR = 0.6, 95% CI = 0.4-1.0, Mantel-Haenszel P = 0.03). Two other SNPs in superkiller viralicidic activity 2-like and tenascin XB that are markers for systemic lupus erythematosus susceptibility showed female-specific associations but due to linkage disequilibrium with HLA-DRB1*15. Our observations supported the epidemiologic link between MS and childhood ALL and added the sex effect to this connection. It appears that only girls born to mothers with MS may have an increased risk of ALL. Investigating the mechanism of these sex-specific associations may help understand the pathogenesis of MS and ALL.

  5. Multiple doses of diacylglycerol and calcium ionophore are necessary to activate AP-1 enhancer activity and induce markers of macrophage differentiation.

    PubMed

    William, F; Wagner, F; Karin, M; Kraft, A S

    1990-10-25

    In contrast to phorbol esters, multiple doses of diacylgycerols are needed to differentiate U937 human monoblastic leukemic cells to a macrophage-like phenotype. Although both of these agents similarly activate protein kinase C in vitro, it is not known why these agents appear to have differing biologic effects. One possibility is that they regulate gene transcription in slightly different ways. Regulation of gene transcription by phorbol esters is complex and involves the stimulation of the transactivating proteins Jun and Fos which form dimers and bind to the AP-1 enhancer elements (5'-TGAGTCA-3'). To understand whether diacylglycerols regulate gene transcription similarly to phorbol esters and to examine whether activation of AP-1 enhancer activity is correlated with differentiation, we have treated U937 human monoblastic leukemic cells with these agents and examined activation of transcription from AP-1 enhancer elements. We find that, although a single dose of diacylglycerol, like phorbol esters, is sufficient to elevate mRNA levels of both the c-jun and c-fos protooncogenes, in contrast to phorbol esters there is no increase in either Jun protein or activation of AP-1 enhancer activity. However, multiple doses of this agent given over 24 h stimulate repeated elevations in c-jun and c-fos mRNA, increases in Jun protein, and enhancer activation. Treatment of U937 cells with ionomycin, a calcium ionophore, also stimulates an increase in c-jun mRNA, but neither activates AP-1 enhancer activity nor stimulates differentiation of these cells. However ionomycin functions to enhance the effects of diacylglycerols both on transcriptional activation and U937 differentiation. These results suggest a complex regulation of AP-1 enhancer activity in U937 cells by diacylglycerols involving both transcriptional and post-transcriptional regulatory mechanisms. Maximal activation of AP-1 enhancer elements, and not changes in jun and fos mRNA, is correlated with increases in

  6. Analyzing multiple endpoints in clinical trials of pain treatments: IMMPACT recommendations. Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials.

    PubMed

    Turk, Dennis C; Dworkin, Robert H; McDermott, Michael P; Bellamy, Nicholas; Burke, Laurie B; Chandler, Julie M; Cleeland, Charles S; Cowan, Penney; Dimitrova, Rozalina; Farrar, John T; Hertz, Sharon; Heyse, Joseph F; Iyengar, Smriti; Jadad, Alejandro R; Jay, Gary W; Jermano, John A; Katz, Nathaniel P; Manning, Donald C; Martin, Susan; Max, Mitchell B; McGrath, Patrick; McQuay, Henry J; Quessy, Steve; Rappaport, Bob A; Revicki, Dennis A; Rothman, Margaret; Stauffer, Joseph W; Svensson, Ola; White, Richard E; Witter, James

    2008-10-31

    The increasing complexity of randomized clinical trials and the practice of obtaining a wide variety of measurements from study participants have made the consideration of multiple endpoints a critically important issue in the design, analysis, and interpretation of clinical trials. Failure to consider important outcomes can limit the validity and utility of clinical trials; specifying multiple endpoints for the evaluation of treatment efficacy, however, can increase the rate of false positive conclusions about the efficacy of a treatment. We describe the use of multiple endpoints in the design, analysis, and interpretation of pain clinical trials, and review available strategies and methods for addressing multiplicity. To decrease the probability of a Type I error (i.e., the likelihood of obtaining statistically significant results by chance) in pain clinical trials, the use of gatekeeping procedures and other methods that correct for multiple analyses is recommended when a single primary endpoint does not adequately reflect the overall benefits of treatment. We emphasize the importance of specifying in advance the outcomes and clinical decision rule that will serve as the basis for determining that a treatment is efficacious and the methods that will be used to control the overall Type I error rate. PMID:18706763

  7. Bone Markers

    MedlinePlus

    ... Alkaline Phosphatase; Osteocalcin; P1NP; Procollagen Type 1 N-Terminal Propeptide Formal name: Biochemical Markers of Bone Remodeling ... tests for evaluating bone turnover: C-telopeptide (C-terminal telopeptide of type 1 collagen (CTx)) – a marker ...

  8. Stability of Markers Used for Real-Time Tumor Tracking After Percutaneous Intrapulmonary Placement

    SciTech Connect

    Voort van Zyp, Noelle C. van der; Hoogeman, Mischa S.; Water, Steven van de; Levendag, Peter C.; Holt, Bronno van der; Heijmen, Ben J.M.; Nuyttens, Joost J.

    2011-11-01

    Purpose: To determine the stability of markers used for real-time tumor tracking after percutaneous intrapulmonary placement. Methods and Materials: A total of 42 patients with 44 lesions, 111 markers, and {>=}2 repeat computed tomography (CT) scans were studied. The tumor on the repeat CT scans was registered with the tumor on the planning CT scan. Next, the three-dimensional marker coordinates were determined on the planning CT scan and repeat CT scans. Marker stability was analyzed by the displacement of the markers and the displacement of the center of mass (COM) of the marker configurations. In addition, we assessed the reliability of using the intermarker distance as a check for displacements in the COM of the marker configurations. Results: The median marker displacement was 1.3 mm (range, 0.1-53.6). The marker displacement was >5 mm in 12% of the markers and >10 mm in 5% of the markers. The causes of marker displacement >5 mm included marker migration (2 of 13) and target volume changes (5 of 13). Nonsynchronous tumor and marker movement during breathing might have been responsible for the displacements >5 mm in the other 6 of 13 markers. The median displacement in the COM of the marker configurations was 1.0 mm (range, 0.1-23.3). Displacements in the COM of the marker configurations of {>=}2.0 mm were detected by changes in the intermarker distance of >1.5 mm in 96% of the treatment fractions. Conclusion: The median marker displacement was small (1.3 mm). Nevertheless, displacements >5 mm occurred in 12% of the markers. Therefore, we recommend the implantation of multiple markers because multiple markers will enable a quick and reliable check of marker displacement by determining the change in the intermarker distance. A displacement in the COM of the marker configuration of {>=}2.0 mm was almost always detected (96%) by a change in the distance between the markers of >1.5 mm. This enabled the displaced marker to be disabled, such that tumor localization

  9. Simplified Digital Spectrum Analyzer

    NASA Technical Reports Server (NTRS)

    Cole, Steven W.

    1992-01-01

    Spectrum analyzer computes approximate cross-correlations between noisy input signal and reference signal of known frequency, yielding measure of amplitude of sinusoidal component of input. Complexity and power consumed less than other digital spectrum analyzers. Performs no multiplications, and because processes data on each frequency independently, focuses on narrow spectral range without processing data on rest of spectrum.

  10. ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems.

    PubMed

    Kaimal, Vivek; Bardes, Eric E; Tabar, Scott C; Jegga, Anil G; Aronow, Bruce J

    2010-07-01

    ToppCluster is a web server application that leverages a powerful enrichment analysis and underlying data environment for comparative analyses of multiple gene lists. It generates heatmaps or connectivity networks that reveal functional features shared or specific to multiple gene lists. ToppCluster uses hypergeometric tests to obtain list-specific feature enrichment P-values for currently 17 categories of annotations of human-ortholog genes, and provides user-selectable cutoffs and multiple testing correction methods to control false discovery. Each nameable gene list represents a column input to a resulting matrix whose rows are overrepresented features, and individual cells per-list P-values and corresponding genes per feature. ToppCluster provides users with choices of tabular outputs, hierarchical clustering and heatmap generation, or the ability to interactively select features from the functional enrichment matrix to be transformed into XGMML or GEXF network format documents for use in Cytoscape or Gephi applications, respectively. Here, as example, we demonstrate the ability of ToppCluster to enable identification of list-specific phenotypic and regulatory element features (both cis-elements and 3'UTR microRNA binding sites) among tissue-specific gene lists. ToppCluster's functionalities enable the identification of specialized biological functions and regulatory networks and systems biology-based dissection of biological states. ToppCluster can be accessed freely at http://toppcluster.cchmc.org.

  11. Gas Analyzer

    NASA Astrophysics Data System (ADS)

    1989-01-01

    The M200 originated in the 1970's under an Ames Research Center/Stanford University contract to develop a small, lightweight gas analyzer for Viking Landers. Although the unit was not used on the spacecraft, it was further developed by The National Institute for Occupational Safety and Health (NIOSH). Three researchers from the project later formed Microsensor Technology, Inc. (MTI) to commercialize the analyzer. The original version (Micromonitor 500) was introduced in 1982, and the M200 in 1988. The M200, a more advanced version, features dual gas chromatograph which separate a gaseous mixture into components and measure concentrations of each gas. It is useful for monitoring gas leaks, chemical spills, etc. Many analyses are completed in less than 30 seconds, and a wide range of mixtures can be analyzed.

  12. Process Analyzer

    NASA Technical Reports Server (NTRS)

    1994-01-01

    The ChemScan UV-6100 is a spectrometry system originally developed by Biotronics Technologies, Inc. under a Small Business Innovation Research (SBIR) contract. It is marketed to the water and wastewater treatment industries, replacing "grab sampling" with on-line data collection. It analyzes the light absorbance characteristics of a water sample, simultaneously detects hundreds of individual wavelengths absorbed by chemical substances in a process solution, and quantifies the information. Spectral data is then processed by ChemScan analyzer and compared with calibration files in the system's memory in order to calculate concentrations of chemical substances that cause UV light absorbance in specific patterns. Monitored substances can be analyzed for quality and quantity. Applications include detection of a variety of substances, and the information provided enables an operator to control a process more efficiently.

  13. Blood Analyzer

    NASA Technical Reports Server (NTRS)

    1992-01-01

    In the 1970's, NASA provided funding for development of an automatic blood analyzer for Skylab at the Oak Ridge National Laboratory (ORNL). ORNL devised "dynamic loading," which employed a spinning rotor to load, transfer, and analyze blood samples by centrifugal processing. A refined, commercial version of the system was produced by ABAXIS and is marketed as portable ABAXIS MiniLab MCA. Used in a doctor's office, the equipment can perform 80 to 100 chemical blood tests on a single drop of blood and report results in five minutes. Further development is anticipated.

  14. Defibrillator analyzers.

    PubMed

    1999-12-01

    Defibrillator analyzers automate the inspection and preventive maintenance (IPM) testing of defibrillators. They need to be able to test at least four basic defibrillator performance characteristics: discharge energy, synchronized-mode operation, automated external defibrillation, and ECG monitoring. We prefer that they also be able to test a defibrillator's external noninvasive pacing function--but this is not essential if a facility already has a pacemaker analyzer that can perform this testing. In this Evaluation, we tested seven defibrillator analyzers from six suppliers. All seven units accurately measure the energies of a variety of discharge wave-forms over a wide range of energy levels--from 1 J for use in a neonatal intensive care unit to 360 J for use on adult patients requiring maximum discharge energy. Most of the analyzers are easy to use. However, only three of the evaluated units could perform the full range of defibrillator tests that we prefer. We rated these units Acceptable--Preferred. Three more units could perform four of the five tests, they could not test the pacing feature of a defibrillator. These units were rated Acceptable. The seventh unit could perform only discharge energy testing and synchronized-mode testing and was difficult to use. We rate that unit Acceptable--Not Recommended. PMID:10604089

  15. Loss of heterozygosity (LOH) for markers on chromosome 8q in a human chondrosarcoma cell line and in a tumor that developed in a man with Hereditary Multiple Exostoses (HME)

    SciTech Connect

    Raskind, W.H.; Conrad, E.U.; Robbins, J.R.

    1994-09-01

    HME is an autosomal dominant disorder in which multiple benign cartilage-capped lesions develop on otherwise histologically normal bones. The majority of chondrosarcomas are sporadic, but the presence of HME greatly increases the risk to develop this tumor. Sarcoma may also arise in sporadically-occurring exostoses. The study of inherited disorders that predispose to malignant diseases has led to discoveries regarding molecular changes involved in carcinogenesis in general. In an analogous manner, somatic mutations in HME genes may be responsible for sporadic exostoses and/or chondrosarcomas. HME is genetically heterogeneous; EXT genes have been assigned to 8q24, the pericentromeric region of 11 and 19p11-p13. We compared chondrosarcoma cell DNA to DNA from white blood cells for LOH at polymorphic loci in these 3 regions. LOH for 4 of 5 markers in 8q24 was detected in a chondrosarcoma that arose in a man with HME. Heterozygosity was retained for markers and chromosomes 11 and 19. We then evaluated cultured cells from 10 sporadic chondrosarcomas. LOH for multiple markers in 8q24 was detected in a cell line, Ch-1, established from an aggressive tumor, but not in 9 other tumors. Of the 9 tumors studied, only the Ch-1 line exhibited LOH for chromosome 11 markers. LOH for a 19p marker was not detected in any of 6 tumors examined, including Ch-1. The karyotype of Ch-1 contains many structurally rearranged chromosomes. The two chromosome 11s appear normal but both chromosome 8 homologues have been replaced by der(8)t(5;8)(q22;q21.2). LOH at 8q24 was also detected in the uncultured tumor. These results suggest that genes responsible for HME may have tumor suppressor functions whose loss may be related to the development of a subset of chondrosarcomas.

  16. Process Analyzer

    NASA Technical Reports Server (NTRS)

    1993-01-01

    Under a NASA Small Business Innovation Research (SBIR) contract, Axiomatics Corporation developed a shunting Dielectric Sensor to determine the nutrient level and analyze plant nutrient solutions in the CELSS, NASA's space life support program. (CELSS is an experimental facility investigating closed-cycle plant growth and food processing for long duration manned missions.) The DiComp system incorporates a shunt electrode and is especially sensitive to changes in dielectric property changes in materials at measurements much lower than conventional sensors. The analyzer has exceptional capabilities for predicting composition of liquid streams or reactions. It measures concentrations and solids content up to 100 percent in applications like agricultural products, petrochemicals, food and beverages. The sensor is easily installed; maintenance is low, and it can be calibrated on line. The software automates data collection and analysis.

  17. Oxygen analyzer

    DOEpatents

    Benner, W.H.

    1984-05-08

    An oxygen analyzer which identifies and classifies microgram quantities of oxygen in ambient particulate matter and for quantitating organic oxygen in solvent extracts of ambient particulate matter. A sample is pyrolyzed in oxygen-free nitrogen gas (N/sub 2/), and the resulting oxygen quantitatively converted to carbon monoxide (CO) by contact with hot granular carbon (C). Two analysis modes are made possible: (1) rapid determination of total pyrolyzable obtained by decomposing the sample at 1135/sup 0/C, or (2) temperature-programmed oxygen thermal analysis obtained by heating the sample from room temperature to 1135/sup 0/C as a function of time. The analyzer basically comprises a pyrolysis tube containing a bed of granular carbon under N/sub 2/, ovens used to heat the carbon and/or decompose the sample, and a non-dispersive infrared CO detector coupled to a mini-computer to quantitate oxygen in the decomposition products and control oven heating.

  18. Oxygen analyzer

    DOEpatents

    Benner, William H.

    1986-01-01

    An oxygen analyzer which identifies and classifies microgram quantities of oxygen in ambient particulate matter and for quantitating organic oxygen in solvent extracts of ambient particulate matter. A sample is pyrolyzed in oxygen-free nitrogen gas (N.sub.2), and the resulting oxygen quantitatively converted to carbon monoxide (CO) by contact with hot granular carbon (C). Two analysis modes are made possible: (1) rapid determination of total pyrolyzable oxygen obtained by decomposing the sample at 1135.degree. C., or (2) temperature-programmed oxygen thermal analysis obtained by heating the sample from room temperature to 1135.degree. C. as a function of time. The analyzer basically comprises a pyrolysis tube containing a bed of granular carbon under N.sub.2, ovens used to heat the carbon and/or decompose the sample, and a non-dispersive infrared CO detector coupled to a mini-computer to quantitate oxygen in the decomposition products and control oven heating.

  19. MULTICHANNEL ANALYZER

    DOEpatents

    Kelley, G.G.

    1959-11-10

    A multichannel pulse analyzer having several window amplifiers, each amplifier serving one group of channels, with a single fast pulse-lengthener and a single novel interrogation circuit serving all channels is described. A pulse followed too closely timewise by another pulse is disregarded by the interrogation circuit to prevent errors due to pulse pileup. The window amplifiers are connected to the pulse lengthener output, rather than the linear amplifier output, so need not have the fast response characteristic formerly required.

  20. Contamination Analyzer

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Measurement of the total organic carbon content in water is important in assessing contamination levels in high purity water for power generation, pharmaceutical production and electronics manufacture. Even trace levels of organic compounds can cause defects in manufactured products. The Sievers Model 800 Total Organic Carbon (TOC) Analyzer, based on technology developed for the Space Station, uses a strong chemical oxidizing agent and ultraviolet light to convert organic compounds in water to carbon dioxide. After ionizing the carbon dioxide, the amount of ions is determined by measuring the conductivity of the deionized water. The new technique is highly sensitive, does not require compressed gas, and maintenance is minimal.

  1. Stress Analyzer

    NASA Technical Reports Server (NTRS)

    1990-01-01

    SPATE 900 Dynamic Stress Analyzer is an acronym for Stress Pattern Analysis by Thermal Emission. It detects stress-induced temperature changes in a structure and indicates the degree of stress. Ometron, Inc.'s SPATE 9000 consists of a scan unit and a data display. The scan unit contains an infrared channel focused on the test structure to collect thermal radiation, and a visual channel used to set up the scan area and interrogate the stress display. Stress data is produced by detecting minute temperature changes, down to one-thousandth of a degree Centigrade, resulting from the application to the structure of dynamic loading. The electronic data processing system correlates the temperature changes with a reference signal to determine stress level.

  2. Optical analyzer

    DOEpatents

    Hansen, A.D.

    1987-09-28

    An optical analyzer wherein a sample of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter is placed in a combustion tube, and light from a light source is passed through the sample. The temperature of the sample is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample is detected as the temperature is raised. A data processor, differentiator and a two pen recorder provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample. These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample. Additional information is obtained by repeating the run in different atmospheres and/or different rates or heating with other samples of the same particulate material collected on other filters. 7 figs.

  3. Optical analyzer

    DOEpatents

    Hansen, Anthony D.

    1989-02-07

    An optical analyzer (10) wherein a sample (19) of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter (20) is placed in a combustion tube (11), and light from a light source (14) is passed through the sample (19). The temperature of the sample (19) is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample (19) is detected (18) as the temperature is raised. A data processor (23), differentiator (28) and a two pen recorder (24) provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample (19). These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample (19). Additional information is obtained by repeating the run in different atmospheres and/or different rates of heating with other samples of the same particulate material collected on other filters.

  4. Optical analyzer

    DOEpatents

    Hansen, Anthony D.

    1989-01-01

    An optical analyzer (10) wherein a sample (19) of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter (20) is placed in a combustion tube (11), and light from a light source (14) is passed through the sample (19). The temperature of the sample (19) is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample (19) is detected (18) as the temperature is raised. A data processor (23), differentiator (28) and a two pen recorder (24) provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample (19). These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample (19). Additional information is obtained by repeating the run in different atmospheres and/or different rates of heating with other samples of the same particulate material collected on other filters.

  5. Trypanosoma brucei s.l.: Microsatellite markers revealed high level of multiple genotypes in the mid-guts of wild tsetse flies of the Fontem sleeping sickness focus of Cameroon.

    PubMed

    Simo, Gustave; Njitchouang, Guy Roger; Njiokou, Flobert; Cuny, Gerard; Asonganyi, Tazoacha

    2011-07-01

    To identify Trypanosoma brucei genotypes which are potentially transmitted in a sleeping sickness focus, microsatellite markers were used to characterize T. brucei found in the mid-guts of wild tsetse flies of the Fontem sleeping sickness focus in Cameroon. For this study, two entomological surveys were performed during which 2685 tsetse flies were collected and 1596 (59.2%) were dissected. Microscopic examination revealed 1.19% (19/1596) mid-gut infections with trypanosomes; the PCR method identified 4.7% (75/1596) infections with T. brucei in the mid-guts. Of these 75 trypanosomes identified in the mid-guts, Trypanosoma brucei gambiense represented 0.81% (13/1596) of them, confirming the circulation of human infective parasite in the Fontem focus. Genetic characterization of the 75 T. brucei samples using five microsatellite markers revealed not only multiple T. brucei genotypes (47%), but also single genotypes (53%) in the mid-guts of the wild tsetse flies. These results show that there is a wide range of trypanosome genotypes circulating in the mid-guts of wild tsetse flies from the Fontem sleeping sickness focus. They open new avenues to undertake investigations on the maturation of multiple infections observed in the tsetse fly mid-guts. Such investigations may allow to understand how the multiple infections evolve from the tsetse flies mid-guts to the salivary glands and also to understand the consequence of these evolutions on the dynamic (which genotype is transmitted to mammals) of trypanosomes transmission.

  6. ABSORPTION ANALYZER

    DOEpatents

    Brooksbank, W.A. Jr.; Leddicotte, G.W.; Strain, J.E.; Hendon, H.H. Jr.

    1961-11-14

    A means was developed for continuously computing and indicating the isotopic assay of a process solution and for automatically controlling the process output of isotope separation equipment to provide a continuous output of the desired isotopic ratio. A counter tube is surrounded with a sample to be analyzed so that the tube is exactly in the center of the sample. A source of fast neutrons is provided and is spaced from the sample. The neutrons from the source are thermalized by causing them to pass through a neutron moderator, and the neutrons are allowed to diffuse radially through the sample to actuate the counter. A reference counter in a known sample of pure solvent is also actuated by the thermal neutrons from the neutron source. The number of neutrons which actuate the detectors is a function of a concentration of the elements in solution and their neutron absorption cross sections. The pulses produced by the detectors responsive to each neu tron passing therethrough are amplified and counted. The respective times required to accumulate a selected number of counts are measured by associated timing devices. The concentration of a particular element in solution may be determined by utilizing the following relation: T2/Ti = BCR, where B is a constant proportional to the absorption cross sections, T2 is the time of count collection for the unknown solution, Ti is the time of count collection for the pure solvent, R is the isotopic ratlo, and C is the molar concentration of the element to be determined. Knowing the slope constant B for any element and when the chemical concentration is known, the isotopic concentration may be readily determined, and conversely when the isotopic ratio is known, the chemical concentrations may be determined. (AEC)

  7. Tetrasomy 13q31.1qter due to an inverted duplicated neocentric marker chromosome in a fetus with multiple malformations.

    PubMed

    Haddad, Véronique; Aboura, Azzedine; Tosca, Lucie; Guediche, Narjes; Mas, Anne-Elisabeth; L'Herminé, Aurore Coulomb; Druart, Luc; Picone, Olivier; Brisset, Sophie; Tachdjian, Gérard

    2012-04-01

    Small supernumerary marker chromosome (sSMC) lacking alpha satellite DNA or endogenous centromere regions are rare and contain fully functional centromeres, called neocentromeres. We report on a woman with a 14-week gestation pregnancy with a cystic hygroma and cerebellar hypoplasia at ultrasound examination. Cytogenetic studies showed a karyotype 47,XY,+mar dn. This sSMC was observed in chorionic villi, lung, and muscle tissue. Array Comparative Genomic Hybridization showed a gain from 13q31.1 to 13qter region. Fluorescent in situ hybridization with pan alpha satellite probe and probes specific for chromosome 13 showed a marker corresponding to an inversion duplication of the 13q distal chromosomal region without alpha satellite DNA sequence, suggesting the presence of a neocentromere. Examination of the fetus showed dysmorphic features, cystic cervical hygroma, postaxial polydactyly of the right hand and left foot with short fingers, malrotation of the gut, and a micropenis with hypospadias. Genotype-phenotype correlation in tetrasomy 13q is discussed according to the four 13q chromosomal breakpoints reported (13q32, 13q31, 13q21, 13q14) for chromosome 13 supernumerary markers.

  8. Construction of multiple recombinant SLA-I proteins by linking heavy chains and light chains in vitro and analyzing their secondary and 3-dimensional structures.

    PubMed

    Gao, Feng-shan; Bai, Jing; Zhang, Qiang; Xu, Chong-bo; Li, Yanmin

    2012-07-10

    Six breeds of swine were used to study the structure of swine leukocyte antigen class I (SLA-I). SLA-I complexes were produced by linking SLA-2 genes and β(2)m genes via a linker encoding a 15 amino acid glycine-rich sequence, (G4S)3, using splicing overlap extension (SOE)-PCR in vitro. The six recombinant SLA-2-linker-β(2)m genes were each inserted into p2X vectors and their expression induced in Escherichia coli TB1. The expressed proteins were detected by SDS-PAGE and western blotting. The maltose binding protein (MBP)-SLA-I fusion proteins were purified by amylose affinity chromatography followed by cleavage with factor Xa and separation of the SLA-I protein monomers from the MBP using a DEAE Ceramic Hyper D F column. The purified SLA-I monomers were detected by circular dichroism (CD) spectroscopy and the 3-dimensional (3D) structure of the constructed single-chain SLA-I molecules were analyzed by homology modeling. Recombinant SLA-2-Linker-β(2)m was successfully amplified from all six breeds of swine by SOE-PCR and expressed as fusion proteins of 84.1 kDa in pMAL-p2X, followed by confirmation by western blotting. After purification and cleavage of the MBP-SLA-I fusion proteins, SLA-I monomeric proteins of 41.6 kDa were separated. CD spectroscopy demonstrated that the SLA-I monomers had an α-helical structure, and the average α-helix, β-sheet, turn and random coil contents were 21.6%, 37.9%, 15.0% and 25.5%, respectively. Homology modeling of recombinant single-chain SLA-I molecules showed that the heavy chain and light chain constituted SLA-I complex with an open antigenic peptide-binding groove. It was concluded that the expressed SLA-I proteins in pMAL-p2X folded correctly and could be used to bind and screen nonameric peptides in vitro.

  9. Molecular Profiling of Multiple Human Cancers Defines an Inflammatory Cancer-Associated Molecular Pattern and Uncovers KPNA2 as a Uniform Poor Prognostic Cancer Marker

    PubMed Central

    Rachidi, Saleh M.; Qin, Tingting; Sun, Shaoli; Zheng, W. Jim; Li, Zihai

    2013-01-01

    Background Immune evasion is one of the recognized hallmarks of cancer. Inflammatory responses to cancer can also contribute directly to oncogenesis. Since the immune system is hardwired to protect the host, there is a possibility that cancers, regardless of their histological origins, endow themselves with a common and shared inflammatory cancer-associated molecular pattern (iCAMP) to promote oncoinflammation. However, the definition of iCAMP has not been conceptually and experimentally investigated. Methods and Findings Genome-wide cDNA expression data was analyzed for 221 normal and 324 cancer specimens from 7 cancer types: breast, prostate, lung, colon, gastric, oral and pancreatic. A total of 96 inflammatory genes with consistent dysregulation were identified, including 44 up-regulated and 52 down-regulated genes. Protein expression was confirmed by immunohistochemistry for some of these genes. The iCAMP contains proteins whose roles in cancer have been implicated and others which are yet to be appreciated. The clinical significance of many iCAMP genes was confirmed in multiple independent cohorts of colon and ovarian cancer patients. In both cases, better prognosis correlated strongly with high CXCL13 and low level of GREM1, LOX, TNFAIP6, CD36, and EDNRA. An “Inflammatory Gene Integrated Score” was further developed from the combination of 18 iCAMP genes in ovarian cancer, which predicted overall survival. Noticeably, as a selective nuclear import protein whose immuno-regulatory function just begins to emerge, karyopherin alpha 2 (KPNA2) is uniformly up-regulated across cancer types. For the first time, the cancer-specific up-regulation of KPNA2 and its clinical significance were verified by tissue microarray analysis in colon and head-neck cancers. Conclusion This work defines an inflammatory signature shared by seven epithelial cancer types and KPNA2 as a consistently up-regulated protein in cancer. Identification of iCAMP may not only serve as a novel

  10. Grave Markers.

    ERIC Educational Resources Information Center

    DeMuro, Ted

    1985-01-01

    Junior high school students studied the cultural uses, symbolic meanings, and general physical forms of tombs and tombstones and then used basic slab building techniques to construct large clay grave markers. (RM)

  11. KIAA1114, a full-length protein encoded by the trophinin gene, is a novel surface marker for isolating tumor-initiating cells of multiple hepatocellular carcinoma subtypes

    PubMed Central

    Kim, Sae Won; Yang, Hyun Gul; Kang, Moon Cheol; Lee, Seungwon; Namkoong, Hong; Lee, Seung-Woo; Sung, Young Chul

    2014-01-01

    Identification of novel biomarkers for tumor-initiating cells (TICs) is of critical importance for developing diagnostic and therapeutic strategies against cancers. Here we identified the role of KIAA1114, a full-length translational product of the trophinin gene, as a distinctive marker for TICs in human liver cancer by developing a DNA vaccine-induced monoclonal antibody targeting the putative extracellular domain of KIAA1114. Compared with other established markers of liver TICs, KIAA1114 was unique in that its expression was detected in both alpha fetoprotein (AFP)-positive and AFP-negative hepatocellular carcinoma (HCC) cell lines with the expression levels of KIAA1114 being positively correlated to their tumorigenic potentials. Notably, KIAA1114 expression was strongly detected in primary hepatic tumor, but neither in the adjacent non-tumorous tissue from the same patient nor normal liver tissue. KIAA1114high cells isolated from HCC cell lines displayed TIC-like features with superior functional and phenotypic traits compared to their KIAA1114low counterparts, including tumorigenic abilities in xenotransplantation model, in vitro colony- and spheroid-forming capabilities, expression of stemness-associated genes, and migratory capacity. Our findings not only address the value of a novel antigen, KIAA1114, as a potential diagnostic factor of human liver cancer, but also as an independent biomarker for identifying TIC populations that could be broadly applied to the heterogeneous HCC subtypes. PMID:24713374

  12. [Serological markers of fibrosis].

    PubMed

    Fernández-Varo, Guillermo

    2012-12-01

    Liver biopsy has classically been considered the gold standard to evaluate the degree of fibrosis, since it allows direct measurement of this entity. However, this technique carries an inherent risk of complications and observer variability and technical limitations can provoke sampling errors, all of which has prompted the search for alternative, noninvasive methods. The use of routine clinical laboratory tests has been investigated and various indexes that combine indirect serological markers have been developed and validated. These indexes are useful, low-cost, noninvasive tests to detect significant fibrosis or cirrhosis. Direct serological markers are those that reflect changes in the composition of the extracellular matrix. Several studies have analyzed the utility of these markers (either individually or combined with other direct and indirect markers) in the detection of the severity and progression of liver fibrosis and in the follow-up of changes related to antiviral therapy. In the last few years, imaging tests based on the measurement of liver stiffness, such as FibroScan or acoustic radiation force impulse (ARFI), have been found to be rapid and reproducible methods to evaluate liver fibrosis. Recently, the results obtained by combining distinct serological markers and imaging techniques have shown a higher diagnostic yield and this strategy seems promising. The present article reviews the most widely discussed noninvasive markers, the most recent alternatives, and the perspectives for their use in clinical practice. PMID:23298654

  13. Judging Quality through Substantive Conversations between Markers

    ERIC Educational Resources Information Center

    Grainger, Peter; Purnell, Ken; Zipf, Reyna

    2008-01-01

    Decisions by markers about quality in student work remain confusing to most students and markers. This may in part be due to the relatively subjective nature of what constitutes a quality response to an assessment task. This paper reports on an experiment that documented the process of decision-making by multiple markers at a university who…

  14. Use of a Time-of-Flight Camera With an Omek Beckon™ Framework to Analyze, Evaluate and Correct in Real Time the Verticality of Multiple Sclerosis Patients during Exercise

    PubMed Central

    Eguíluz, Gonzalo; García, María Begoña

    2013-01-01

    Any person with Multiple Sclerosis (MS), regardless of the severity of their disability, needs regular physical activity. Poorly performed exercises could aggravate muscle imbalances and worsen the patient’s health. In this paper, we propose a human body verticality detection system using a time-of-flight camera as a tool to detect incorrect postures and improve them in real time. The prototype uses Omek’s Beckon™ Framework to analyze and evaluate the position of patients during exercise. Preliminary results, based on objective questionnaires, indicate an improvement in patients’ evolution through better positions and performance of the exercises. PMID:24192790

  15. Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat

    PubMed Central

    Bernardo, Amy; Wang, Shan; St. Amand, Paul; Bai, Guihua

    2015-01-01

    With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat (Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat. PMID:26625271

  16. Use of multiple markers demonstrates a cryptic western refugium and postglacial colonisation routes of Atlantic salmon (Salmo salar L.) in Northwest Europe.

    PubMed

    Finnegan, A K; Griffiths, A M; King, R A; Machado-Schiaffino, G; Porcher, J-P; Garcia-Vazquez, E; Bright, D; Stevens, J R

    2013-07-01

    Glacial and postglacial processes are known to be important determinants of contemporary population structuring for many species. In Europe, refugia in the Italian, Balkan and Iberian peninsulas are believed to be the main sources of species colonising northern Europe after the glacial retreat; however, there is increasing evidence of small, cryptic refugia existing north of these for many cold-tolerant species. This study examined the glacial history of Atlantic salmon in western Europe using two independent classes of molecular markers, microsatellites (nuclear) and mitochondrial DNA variation. Alongside the well-documented refuge in the Iberian Peninsula, evidence for a cryptic refuge in northwest France is also presented. Critically, methods utilised to estimate divergence times between the refugia indicated that salmon in these two regions had diverged a long time before the last glacial maximum; coalescence analysis (as implemented in the program IMa2) estimated divergence times at around 60 000 years before present. Through the examination of haplotype frequencies, previously glaciated areas of northwest Europe, that is, Britain and Ireland, appear to have been colonised from salmon expanding out of both refugia, with the southwest of England being the primary contact zone and exhibiting the highest genetic diversity.

  17. Use of multiple markers demonstrates a cryptic western refugium and postglacial colonisation routes of Atlantic salmon (Salmo salar L.) in northwest Europe

    PubMed Central

    Finnegan, A K; Griffiths, A M; King, R A; Machado-Schiaffino, G; Porcher, J-P; Garcia-Vazquez, E; Bright, D; Stevens, J R

    2013-01-01

    Glacial and postglacial processes are known to be important determinants of contemporary population structuring for many species. In Europe, refugia in the Italian, Balkan and Iberian peninsulas are believed to be the main sources of species colonising northern Europe after the glacial retreat; however, there is increasing evidence of small, cryptic refugia existing north of these for many cold-tolerant species. This study examined the glacial history of Atlantic salmon in western Europe using two independent classes of molecular markers, microsatellites (nuclear) and mitochondrial DNA variation. Alongside the well-documented refuge in the Iberian Peninsula, evidence for a cryptic refuge in northwest France is also presented. Critically, methods utilised to estimate divergence times between the refugia indicated that salmon in these two regions had diverged a long time before the last glacial maximum; coalescence analysis (as implemented in the program IMa2) estimated divergence times at around 60 000 years before present. Through the examination of haplotype frequencies, previously glaciated areas of northwest Europe, that is, Britain and Ireland, appear to have been colonised from salmon expanding out of both refugia, with the southwest of England being the primary contact zone and exhibiting the highest genetic diversity. PMID:23512011

  18. A DNA marker closely linked to the vrs1 locus (row-type gene) indicates multiple origins of six-rowed cultivated barley ( Hordeum vulgare L.).

    PubMed

    Tanno, K; Taketa, S; Takeda, K; Komatsuda, T

    2002-01-01

    The origin of six-rowed cultivated barley was studied using a DNA marker cMWG699 closely linked to the vrs1 locus. Restriction patterns of the PCR-amplified product of the cMWG699 locus were examined in 280 cultivated ( Hordeum vulgare ssp. vulgare) and 183 wild ( H. vulgare ssp. spontaneum) barleys. Nucleotide sequences of the PCR products were also examined in selected accessions. Six-rowed cultivated barleys were divided into two distinct groups, types I and II. Type I six-rowed cultivated barley was distributed widely while type II six-rowed cultivated barley was found only in the Mediterranean region. The type I sequence was also found in a wild barley accession from Turkmenistan whereas the type II sequence was also found in a two-rowed cultivated barley from North Africa and a wild barley from Morocco. These results suggested that the six-rowed type I and II barleys were derived from two-rowed type I and II barleys, respectively, by independent mutations at the vrs1 locus.

  19. A genetic map of chromosome 20q12-q13. 1: Multiple highly polymorphic microsatellite and RFLP markers linked to the maturity-onset diabetes of the Young (MODY) locus

    SciTech Connect

    Rothschild, C.B.; Akots, G.; Hayworth, R.; Pettenati, M.J.; Rao, P.N.; Wood, P. ); Stolz, F.M.; Hansmann, I. ); Serino, K.; Keith, T.P. ); Fajans, S.S. )

    1993-01-01

    Multiple highly polymorphic markers have been used to construct a genetic map of the q12-q13.1 region of chromosome 20 and to map the location of the maturity-onset diabetes of the young (MODY) locus. The genetic map encompasses 23 cM and includes 11 loci with PIC values >.50, seven of which have PICs >.70. New dinucleotide repeat polymorphisms associated with the D20S17, PPGB, and ADA loci have been identified and mapped. The dinucleotide repeat polymorphisms have increased the PIC of the ADA locus to .89 and, with an additional RFLP at the D20S17 locus, the PIC of the D20S17 locus to .88. The order of the D20S17 and ADA loci determined genetically (cen-ADA-D20S17-qter) was confirmed by multicolor fluorescence in situ hybridization. The previously unmapped PPGB marker is closely linked to D20S17, with a two-point lod score of 50.53 at [cflx [theta

  20. Herbs and spices: characterization and quantitation of biologically-active markers for routine quality control by multiple headspace solid-phase microextraction combined with separative or non-separative analysis.

    PubMed

    Sgorbini, Barbara; Bicchi, Carlo; Cagliero, Cecilia; Cordero, Chiara; Liberto, Erica; Rubiolo, Patrizia

    2015-01-01

    Herbs and spices are used worldwide as food flavoring, thus determination of their identity, origin, and quality is mandatory for safe human consumption. An analysis strategy based on separative (HS-SPME-GC-MS) and non-separative (HS-SPME-MS) approaches is proposed for the volatile fraction of herbs and spices, for quality control and to quantify the aromatic markers with a single analysis directly on the plant material as such. Eight-to-ten lots of each of the following herbs/spices were considered: cloves (Syzygium aromaticum (L.) Merr. & Perry), American peppertree (Schinus molle L.), black pepper and white pepper (Piper nigrum L.), rosemary (Rosmarinus officinalis L.), sage (Salvia officinalis L.) and thyme (Thymus vulgaris L.). Homogeneity, origin, and chemotypes of the investigated lots of each herb/spice were defined by fingerprinting, through statistical elaboration with principal component analysis (PCA). Characterizing aromatic markers were directly quantified on the solid matrix through multiple headspace extraction-HS-SPME (MHS-SPME). Reliable results were obtained with both separative and non-separative methods (where the latter were applicable); the two were in full agreement, RSD% ranging from 1.8 to 7.7% for eugenol in cloves, 2.2-18.4% for carvacrol+thymol in thyme, and 3.1-16.8% for thujones in sage. PMID:25541091

  1. Herbs and spices: characterization and quantitation of biologically-active markers for routine quality control by multiple headspace solid-phase microextraction combined with separative or non-separative analysis.

    PubMed

    Sgorbini, Barbara; Bicchi, Carlo; Cagliero, Cecilia; Cordero, Chiara; Liberto, Erica; Rubiolo, Patrizia

    2015-01-01

    Herbs and spices are used worldwide as food flavoring, thus determination of their identity, origin, and quality is mandatory for safe human consumption. An analysis strategy based on separative (HS-SPME-GC-MS) and non-separative (HS-SPME-MS) approaches is proposed for the volatile fraction of herbs and spices, for quality control and to quantify the aromatic markers with a single analysis directly on the plant material as such. Eight-to-ten lots of each of the following herbs/spices were considered: cloves (Syzygium aromaticum (L.) Merr. & Perry), American peppertree (Schinus molle L.), black pepper and white pepper (Piper nigrum L.), rosemary (Rosmarinus officinalis L.), sage (Salvia officinalis L.) and thyme (Thymus vulgaris L.). Homogeneity, origin, and chemotypes of the investigated lots of each herb/spice were defined by fingerprinting, through statistical elaboration with principal component analysis (PCA). Characterizing aromatic markers were directly quantified on the solid matrix through multiple headspace extraction-HS-SPME (MHS-SPME). Reliable results were obtained with both separative and non-separative methods (where the latter were applicable); the two were in full agreement, RSD% ranging from 1.8 to 7.7% for eugenol in cloves, 2.2-18.4% for carvacrol+thymol in thyme, and 3.1-16.8% for thujones in sage.

  2. Reference levels of the tumor markers carcinoembryonic antigen, the carbohydrate antigens 19-9 and 72-4, and cytokeratin fragment 19 using the Elecsys Relecsys 1010 analyzer in a normal population in Kuwait. The importance of the determination of local reference levels.

    PubMed

    Behbehani, A I; Mathew, A; Farghaly, M; van Dalen, A

    2002-01-01

    The tumor markers CEA, CA 19-9, CA 72-4 and CYFRA 21-1 were analyzed in a group of apparently healthy subjects (n=232) in Kuwait using the Elecsys Relecsys 1010 analyzer. The distribution of the tumour marker levels was analyzed separately in Kuwaitis (n=103), non-Kuwaitis (n=129), smokers (n=68), non-smokers (n=164), males (n=138) and females (n=94). The distribution of CEA was significantly different in Kuwaitis vs. non-Kuwaitis in the total population (p=0.033) and in non-smokers (p=0.049); in males vs. females in the total population (p<0.0001) and in non-smokers (p=0.0002); and in smokers vs. non-smokers in the total population (p<0.0001) using the non-parametric Mann-Whitney U test. None of the other tumour markers showed significant differences in the subgroups. The upper reference level was defined as the 95th percentile of the normal values in each group. A higher reference level of CEA was observed in smokers (vs. non-smokers) in the total population. Also higher reference levels of CEA were observed in males (vs. females) both in the total population and in non-smokers. In the total population the respective reference levels were: CEA: 4.4 microg/L, CA 19-9: 35 kU/L, CA 72.4: 2.4 kU/L, and CYFRA 21.1: 2.1 microg/L. These results were compared with data in the kit inserts and literature data. The impact of 95th percentiles in a local heterogeneous population is discussed.

  3. & Source apportionment of particulate matter in the United States and associations with lung inflammatory Markers

    EPA Science Inventory

    Size-fractionated particulate matter (PM) samples were collected from six U.S. cities and chemically analyzed as part of the Multiple Air Pollutant Study. Particles were administered to cultured lung cells and the production of three different proinflammatory markers was measured...

  4. Tumor Markers

    MedlinePlus

    ... types: Germ cell tumors, lymphoma, leukemia, melanoma, and neuroblastoma Tissue analyzed: Blood How used: To assess stage, ... NSE) Cancer types: Small cell lung cancer and neuroblastoma Tissue analyzed: Blood How used: To help in ...

  5. A calibration means for spectrum analyzers

    NASA Technical Reports Server (NTRS)

    Larson, M. S.

    1967-01-01

    Spectrum analyzer calibration system is rapid and provides an accurate family of adjustable markers at any point in the spectrum. Pulse width controls determine the number of markers. The unit operates with a repetition rate from 300 cps to 40 kc at a center frequency from 10 kc to 2 Mc.

  6. Thalidomide-prednisone maintenance following autologous stem cell transplant for multiple myeloma: effect on thrombin generation and procoagulant markers in NCIC CTG MY.10.

    PubMed

    Kovacs, Michael J; Davies, Gwynivere A; Chapman, Judy-Anne W; Bahlis, Nizar; Voralia, Michael; Roy, Jean; Kouroukis, C Tom; Chen, Christine; Belch, Andrew; Reece, Donna; Zhu, Liting; Meyer, Ralph M; Shepherd, Lois; Stewart, Keith A

    2015-02-01

    Venous thromboembolism (VTE) has an increased incidence in patients with multiple myeloma (MM), especially during chemotherapy. Mechanisms including upregulation of procoagulant factors, such as factor VIII, have been postulated. The National Cancer Institute of Canada Clinical Trials Group MY.10 phase III clinical trial compared thalidomide-prednisone to observation for 332 patients with MM post-autologous stem cell transplantation (ASCT), with a primary endpoint of overall survival and various secondary endpoints including the incidence of VTE. One hundred and fifty-three patients had biomarker data, including D-dimer, factor VIII and thrombin anti-thrombin (TAT) levels collected post-ASCT at baseline and 2 months after intervention investigating in-vivo thrombin generation. Differences between the time-points included a significant reduction over time in D-dimer, factor VIII and TAT levels in the observation group and sustained elevation of D-dimer, significant increase in factor VIII and reduction in TAT levels in the thalidomide-prednisone group. Eight VTE events were reported in this subset of study patients, all in the thalidomide-prednisone arm, with a trend to increase in D-dimer levels over time in those patients with VTE. This study provides physiological and clinical evidence for an increased risk of VTE associated with thalidomide-prednisone maintenance therapy post-ASCT for MM.

  7. Different sleep onset criteria at the multiple sleep latency test (MSLT): an additional marker to differentiate central nervous system (CNS) hypersomnias.

    PubMed

    Pizza, Fabio; Vandi, Stefano; Detto, Stefania; Poli, Francesca; Franceschini, Christian; Montagna, Pasquale; Plazzi, Giuseppe

    2011-03-01

    Excessive daytime sleepiness (EDS) has different correlates in non-rapid eye movement (NREM) [idiopathic hypersomnia (IH) without long sleep time] and REM sleep [narcolepsy without cataplexy (NwoC) and narcolepsy with cataplexy (NC)]-related hypersomnias of central origin. We analysed sleep onset characteristics at the multiple sleep latency test (MSLT) applying simultaneously two sleep onset criteria in 44 NC, seven NwoC and 16 IH consecutive patients referred for subjective EDS complaint. Sleep latency (SL) at MSLT was assessed both as the time elapsed to the occurrence of a single epoch of sleep Stage 1 NREM (SL) and of unequivocal sleep [three sleep Stage 1 NREM epochs or any other sleep stage epoch, sustained SL (SusSL)]. Idiopathic hypersomnia patients showed significantly (P<0.0001) longer SusSL than SL (7.7±2.5 versus 5.6±1.3 min, respectively) compared to NwoC (5.8±2.5 versus 5.3±2.2 min) and NC patients (4.1±3 versus 3.9±3 min). A mean difference threshold between SusSL and SL ≥27 s reached a diagnostic value to discriminate IH versus NC and NwoC sufferers (sensitivity 88%; specificity 82%). Moreover, NC patients showed better subjective sleepiness perception than NwoC and IH cases in the comparison between naps with or without sleep occurrence. Simultaneous application of the two widely used sleep onset criteria differentiates IH further from NC and NwoC patients: IH fluctuate through a wake-Stage 1 NREM sleep state before the onset of sustained sleep, while NC and NwoC shift abruptly into a sustained sleep. The combination of SusSL and SL determination at MSLT should be tested as an additional objective differential criterion for EDS disorders.

  8. Marker evaluation of human breast and bladder cancers

    SciTech Connect

    Mayall, B.H.; Carroll, P.R.; Chen, Ling-Chun; Cohen, M.B.; Goodson, W.H. III; Smith, H.S.; Waldman, F.M. )

    1990-11-02

    We are investigating multiple markers in human breast and bladder cancers. Our aim is to identify markers that are clinically relevant and that contribute to our understanding of the disease process in individual patients. Good markers accurately assess the malignant potential of a cancer in an individual patient. Thus, they help identify those cancers that will recur, and they may be used to predict more accurately time to recurrence, response to treatment, and overall prognosis. Therapy and patient management may then be optimized to the individual patient. Relevant markers reflect the underlying pathobiology of individual tumors. As a tissue undergoes transformation from benign to malignant, the cells lose their differentiated phenotype. As a generalization, the more the cellular phenotype, cellular proliferation and cellular genotype depart from normal, the more advanced is the tumor in its biological evolution and the more likely it is that the patient has a poor prognosis. We use three studies to illustrate our investigation of potential tumor markers. Breast cancers are labeled in vivo with 5-bromodeoxyuridine (BrdUrd) to give a direct measure of the tumor labeling index. Bladder cancers are analyzed immunocytochemically using an antibody against proliferation. Finally, the techniques of molecular genetics are used to detect allelic loss in breast cancers. 6 refs., 3 figs.

  9. Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.))

    PubMed Central

    Hu, Xin; Ren, Jing; Ren, Xifeng; Huang, Sisi; Sabiel, Salih A. I.; Luo, Mingcheng; Nevo, Eviatar; Fu, Chunjie; Peng, Junhua; Sun, Dongfa

    2015-01-01

    Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection. PMID:26110423

  10. Analysis of Genome-Wide Association Studies with Multiple Outcomes Using Penalization

    PubMed Central

    Liu, Jin; Huang, Jian; Ma, Shuangge

    2012-01-01

    Genome-wide association studies have been extensively conducted, searching for markers for biologically meaningful outcomes and phenotypes. Penalization methods have been adopted in the analysis of the joint effects of a large number of SNPs (single nucleotide polymorphisms) and marker identification. This study is partly motivated by the analysis of heterogeneous stock mice dataset, in which multiple correlated phenotypes and a large number of SNPs are available. Existing penalization methods designed to analyze a single response variable cannot accommodate the correlation among multiple response variables. With multiple response variables sharing the same set of markers, joint modeling is first employed to accommodate the correlation. The group Lasso approach is adopted to select markers associated with all the outcome variables. An efficient computational algorithm is developed. Simulation study and analysis of the heterogeneous stock mice dataset show that the proposed method can outperform existing penalization methods. PMID:23272092

  11. CAPS markers improved by cluster-specific amplification for identification of octoploid strawberry (Fragaria x ananassa Duch.) cultivars, and their disomic inheritance.

    PubMed

    Kunihisa, M; Fukino, N; Matsumoto, S

    2005-05-01

    Cleavage amplified polymorphic sequence (CAPS) markers of strawberry (Fragaria x ananassa Duch.) can be useful for identifying mislabeled or patent-infringing cultivars in the marketplace. However, CAPS markers in octoploid strawberry tend to give unclear bands because multiple homologous sites are simultaneously amplified by the non-selective PCR. To overcome this problem, we used "cluster-specific amplification" based on the nucleotide sequences of PCR products and were able to improve the band clarity of 18 CAPS markers. By analyzing the marker segregation ratio, we demonstrated that 13 clarified markers were derived from single diploid loci that were transmitted to progeny in a manner consistent with Mendelian inheritance. We discuss the genomic structure of octoploid strawberry from the viewpoint of cluster and segregation analysis and suggest that it comprises independent genomes. We tested the utility of all of the markers we developed for cultivar identification and confirmed their ability to distinguish among 64 strawberry cultivars.

  12. Global real-time quantitative reverse transcription-polymerase chain reaction detecting proto-oncogenes associated with 14q32 chromosomal translocation as a valuable marker for predicting survival in multiple myeloma.

    PubMed

    Inagaki, Atsushi; Tajima, Emi; Uranishi, Miyuki; Totani, Haruhito; Asao, Yu; Ogura, Hiroka; Masaki, Ayako; Yoshida, Tatsuya; Mori, Fumiko; Ito, Asahi; Yano, Hiroki; Ri, Masaki; Kayukawa, Satoshi; Kataoka, Takae; Kusumoto, Shigeru; Ishida, Takashi; Hayami, Yoshihito; Hanamura, Ichiro; Komatsu, Hirokazu; Inagaki, Hiroshi; Matsuda, Yasufumi; Ueda, Ryuzo; Iida, Shinsuke

    2013-12-01

    CCND1, FGFR3 and c-MAF mRNA expression of tumor samples from 123 multiple myeloma patients were analyzed by global RQ/RT-PCR. CCND1, FGFR3 and c-MAF were positive in 44 (36%), 28 (23%) and 16 (13%) of patients, respectively. In 7 patients, both FGFR3 and c-MAF were positive. The expression of c-MAF was independent unfavorable prognostic factors for overall survival (OS). Autologous stem cell transplantation improved progression-free survival of CCND1-positive patients. Bortezomib, thalidomide or lenalidomide extended OS of FGFR3 and/or c-MAF-positive patients. Thus, CCND1, FGFR3 and c-MAF mRNA expression can predict survival and is useful for planning stratified treatment strategies for myeloma patients.

  13. Downhole Fluid Analyzer Development

    SciTech Connect

    Bill Turner

    2006-11-28

    A novel fiber optic downhole fluid analyzer has been developed for operation in production wells. This device will allow real-time determination of the oil, gas and water fractions of fluids from different zones in a multizone or multilateral completion environment. The device uses near infrared spectroscopy and induced fluorescence measurement to unambiguously determine the oil, water and gas concentrations at all but the highest water cuts. The only downhole components of the system are the fiber optic cable and windows. All of the active components--light sources, sensors, detection electronics and software--will be located at the surface, and will be able to operate multiple downhole probes. Laboratory testing has demonstrated that the sensor can accurately determine oil, water and gas fractions with a less than 5 percent standard error. Once installed in an intelligent completion, this sensor will give the operating company timely information about the fluids arising from various zones or multilaterals in a complex completion pattern, allowing informed decisions to be made on controlling production. The research and development tasks are discussed along with a market analysis.

  14. Acoustical markers for CAD-detected pulmonary nodules in chest CT: A way to avoid suggestion and distraction of radiologist's attention?

    NASA Astrophysics Data System (ADS)

    Beyer, Florian; Heindel, Walter; Wormanns, Dag

    2009-02-01

    Purpose: To compare the influence of visual and acoustical CAD markers on radiologist's performance with regard to suggestive and distractive effects. Materials and methods: Ten radiologists analyzed 150 pictures of chest CT slices. Every picture contained a visual CAD marker. 100 pictures showed one nodule: CAD marker marked this in 50 cases and in 50 cases a false positive finding (f.p.). The other 50 cases showed no nodule but an f.p. marker. After 3 years same images were presented to thirteen radiologists with only a sound as CAD marker. 55 of 150 images were marked, 30 true positive and 25 f.p. Sensitivity and f.p. rate were calculated for both marker types. Significance between sensitivities and f.p. rates were calculated by multiple-analysis-of-variance (MANOVA). Results: Without CAD mean sensitivity resp. f.p. were 57.7% /.13. In case of correct optical resp. acoustical marker sensitivity increased to 75.6% resp. 63.1%. For incorrect set marker mean f.p. rate increased to .31 resp. .24. MANOVA showed that marker's correctness highly significantly influenced sensitivity (p<.001) and f.n. (p=.005). Type of marker showed no significant influence on sensitivity (p=.26) or f.n. (p=.23) but on f.p. (p<.001). New work to be presented: Acoustical markers are a new means to increase radiologist's awareness of the presence of pulmonary nodules at CT scans with much less suggestive effect compared to optical markers. Conclusion: We found an unexpectedly low distraction effect for misplaced CAD markers. A suggestive effect was remarkable especially for optical markers. However acoustical markers offered less increase of sensitivity.

  15. Multiple homicides.

    PubMed

    Copeland, A R

    1989-09-01

    A study of multiple homicides or multiple deaths involving a solitary incident of violence by another individual was performed on the case files of the Office of the Medical Examiner of Metropolitan Dade County in Miami, Florida, during 1983-1987. A total of 107 multiple homicides were studied: 88 double, 17 triple, one quadruple, and one quintuple. The 236 victims were analyzed regarding age, race, sex, cause of death, toxicologic data, perpetrator, locale of the incident, and reason for the incident. This article compares this type of slaying with other types of homicide including those perpetrated by serial killers. Suggestions for future research in this field are offered.

  16. Blood Gas Analyzers.

    PubMed

    Gonzalez, Anthony L; Waddell, Lori S

    2016-03-01

    Acid-base and respiratory disturbances are common in sick and hospitalized veterinary patients; therefore, blood gas analyzers have become integral diagnostic and monitoring tools. This article will discuss uses of blood gas analyzers, types of samples that can be used, sample collection methods, potential sources of error, and potential alternatives to blood gas analyzers and their limitations. It will also discuss the types of analyzers that are available, logistical considerations that should be taken into account when purchasing an analyzer, and the basic principles of how these analyzers work. PMID:27451046

  17. Ceramic subsurface marker prototypes

    SciTech Connect

    Lukens, C.E.

    1985-05-02

    The client submitted 5 sets of porcelain and stoneware subsurface (radioactive site) marker prototypes (31 markers each set). The following were determined: compressive strength, thermal shock resistance, thermal crazing resistance, alkali resistance, color retention, and chemical resistance.

  18. Multiple epiphyseal dysplasia

    PubMed Central

    2009-01-01

    Background Multiple epiphyseal dysplasia (MED) is a common genetically and clinically heterogeneous skeletal dysplasia characterized by early-onset osteoarthritis, mainly in the hip and knee, and mild-to-moderate short stature. Here we report on a 6-generation MED family with 17 affected members. Method The clinical and radiographic data on the 12 affected members still living were scrutinized. A structured inquiry comprising state of health and MED-related symptoms since birth up to the present time and the osteoarthritis outcome (KOOS) questionnaire were sent to all living family members with MED. The 5 known gene loci for autosomal dominant MED were analyzed for linkage, using fluorescence-labeled microsatellite markers. Linkage was ascertained with markers close to the COL9A2 gene, which was analyzed for mutations by sequencing. Results We identified an exon 3 donor splice mutation in the COL9A2 gene in all affected family members. Clinical, radiographic, and questionnaire data from affected family members suggested that MED caused by COL9A2 mutations starts in early childhood with knee pain accompanied by delayed ossification of femoral epiphyses. The disease then either stabilizes during puberty or progresses with additional joints becoming affected; joint surgery might be necessary. The progression of the disease also affects muscles, with increasing atrophy, resulting in muscle fatigue and pain. Muscular atrophy has not been reported earlier in cases with COL9A2 mutations. Interpretation In a patient with clinically suspected or verified MED, it is important to perform DNA-based analysis to identify a possible disease-causing mutation. This information can be used to carry out genetic risk assessment of other family members and to achieve an early and correct diagnosis in the children. PMID:19995321

  19. Wideband digital spectrum analyzer

    NASA Technical Reports Server (NTRS)

    Morris, G. A., Jr.; Wilck, H. C.

    1979-01-01

    Modular spectrum analyzer consisting of RF receiver, fast fourier transform spectrum analyzer, and data processor samples stochastic signals in 220 channels. Construction reduces design and fabrication costs of assembled unit.

  20. Image quality analyzer

    NASA Astrophysics Data System (ADS)

    Lukin, V. P.; Botugina, N. N.; Emaleev, O. N.; Antoshkin, L. V.; Konyaev, P. A.

    2012-07-01

    Image quality analyzer (IQA) which used as device for efficiency analysis of adaptive optics application is described. In analyzer marketed possibility estimations quality of images on three different criterions of quality images: contrast, sharpnesses and the spectral criterion. At present given analyzer is introduced on Big Solar Vacuum Telescope in stale work that allows at observations to conduct the choice of the most contrasting images of Sun. Is it hereinafter planned use the analyzer in composition of the ANGARA adaptive correction system.

  1. Crew Activity Analyzer

    NASA Technical Reports Server (NTRS)

    Murray, James; Kirillov, Alexander

    2008-01-01

    The crew activity analyzer (CAA) is a system of electronic hardware and software for automatically identifying patterns of group activity among crew members working together in an office, cockpit, workshop, laboratory, or other enclosed space. The CAA synchronously records multiple streams of data from digital video cameras, wireless microphones, and position sensors, then plays back and processes the data to identify activity patterns specified by human analysts. The processing greatly reduces the amount of time that the analysts must spend in examining large amounts of data, enabling the analysts to concentrate on subsets of data that represent activities of interest. The CAA has potential for use in a variety of governmental and commercial applications, including planning for crews for future long space flights, designing facilities wherein humans must work in proximity for long times, improving crew training and measuring crew performance in military settings, human-factors and safety assessment, development of team procedures, and behavioral and ethnographic research. The data-acquisition hardware of the CAA (see figure) includes two video cameras: an overhead one aimed upward at a paraboloidal mirror on the ceiling and one mounted on a wall aimed in a downward slant toward the crew area. As many as four wireless microphones can be worn by crew members. The audio signals received from the microphones are digitized, then compressed in preparation for storage. Approximate locations of as many as four crew members are measured by use of a Cricket indoor location system. [The Cricket indoor location system includes ultrasonic/radio beacon and listener units. A Cricket beacon (in this case, worn by a crew member) simultaneously transmits a pulse of ultrasound and a radio signal that contains identifying information. Each Cricket listener unit measures the difference between the times of reception of the ultrasound and radio signals from an identified beacon

  2. Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm

    PubMed Central

    Wang, Boyi; Tan, Hua-Wei; Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Matsumoto, Tracie; Zhang, Dapeng

    2015-01-01

    Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (Fst=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification. PMID:26504559

  3. Analyzing Peace Pedagogies

    ERIC Educational Resources Information Center

    Haavelsrud, Magnus; Stenberg, Oddbjorn

    2012-01-01

    Eleven articles on peace education published in the first volume of the Journal of Peace Education are analyzed. This selection comprises peace education programs that have been planned or carried out in different contexts. In analyzing peace pedagogies as proposed in the 11 contributions, we have chosen network analysis as our method--enabling…

  4. Portable automatic blood analyzer

    NASA Technical Reports Server (NTRS)

    Coleman, R. L.

    1975-01-01

    Analyzer employs chemical-sensing electrodes for determination of blood, gas, and ion concentrations. It is rugged, easily serviced, and comparatively simple to operate. System can analyze up to eight parameters and can be modified to measure other blood constituents including nonionic species, such as urea, glucose, and oxygen.

  5. Analyzing Costs of Services.

    ERIC Educational Resources Information Center

    Cox, James O.; Black, Talbot

    A simplified method to gather and analyze cost data is presented for administrators of Handicapped Children's Early Education Programs, and specifically for members of the Technical Assistance Development System, North Carolina. After identifying benefits and liabilities associated with analyzing program costs, attention is focused on the internal…

  6. Plasmodium falciparum: A novel method for analyzing haplotypes in mixed infections

    PubMed Central

    Certain, Laura K.; Sibley, Carol H.

    2007-01-01

    Studying the population genetics of Plasmodium falciparum is necessary for understanding the spread of drug resistance. However, these studies are hampered by the inability to determine haplotypes from patient samples that contain multiple parasite populations. Therefore, we have developed a method for separating for genetic analysis the individual strains in a mixed infection. We amplified a 6 kb region of chromosome 4, including the dihydrofolate reductase gene and upstream microsatellite markers. This PCR product was inserted by recombination into a gapped yeast shuttle plasmid containing both selectable and counter-selectable markers. Because each plasmid contains only one insert and each yeast colony contains only one plasmid, the individual strains are now separate. We analyzed mixtures of 3D7, K1, and Dd2 DNA and correctly identified a haplotype in each case. PMID:17049516

  7. Microwave transient analyzer

    DOEpatents

    Gallegos, C.H.; Ogle, J.W.; Stokes, J.L.

    1992-11-24

    A method and apparatus for capturing and recording indications of frequency content of electromagnetic signals and radiation is disclosed including a laser light source and a Bragg cell for deflecting a light beam at a plurality of deflection angles dependent upon frequency content of the signal. A streak camera and a microchannel plate intensifier are used to project Bragg cell output onto either a photographic film or a charge coupled device (CCD) imager. Timing markers are provided by a comb generator and a one shot generator, the outputs of which are also routed through the streak camera onto the film or the CCD imager. Using the inventive method, the full range of the output of the Bragg cell can be recorded as a function of time. 5 figs.

  8. Microwave transient analyzer

    DOEpatents

    Gallegos, Cenobio H.; Ogle, James W.; Stokes, John L.

    1992-01-01

    A method and apparatus for capturing and recording indications of frequency content of electromagnetic signals and radiation is disclosed including a laser light source (12) and a Bragg cell (14) for deflecting a light beam (22) at a plurality of deflection angles (36) dependent upon frequency content of the signal. A streak camera (26) and a microchannel plate intensifier (28) are used to project Bragg cell (14) output onto either a photographic film (32) or a charge coupled device (CCD) imager (366). Timing markers are provided by a comb generator (50) and a one shot generator (52), the outputs of which are also routed through the streak camera (26) onto the film (32) or the CCD imager (366). Using the inventive method, the full range of the output of the Bragg cell (14) can be recorded as a function of time.

  9. Software Design Analyzer System

    NASA Technical Reports Server (NTRS)

    Tausworthe, R. C.

    1985-01-01

    CRISP80 software design analyzer system a set of programs that supports top-down, hierarchic, modular structured design, and programing methodologies. CRISP80 allows for expression of design as picture of program.

  10. Automatic amino acid analyzer

    NASA Technical Reports Server (NTRS)

    Berdahl, B. J.; Carle, G. C.; Oyama, V. I.

    1971-01-01

    Analyzer operates unattended or up to 15 hours. It has an automatic sample injection system and can be programmed. All fluid-flow valve switching is accomplished pneumatically from miniature three-way solenoid pilot valves.

  11. Analyzing binding data.

    PubMed

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  12. Prevalence of heroin markers in urine for pain management patients.

    PubMed

    Knight, Julie; Puet, Brandi L; DePriest, Anne; Heltsley, Rebecca; Hild, Cheryl; Black, David L; Robert, Timothy; Caplan, Yale H; Cone, Edward J

    2014-10-01

    Surveys of current trends indicate heroin abuse is associated with nonmedical use of pain relievers. Consequently, there is an interest in evaluating the presence of heroin-specific markers in chronic pain patients who are prescribed controlled substances. A total of 926,084 urine specimens from chronic pain patients were tested for heroin/diacetylmorphine (DAM), 6-acetylmorphine (6AM), 6-acetylcodeine (6AC), codeine (COD), and morphine (MOR). Heroin and markers were analyzed using liquid chromatography tandem mass spectrometry (LC-MS-MS). Opiates were analyzed following hydrolysis using LC-MS-MS. The prevalence of heroin use was 0.31%, as 2871 were positive for one or more heroin-specific markers including DAM, 6AM, or 6AC (a known contaminant of illicit heroin). Of these, 1884 were additionally tested for the following markers of illicit drug use: 3,4-methylenedioxymethamphetamine (MDMA), 3,4-methylenedioxyamphetamine (MDA), methamphetamine (MAMP), 11-nor-9-carboxy-Δ(9)-tetracannabinol (THCCOOH), and benzoylecgonine (BZE); 654 (34.7%) had positive findings for one or more of these analytes. The overall prevalence of heroin markers were as follows: DAM 1203 (41.9%), 6AM 2570 (89.5%), 6AC 1082 (37.7%). MOR was present in 2194 (76.4%) and absent (multiple heroin markers may be useful to assess for

  13. Soil Rock Analyzer

    NASA Technical Reports Server (NTRS)

    1985-01-01

    A redesigned version of a soil/rock analyzer developed by Martin Marietta under a Langley Research Center contract is being marketed by Aurora Tech, Inc. Known as the Aurora ATX-100, it has self-contained power, an oscilloscope, a liquid crystal readout, and a multichannel spectrum analyzer. It measures energy emissions to determine what elements in what percentages a sample contains. It is lightweight and may be used for mineral exploration, pollution monitoring, etc.

  14. Serotonin, neural markers, and memory

    PubMed Central

    Meneses, Alfredo

    2015-01-01

    Diverse neuropsychiatric disorders present dysfunctional memory and no effective treatment exits for them; likely as result of the absence of neural markers associated to memory. Neurotransmitter systems and signaling pathways have been implicated in memory and dysfunctional memory; however, their role is poorly understood. Hence, neural markers and cerebral functions and dysfunctions are revised. To our knowledge no previous systematic works have been published addressing these issues. The interactions among behavioral tasks, control groups and molecular changes and/or pharmacological effects are mentioned. Neurotransmitter receptors and signaling pathways, during normal and abnormally functioning memory with an emphasis on the behavioral aspects of memory are revised. With focus on serotonin, since as it is a well characterized neurotransmitter, with multiple pharmacological tools, and well characterized downstream signaling in mammals' species. 5-HT1A, 5-HT4, 5-HT5, 5-HT6, and 5-HT7 receptors as well as SERT (serotonin transporter) seem to be useful neural markers and/or therapeutic targets. Certainly, if the mentioned evidence is replicated, then the translatability from preclinical and clinical studies to neural changes might be confirmed. Hypothesis and theories might provide appropriate limits and perspectives of evidence. PMID:26257650

  15. Total organic carbon analyzer

    NASA Technical Reports Server (NTRS)

    Godec, Richard G.; Kosenka, Paul P.; Smith, Brian D.; Hutte, Richard S.; Webb, Johanna V.; Sauer, Richard L.

    1991-01-01

    The development and testing of a breadboard version of a highly sensitive total-organic-carbon (TOC) analyzer are reported. Attention is given to the system components including the CO2 sensor, oxidation reactor, acidification module, and the sample-inlet system. Research is reported for an experimental reagentless oxidation reactor, and good results are reported for linearity, sensitivity, and selectivity in the CO2 sensor. The TOC analyzer is developed with gravity-independent components and is designed for minimal additions of chemical reagents. The reagentless oxidation reactor is based on electrolysis and UV photolysis and is shown to be potentially useful. The stability of the breadboard instrument is shown to be good on a day-to-day basis, and the analyzer is capable of 5 sample analyses per day for a period of about 80 days. The instrument can provide accurate TOC and TIC measurements over a concentration range of 20 ppb to 50 ppm C.

  16. Electrosurgical unit analyzers.

    PubMed

    1998-07-01

    Electrosurgical unit (ESU) analyzers automate the testing and inspection of the output circuits and safety features of ESUs. They perform testing that would otherwise require several other pieces of equipment, as well as considerably more time and greater technician expertise. They are used largely by clinical engineering departments for routine inspection and preventive maintenance (IPM) procedures and, less often, for accident investigations and troubleshooting. In this Evaluation, we tested three ESU analyzers from three suppliers. We rated all three analyzers Acceptable and ranked them in two groupings. In ranking the units, we placed the greatest weight on ease of use for routine ESU inspections, and gave additional consideration to versatility for advanced applications such as ESU research. The unit in Group 1 was the easiest to use, especially for infrequent users. The units in Group 2 were satisfactory but require more frequent use to maintain proficiency and to avoid user errors. PMID:9689540

  17. Analyzing radioligand binding data.

    PubMed

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  18. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing

    PubMed Central

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.

  19. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.

    PubMed

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.

  20. Analyzing Bilingual Education Costs.

    ERIC Educational Resources Information Center

    Bernal, Joe J.

    This paper examines the particular problems involved in analyzing the costs of bilingual education and suggests that cost analysis of bilingual education requires a fundamentally different approach than that followed in other recent school finance studies. Focus of the discussion is the Intercultural Development Research Association's (IDRA)…

  1. List mode multichannel analyzer

    SciTech Connect

    Archer, Daniel E.; Luke, S. John; Mauger, G. Joseph; Riot, Vincent J.; Knapp, David A.

    2007-08-07

    A digital list mode multichannel analyzer (MCA) built around a programmable FPGA device for onboard data analysis and on-the-fly modification of system detection/operating parameters, and capable of collecting and processing data in very small time bins (<1 millisecond) when used in histogramming mode, or in list mode as a list mode MCA.

  2. Analyzing Workforce Education. Monograph.

    ERIC Educational Resources Information Center

    Texas Community & Technical Coll. Workforce Education Consortium.

    This monograph examines the issue of task analysis as used in workplace literacy programs, debating the need for it and how to perform it in a rapidly changing environment. Based on experiences of community colleges in Texas, the report analyzes ways that task analysis can be done and how to implement work force education programs more quickly.…

  3. Electronic sleep analyzer

    NASA Technical Reports Server (NTRS)

    Frost, J. D., Jr.

    1970-01-01

    Electronic instrument automatically monitors the stages of sleep of a human subject. The analyzer provides a series of discrete voltage steps with each step corresponding to a clinical assessment of level of consciousness. It is based on the operation of an EEG and requires very little telemetry bandwidth or time.

  4. Micro acoustic spectrum analyzer

    DOEpatents

    Schubert, W. Kent; Butler, Michael A.; Adkins, Douglas R.; Anderson, Larry F.

    2004-11-23

    A micro acoustic spectrum analyzer for determining the frequency components of a fluctuating sound signal comprises a microphone to pick up the fluctuating sound signal and produce an alternating current electrical signal; at least one microfabricated resonator, each resonator having a different resonant frequency, that vibrate in response to the alternating current electrical signal; and at least one detector to detect the vibration of the microfabricated resonators. The micro acoustic spectrum analyzer can further comprise a mixer to mix a reference signal with the alternating current electrical signal from the microphone to shift the frequency spectrum to a frequency range that is a better matched to the resonant frequencies of the microfabricated resonators. The micro acoustic spectrum analyzer can be designed specifically for portability, size, cost, accuracy, speed, power requirements, and use in a harsh environment. The micro acoustic spectrum analyzer is particularly suited for applications where size, accessibility, and power requirements are limited, such as the monitoring of industrial equipment and processes, detection of security intrusions, or evaluation of military threats.

  5. Molecular Marker Systems for Oenothera Genetics

    PubMed Central

    Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G.; Greiner, Stephan

    2008-01-01

    The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome–genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9·8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed. PMID:18791241

  6. Alzheimer's disease: analyzing the missing heritability.

    PubMed

    Ridge, Perry G; Mukherjee, Shubhabrata; Crane, Paul K; Kauwe, John S K

    2013-01-01

    Alzheimer's disease (AD) is a complex disorder influenced by environmental and genetic factors. Recent work has identified 11 AD markers in 10 loci. We used Genome-wide Complex Trait Analysis to analyze >2 million SNPs for 10,922 individuals from the Alzheimer's Disease Genetics Consortium to assess the phenotypic variance explained first by known late-onset AD loci, and then by all SNPs in the Alzheimer's Disease Genetics Consortium dataset. In all, 33% of total phenotypic variance is explained by all common SNPs. APOE alone explained 6% and other known markers 2%, meaning more than 25% of phenotypic variance remains unexplained by known markers, but is tagged by common SNPs included on genotyping arrays or imputed with HapMap genotypes. Novel AD markers that explain large amounts of phenotypic variance are likely to be rare and unidentifiable using genome-wide association studies. Based on our findings and the current direction of human genetics research, we suggest specific study designs for future studies to identify the remaining heritability of Alzheimer's disease.

  7. PULSE AMPLITUDE ANALYZER

    DOEpatents

    Greenblatt, M.H.

    1958-03-25

    This patent pertains to pulse amplitude analyzers for sorting and counting a serles of pulses, and specifically discloses an analyzer which ls simple in construction and presents the puise height distribution visually on an oscilloscope screen. According to the invention, the pulses are applied to the vertical deflection plates of an oscilloscope and trigger the horizontal sweep. Each pulse starts at the same point on the screen and has a maximum amplitude substantially along the same vertical line. A mask is placed over the screen except for a slot running along the line where the maximum amplitudes of the pulses appear. After the slot has been scanned by a photocell in combination with a slotted rotating disk, the photocell signal is displayed on an auxiliary oscilloscope as vertical deflection along a horizontal time base to portray the pulse amplitude distribution.

  8. Analyzing radioligand binding data.

    PubMed

    Motulsky, H; Neubig, R

    2001-05-01

    A radioligand is a radioactively labeled drug that can associate with a receptor, transporter, enzyme, or any protein of interest. Measuring the rate and extent of binding provides information on the number of binding sites, and their affinity and accessibility for various drugs. Radioligand binding experiments are easy to perform, and provide useful data in many fields. For example, radioligand binding studies are used to study receptor regulation, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  9. Identification of fecal contamination sources in water using host-associated markers.

    PubMed

    Krentz, Corinne A; Prystajecky, Natalie; Isaac-Renton, Judith

    2013-03-01

    In British Columbia, Canada, drinking water is tested for total coliforms and Escherichia coli, but there is currently no routine follow-up testing to investigate fecal contamination sources in samples that test positive for indicator bacteria. Reliable microbial source tracking (MST) tools to rapidly test water samples for multiple fecal contamination markers simultaneously are currently lacking. The objectives of this study were (i) to develop a qualitative MST tool to identify fecal contamination from different host groups, and (ii) to evaluate the MST tool using water samples with evidence of fecal contamination. Singleplex and multiplex polymerase chain reaction (PCR) were used to test (i) water from polluted sites and (ii) raw and drinking water samples for presence of bacterial genetic markers associated with feces from humans, cattle, seagulls, pigs, chickens, and geese. The multiplex MST assay correctly identified suspected contamination sources in contaminated waterways, demonstrating that this test may have utility for heavily contaminated sites. Most raw and drinking water samples analyzed using singleplex PCR contained at least one host-associated marker. Singleplex PCR was capable of detecting host-associated markers in small sample volumes and is therefore a promising tool to further analyze water samples submitted for routine testing and provide information useful for water quality management.

  10. Analyzing Optical Communications Links

    NASA Technical Reports Server (NTRS)

    Marshall, William K.; Burk, Brian D.

    1990-01-01

    Optical Communication Link Analysis Program, OPTI, analyzes optical and near-infrared communication links using pulse-position modulation (PPM) and direct detention. Link margins and design-control tables generated from input parameters supplied by user. Enables user to save sets of input parameters that define given link and read them back into program later. Alters automatically any of input parameters to achieve desired link margin. Written in FORTRAN 77.

  11. Magnetoresistive emulsion analyzer.

    PubMed

    Lin, Gungun; Baraban, Larysa; Han, Luyang; Karnaushenko, Daniil; Makarov, Denys; Cuniberti, Gianaurelio; Schmidt, Oliver G

    2013-01-01

    We realize a magnetoresistive emulsion analyzer capable of detection, multiparametric analysis and sorting of ferrofluid-containing nanoliter-droplets. The operation of the device in a cytometric mode provides high throughput and quantitative information about the dimensions and magnetic content of the emulsion. Our method offers important complementarity to conventional optical approaches involving ferrofluids, and paves the way to the development of novel compact tools for diagnostics and nanomedicine including drug design and screening. PMID:23989504

  12. Analyzing Leakage Through Cracks

    NASA Technical Reports Server (NTRS)

    Romine, William D.

    1993-01-01

    Two related computer programs written for use in analyzing leakage through cracks. Leakage flow laminar or turbulent. One program used to determine dimensions of crack under given flow conditions and given measured rate of leakage. Other used to determine rate of leakage of gas through crack of given dimensions under given flow conditions. Programs, written in BASIC language, accelerate and facilitate iterative calculations and parametric analyses. Solve equations of Fanno flow. Enables rapid solution of leakage problem.

  13. Magnetoresistive Emulsion Analyzer

    PubMed Central

    Lin, Gungun; Baraban, Larysa; Han, Luyang; Karnaushenko, Daniil; Makarov, Denys; Cuniberti, Gianaurelio; Schmidt, Oliver G.

    2013-01-01

    We realize a magnetoresistive emulsion analyzer capable of detection, multiparametric analysis and sorting of ferrofluid-containing nanoliter-droplets. The operation of the device in a cytometric mode provides high throughput and quantitative information about the dimensions and magnetic content of the emulsion. Our method offers important complementarity to conventional optical approaches involving ferrofluids, and paves the way to the development of novel compact tools for diagnostics and nanomedicine including drug design and screening. PMID:23989504

  14. Coaxial charged particle energy analyzer

    NASA Technical Reports Server (NTRS)

    Kelly, Michael A. (Inventor); Bryson, III, Charles E. (Inventor); Wu, Warren (Inventor)

    2011-01-01

    A non-dispersive electrostatic energy analyzer for electrons and other charged particles having a generally coaxial structure of a sequentially arranged sections of an electrostatic lens to focus the beam through an iris and preferably including an ellipsoidally shaped input grid for collimating a wide acceptance beam from a charged-particle source, an electrostatic high-pass filter including a planar exit grid, and an electrostatic low-pass filter. The low-pass filter is configured to reflect low-energy particles back towards a charged particle detector located within the low-pass filter. Each section comprises multiple tubular or conical electrodes arranged about the central axis. The voltages on the lens are scanned to place a selected energy band of the accepted beam at a selected energy at the iris. Voltages on the high-pass and low-pass filters remain substantially fixed during the scan.

  15. Fractional channel multichannel analyzer

    DOEpatents

    Brackenbush, Larry W.; Anderson, Gordon A.

    1994-01-01

    A multichannel analyzer incorporating the features of the present invention obtains the effect of fractional channels thus greatly reducing the number of actual channels necessary to record complex line spectra. This is accomplished by using an analog-to-digital converter in the asynscronous mode, i.e., the gate pulse from the pulse height-to-pulse width converter is not synchronized with the signal from a clock oscillator. This saves power and reduces the number of components required on the board to achieve the effect of radically expanding the number of channels without changing the circuit board.

  16. Portable Gas Analyzer

    NASA Technical Reports Server (NTRS)

    1986-01-01

    The Michromonitor M500 universal gas analyzer contains a series of miniature modules, each of which is a complete gas chromatograph, an instrument which separates a gaseous mixture into its components and measures the concentrations of each gas in the mixture. The system is manufactured by Microsensor Technology, and is used for environmental analysis, monitoring for gas leaks and chemical spills, compliance with pollution laws, etc. The technology is based on a Viking attempt to detect life on Mars. Ames/Stanford miniaturized the system and NIOSH funded further development. Three Stanford researchers commercialized the technology, which can be operated by unskilled personnel.

  17. RELAPS desktop analyzer

    SciTech Connect

    Beelman, R.J.; Grush, W.H.; Mortensen, G.A.; Snider, D.M.; Wagner, K.L.

    1989-01-01

    The previously mainframe bound RELAP5 reactor safety computer code has been installed on a microcomputer. A simple color-graphic display driver has been developed to enable the user to view the code results as the calculation advances. In order to facilitate future interactive desktop applications, the Nuclear Plant Analyzer (NPA), also previously mainframe bound, is being redesigned to encompass workstation applications. The marriage of RELAP5 simulation capabilities with NPA interactive graphics on a desktop workstation promises to revolutionize reactor safety analysis methodology. 8 refs.

  18. Fluorescence analyzer for lignin

    DOEpatents

    Berthold, John W.; Malito, Michael L.; Jeffers, Larry

    1993-01-01

    A method and apparatus for measuring lignin concentration in a sample of wood pulp or black liquor comprises a light emitting arrangement for emitting an excitation light through optical fiber bundles into a probe which has an undiluted sensing end facing the sample. The excitation light causes the lignin concentration to produce fluorescent emission light which is then conveyed through the probe to analyzing equipment which measures the intensity of the emission light. Measures a This invention was made with Government support under Contract Number DOE: DE-FC05-90CE40905 awarded by the Department of Energy (DOE). The Government has certain rights in this invention.

  19. Today's oxidative stress markers.

    PubMed

    Czerska, Marta; Mikołajewska, Karolina; Zieliński, Marek; Gromadzińska, Jolanta; Wąsowicz, Wojciech

    2015-01-01

    Oxidative stress represents a situation where there is an imbalance between the reactive oxygen species (ROS) and the availability and the activity of antioxidants. This balance is disturbed by increased generation of free radicals or decreased antioxidant activity. It is very important to develop methods and find appropriate biomarkers that may be used to assess oxidative stress in vivo. It is significant because appropriate measurement of such stress is necessary in identifying its role in lifestyle-related diseases. Previously used markers of oxidative stress, such as thiobarbituric acid reactive substances (TBARS) or malondialdehyde (MDA), are progressively being supplemented by new ones, such as isoprostanes (IsoPs) and their metabolites or allantoin. This paper is focusing on the presentation of new ones, promising markers of oxidative stress (IsoPs, their metabolites and allantoin), taking into account the advantage of those markers over markers used previously. PMID:26325052

  20. Acupuncture Stimulation Analyzed from Multiple Aspects of Western Medical Science.

    PubMed

    Inanç, Betül Battaloğlu

    2016-01-01

    Skin is the biggest and most important organ of us. It has a large surface area and it is easily accessible. While we touch skin, piezoelectric stimulation starts, fundamental property of biological tissues, pressure electrification. And after this stimulation, ferroelectric and pyroelectric effects occur. While we insert the acupuncture needle into skin, we have created a conscious trauma and damage. After this, inflammatory phase, proliferation and tissue formation phase and tissue remodeling phase start. With embryological perspective, at that moment, we give stimulus ectodermal and mesodermal layer of the skin also. We stimulate these embryologic layers and cells not only into skin but also whole body. Because, while we start stimulation with a cell, cell stimulates other cells and cells stimulate body. Also we stimulate neuropeptides, neurotransmitters, neuro-hormones and receptors. The skin is the largest immunologically active receptor organ in the body. And we see, peripheral local stress response (brain-skin) works same as hypothalamic-pituitary-adrenal axis. So, what we have done? We only insert the acupuncture needle into skin consciously. PMID:27244951

  1. Analyzing hyperspectral images into multiple subspaces using Gaussian mixture models

    NASA Astrophysics Data System (ADS)

    Spence, Clay D.

    2016-05-01

    I argue that the spectra in a hyperspectral datacube will usually lie in several low-dimensional subspaces, and that these subspaces are more easily estimated from the data than the endmembers. I present an algorithm for finding the subspaces. The algorithm fits the data with a Gaussian mixture model, in which the means and covariance matrices are parameterized in terms of the subspaces. The locations of materials can be inferred from the fit of library spectra to the subspaces. The algorithm can be modified to perform material detection. This has better performance than standard algorithms such as ACE, and runs in real time.

  2. Analyzing Aeroelasticity in Turbomachines

    NASA Technical Reports Server (NTRS)

    Reddy, T. S. R.; Srivastava, R.

    2003-01-01

    ASTROP2-LE is a computer program that predicts flutter and forced responses of blades, vanes, and other components of such turbomachines as fans, compressors, and turbines. ASTROP2-LE is based on the ASTROP2 program, developed previously for analysis of stability of turbomachinery components. In developing ASTROP2- LE, ASTROP2 was modified to include a capability for modeling forced responses. The program was also modified to add a capability for analysis of aeroelasticity with mistuning and unsteady aerodynamic solutions from another program, LINFLX2D, that solves the linearized Euler equations of unsteady two-dimensional flow. Using LINFLX2D to calculate unsteady aerodynamic loads, it is possible to analyze effects of transonic flow on flutter and forced response. ASTROP2-LE can be used to analyze subsonic, transonic, and supersonic aerodynamics and structural mistuning for rotors with blades of differing structural properties. It calculates the aerodynamic damping of a blade system operating in airflow so that stability can be assessed. The code also predicts the magnitudes and frequencies of the unsteady aerodynamic forces on the airfoils of a blade row from incoming wakes. This information can be used in high-cycle fatigue analysis to predict the fatigue lives of the blades.

  3. Ring Image Analyzer

    NASA Technical Reports Server (NTRS)

    Strekalov, Dmitry V.

    2012-01-01

    Ring Image Analyzer software analyzes images to recognize elliptical patterns. It determines the ellipse parameters (axes ratio, centroid coordinate, tilt angle). The program attempts to recognize elliptical fringes (e.g., Newton Rings) on a photograph and determine their centroid position, the short-to-long-axis ratio, and the angle of rotation of the long axis relative to the horizontal direction on the photograph. These capabilities are important in interferometric imaging and control of surfaces. In particular, this program has been developed and applied for determining the rim shape of precision-machined optical whispering gallery mode resonators. The program relies on a unique image recognition algorithm aimed at recognizing elliptical shapes, but can be easily adapted to other geometric shapes. It is robust against non-elliptical details of the image and against noise. Interferometric analysis of precision-machined surfaces remains an important technological instrument in hardware development and quality analysis. This software automates and increases the accuracy of this technique. The software has been developed for the needs of an R&TD-funded project and has become an important asset for the future research proposal to NASA as well as other agencies.

  4. Plutonium solution analyzer

    SciTech Connect

    Burns, D.A.

    1994-09-01

    A fully automated analyzer has been developed for plutonium solutions. It was assembled from several commercially available modules, is based upon segmented flow analysis, and exhibits precision about an order of magnitude better than commercial units (0.5%-O.05% RSD). The system was designed to accept unmeasured, untreated liquid samples in the concentration range 40-240 g/L and produce a report with sample identification, sample concentrations, and an abundance of statistics. Optional hydraulics can accommodate samples in the concentration range 0.4-4.0 g/L. Operating at a typical rate of 30 to 40 samples per hour, it consumes only 0.074 mL of each sample and standard, and generates waste at the rate of about 1.5 mL per minute. No radioactive material passes through its multichannel peristaltic pump (which remains outside the glovebox, uncontaminated) but rather is handled by a 6-port, 2-position chromatography-type loop valve. An accompanying computer is programmed in QuickBASIC 4.5 to provide both instrument control and data reduction. The program is truly user-friendly and communication between operator and instrument is via computer screen displays and keyboard. Two important issues which have been addressed are waste minimization and operator safety (the analyzer can run in the absence of an operator, once its autosampler has been loaded).

  5. Field Deployable DNA analyzer

    SciTech Connect

    Wheeler, E; Christian, A; Marion, J; Sorensen, K; Arroyo, E; Vrankovich, G; Hara, C; Nguyen, C

    2005-02-09

    This report details the feasibility of a field deployable DNA analyzer. Steps for swabbing cells from surfaces and extracting DNA in an automatable way are presented. Since enzymatic amplification reactions are highly sensitive to environmental contamination, sample preparation is a crucial step to make an autonomous deployable instrument. We perform sample clean up and concentration in a flow through packed bed. For small initial samples, whole genome amplification is performed in the packed bed resulting in enough product for subsequent PCR amplification. In addition to DNA, which can be used to identify a subject, protein is also left behind, the analysis of which can be used to determine exposure to certain substances, such as radionuclides. Our preparative step for DNA analysis left behind the protein complement as a waste stream; we determined to learn if the proteins themselves could be analyzed in a fieldable device. We successfully developed a two-step lateral flow assay for protein analysis and demonstrate a proof of principle assay.

  6. [Biological markers of alcoholism].

    PubMed

    Marcos Martín, M; Pastor Encinas, I; Laso Guzmán, F J

    2005-09-01

    Diagnosis of alcoholism is very important, given its high prevalence and possibility of influencing the disease course. For this reason, the so-called biological markers of alcoholism are useful. These are analytic parameters that alter in the presence of excessive alcohol consumption. The two most relevant markers are the gamma-glutamyltranspeptidase and carbohydrate deficient transferrin. With this clinical comment, we aim to contribute to the knowledge of these tests and promote its use in the clinical practice. PMID:16194480

  7. Study of Aided Diagnosis of Hepatic Carcinoma Based on Artificial Neural Network Combined with Tumor Marker Group

    NASA Astrophysics Data System (ADS)

    Tan, Shanjuan; Feng, Feifei; Wu, Yongjun; Wu, Yiming

    To develop a computer-aided diagnostic scheme by using an artificial neural network (ANN) combined with tumor markers for diagnosis of hepatic carcinoma (HCC) as a clinical assistant method. 140 serum samples (50 malignant, 40 benign and 50 normal) were analyzed for α-fetoprotein (AFP), carbohydrate antigen 125 (CA125), carcinoembryonic antigen (CEA), sialic acid (SA) and calcium (Ca). The five tumor marker values were then used as ANN inputs data. The result of ANN was compared with that of discriminant analysis by receiver operating characteristic (ROC) curve (AUC) analysis. The diagnostic accuracy of ANN and discriminant analysis among all samples of the test group was 95.5% and 79.3%, respectively. Analysis of multiple tumor markers based on ANN may be a better choice than the traditional statistical methods for differentiating HCC from benign or normal.

  8. Methodological issues associated with tumor marker development. Biostatistical aspects.

    PubMed

    Faraggi; Kramar

    2000-09-01

    The search for markers as potential prognostic factors for different stages of disease is becoming a major task in clinical research. Enormous amounts of information on the effectiveness of tumor markers are being published, and many of these results are conflicting and thus adding confusion to the area. In this paper we discuss the problem of multiplicity that we believe is one of the major statistical reasons for the conflicting results. We further review the ROC curve and the area under it as a popular statistical tool for evaluating the ability of a marker to distinguish between two populations. Finally we provide an extension to the ROC analysis when several markers are available.

  9. L-split marker for augmented reality in aircraft assembly

    NASA Astrophysics Data System (ADS)

    Han, Pengfei; Zhao, Gang

    2016-04-01

    In order to improve the performance of conventional square markers widely used by marker-based augmented reality systems in aircraft assembly environments, an L-split marker is proposed. Every marker consists of four separate L-shaped parts and each of them contains partial information about the marker. Geometric features of the L-shape, which are more discriminate than the symmetrical square shape adopted by conventional markers, are used to detect proposed markers from the camera images effectively. The marker is split into four separate parts in order to improve the robustness to occlusion and curvature to some extent. The registration process can be successfully completed as long as three parts are detected (up to about 80% of the area could be occluded). Moreover, when we attach the marker on nonplanar surfaces, the curvature status of the marker can be roughly analyzed with every part's normal direction, which can be obtained since their six corners have been explicitly determined in the previous detection process. And based on the marker design, new detection and recognition algorithms are proposed and detailed. The experimental results show that the marker and the algorithms are effective.

  10. Evaluation of Tumor Shape Variability in Head-and-Neck Cancer Patients Over the Course of Radiation Therapy Using Implanted Gold Markers

    SciTech Connect

    Hamming-Vrieze, Olga; Kranen, Simon Robert van; Beek, Suzanne van; Heemsbergen, Wilma; Herk, Marcel van; Brekel, Michiel Wilhelmus Maria van den; Sonke, Jan-Jakob; Rasch, Coenraad Robert Nico

    2012-10-01

    Purpose: This study quantifies tumor shape variability in head-and-neck cancer patients during radiation therapy using implanted markers. Methods and Materials: Twenty-seven patients with oropharyngeal tumors treated with (chemo)radiation were included. Helical gold markers (0.35 Multiplication-Sign 2 mm, 3-10/patient, average 6) were implanted around the tumor. Markers were identified on planning computed tomography (CT) and daily cone beam CT (CBCT). After bony anatomy registration, the daily vector length on CBCT in reference to the planning CT and daily marker movement perpendicular to the gross tumor volume (GTV) surface at planning CT (d{sub normal}) of each marker were analyzed. Time trends were assessed with linear regression of the {sub markers}. In 2 patients, 2 markers were implanted in normal tissue to evaluate migration by measuring intermarker distances. Results: Marker implantation was feasible without complications. Three-dimensional vectors (4827 measurements, mean 0.23 cm, interquartile ratio 0.24 cm) were highest in base of tongue sublocalization (P<.001) and bulky tumors (vectors exceeded 0.5 cm in 5.7% [0-20 mL], 12.0% [21-40 mL], and 21.7% [{>=}41 mL], respectively [P<.001] of measurements). The measured inward time trend in 11/27 patients correlated with the visual observed marker pattern. In patients with an outward trend (5/27) or no trend (11/27), visual observation showed predominantly an inhomogeneous pattern. Remarkably, in 6 patients, outward marker movement was observed in the posterior pharyngeal wall. The difference in distance between normal tissue markers (1 SD) was 0.05-0.06 cm without time trend, indicating that implanted markers did not migrate. Conclusions: During head-and-neck radiation therapy, normal tissue markers remained stable. Changes in position of tumor markers depended on sublocalization and tumor volume. Large differences in marker patterns between patients as well as within patients were observed

  11. Analyzing Water's Optical Absorption

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A cooperative agreement between World Precision Instruments (WPI), Inc., and Stennis Space Center has led the UltraPath(TM) device, which provides a more efficient method for analyzing the optical absorption of water samples at sea. UltraPath is a unique, high-performance absorbance spectrophotometer with user-selectable light path lengths. It is an ideal tool for any study requiring precise and highly sensitive spectroscopic determination of analytes, either in the laboratory or the field. As a low-cost, rugged, and portable system capable of high- sensitivity measurements in widely divergent waters, UltraPath will help scientists examine the role that coastal ocean environments play in the global carbon cycle. UltraPath(TM) is a trademark of World Precision Instruments, Inc. LWCC(TM) is a trademark of World Precision Instruments, Inc.

  12. Motion detector and analyzer

    DOEpatents

    Unruh, W.P.

    1987-03-23

    Method and apparatus are provided for deriving positive and negative Doppler spectrum to enable analysis of objects in motion, and particularly, objects having rotary motion. First and second returned radar signals are mixed with internal signals to obtain an in-phase process signal and a quadrature process signal. A broad-band phase shifter shifts the quadrature signal through 90/degree/ relative to the in-phase signal over a predetermined frequency range. A pair of signals is output from the broad-band phase shifter which are then combined to provide a first side band signal which is functionally related to a negative Doppler shift spectrum. The distinct positive and negative Doppler spectra may then be analyzed for the motion characteristics of the object being examined.

  13. Analyzing geographic clustered response

    SciTech Connect

    Merrill, D.W.; Selvin, S.; Mohr, M.S.

    1991-08-01

    In the study of geographic disease clusters, an alternative to traditional methods based on rates is to analyze case locations on a transformed map in which population density is everywhere equal. Although the analyst's task is thereby simplified, the specification of the density equalizing map projection (DEMP) itself is not simple and continues to be the subject of considerable research. Here a new DEMP algorithm is described, which avoids some of the difficulties of earlier approaches. The new algorithm (a) avoids illegal overlapping of transformed polygons; (b) finds the unique solution that minimizes map distortion; (c) provides constant magnification over each map polygon; (d) defines a continuous transformation over the entire map domain; (e) defines an inverse transformation; (f) can accept optional constraints such as fixed boundaries; and (g) can use commercially supported minimization software. Work is continuing to improve computing efficiency and improve the algorithm. 21 refs., 15 figs., 2 tabs.

  14. System performance analyzer

    NASA Technical Reports Server (NTRS)

    Helbig, H. R.

    1981-01-01

    The System Performance Analyzer (SPA) designed to provide accurate real time information about the operation of complex systems and developed for use on the Airborne Data Analysis/Monitor System (ADAMS), a ROLM 1666 based system is described. The system uses an external processor to operate an intelligent, simulated control panel. Also provided are functions to trace operations, determine frequency of use of memory areas, and time or count user tasks in a multitask environment. This augments the information available from the standard debugger and control panel, and reduces the time and effort needed by ROLM 1666 users in optimizing their system, as well as providing documentation of the effect of any changes. The operation and state of the system are evaluated.

  15. Analyzing a Cometary 'Sneeze'

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Figure 1: Analyzing a Cometary 'Sneeze'

    This display shows highly processed images of the outburst of comet Tempel 1 between June 22 and 23, 2005. The pictures were taken by Deep Impact's medium-resolution camera. An average image of the comet has been subtracted from each picture to provide an enhanced view of the outburst. The intensity has also been stretched to show the faintest parts. This processing enables measurement of the outflow speed and the details of the dissipation of the outburst. The left image was taken when the comet was very close to its normal, non-bursting state, so almost nothing is visible.

  16. Residual gas analyzer calibration

    NASA Technical Reports Server (NTRS)

    Lilienkamp, R. H.

    1972-01-01

    A technique which employs known gas mixtures to calibrate the residual gas analyzer (RGA) is described. The mass spectra from the RGA are recorded for each gas mixture. This mass spectra data and the mixture composition data each form a matrix. From the two matrices the calibration matrix may be computed. The matrix mathematics requires the number of calibration gas mixtures be equal to or greater than the number of gases included in the calibration. This technique was evaluated using a mathematical model of an RGA to generate the mass spectra. This model included shot noise errors in the mass spectra. Errors in the gas concentrations were also included in the valuation. The effects of these errors was studied by varying their magnitudes and comparing the resulting calibrations. Several methods of evaluating an actual calibration are presented. The effects of the number of gases in then, the composition of the calibration mixture, and the number of mixtures used are discussed.

  17. A Meta-Regression Method for Studying Etiological Heterogeneity Across Disease Subtypes Classified by Multiple Biomarkers.

    PubMed

    Wang, Molin; Kuchiba, Aya; Ogino, Shuji

    2015-08-01

    In interdisciplinary biomedical, epidemiologic, and population research, it is increasingly necessary to consider pathogenesis and inherent heterogeneity of any given health condition and outcome. As the unique disease principle implies, no single biomarker can perfectly define disease subtypes. The complex nature of molecular pathology and biology necessitates biostatistical methodologies to simultaneously analyze multiple biomarkers and subtypes. To analyze and test for heterogeneity hypotheses across subtypes defined by multiple categorical and/or ordinal markers, we developed a meta-regression method that can utilize existing statistical software for mixed-model analysis. This method can be used to assess whether the exposure-subtype associations are different across subtypes defined by 1 marker while controlling for other markers and to evaluate whether the difference in exposure-subtype association across subtypes defined by 1 marker depends on any other markers. To illustrate this method in molecular pathological epidemiology research, we examined the associations between smoking status and colorectal cancer subtypes defined by 3 correlated tumor molecular characteristics (CpG island methylator phenotype, microsatellite instability, and the B-Raf protooncogene, serine/threonine kinase (BRAF), mutation) in the Nurses' Health Study (1980-2010) and the Health Professionals Follow-up Study (1986-2010). This method can be widely useful as molecular diagnostics and genomic technologies become routine in clinical medicine and public health.

  18. Lorentz force particle analyzer

    NASA Astrophysics Data System (ADS)

    Wang, Xiaodong; Thess, André; Moreau, René; Tan, Yanqing; Dai, Shangjun; Tao, Zhen; Yang, Wenzhi; Wang, Bo

    2016-07-01

    A new contactless technique is presented for the detection of micron-sized insulating particles in the flow of an electrically conducting fluid. A transverse magnetic field brakes this flow and tends to become entrained in the flow direction by a Lorentz force, whose reaction force on the magnetic-field-generating system can be measured. The presence of insulating particles suspended in the fluid produce changes in this Lorentz force, generating pulses in it; these pulses enable the particles to be counted and sized. A two-dimensional numerical model that employs a moving mesh method demonstrates the measurement principle when such a particle is present. Two prototypes and a three-dimensional numerical model are used to demonstrate the feasibility of a Lorentz force particle analyzer (LFPA). The findings of this study conclude that such an LFPA, which offers contactless and on-line quantitative measurements, can be applied to an extensive range of applications. These applications include measurements of the cleanliness of high-temperature and aggressive molten metal, such as aluminum and steel alloys, and the clean manufacturing of semiconductors.

  19. Analyzing nocturnal noise stratification.

    PubMed

    Rey Gozalo, Guillermo; Barrigón Morillas, Juan Miguel; Gómez Escobar, Valentín

    2014-05-01

    Pollution associated to traffic can be considered as one of the most relevant pollution sources in our cities; noise is one of the major components of traffic pollution; thus, efforts are necessary to search adequate noise assessment methods and low pollution city designs. Different methods have been proposed for the evaluation of noise in cities, including the categorization method, which is based on the functionality concept. Until now, this method has only been studied (with encouraging results) for short-term, diurnal measurements, but nocturnal noise presents a behavior clearly different on respect to the diurnal one. In this work 45 continuous measurements of approximately one week each in duration are statistically analyzed to identify differences between the proposed categories. The results show that the five proposed categories highlight the noise stratification of the studied city in each period of the day (day, evening, and night). A comparison of the continuous measurements with previous short-term measurements indicates that the latter can be a good approximation of the former in diurnal period, reducing the resource expenditure for noise evaluation. Annoyance estimated from the measured noise levels was compared with the response of population obtained from a questionnaire with good agreement. The categorization method can yield good information about the distribution of a pollutant associated to traffic in our cities in each period of the day and, therefore, is a powerful tool for town planning and the design of pollution prevention policies.

  20. TEAMS Model Analyzer

    NASA Technical Reports Server (NTRS)

    Tijidjian, Raffi P.

    2010-01-01

    The TEAMS model analyzer is a supporting tool developed to work with models created with TEAMS (Testability, Engineering, and Maintenance System), which was developed by QSI. In an effort to reduce the time spent in the manual process that each TEAMS modeler must perform in the preparation of reporting for model reviews, a new tool has been developed as an aid to models developed in TEAMS. The software allows for the viewing, reporting, and checking of TEAMS models that are checked into the TEAMS model database. The software allows the user to selectively model in a hierarchical tree outline view that displays the components, failure modes, and ports. The reporting features allow the user to quickly gather statistics about the model, and generate an input/output report pertaining to all of the components. Rules can be automatically validated against the model, with a report generated containing resulting inconsistencies. In addition to reducing manual effort, this software also provides an automated process framework for the Verification and Validation (V&V) effort that will follow development of these models. The aid of such an automated tool would have a significant impact on the V&V process.

  1. PULSE HEIGHT ANALYZER

    DOEpatents

    Johnstone, C.W.

    1958-01-21

    An anticoincidence device is described for a pair of adjacent channels of a multi-channel pulse height analyzer for preventing the lower channel from generating a count pulse in response to an input pulse when the input pulse has sufficient magnitude to reach the upper level channel. The anticoincidence circuit comprises a window amplifier, upper and lower level discriminators, and a biased-off amplifier. The output of the window amplifier is coupled to the inputs of the discriminators, the output of the upper level discriminator is connected to the resistance end of a series R-C network, the output of the lower level discriminator is coupled to the capacitance end of the R-C network, and the grid of the biased-off amplifier is coupled to the junction of the R-C network. In operation each discriminator produces a negative pulse output when the input pulse traverses its voltage setting. As a result of the connections to the R-C network, a trigger pulse will be sent to the biased-off amplifier when the incoming pulse level is sufficient to trigger only the lower level discriminator.

  2. Analyzing Spacecraft Telecommunication Systems

    NASA Technical Reports Server (NTRS)

    Kordon, Mark; Hanks, David; Gladden, Roy; Wood, Eric

    2004-01-01

    Multi-Mission Telecom Analysis Tool (MMTAT) is a C-language computer program for analyzing proposed spacecraft telecommunication systems. MMTAT utilizes parameterized input and computational models that can be run on standard desktop computers to perform fast and accurate analyses of telecommunication links. MMTAT is easy to use and can easily be integrated with other software applications and run as part of almost any computational simulation. It is distributed as either a stand-alone application program with a graphical user interface or a linkable library with a well-defined set of application programming interface (API) calls. As a stand-alone program, MMTAT provides both textual and graphical output. The graphs make it possible to understand, quickly and easily, how telecommunication performance varies with variations in input parameters. A delimited text file that can be read by any spreadsheet program is generated at the end of each run. The API in the linkable-library form of MMTAT enables the user to control simulation software and to change parameters during a simulation run. Results can be retrieved either at the end of a run or by use of a function call at any time step.

  3. PULSE HEIGHT ANALYZER

    DOEpatents

    Goldsworthy, W.W.

    1958-06-01

    A differential pulse-height discriminator circuit is described which is readily adaptable for operation in a single-channel pulse-height analyzer. The novel aspect of the circuit lies in the specific arrangement of differential pulse-height discriminator which includes two pulse-height discriminators having a comnnon input and an anticoincidence circuit having two interconnected vacuum tubes with a common cathode resistor. Pulses from the output of one discriminator circuit are delayed and coupled to the grid of one of the anticoincidence tubes by a resistor. The output pulses from the other discriminator circuit are coupled through a cathode follower circuit, which has a cathode resistor of such value as to provide a long time constant with the interelectrode capacitance of the tube, to lenthen the output pulses. The pulses are then fed to the grid of the other anticoincidence tube. With such connections of the circuits, only when the incoming pulse has a pesk value between the operating levels of the two discriminators does an output pulse occur from the anticoincidence circuit.

  4. Analyzing Atmospheric Neutrino Oscillations

    SciTech Connect

    Escamilla, J.; Ernst, D. J.; Latimer, D. C.

    2007-10-26

    We provide a pedagogic derivation of the formula needed to analyze atmospheric data and then derive, for the subset of the data that are fully-contained events, an analysis tool that is quantitative and numerically efficient. Results for the full set of neutrino oscillation data are then presented. We find the following preliminary results: 1.) the sub-dominant approximation provides reasonable values for the best fit parameters for {delta}{sub 32}, {theta}{sub 23}, and {theta}{sub 13} but does not quantitatively provide the errors for these three parameters; 2.) the size of the MSW effect is suppressed in the sub-dominant approximation; 3.) the MSW effect reduces somewhat the extracted error for {delta}{sub 32}, more so for {theta}{sub 23} and {theta}{sub 13}; 4.) atmospheric data alone constrains the allowed values of {theta}{sub 13} only in the sub-dominant approximation, the full three neutrino calculations requires CHOOZ to get a clean constraint; 5.) the linear in {theta}{sub 13} terms are not negligible; and 6.) the minimum value of {theta}{sub 13} is found to be negative, but at a statistically insignificant level.

  5. Pseudostupidity and analyzability.

    PubMed

    Cohn, L S

    1989-01-01

    This paper seeks to heighten awareness of pseudostupidity and the potential analyzability of patients who manifest it by defining and explicating it, reviewing the literature, and presenting in detail the psychoanalytic treatment of a pseudostupid patient. Pseudostupidity is caused by an inhibition of the integration and synthesis of thoughts resulting in a discrepancy between intellectual capacity and apparent intellect. The patient's pseudostupidity was determined in part by his need to prevent his being more successful than father, i.e., defeating his oedipal rival. Knowing and learning were instinctualized. The patient libidinally and defensively identified with father's passive, masochistic position. He needed to frustrate the analyst as he had felt excited and frustrated by his parents' nudity and thwarted by his inhibitions. He wanted to cause the analyst to feel as helpless as he, the patient, felt. Countertransference frustration was relevant and clinically useful in the analysis. Interpretation of evolving relevant issues led to more anxiety and guilt, less pseudostupidity, a heightened alliance, and eventual working through. Negative therapeutic reactions followed the resolution of pseudostupidity. PMID:2708771

  6. Effect of long-term treatment with antioxidants (vitamin C, vitamin E, coenzyme Q10 and selenium) on arterial compliance, humoral factors and inflammatory markers in patients with multiple cardiovascular risk factors

    PubMed Central

    2010-01-01

    Background Antioxidant supplementations have the potential to alleviate the atherosclerotic damage caused by excessive production of reactive oxygen species (ROS). The present study evaluated the effects of prolonged antioxidant treatment on arterial elasticity, inflammatory and metabolic measures in patients with multiple cardiovascular risk factors. Methods Study participants were randomly assigned to two groups. Group 1 received oral supplementation with 2 capsules per day of Mid Life Guard, SupHerb, Israel. In each capsule vitamin C (500 mg) vitamin E (200 iu), co-enzyme Q10 (60 mg) and selenium (100 mcg), Group 2 received matching placebo(SupHerb) for 6 months. Patients were evaluated for lipid profile, HbA1C, insulin, C-peptide, hs-CRP, endothelin, aldosterone, plasma renin activity and Homeostasis model assessment-insulin resistance (HOMA-IR). Arterial elasticity was evaluated using pulse wave contour analysis (HDI CR 2000, Eagan, Minnesota). Results Antioxidant-treated patients exhibited significant increases in large arterial elasticity index (LAEI) as well as small arterial elasticity index (SAEI). A significant decline HbA1C and a significant increase in HDL-cholesterol were also observed. In the placebo group, significant changes in LAEI, SAEI or metabolic measures were not observed. Conclusions Antioxidant supplementation significantly increased large and small artery elasticity in patients with multiple cardiovascular risk factors. This beneficial vascular effect was associated with an improvement in glucose and lipid metabolism as well as decrease in blood pressure. PMID:20604917

  7. Digital Microfluidics Sample Analyzer

    NASA Technical Reports Server (NTRS)

    Pollack, Michael G.; Srinivasan, Vijay; Eckhardt, Allen; Paik, Philip Y.; Sudarsan, Arjun; Shenderov, Alex; Hua, Zhishan; Pamula, Vamsee K.

    2010-01-01

    Three innovations address the needs of the medical world with regard to microfluidic manipulation and testing of physiological samples in ways that can benefit point-of-care needs for patients such as premature infants, for which drawing of blood for continuous tests can be life-threatening in their own right, and for expedited results. A chip with sample injection elements, reservoirs (and waste), droplet formation structures, fluidic pathways, mixing areas, and optical detection sites, was fabricated to test the various components of the microfluidic platform, both individually and in integrated fashion. The droplet control system permits a user to control droplet microactuator system functions, such as droplet operations and detector operations. Also, the programming system allows a user to develop software routines for controlling droplet microactuator system functions, such as droplet operations and detector operations. A chip is incorporated into the system with a controller, a detector, input and output devices, and software. A novel filler fluid formulation is used for the transport of droplets with high protein concentrations. Novel assemblies for detection of photons from an on-chip droplet are present, as well as novel systems for conducting various assays, such as immunoassays and PCR (polymerase chain reaction). The lab-on-a-chip (a.k.a., lab-on-a-printed-circuit board) processes physiological samples and comprises a system for automated, multi-analyte measurements using sub-microliter samples of human serum. The invention also relates to a diagnostic chip and system including the chip that performs many of the routine operations of a central labbased chemistry analyzer, integrating, for example, colorimetric assays (e.g., for proteins), chemiluminescence/fluorescence assays (e.g., for enzymes, electrolytes, and gases), and/or conductometric assays (e.g., for hematocrit on plasma and whole blood) on a single chip platform.

  8. Soft Decision Analyzer

    NASA Technical Reports Server (NTRS)

    Steele, Glen; Lansdowne, Chatwin; Zucha, Joan; Schlensinger, Adam

    2013-01-01

    The Soft Decision Analyzer (SDA) is an instrument that combines hardware, firmware, and software to perform realtime closed-loop end-to-end statistical analysis of single- or dual- channel serial digital RF communications systems operating in very low signal-to-noise conditions. As an innovation, the unique SDA capabilities allow it to perform analysis of situations where the receiving communication system slips bits due to low signal-to-noise conditions or experiences constellation rotations resulting in channel polarity in versions or channel assignment swaps. SDA s closed-loop detection allows it to instrument a live system and correlate observations with frame, codeword, and packet losses, as well as Quality of Service (QoS) and Quality of Experience (QoE) events. The SDA s abilities are not confined to performing analysis in low signal-to-noise conditions. Its analysis provides in-depth insight of a communication system s receiver performance in a variety of operating conditions. The SDA incorporates two techniques for identifying slips. The first is an examination of content of the received data stream s relation to the transmitted data content and the second is a direct examination of the receiver s recovered clock signals relative to a reference. Both techniques provide benefits in different ways and allow the communication engineer evaluating test results increased confidence and understanding of receiver performance. Direct examination of data contents is performed by two different data techniques, power correlation or a modified Massey correlation, and can be applied to soft decision data widths 1 to 12 bits wide over a correlation depth ranging from 16 to 512 samples. The SDA detects receiver bit slips within a 4 bits window and can handle systems with up to four quadrants (QPSK, SQPSK, and BPSK systems). The SDA continuously monitors correlation results to characterize slips and quadrant change and is capable of performing analysis even when the

  9. Regolith Evolved Gas Analyzer

    NASA Technical Reports Server (NTRS)

    Hoffman, John H.; Hedgecock, Jud; Nienaber, Terry; Cooper, Bonnie; Allen, Carlton; Ming, Doug

    2000-01-01

    The Regolith Evolved Gas Analyzer (REGA) is a high-temperature furnace and mass spectrometer instrument for determining the mineralogical composition and reactivity of soil samples. REGA provides key mineralogical and reactivity data that is needed to understand the soil chemistry of an asteroid, which then aids in determining in-situ which materials should be selected for return to earth. REGA is capable of conducting a number of direct soil measurements that are unique to this instrument. These experimental measurements include: (1) Mass spectrum analysis of evolved gases from soil samples as they are heated from ambient temperature to 900 C; and (2) Identification of liberated chemicals, e.g., water, oxygen, sulfur, chlorine, and fluorine. REGA would be placed on the surface of a near earth asteroid. It is an autonomous instrument that is controlled from earth but does the analysis of regolith materials automatically. The REGA instrument consists of four primary components: (1) a flight-proven mass spectrometer, (2) a high-temperature furnace, (3) a soil handling system, and (4) a microcontroller. An external arm containing a scoop or drill gathers regolith samples. A sample is placed in the inlet orifice where the finest-grained particles are sifted into a metering volume and subsequently moved into a crucible. A movable arm then places the crucible in the furnace. The furnace is closed, thereby sealing the inner volume to collect the evolved gases for analysis. Owing to the very low g forces on an asteroid compared to Mars or the moon, the sample must be moved from inlet to crucible by mechanical means rather than by gravity. As the soil sample is heated through a programmed pattern, the gases evolved at each temperature are passed through a transfer tube to the mass spectrometer for analysis and identification. Return data from the instrument will lead to new insights and discoveries including: (1) Identification of the molecular masses of all of the gases

  10. Frailty Markers and Treatment Decisions in Patients Seen in Oncogeriatric Clinics: Results from the ASRO Pilot Study

    PubMed Central

    de Decker, Laure; Pauly, Vanessa; Rousseau, Frédérique; Bergman, Howard; Molines, Catherine

    2016-01-01

    Background Comprehensive Geriatric Assessment (CGA) is the gold standard to help oncologists select the best cancer treatment for their older patients. Some authors have suggested that the concept of frailty could be a more useful approach in this population. We investigated whether frailty markers are associated with treatment recommendations in an oncogeriatric clinic. Methods This prospective study included 70 years and older patients with solid tumors and referred for an oncogeriatric assessment. The CGA included nine domains: autonomy, comorbidities, medication, cognition, nutrition, mood, neurosensory deficits, falls, and social status. Five frailty markers were assessed (nutrition, physical activity, energy, mobility, and strength). Patients were categorized as Frail (three or more frailty markers), pre-frail (one or two frailty markers), or not-frail (no frailty marker). Treatment recommendations were classified into two categories: standard treatment with and without any changes and supportive/palliative care. Multiple logistic regression models were used to analyze factors associated with treatment recommendations. Results 217 patients, mean age 83 years (± Standard deviation (SD) 5.3), were included. In the univariate analysis, number of frailty markers, grip strength, physical activity, mobility, nutrition, energy, autonomy, depression, Eastern Cooperative Oncology Group Scale of Performance Status (ECOG-PS), and falls were significantly associated with final treatment recommendations. In the multivariate analysis, the number of frailty markers and basic Activities of Daily Living (ADL) were significantly associated with final treatment recommendations (p<0.001 and p = 0.010, respectively). Conclusion Frailty markers are associated with final treatment recommendations in older cancer patients. Longitudinal studies are warranted to better determine their use in a geriatric oncology setting. PMID:26918947

  11. Analyzes Data from Semiconductor Wafers

    2002-07-23

    This program analyzes reflectance data from semiconductor wafers taken during the deposition or evolution of a thin film, typically via chemical vapor deposition (CVD) or molecular beam epitaxy (MBE). It is used to determine the growth rate and optical constants of the deposited thin films using a virtual interface concept. Growth rates and optical constants of multiple-layer structures is possible by selecting appropriate sections in the reflectance vs time waveform. No prior information or estimatesmore » of growth rates and materials properties is required if an absolute reflectance waveform is used. If the optical constants of a thin film are known, then the growth rate may be extracted from a relative reflectance data set. The analysis is valid for either s or p polarized light at any incidence angle and wavelength. The analysis package is contained within an easy-to-use graphical user interface. The program is based on the algorighm described in the following two publications: W.G. Breiland and K.P. Killen, J. Appl. Phys. 78 (1995) 6726, and W. G. Breiland, H.Q. Hou, B.E. Hammons, and J.F. Klem, Proc. XXVIII SOTAPOCS Symp. Electrochem. Soc. San Diego, May 3-8, 1998. It relies on the fact that any multiple-layer system has a reflectance spectrum that is mathematically equivalent to a single-layer thin film on a virtual substrate. The program fits the thin film reflectance with five adjustable parameters: 1) growth rate, 2) real part of complex refractive index, 3) imaginary part of refractive index, 4) amplitude of virtual interface reflectance, 5) phase of virtual interface reflectance.« less

  12. Glycomics and Disease Markers

    PubMed Central

    An, Hyun Joo; Kronewitter, Scott R.; de Leoz, Maria Lorna A.; Lebrilla, Carlito B.

    2009-01-01

    Summary of Recent Advances Glycomics is the comprehensive study of all glycans expressed in biological systems. The biosynthesis of glycan relies on a number of highly competitive processes involving glycosyl transferase. Glycosylation is therefore highly sensitive to the biochemical environment and has been implicated in many diseases including cancer. Recently, interest in profiling the glycome has increased due to the potential of glycans for disease markers. In this regard, mass spectrometry is emerging as a powerful technique for profiling the glycome. Global glycan profiling of human serum based on mass spectrometry has already led to several potentially promising markers for several types of cancer and diseases. PMID:19775929

  13. Prognostic molecular markers in early breast cancer

    PubMed Central

    Esteva, Francisco J; Hortobagyi, Gabriel N

    2004-01-01

    A multitude of molecules involved in breast cancer biology have been studied as potential prognostic markers. In the present review we discuss the role of established molecular markers, as well as potential applications of emerging new technologies. Those molecules used routinely to make treatment decisions in patients with early-stage breast cancer include markers of proliferation (e.g. Ki-67), hormone receptors, and the human epidermal growth factor receptor 2. Tumor markers shown to have prognostic value but not used routinely include cyclin D1 and cyclin E, urokinase-like plasminogen activator/plasminogen activator inhibitor, and cathepsin D. The level of evidence for other molecular markers is lower, in part because most studies were retrospective and not adequately powered, making their findings unsuitable for choosing treatments for individual patients. Gene microarrays have been successfuly used to classify breast cancers into subtypes with specific gene expression profiles and to evaluate prognosis. RT-PCR has also been used to evaluate expression of multiple genes in archival tissue. Proteomics technologies are in development. PMID:15084231

  14. Systems Analyze Water Quality in Real Time

    NASA Technical Reports Server (NTRS)

    2010-01-01

    A water analyzer developed under Small Business Innovation Research (SBIR) contracts with Kennedy Space Center now monitors treatment processes at water and wastewater facilities around the world. Originally designed to provide real-time detection of nutrient levels in hydroponic solutions for growing plants in space, the ChemScan analyzer, produced by ASA Analytics Inc., of Waukesha, Wisconsin, utilizes spectrometry and chemometric algorithms to automatically analyze multiple parameters in the water treatment process with little need for maintenance, calibration, or operator intervention. The company has experienced a compound annual growth rate of 40 percent over its 15-year history as a direct result of the technology's success.

  15. Multiple Sporadic Colorectal Cancers Display a Unique Methylation Phenotype

    PubMed Central

    Gonzalo, Victoria; Lozano, Juan Jose; Alonso-Espinaco, Virginia; Moreira, Leticia; Muñoz, Jenifer; Pellisé, Maria; Castellví-Bel, Sergi; Bessa, Xavier; Andreu, Montserrat; Xicola, Rosa M.; Llor, Xavier; Ruiz-Ponte, Clara; Carracedo, Angel; Jover, Rodrigo; Castells, Antoni; Balaguer, Francesc

    2014-01-01

    Epigenetics are thought to play a major role in the carcinogenesis of multiple sporadic colorectal cancers (CRC). Previous studies have suggested concordant DNA hypermethylation between tumor pairs. However, only a few methylation markers have been analyzed. This study was aimed at describing the epigenetic signature of multiple CRC using a genome-scale DNA methylation profiling. We analyzed 12 patients with synchronous CRC and 29 age-, sex-, and tumor location-paired patients with solitary tumors from the EPICOLON II cohort. DNA methylation profiling was performed using the Illumina Infinium HM27 DNA methylation assay. The most significant results were validated by Methylight. Tumors samples were also analyzed for the CpG Island Methylator Phenotype (CIMP); KRAS and BRAF mutations and mismatch repair deficiency status. Functional annotation clustering was performed. We identified 102 CpG sites that showed significant DNA hypermethylation in multiple tumors with respect to the solitary counterparts (difference in β value ≥0.1). Methylight assays validated the results for 4 selected genes (p = 0.0002). Eight out of 12(66.6%) multiple tumors were classified as CIMP-high, as compared to 5 out of 29(17.2%) solitary tumors (p = 0.004). Interestingly, 76 out of the 102 (74.5%) hypermethylated CpG sites found in multiple tumors were also seen in CIMP-high tumors. Functional analysis of hypermethylated genes found in multiple tumors showed enrichment of genes involved in different tumorigenic functions. In conclusion, multiple CRC are associated with a distinct methylation phenotype, with a close association between tumor multiplicity and CIMP-high. Our results may be important to unravel the underlying mechanism of tumor multiplicity. PMID:24643221

  16. The Swift Turbidity Marker

    ERIC Educational Resources Information Center

    Omar, Ahmad Fairuz; MatJafri, Mohd Zubir

    2011-01-01

    The Swift Turbidity Marker is an optical instrument developed to measure the level of water turbidity. The components and configuration selected for the system are based on common turbidity meter design concepts but use a simplified methodology to produce rapid turbidity measurements. This work is aimed at high school physics students and is the…

  17. Dual-Byte-Marker Algorithm for Detecting JFIF Header

    NASA Astrophysics Data System (ADS)

    Mohamad, Kamaruddin Malik; Herawan, Tutut; Deris, Mustafa Mat

    The use of efficient algorithm to detect JPEG file is vital to reduce time taken for analyzing ever increasing data in hard drive or physical memory. In the previous paper, single-byte-marker algorithm is proposed for header detection. In this paper, another novel header detection algorithm called dual-byte-marker is proposed. Based on the experiments done on images from hard disk, physical memory and data set from DFRWS 2006 Challenge, results showed that dual-byte-marker algorithm gives better performance with better execution time for header detection as compared to single-byte-marker.

  18. Clinical laboratory data: acquire, analyze, communicate, liberate.

    PubMed

    Azzazy, Hassan M E; Elbehery, Ali H A

    2015-01-01

    The availability of portable healthcare devices, which can acquire and transmit medical data to remote experts would dramatically affect healthcare in areas with poor infrastructure. Smartphones, which feature touchscreen computer capabilities and sophisticated cameras, have become widely available with over billion units shipped in 2013. In the clinical laboratory, smartphones have recently brought the capabilities of key instruments such as spectrophotometers, fluorescence analyzers and microscopes into the palm of the hand. Several research groups have developed sensitive and low-cost smartphone-based diagnostic assay prototypes for testing cholesterol, albumin, vitamin D, tumor markers, and the detection of infectious agents. This review covers the use of smartphones to acquire, analyze, communicate, and liberate clinical laboratory data. Smartphones promise to dramatically improve the quality and quantity of healthcare offered in resource-limited areas.

  19. Analyzing Association Mapping in Pedigree-Based GWAS Using a Penalized Multitrait Mixed Model.

    PubMed

    Liu, Jin; Yang, Can; Shi, Xingjie; Li, Cong; Huang, Jian; Zhao, Hongyu; Ma, Shuangge

    2016-07-01

    Genome-wide association studies (GWAS) have led to the identification of many genetic variants associated with complex diseases in the past 10 years. Penalization methods, with significant numerical and statistical advantages, have been extensively adopted in analyzing GWAS. This study has been partly motivated by the analysis of Genetic Analysis Workshop (GAW) 18 data, which have two notable characteristics. First, the subjects are from a small number of pedigrees and hence related. Second, for each subject, multiple correlated traits have been measured. Most of the existing penalization methods assume independence between subjects and traits and can be suboptimal. There are a few methods in the literature based on mixed modeling that can accommodate correlations. However, they cannot fully accommodate the two types of correlations while conducting effective marker selection. In this study, we develop a penalized multitrait mixed modeling approach. It accommodates the two different types of correlations and includes several existing methods as special cases. Effective penalization is adopted for marker selection. Simulation demonstrates its satisfactory performance. The GAW 18 data are analyzed using the proposed method. PMID:27247027

  20. Referential Markers and Agreement Markers in Functional Discourse Grammar

    ERIC Educational Resources Information Center

    Hengeveld, Kees

    2012-01-01

    It follows from the ordering principles that are applied in Functional Discourse Grammar that the positional possibilities of markers of agreement and those of cross-reference are different. Markers of cross reference are predicted to occur closer to the verb stem, while markers of agreement would occupy peripheral positions. This paper tests…

  1. Lipoprotein marker for hypertriglyceridemia

    DOEpatents

    Cubicciotti, Roger S.; Karu, Alexander E.; Krauss, Ronald M.

    1986-01-01

    Methods and compositions are provided for the detection of a particular low density lipoprotein which has been found to be a marker for patients suffering from type IV hypertriglyceridemia. A monoclonal antibody capable of specifically binding to a characteristic epitopic site on this LDL subspecies can be utilized in a wide variety of immunoassays. Hybridoma cell line SPL.IVA5A1 was deposited at the American Type Culture Collection on Mar. 29, 1984, and granted accession no. HB 8535.

  2. [Tumor markers in gastric cancer].

    PubMed

    Ohkura, Hisanao

    2002-04-01

    There are two markers, pepsinogen isoenzymes and antibody against Helicobactor pyroli, for screening of high-risk group for gastric cancer. Most of markers are used in diagnosis, staging, monitoring and differentiating subgroups of gastric cancer. Markers in ascitic fluid are used for diagnosing peritoneal invasion of gastric cancer. PMID:11977555

  3. Korean Syntax: Case Markers, Delimiters, Complementation, and Relativization. Working Papers in Linguistics, Volume 4, Number 6.

    ERIC Educational Resources Information Center

    Yang, In-Seok

    This generative grammar of Korean analyzes the syntactic aspects of case markers, delimiters, complementation, and relativization. C. J. Fillmore's case grammar is adopted as the overall framework. Case markers and delimiters are seen to interact in two ways: one is obligatory deletion of the nominative and accusative markers before any delimiter,…

  4. Expression of squamous cell carcinoma markers and adenocarcinoma markers in primary pulmonary neuroendocrine carcinomas.

    PubMed

    Masai, Kyohei; Tsuta, Koji; Kawago, Mitsumasa; Tatsumori, Takahiro; Kinno, Tomoaki; Taniyama, Tomoko; Yoshida, Akihiko; Asamura, Hisao; Tsuda, Hitoshi

    2013-07-01

    Recent clinical trials have revealed that accurate histologic typing of non-small cell lung cancer is essential. Until now, squamous cell carcinoma (SQC) and adenocarcinoma (ADC) markers have not been thoroughly analyzed for pulmonary neuroendocrine carcinomas (NECs). We analyzed the expression of 8 markers [p63, cytokeratin (CK) 5/6, SOX2, CK7, desmocollin 3, thyroid transcription factor-1 (8G7G3/1 and SPT24), and napsin A] in 224 NECs. SOX2 (76.2%) had the greatest expression for NECs. CK5/6 (1.4%), desmocollin 3 (0.5%), and napsin A (0%) were expressed less or not at all in NECs. Although our investigated markers have been reported useful for differentiating between SQC and ADC, some of them were also present in a portion of pulmonary NECs. In our study, CK5/6 and desmocollin 3 were highly specific markers for SQC, and napsin A was highly specific for ADC. These markers are recommended for diagnosis of poorly differentiated non-small cell lung cancer.

  5. Fiducial marker for correlating images

    DOEpatents

    Miller, Lisa Marie; Smith, Randy J.; Warren, John B.; Elliott, Donald

    2011-06-21

    The invention relates to a fiducial marker having a marking grid that is used to correlate and view images produced by different imaging modalities or different imaging and viewing modalities. More specifically, the invention relates to the fiducial marking grid that has a grid pattern for producing either a viewing image and/or a first analytical image that can be overlaid with at least one other second analytical image in order to view a light path or to image different imaging modalities. Depending on the analysis, the grid pattern has a single layer of a certain thickness or at least two layers of certain thicknesses. In either case, the grid pattern is imageable by each imaging or viewing modality used in the analysis. Further, when viewing a light path, the light path of the analytical modality cannot be visualized by viewing modality (e.g., a light microscope objective). By correlating these images, the ability to analyze a thin sample that is, for example, biological in nature but yet contains trace metal ions is enhanced. Specifically, it is desired to analyze both the organic matter of the biological sample and the trace metal ions contained within the biological sample without adding or using extrinsic labels or stains.

  6. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.

    PubMed

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar. PMID:27679641

  7. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing

    PubMed Central

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar. PMID:27679641

  8. Monte Carlo simulations on marker grouping and ordering.

    PubMed

    Wu, J; Jenkins, J; Zhu, J; McCarty, J; Watson, C

    2003-08-01

    Four global algorithms, maximum likelihood (ML), sum of adjacent LOD score (SALOD), sum of adjacent recombinant fractions (SARF) and product of adjacent recombinant fraction (PARF), and one approximation algorithm, seriation (SER), were used to compare the marker ordering efficiencies for correctly given linkage groups based on doubled haploid (DH) populations. The Monte Carlo simulation results indicated the marker ordering powers for the five methods were almost identical. High correlation coefficients were greater than 0.99 between grouping power and ordering power, indicating that all these methods for marker ordering were reliable. Therefore, the main problem for linkage analysis was how to improve the grouping power. Since the SER approach provided the advantage of speed without losing ordering power, this approach was used for detailed simulations. For more generality, multiple linkage groups were employed, and population size, linkage cutoff criterion, marker spacing pattern (even or uneven), and marker spacing distance (close or loose) were considered for obtaining acceptable grouping powers. Simulation results indicated that the grouping power was related to population size, marker spacing distance, and cutoff criterion. Generally, a large population size provided higher grouping power than small population size, and closely linked markers provided higher grouping power than loosely linked markers. The cutoff criterion range for achieving acceptable grouping power and ordering power differed for varying cases; however, combining all situations in this study, a cutoff criterion ranging from 50 cM to 60 cM was recommended for achieving acceptable grouping power and ordering power for different cases.

  9. Multiple interval mapping for quantitative trait loci.

    PubMed Central

    Kao, C H; Zeng, Z B; Teasdale, R D

    1999-01-01

    A new statistical method for mapping quantitative trait loci (QTL), called multiple interval mapping (MIM), is presented. It uses multiple marker intervals simultaneously to fit multiple putative QTL directly in the model for mapping QTL. The MIM model is based on Cockerham's model for interpreting genetic parameters and the method of maximum likelihood for estimating genetic parameters. With the MIM approach, the precision and power of QTL mapping could be improved. Also, epistasis between QTL, genotypic values of individuals, and heritabilities of quantitative traits can be readily estimated and analyzed. Using the MIM model, a stepwise selection procedure with likelihood ratio test statistic as a criterion is proposed to identify QTL. This MIM method was applied to a mapping data set of radiata pine on three traits: brown cone number, tree diameter, and branch quality scores. Based on the MIM result, seven, six, and five QTL were detected for the three traits, respectively. The detected QTL individually contributed from approximately 1 to 27% of the total genetic variation. Significant epistasis between four pairs of QTL in two traits was detected, and the four pairs of QTL contributed approximately 10.38 and 14.14% of the total genetic variation. The asymptotic variances of QTL positions and effects were also provided to construct the confidence intervals. The estimated heritabilities were 0.5606, 0.5226, and 0. 3630 for the three traits, respectively. With the estimated QTL effects and positions, the best strategy of marker-assisted selection for trait improvement for a specific purpose and requirement can be explored. The MIM FORTRAN program is available on the worldwide web (http://www.stat.sinica.edu.tw/chkao/). PMID:10388834

  10. Soft Decision Analyzer and Method

    NASA Technical Reports Server (NTRS)

    Steele, Glen F. (Inventor); Lansdowne, Chatwin (Inventor); Zucha, Joan P. (Inventor); Schlesinger, Adam M. (Inventor)

    2016-01-01

    A soft decision analyzer system is operable to interconnect soft decision communication equipment and analyze the operation thereof to detect symbol wise alignment between a test data stream and a reference data stream in a variety of operating conditions.

  11. Soft Decision Analyzer and Method

    NASA Technical Reports Server (NTRS)

    Steele, Glen F. (Inventor); Lansdowne, Chatwin (Inventor); Zucha, Joan P. (Inventor); Schlesinger, Adam M. (Inventor)

    2015-01-01

    A soft decision analyzer system is operable to interconnect soft decision communication equipment and analyze the operation thereof to detect symbol wise alignment between a test data stream and a reference data stream in a variety of operating conditions.

  12. Droplet actuator analyzer with cartridge

    NASA Technical Reports Server (NTRS)

    Smith, Gregory F. (Inventor); Sturmer, Ryan A. (Inventor); Paik, Philip Y. (Inventor); Srinivasan, Vijay (Inventor); Pollack, Michael G. (Inventor); Pamula, Vamsee K. (Inventor); Brafford, Keith R. (Inventor); West, Richard M. (Inventor)

    2011-01-01

    A droplet actuator with cartridge is provided. According to one embodiment, a sample analyzer is provided and includes an analyzer unit comprising electronic or optical receiving means, a cartridge comprising self-contained droplet handling capabilities, and a wherein the cartridge is coupled to the analyzer unit by a means which aligns electronic and/or optical outputs from the cartridge with electronic or optical receiving means on the analyzer unit. According to another embodiment, a sample analyzer is provided and includes a sample analyzer comprising a cartridge coupled thereto and a means of electrical interface and/or optical interface between the cartridge and the analyzer, whereby electrical signals and/or optical signals may be transmitted from the cartridge to the analyzer.

  13. [Markers of hepatitis virus].

    PubMed

    Suzuki, Fumitaka

    2008-11-01

    Hepatitis B virus (HBV) and hepatitis C virus (HCV) are the major viruses known to cause viral hepatitis. Serological markers are commonly used as diagnostic and/or prognostic indicators of acute or chronic HBV or HCV infection. The ability to detect HBV DNA in serum has been reported to have prognostic value for the outcome of chronic HBV infection. A rapid and sustained drop in HBV DNA or HCV RNA levels in patients under therapy has been shown to be a predictive factor for a favourable treatment outcome. Various techniques for detecting HBV DNA or HCV RNA have already been described; however, there are various problems with the sensitivity or detection range of those methods. New virus measuring methods have recently been reported and used. The Cobas Taq Man HCV Test is a new method to detect HBV DNA and HCV RNA with higher sensitivity and a broader range of quantitation than conventional methods. Some reports have shown that these methods improve therapy monitoring and the management of HBV or HCV infection. Moreover, hepatitis E virus (HEV) infection has been reported in Japan. The clinical features and viral markers of HEV have also been described. PMID:19086457

  14. Magnetic Resonance Imaging (MRI) Markers for MRI-Guided High-Dose-Rate Brachytherapy: Novel Marker-Flange for Cervical Cancer and Marker Catheters for Prostate Cancer

    SciTech Connect

    Schindel, Joshua; Muruganandham, Manickam; Pigge, F. Christopher; Anderson, James; Kim, Yusung

    2013-06-01

    Purpose: To present a novel marker-flange, addressing source-reconstruction uncertainties due to the artifacts of a titanium intracavitary applicator used for magnetic resonance imaging (MRI)-guided high-dose-rate (HDR) brachytherapy (BT); and to evaluate 7 different MRI marker agents used for interstitial prostate BT and intracavitary gynecologic HDR BT when treatment plans are guided by MRI. Methods and Materials: Seven MRI marker agents were analyzed: saline solution, Conray-60, copper sulfate (CuSO{sub 4}) (1.5 g/L), liquid vitamin E, fish oil, 1% agarose gel (1 g agarose powder per 100 mL distilled water), and a cobalt–chloride complex contrast (C4) (CoCl{sub 2}/glycine = 4:1). A plastic, ring-shaped marker-flange was designed and tested on both titanium and plastic applicators. Three separate phantoms were designed to test the marker-flange, interstitial catheters for prostate BT, and intracavitary catheters for gynecologic HDR BT. T1- and T2-weighted MRI were analyzed for all markers in each phantom and quantified as percentages compared with a 3% agarose gel background. The geometric accuracy of the MR signal for the marker-flange was measured using an MRI-CT fusion. Results: The CuSO{sub 4} and C4 markers on T1-weighted MRI and saline on T2-weighted MRI showed the highest signals. The marker-flange showed hyper-signals of >500% with CuSO{sub 4} and C4 on T1-weighted MRI and of >400% with saline on T2-weighted MRI on titanium applicators. On T1-weighted MRI, the MRI signal inaccuracies of marker-flanges were measured <2 mm, regardless of marker agents, and that of CuSO{sub 4} was 0.42 ± 0.14 mm. Conclusion: The use of interstitial/intracavitary markers for MRI-guided prostate/gynecologic BT was observed to be feasible, providing accurate source pathway reconstruction. The novel marker-flange can produce extremely intense, accurate signals, demonstrating its feasibility for gynecologic HDR BT.

  15. Multiple Pregnancy

    MedlinePlus

    ... is called multiple pregnancy . If more than one egg is released during the menstrual cycle and each ... fraternal twins (or more). When a single fertilized egg splits, it results in multiple identical embryos. This ...

  16. Multiple myeloma

    MedlinePlus

    Plasma cell dyscrasia; Plasma cell myeloma; Malignant plasmacytoma; Plasmacytoma of bone; Myeloma - multiple ... Multiple myeloma most commonly causes: Low red blood cell count ( anemia ), which can lead to fatigue and ...

  17. Multiple Sclerosis

    MedlinePlus

    Multiple sclerosis (MS) is a nervous system disease that affects your brain and spinal cord. It damages the ... attacks healthy cells in your body by mistake. Multiple sclerosis affects women more than men. It often begins ...

  18. [Future challenges in multiple sclerosis].

    PubMed

    Fernández, Óscar

    2014-12-01

    Multiple sclerosis occurs in genetically susceptible individuals, in whom an unknown environmental factor triggers an immune response, giving rise to a chronic and disabling autoimmune disease. Currently, significant progress is being made in our knowledge of the frequency and distribution of multiple sclerosis and its risk factors, genetics, pathology, pathogenesis, diagnostic and prognostic markers, and treatment. This has radically changed patients' and clinicians' expectations of multiple sclerosis and has raised hope that there will soon be a way to control the disease. PMID:25732950

  19. Occurrence of bacteria and biochemical markers on public surfaces.

    PubMed

    Reynolds, Kelly A; Watt, Pamela M; Boone, Stephanie A; Gerba, Charles P

    2005-06-01

    From 1999-2003, the hygiene of 1061 environmental surfaces from shopping, daycare, and office environments, personal items, and miscellaneous activities (i.e., gymnasiums, airports, movie theaters, restaurants, etc.), in four US cities, was monitored. Samples were analyzed for fecal and total coliform bacteria, protein, and biochemical markers. Biochemical markers, i.e., hemoglobin (blood marker), amylase (mucus, saliva, sweat, and urine marker), and urea (urine and sweat marker) were detected on 3% (26/801); 15% (120/801), and 6% (48/801) of the surfaces, respectively. Protein (general hygiene marker) levels > or = 200 microg/10 cm2 were present on 26% (200/801) of the surfaces tested. Surfaces from children's playground equipment and daycare centers were the most frequently contaminated (biochemical markers on 36%; 15/42 and 46%; 25/54, respectively). Surfaces from the shopping, miscellaneous activities, and office environments were positive for biochemical markers with a frequency of 21% (69/333), 21% (66/308), and 11% (12/105), respectively). Sixty samples were analyzed for biochemical markers and bacteria. Total and fecal coliforms were detected on 20% (12/60) and 7% (4/ 60) of the surfaces, respectively. Half and one-third of the sites positive for biochemical markers were also positive for total and fecal coliforms, respectively. Artificial contamination of public surfaces with an invisible fluorescent tracer showed that contamination from outside surfaces was transferred to 86% (30/ 35) of exposed individual's hands and 82% (29/35) tracked the tracer to their home or personal belongings hours later. Results provide information on the relative hygiene of commonly encountered public surfaces and aid in the identification of priority environments where contaminant occurrence and risk of exposure may be greatest. Children's playground equipment is identified as a priority surface for additional research on the occurrence of and potential exposure to infectious

  20. Finger Multiplication

    ERIC Educational Resources Information Center

    Simanihuruk, Mudin

    2011-01-01

    Multiplication facts are difficult to teach. Therefore many researchers have put a great deal of effort into finding multiplication strategies. Sherin and Fuson (2005) provided a good survey paper on the multiplication strategies research area. Kolpas (2002), Rendtorff (1908), Dabell (2001), Musser (1966) and Markarian (2009) proposed the finger…

  1. Multiple Sclerosis

    MedlinePlus

    ... Awards Enhancing Diversity Find People About NINDS NINDS Multiple Sclerosis Information Page Condensed from Multiple Sclerosis: Hope Through ... en Español Additional resources from MedlinePlus What is Multiple Sclerosis? An unpredictable disease of the central nervous system, ...

  2. Genotyping markers used for multi locus VNTR analysis with ompA (MLVA-ompA) and multi sequence typing (MST) retain stability in Chlamydia trachomatis.

    PubMed

    Labiran, Clare; Clarke, Ian N; Cutcliffe, Lesley T; Wang, Yibing; Skilton, Rachel J; Persson, Kenneth; Bjartling, Carina; Herrmann, Björn; Christerson, Linus; Marsh, Peter

    2012-01-01

    We aimed to evaluate the stability of the Chlamydia trachomatis multi locus VNTR analysis (MLVA-ompA) and multi sequence typing (MST) systems through multiple passages in tissue culture. Firstly, we analyzed the stability of these markers through adaptation of C. trachomatis to tissue culture and secondly, we examined the stability of a four-locus MLVA-ompA and a five-locus MST system after multiple passages in tissue culture. Marker sequences were monitored through successive chlamydial developmental cycles to evaluate the stability of the individual DNA markers through many bacterial divisions and this, in turn, informed us of the usefulness of using such typing systems for short and long-term molecular epidemiology. Southampton genitourinary medicine (GUM) clinic isolates from endocervical swabs collected from C. trachomatis positive women were passaged through tissue culture. MLVA-ompA typing was applied to primary swab samples and to the same samples after C. trachomatis had been passaged through cell culture (eight passages). Sequence data from time-zero and passage-eight isolates were aligned with reference sequences to determine the stability of the markers. The Swedish new variant (nvCT) underwent 72 passages in cell culture and the markers of the two schemes were similarly analyzed. Analysis of genetic markers of the MLVA-ompA typing system before and after the isolates were introduced to tissue culture showed no change in the dominant sequence. The nvCT that had been passaged 72 times over the duration of a year also showed no variation in the dominant sequence for both the genotyping schemes. MLVA-ompA and MST markers are stable upon adaptation of C. trachomatis to tissue culture following isolation of strains from primary endocervical swab samples. These markers remain stable throughout multiple rounds of cell-division in tissue culture, concomitant with the incubation period and appearance of symptoms normally associated with host-infection. Both

  3. Genotyping markers used for multi locus VNTR analysis with ompA (MLVA-ompA) and multi sequence typing (MST) retain stability in Chlamydia trachomatis

    PubMed Central

    Labiran, Clare; Clarke, Ian N.; Cutcliffe, Lesley T.; Wang, Yibing; Skilton, Rachel J.; Persson, Kenneth; Bjartling, Carina; Herrmann, Björn; Christerson, Linus; Marsh, Peter

    2012-01-01

    We aimed to evaluate the stability of the Chlamydia trachomatis multi locus VNTR analysis (MLVA-ompA) and multi sequence typing (MST) systems through multiple passages in tissue culture. Firstly, we analyzed the stability of these markers through adaptation of C. trachomatis to tissue culture and secondly, we examined the stability of a four-locus MLVA-ompA and a five-locus MST system after multiple passages in tissue culture. Marker sequences were monitored through successive chlamydial developmental cycles to evaluate the stability of the individual DNA markers through many bacterial divisions and this, in turn, informed us of the usefulness of using such typing systems for short and long-term molecular epidemiology. Southampton genitourinary medicine (GUM) clinic isolates from endocervical swabs collected from C. trachomatis positive women were passaged through tissue culture. MLVA-ompA typing was applied to primary swab samples and to the same samples after C. trachomatis had been passaged through cell culture (eight passages). Sequence data from time-zero and passage-eight isolates were aligned with reference sequences to determine the stability of the markers. The Swedish new variant (nvCT) underwent 72 passages in cell culture and the markers of the two schemes were similarly analyzed. Analysis of genetic markers of the MLVA-ompA typing system before and after the isolates were introduced to tissue culture showed no change in the dominant sequence. The nvCT that had been passaged 72 times over the duration of a year also showed no variation in the dominant sequence for both the genotyping schemes. MLVA-ompA and MST markers are stable upon adaptation of C. trachomatis to tissue culture following isolation of strains from primary endocervical swab samples. These markers remain stable throughout multiple rounds of cell-division in tissue culture, concomitant with the incubation period and appearance of symptoms normally associated with host-infection. Both

  4. Extent and consistency of linkage disequilibrium and identification of DNA markers for production and egg quality traits in commercial layer chicken populations

    PubMed Central

    2009-01-01

    Background The genome sequence and a high-density SNP map are now available for the chicken and can be used to identify genetic markers for use in marker-assisted selection (MAS). Effective MAS requires high linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), and sustained marker-QTL LD over generations. This study used data from a 3,000 SNP panel to assess the level and consistency of LD between single nucleotide polymorphisms (SNPs) over consecutive years in two egg-layer chicken lines, and analyzed one line by two methods (SNP-wise association and genome-wise Bayesian analysis) to identify markers associated with egg-quality and egg-production phenotypes. Results The LD between markers pairs was high at short distances (r2 > 0.2 at < 2 Mb) and remained high after one generation (correlations of 0.80 to 0.92 at < 5 Mb) in both lines. Single- and 3-SNP regression analyses using a mixed model with SNP as fixed effect resulted in 159 and 76 significant tests (P < 0.01), respectively, across 12 traits. A Bayesian analysis called BayesB, that fits all SNPs simultaneously as random effects and uses model averaging procedures, identified 33 SNPs that were included in the model >20% of the time (φ > 0.2) and an additional ten 3-SNP windows that had a sum of φ greater than 0.35. Generally, SNPs included in the Bayesian model also had a small P-value in the 1-SNP analyses. Conclusion High LD correlations between markers at short distances across two generations indicate that such markers will retain high LD with linked QTL and be effective for MAS. The different association analysis methods used provided consistent results. Multiple single SNPs and 3-SNP windows were significantly associated with egg-related traits, providing genomic positions of QTL that can be useful for both MAS and to identify causal mutations. PMID:19607653

  5. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome.

    PubMed

    Fan, Guang Yao; Ye, Yi; Hou, Yi Ping

    2016-01-01

    Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification. PMID:27535707

  6. Variability of Marker-Based Rectal Dose Evaluation in HDR Cervical Brachytherapy

    SciTech Connect

    Wang Zhou; Jaggernauth, Wainwright; Malhotra, Harish K.; Podgorsak, Matthew B.

    2010-01-01

    In film-based intracavitary brachytherapy for cervical cancer, position of the rectal markers may not accurately represent the anterior rectal wall. This study was aimed at analyzing the variability of rectal dose estimation as a result of interfractional variation of marker placement. A cohort of five patients treated with multiple-fraction tandem and ovoid high-dose-rate (HDR) brachytherapy was studied. The cervical os point and the orientation of the applicators were matched among all fractional plans for each patient. Rectal points obtained from all fractions were then input into each clinical treated plan. New fractional rectal doses were obtained and a new cumulative rectal dose for each patient was calculated. The maximum interfractional variation of distances between rectal dose points and the closest source positions was 1.1 cm. The corresponding maximum variability of fractional rectal dose was 65.5%. The percentage difference in cumulative rectal dose estimation for each patient was 5.4%, 19.6%, 34.6%, 23.4%, and 13.9%, respectively. In conclusion, care should be taken when using rectal markers as reference points for estimating rectal dose in HDR cervical brachytherapy. The best estimate of true rectal dose for each fraction should be determined by the most anterior point among all fractions.

  7. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

    PubMed Central

    Fan, Guang Yao; Ye, Yi; Hou, Yi Ping

    2016-01-01

    Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification. PMID:27535707

  8. Preliminary clinical evaluation of a protein chip for tumor marker serodiagnosis of various cancers.

    PubMed

    Balachandra, Kruavon; Laisupasin, Pikul; Dhepakson, Panadda; Warachit, Jiranan; Jantraraksri, Udom; Issaragrisil, Surapol; Yang, Xiao-Li; Hus, Geng-Xi

    2003-09-01

    This preliminary study aimed to investigate sensitivity and specificity of a protein chip system for multi-tumor marker serodiagnosis of ten types of cancers, and to understand the possible clinical applications of this protein chip for the Thai population. The specific cancers diagnosed by this protein chip are lung, breast, liver, cervix, colo-rectal, stomach, ovary, esophagus, prostate and pancreas cancers. We analyzed 215 serum samples of which 165 were obtained from clinically confirmed cancer patients and 50 from healthy people with no evidence of cancer. The sensitivity and specificity of the protein chip were 82.4% and 94.0%, respectively. The success rate of the protein chip for detecting all 10 types of cancers varied from 57% to 100%. The value of the simultaneous measurement of multiple tumor markers using the protein chip for cancer screening lied in the higher sensitivity compared to using single tumor markers for each type of cancer. In short, protein chips may be useful in mass screening for cancer during health checkups as well as for metastasis follow-up of cancer patients.

  9. Archival bone marrow samples: suitable for multiple biomarker analysis.

    PubMed

    Lund, Bendik; Najmi, Laeya A; Wesolowska-Andersen, Agata; Landsem, Veslemøy M; Rasmussen, Kirsten K; Borst, Louise; Gupta, Ramneek; Schmiegelow, Kjeld; Klungland, Helge

    2015-01-01

    AB Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP analysis seems feasible, but the method has to be further optimized.

  10. Interpolation Errors in Spectrum Analyzers

    NASA Technical Reports Server (NTRS)

    Martin, J. L.

    1996-01-01

    To obtain the proper measurement amplitude with a spectrum analyzer, the correct frequency-dependent transducer factor must be added to the voltage measured by the transducer. This report examines how entering transducer factors into a spectrum analyzer can cause significant errors in field amplitude due to the misunderstanding of the analyzer's interpolation methods. It also discusses how to reduce these errors to obtain a more accurate field amplitude reading.

  11. Multiplicity Counting

    SciTech Connect

    Geist, William H.

    2015-12-01

    This set of slides begins by giving background and a review of neutron counting; three attributes of a verification item are discussed: 240Pueff mass; α, the ratio of (α,n) neutrons to spontaneous fission neutrons; and leakage multiplication. It then takes up neutron detector systems – theory & concepts (coincidence counting, moderation, die-away time); detector systems – some important details (deadtime, corrections); introduction to multiplicity counting; multiplicity electronics and example distributions; singles, doubles, and triples from measured multiplicity distributions; and the point model: multiplicity mathematics.

  12. Urinary markers for bladder cancer

    PubMed Central

    Smith, Zachary L.

    2013-01-01

    Bladder cancer has the fifth highest incidence of all malignancies in the United States, with a propensity to recur, requiring lifelong surveillance after diagnosis. Urinary markers of disease have been of extreme interest in this field in an effort to simplify surveillance schedules and improve early detection of tumors. Many markers have been described, but most remain investigational. However, some markers have undergone clinical trials and are approved for clinical use. In this review, urinary markers and their application for screening and surveillance of bladder cancer are discussed. PMID:23864929

  13. Markers of vulnerability in schizophrenia

    PubMed Central

    Prelipceanu, D

    2009-01-01

    Vulnerability in schizophrenia is an integrative concept, which tries to explain the development of schizophrenia as an interaction between different individual susceptibility factors and environmental risk factors. Vulnerability markers used in genetic studies include biochemical indicators, neuroanatomical, neurophysiologic, and cognitive abnormalities. Among those, the most extensive studied markers were: evoked potentials, smooth pursuit eye movements, and attentional deficits. Some of the potential indicators presented in this paper satisfy most of the criteria necessary for a vulnerability marker, but none meets all of them. Nevertheless, they represent important markers of risk to schizophrenia. Key words: vulnerability, evoked potentials, eye movements, attentional deficits PMID:20108534

  14. Rapid detection of autosomal aneuploidy using microsatellite markers

    SciTech Connect

    Ray, P.N.; Teshima, I.E.; Winsor, E.J.T.

    1994-09-01

    Trisomy occurs in at least 4% of all clinically recognized pregnancies, making it the most common type of chromosome abnormality in humans. The most commonly occurring trisomies are those of chromosomes 13, 18, 21 and aneuploidy of X and Y, accounting for about 0.3% of all newborns and a much higher percentage of conceptuses. In Canada, prenatal chromosome analysis by amniocentesis is offered to those women {ge} 35 years of age at the time of delivery or equivalent risk by maternal serum screen. We are developing a rapid molecular diagnostic test to detect the most common autosomal aneuploidies in prenatal and neonatal samples. The tests makes use of highly polymorphic short tandem repeat markers labeled with fluorescent tags which allow analysis on a GENESCANNER automated fragment analyzer (ABI). Multiple polymorphic markers have been selected on each of chromosomes 13, 18 and 21. At a given locus, trisomic fetuses/neonates will have either three alleles or two alleles with one allele having twice the intensity of the other. Unaffected individuals have two equal intensity alleles. We are conducting a blind study that will compare the detection efficiencies of FISH analysis on uncultured cells and the molecular method on confirmation amniotic fluid samples collected at the time of termination of affected fetuses. Results on cultured amniocytes from one such patient confirmed that trisomy 21 can be detected. FISH was not done on this sample. In addition, detection efficiency of the molecular method in whole blood samples from affected neonates is also being studied. To date, two such samples have been tested, one with trisomy 13 and one with trisomy 18, and both samples were diagnosed correctly. Preliminary results suggest that this method may provide a valuable tool for the rapid diagnosis of aneuploidy.

  15. Recycling selectable markers in mouse embryonic stem cells.

    PubMed Central

    Abuin, A; Bradley, A

    1996-01-01

    As a result of gene targeting, selectable markers are usually permanently introduced into the mammalian genome. Multiple gene targeting events in the same cell line can therefore exhaust the pool of markers available and limit subsequent manipulations or genetic analysis. In this study, we describe the combined use of homologous and CRE-loxP-mediated recombination to generate mouse embryonic stem cell lines carrying up to four targeted mutations and devoid of exogenous selectable markers. A cassette that contains both positive and negative selectable markers flanked by loxP sites, rendering it excisable by the CRE protein, was constructed. Homologous recombination and positive selection were used to disrupt the Rep-3 locus, a gene homologous to members of the mutS family of DNA mismatch repair genes. CRE-loxP-mediated recombination and negative selection were then used to recover clones in which the cassette had been excised. The remaining allele of Rep-3 was then subjected to a second round of targeting and excision with the same construct to generate homozygous, marker-free cell lines. Subsequently, both alleles of mMsh2, another mutS homolog, were disrupted in the same fashion to obtain cell lines homozygous for targeted mutations at both the Rep-3 and mMsh2 loci and devoid of selectable markers. Thus, embryonic stem cell lines obtained in this fashion are suitable for further manipulation and analysis involving the use of selectable markers. PMID:8657161

  16. 53BP1 foci as a marker of tumor cell radiosensitivity.

    PubMed

    Markova, E; Vasilyev, S; Belyaev, I

    2015-01-01

    Predicting tumor radiosensitivity has yet to be routinely integrated into radiotherapy. We analyzed the possibility to assess radiosensitivity of tumor cells based on endogenous and radiation-induced 53BP1 foci which are molecular markers of DNA double strand breaks (DSB). In eleven tumor cell lines of different origin, radiosensitivity was assessed by surviving cell fraction following irradiation with 2 Gy (SF2). 53BP1 foci were measured at 4 and 12 h post-irradiation by confocal laser microscopy and dedicated software. The correlation of 53BP1 foci and their post-irradiation kinetics with SF2 was assessed using Spearman rank test. The SF2 correlated with both excess of radiation-induced 53BP1 foci per cell at 4 h after irradiation and decay in number of 53BP1 foci from 4 to 12 h post-irradiation. The fraction of cells with multiple endogenous 53BP1 foci also correlated with SF2 of tumor cells. We conclude that the radiosensitivity of tumor cells can be predicted by kinetics of formation and decay of 53BP1 foci after irradiation. For the first time we report that the fraction of cells with multiple endogenous 53BP1 foci can be used as a marker of tumor cell radiosensitivity. PMID:26278144

  17. Expert judgment on markers to deter inadvertent human intrusion into the Waste Isolation Pilot Plant

    SciTech Connect

    Trauth, K.M.; Hora, S.C.; Guzowski, R.V.

    1993-11-01

    The expert panel identified basic principles to guide current and future marker development efforts: (1) the site must be marked, (2) message(s) must be truthful and informative, (3) multiple components within a marker system, (4) multiple means of communication (e.g., language, pictographs, scientific diagrams), (5) multiple levels of complexity within individual messages on individual marker system elements, (6) use of materials with little recycle value, and (7) international effort to maintain knowledge of the locations and contents of nuclear waste repositories. The efficacy of the markers in deterring inadvertent human intrusion was estimated to decrease with time, with the probability function varying with the mode of intrusion (who is intruding and for what purpose) and the level of technological development of the society. The development of a permanent, passive marker system capable of surviving and remaining interpretable for 10,000 years will require further study prior to implementation.

  18. Curiosity analyzes Martian soil samples

    NASA Astrophysics Data System (ADS)

    Showstack, Randy; Balcerak, Ernie

    2012-12-01

    NASA's Mars Curiosity rover has conducted its first analysis of Martian soil samples using multiple instruments, the agency announced at a 3 December news briefing at the AGU Fall Meeting in San Francisco. "These results are an unprecedented look at the chemical diversity in the area," said NASA's Michael Meyer, program scientist for Curiosity.

  19. Integrative prescreening in analysis of multiple cancer genomic studies

    PubMed Central

    2012-01-01

    Background In high throughput cancer genomic studies, results from the analysis of single datasets often suffer from a lack of reproducibility because of small sample sizes. Integrative analysis can effectively pool and analyze multiple datasets and provides a cost effective way to improve reproducibility. In integrative analysis, simultaneously analyzing all genes profiled may incur high computational cost. A computationally affordable remedy is prescreening, which fits marginal models, can be conducted in a parallel manner, and has low computational cost. Results An integrative prescreening approach is developed for the analysis of multiple cancer genomic datasets. Simulation shows that the proposed integrative prescreening has better performance than alternatives, particularly including prescreening with individual datasets, an intensity approach and meta-analysis. We also analyze multiple microarray gene profiling studies on liver and pancreatic cancers using the proposed approach. Conclusions The proposed integrative prescreening provides an effective way to reduce the dimensionality in cancer genomic studies. It can be coupled with existing analysis methods to identify cancer markers. PMID:22799431

  20. Nuclear fuel microsphere gamma analyzer

    DOEpatents

    Valentine, Kenneth H.; Long, Jr., Ernest L.; Willey, Melvin G.

    1977-01-01

    A gamma analyzer system is provided for the analysis of nuclear fuel microspheres and other radioactive particles. The system consists of an analysis turntable with means for loading, in sequence, a plurality of stations within the turntable; a gamma ray detector for determining the spectrum of a sample in one section; means for analyzing the spectrum; and a receiver turntable to collect the analyzed material in stations according to the spectrum analysis. Accordingly, particles may be sorted according to their quality; e.g., fuel particles with fractured coatings may be separated from those that are not fractured, or according to other properties.

  1. Compact fast analyzer of rotary cuvette type

    DOEpatents

    Thacker, Louis H.

    1976-01-01

    A compact fast analyzer of the rotary cuvette type is provided for simultaneously determining concentrations in a multiplicity of discrete samples using either absorbance or fluorescence measurement techniques. A rigid, generally rectangular frame defines optical passageways for the absorbance and fluorescence measurement systems. The frame also serves as a mounting structure for various optical components as well as for the cuvette rotor mount and drive system. A single light source and photodetector are used in making both absorbance and fluorescence measurements. Rotor removal and insertion are facilitated by a swing-out drive motor and rotor mount. BACKGROUND OF THE INVENTION The invention relates generally to concentration measuring instruments and more specifically to a compact fast analyzer of the rotary cuvette type which is suitable for making either absorbance or fluorescence measurements. It was made in the course of, or under, a contract with the U.S. Atomic Energy Commission.

  2. Real-time airborne particle analyzer

    DOEpatents

    Reilly, Peter T.A.

    2012-10-16

    An aerosol particle analyzer includes a laser ablation chamber, a gas-filled conduit, and a mass spectrometer. The laser ablation chamber can be operated at a low pressure, which can be from 0.1 mTorr to 30 mTorr. The ablated ions are transferred into a gas-filled conduit. The gas-filled conduit reduces the electrical charge and the speed of ablated ions as they collide and mix with buffer gases in the gas-filled conduit. Preferably, the gas filled-conduit includes an electromagnetic multipole structure that collimates the nascent ions into a beam, which is guided into the mass spectrometer. Because the gas-filled conduit allows storage of vast quantities of the ions from the ablated particles, the ions from a single ablated particle can be analyzed multiple times and by a variety of techniques to supply statistically meaningful analysis of composition and isotope ratios.

  3. Automated genotyping of dinucleotide repeat markers

    SciTech Connect

    Perlin, M.W.; Hoffman, E.P. |

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  4. Market study: Whole blood analyzer

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A market survey was conducted to develop findings relative to the commercialization potential and key market factors of the whole blood analyzer which is being developed in conjunction with NASA's Space Shuttle Medical System.

  5. Molecular wake shield gas analyzer

    NASA Technical Reports Server (NTRS)

    Hoffman, J. H.

    1980-01-01

    Techniques for measuring and characterizing the ultrahigh vacuum in the wake of an orbiting spacecraft are studied. A high sensitivity mass spectrometer that contains a double mass analyzer consisting of an open source miniature magnetic sector field neutral gas analyzer and an identical ion analyzer is proposed. These are configured to detect and identify gas and ion species of hydrogen, helium, nitrogen, oxygen, nitric oxide, and carbon dioxide and any other gas or ion species in the 1 to 46 amu mass range. This range covers the normal atmospheric constituents. The sensitivity of the instrument is sufficient to measure ambient gases and ion with a particle density of the order of one per cc. A chemical pump, or getter, is mounted near the entrance aperture of the neutral gas analyzer which integrates the absorption of ambient gases for a selectable period of time for subsequent release and analysis. The sensitivity is realizable for all but rare gases using this technique.

  6. A Categorization of Dynamic Analyzers

    NASA Technical Reports Server (NTRS)

    Lujan, Michelle R.

    1997-01-01

    Program analysis techniques and tools are essential to the development process because of the support they provide in detecting errors and deficiencies at different phases of development. The types of information rendered through analysis includes the following: statistical measurements of code, type checks, dataflow analysis, consistency checks, test data,verification of code, and debugging information. Analyzers can be broken into two major categories: dynamic and static. Static analyzers examine programs with respect to syntax errors and structural properties., This includes gathering statistical information on program content, such as the number of lines of executable code, source lines. and cyclomatic complexity. In addition, static analyzers provide the ability to check for the consistency of programs with respect to variables. Dynamic analyzers in contrast are dependent on input and the execution of a program providing the ability to find errors that cannot be detected through the use of static analysis alone. Dynamic analysis provides information on the behavior of a program rather than on the syntax. Both types of analysis detect errors in a program, but dynamic analyzers accomplish this through run-time behavior. This paper focuses on the following broad classification of dynamic analyzers: 1) Metrics; 2) Models; and 3) Monitors. Metrics are those analyzers that provide measurement. The next category, models, captures those analyzers that present the state of the program to the user at specified points in time. The last category, monitors, checks specified code based on some criteria. The paper discusses each classification and the techniques that are included under them. In addition, the role of each technique in the software life cycle is discussed. Familiarization with the tools that measure, model and monitor programs provides a framework for understanding the program's dynamic behavior from different, perspectives through analysis of the input

  7. PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

    PubMed Central

    Lei, Runhua; Rowley, Thaine W.; Zhu, Lifeng; Bailey, Carolyn A.; Engberg, Shannon E.; Wood, Mindy L.; Christman, Mary C.; Perry, George H.; Louis, Edward E.; Lu, Guoqing

    2012-01-01

    Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/.

  8. Analyzing clonal fidelity of micropropagated Psidium guajava L. plants using simple sequence repeat markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Micropropagation of Psidium guajava L. (guava) is a viable alternative to currently adopted techniques for large-scale plant propagation of commercial cultivars. Assessment of clonal fidelity in micropropagated plants is the first step towards ensuring genetic uniformity in mass production of planti...

  9. Characterizing seasonal markers using high-resolution water temperature data from small mountain ponds

    NASA Astrophysics Data System (ADS)

    Daly, J.; Engel, B.; Hansen, J.

    2010-12-01

    Small mountain ponds in western Maine are near local topographic highs and are typically associated with distinctive ecological zones because of their elevation. Long-term historic records of seasonal markers such as ice-out for large, low elevation lakes in the region indicate that climate warming is affecting these large water bodies, but little data exist for the smaller, remote, higher elevation ponds. These ponds are typically 700 m elevation, have a surface area of about 4 hectares, and a maximum depth of 10 m. Because these ponds are associated with habitats restricted from migrating in response to climate change, characterizing and documenting the timing of seasonal markers such as ice-out and other events is important to assess whether these smaller ponds are following similar trends to the larger lakes, or if they might be more sensitive to climate forcing. High-resolution water temperature and light data collected at several depths by data loggers at study sites across the region since 2007 have been analyzed to characterize major seasonal markers that cannot be otherwise determined because of the remote character of the ponds. Ice-in and ice-out dates can be identified by characteristic signatures in the surface and bottom water temperatures; differences in the timing of the events among sites may be explained by elevation or basin aspect. Summer temperatures records also revealed multiple turnover events during some summer seasons, indicating that these ponds should be classified as discontinuous cold polymictic water bodies . These turnover events were nearly simultaneous at multiple study sites fifty kilometers apart, suggesting forcing by regional weather events. These high-resolution records permit long-term monitoring of sensitive, remote sites that will contribute to understanding the magnitude of the response to climate change in these small subalpine watersheds, as well as the spatial and temporal complexity of climate change in the

  10. Representing Multiplication

    ERIC Educational Resources Information Center

    Harries, Tony; Barmby, Patrick

    2008-01-01

    In this study, the authors wish to explore the use of visual representations in facilitating the understanding of multiplication. In doing so, they examine the different aspects of multiplication that they can access through different representations. In addition, they draw on a study that they have been carrying out looking at pupils' actual use…

  11. Reproducibility of Immunological Tests Used To Assess Multiple Chemical Sensitivity Syndrome

    PubMed Central

    Hoover, Donald R.; Donnay, Albert; Mitchell, Clifford S.; Ziem, Grace; Rose, Noel R.; Sabath, Daniel E.; Yurkow, Edward J.; Nakamura, Robert; Vogt, Robert F.; Waxdal, Myron; Margolick, Joseph B.

    2003-01-01

    Whether persons with multiple chemical sensitivity syndrome (MCS) have immunological abnormalities is unknown. To assess the reliability of selected immunological tests that have been hypothesized to be associated with MCS, replicate blood samples from 19 healthy volunteers, 15 persons diagnosed with MCS, and 11 persons diagnosed with autoimmune disease were analyzed in five laboratories for expression of four T-cell surface activation markers (CD25, CD26, CD38, and HLA-DR) and in four laboratories for autoantibodies (to smooth muscle, thyroid antigens, and myelin). For T-cell activation markers, the intralaboratory reproducibility was very good, with 90% of the replicates analyzed in the same laboratory differing by ≤3%. Interlaboratory differences were statistically significant for all T-cell subsets except CD4+ cells, ranging from minor to eightfold for CD25+ subsets. Within laboratories, the date of analysis was significantly associated with the values for all cellular activation markers. Although reproducibility of autoantibodies could not be precisely assessed due to the rarity of abnormal results, there were inconsistencies across laboratories. The effect of shipping on all measurements, while sometimes statistically significant, was very small. These results support the reliability of fresh and shipped samples for detecting large (but perhaps not small) differences between groups of donors in the T-cell subsets tested. When comparing markers that are not well standardized, it may be important to distribute samples from different study groups evenly over time. PMID:14607863

  12. Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster

    SciTech Connect

    Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

    2001-04-16

    For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that have recently revolutionized human, mouse and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila using an STS-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that the genome. The majority of these markers are single nucleotide polymorphisms (SNPs) and sequences for these variants are provided in an accessible format. The average density of the new markers is 1 marker per 225 kb on the autosomes and 1 marker per 1 Mb on the X chromosome. We include in this survey a set of P-element strains that provide additional utility for high-resolution mapping. We demonstrate one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community.

  13. Analysis of morphological markers of chromosomal instability in ascitic fluid.

    PubMed

    Tyagi, Ruchita; Dey, Pranab; Uppal, Radha; Rajwanshi, Arvind

    2015-10-01

    Chromosomal instability (CI) plays a major role in the carcinogenesis. Micronuclei, nuclear budding, chromatin bridges,and multipolar mitoses are the morphological markers of CI and have never been studied in routine cytological specimens. Aims of the study is to analyze the significance of morphological markers of CI in malignant and benign ascitic fluid smears. A total of sixty benign and 40 malignant ascitic fluid samples were selected for this study. All the cases with malignant ascitic fluid showed histopathological evidence of malignancy in ovary and omentum. Chromatin bridges, multipolar mitosis (MPM), micronuclei and nuclear budding were counted in 1000 cells in representative May Grunwald Giemsa (MGG) stained smears. The CI markers were correlated with the cytological diagnosis of effusion. The mean number of micronuclei, nuclear budding, chromatin bridge and multipolar mitoses found in malignant effusions were 13.2611.79, 10.1067.07, 2.5362.67, 1.964.5, respectively. The mean number of micronuclei, nuclear budding, anaphase bridges, and MPM found in benign effusion cases were 0.566761.07934, 0.516761.33, 0.66760.25, and 0, respectively. The student t test showed significant differences between malignant and benign ascitic fluid samples for each marker of CI. This is the first comprehensive study of morphological markers of CI in ascitic fluid smears. This study has shown strong correlation between markers of CI and cytological diagnosis of malignancy. In future, the knowledge of these markers can be applied to diagnose malignancy in suspected cases of effusion in difficult situations.

  14. GTA: a game theoretic approach to identifying cancer subnetwork markers.

    PubMed

    Farahmand, S; Goliaei, S; Ansari-Pour, N; Razaghi-Moghadam, Z

    2016-03-01

    The identification of genetic markers (e.g. genes, pathways and subnetworks) for cancer has been one of the most challenging research areas in recent years. A subset of these studies attempt to analyze genome-wide expression profiles to identify markers with high reliability and reusability across independent whole-transcriptome microarray datasets. Therefore, the functional relationships of genes are integrated with their expression data. However, for a more accurate representation of the functional relationships among genes, utilization of the protein-protein interaction network (PPIN) seems to be necessary. Herein, a novel game theoretic approach (GTA) is proposed for the identification of cancer subnetwork markers by integrating genome-wide expression profiles and PPIN. The GTA method was applied to three distinct whole-transcriptome breast cancer datasets to identify the subnetwork markers associated with metastasis. To evaluate the performance of our approach, the identified subnetwork markers were compared with gene-based, pathway-based and network-based markers. We show that GTA is not only capable of identifying robust metastatic markers, it also provides a higher classification performance. In addition, based on these GTA-based subnetworks, we identified a new bonafide candidate gene for breast cancer susceptibility. PMID:26750920

  15. On-Demand Urine Analyzer

    NASA Technical Reports Server (NTRS)

    Farquharson, Stuart; Inscore, Frank; Shende, Chetan

    2010-01-01

    A lab-on-a-chip was developed that is capable of extracting biochemical indicators from urine samples and generating their surface-enhanced Raman spectra (SERS) so that the indicators can be quantified and identified. The development was motivated by the need to monitor and assess the effects of extended weightlessness, which include space motion sickness and loss of bone and muscle mass. The results may lead to developments of effective exercise programs and drug regimes that would maintain astronaut health. The analyzer containing the lab-on-a- chip includes materials to extract 3- methylhistidine (a muscle-loss indicator) and Risedronate (a bone-loss indicator) from the urine sample and detect them at the required concentrations using a Raman analyzer. The lab-on- a-chip has both an extractive material and a SERS-active material. The analyzer could be used to monitor the onset of diseases, such as osteoporosis.

  16. Rotor for centrifugal fast analyzers

    DOEpatents

    Lee, N.E.

    1984-01-01

    The invention is an improved photometric analyzer of the rotary cuvette type, the analyzer incorporating a multicuvette rotor of novel design. The rotor (a) is leaktight, (b) permits operation in the 90/sup 0/ and 180/sup 0/ excitation modes, (c) is compatible with extensively used Centrifugal Fast Analyzers, and (d) can be used thousands of times. The rotor includes an assembly comprising a top plate, a bottom plate, and a central plate, the rim of the central plate being formed with circumferentially spaced indentations. A uv-transmitting ring is sealably affixed to the indented rim to define with the indentations an array of cuvettes. The ring serves both as a sealing means and an end window for the cuvettes.

  17. Rotor for centrifugal fast analyzers

    DOEpatents

    Lee, Norman E.

    1985-01-01

    The invention is an improved photometric analyzer of the rotary cuvette type, the analyzer incorporating a multicuvette rotor of novel design. The rotor (a) is leaktight, (b) permits operation in the 90.degree. and 180.degree. excitation modes, (c) is compatible with extensively used Centrifugal Fast Analyzers, and (d) can be used thousands of times. The rotor includes an assembly comprising a top plate, a bottom plate, and a central plate, the rim of the central plate being formed with circumferentially spaced indentations. A UV-transmitting ring is sealably affixed to the indented rim to define with the indentations an array of cuvettes. The ring serves both as a sealing means and an end window for the cuvettes.

  18. Real time infrared aerosol analyzer

    DOEpatents

    Johnson, Stanley A.; Reedy, Gerald T.; Kumar, Romesh

    1990-01-01

    Apparatus for analyzing aerosols in essentially real time includes a virtual impactor which separates coarse particles from fine and ultrafine particles in an aerosol sample. The coarse and ultrafine particles are captured in PTFE filters, and the fine particles impact onto an internal light reflection element. The composition and quantity of the particles on the PTFE filter and on the internal reflection element are measured by alternately passing infrared light through the filter and the internal light reflection element, and analyzing the light through infrared spectrophotometry to identify the particles in the sample.

  19. Predicting Missing Marker Trajectories in Human Motion Data Using Marker Intercorrelations

    PubMed Central

    2016-01-01

    Missing information in motion capture data caused by occlusion or detachment of markers is a common problem that is difficult to avoid entirely. The aim of this study was to develop and test an algorithm for reconstruction of corrupted marker trajectories in datasets representing human gait. The reconstruction was facilitated using information of marker inter-correlations obtained from a principal component analysis, combined with a novel weighting procedure. The method was completely data-driven, and did not require any training data. We tested the algorithm on datasets with movement patterns that can be considered both well suited (healthy subject walking on a treadmill) and less suited (transitioning from walking to running and the gait of a subject with cerebral palsy) to reconstruct. Specifically, we created 50 copies of each dataset, and corrupted them with gaps in multiple markers at random temporal and spatial positions. Reconstruction errors, quantified by the average Euclidian distance between predicted and measured marker positions, was ≤ 3 mm for the well suited dataset, even when there were gaps in up to 70% of all time frames. For the less suited datasets, median reconstruction errors were in the range 5–6 mm. However, a few reconstructions had substantially larger errors (up to 29 mm). Our results suggest that the proposed algorithm is a viable alternative both to conventional gap-filling algorithms and state-of-the-art reconstruction algorithms developed for motion capture systems. The strengths of the proposed algorithm are that it can fill gaps anywhere in the dataset, and that the gaps can be considerably longer than when using conventional interpolation techniques. Limitations are that it does not enforce musculoskeletal constraints, and that the reconstruction accuracy declines if applied to datasets with less predictable movement patterns. PMID:27031243

  20. Predicting Missing Marker Trajectories in Human Motion Data Using Marker Intercorrelations.

    PubMed

    Gløersen, Øyvind; Federolf, Peter

    2016-01-01

    Missing information in motion capture data caused by occlusion or detachment of markers is a common problem that is difficult to avoid entirely. The aim of this study was to develop and test an algorithm for reconstruction of corrupted marker trajectories in datasets representing human gait. The reconstruction was facilitated using information of marker inter-correlations obtained from a principal component analysis, combined with a novel weighting procedure. The method was completely data-driven, and did not require any training data. We tested the algorithm on datasets with movement patterns that can be considered both well suited (healthy subject walking on a treadmill) and less suited (transitioning from walking to running and the gait of a subject with cerebral palsy) to reconstruct. Specifically, we created 50 copies of each dataset, and corrupted them with gaps in multiple markers at random temporal and spatial positions. Reconstruction errors, quantified by the average Euclidian distance between predicted and measured marker positions, was ≤ 3 mm for the well suited dataset, even when there were gaps in up to 70% of all time frames. For the less suited datasets, median reconstruction errors were in the range 5-6 mm. However, a few reconstructions had substantially larger errors (up to 29 mm). Our results suggest that the proposed algorithm is a viable alternative both to conventional gap-filling algorithms and state-of-the-art reconstruction algorithms developed for motion capture systems. The strengths of the proposed algorithm are that it can fill gaps anywhere in the dataset, and that the gaps can be considerably longer than when using conventional interpolation techniques. Limitations are that it does not enforce musculoskeletal constraints, and that the reconstruction accuracy declines if applied to datasets with less predictable movement patterns. PMID:27031243

  1. Software-Design-Analyzer System

    NASA Technical Reports Server (NTRS)

    Tausworthe, Robert C.

    1991-01-01

    CRISP-90 software-design-analyzer system, update of CRISP-80, is set of computer programs constituting software tool for design and documentation of other software and supporting top-down, hierarchical, modular, structured methodologies for design and programming. Written in Microsoft QuickBasic.

  2. Analyzing Software Piracy in Education.

    ERIC Educational Resources Information Center

    Lesisko, Lee James

    This study analyzes the controversy of software piracy in education. It begins with a real world scenario that presents the setting and context of the problem. The legalities and background of software piracy are explained and true court cases are briefly examined. Discussion then focuses on explaining why individuals and organizations pirate…

  3. Strategies for Analyzing Tone Languages

    ERIC Educational Resources Information Center

    Coupe, Alexander R.

    2014-01-01

    This paper outlines a method of auditory and acoustic analysis for determining the tonemes of a language starting from scratch, drawing on the author's experience of recording and analyzing tone languages of north-east India. The methodology is applied to a preliminary analysis of tone in the Thang dialect of Khiamniungan, a virtually undocumented…

  4. FORTRAN Static Source Code Analyzer

    NASA Technical Reports Server (NTRS)

    Merwarth, P.

    1982-01-01

    FORTRAN Static Source Code Analyzer program (SAP) automatically gathers and reports statistics on occurrences of statements and structures within FORTRAN program. Provisions are made for weighting each statistic, providing user with overall figure of complexity. Statistics, as well as figures of complexity, are gathered on module-by-module basis. Overall summed statistics are accumulated for complete input source file.

  5. FORTRAN Static Source Code Analyzer

    NASA Technical Reports Server (NTRS)

    Merwarth, P.

    1984-01-01

    FORTRAN Static Source Code Analyzer program, SAP (DEC VAX version), automatically gathers statistics on occurrences of statements and structures within FORTRAN program and provides reports of those statistics. Provisions made for weighting each statistic and provide an overall figure of complexity.

  6. Gene markers of cellular aging in human multipotent stromal cells in culture

    PubMed Central

    2014-01-01

    Introduction Human multipotent stromal cells (MSCs) isolated from bone marrow or other tissue sources have great potential to treat a wide range of injuries and disorders in the field of regenerative medicine and tissue engineering. In particular, MSCs have inherent characteristics to suppress the immune system and are being studied in clinical studies to prevent graft-versus-host disease. MSCs can be expanded in vitro and have potential for differentiation into multiple cell lineages. However, the impact of cell passaging on gene expression and function of the cells has not been determined. Methods Commercially available human MSCs derived from bone marrow from six different donors, grown under identical culture conditions and harvested at cell passages 3, 5, and 7, were analyzed with gene-expression profiling by using microarray technology. Results The phenotype of these cells did not change as reported previously; however, a statistical analysis revealed a set of 78 significant genes that were distinguishable in expression between passages 3 and 7. None of these significant genes corresponded to the markers established by the International Society for Cellular Therapy (ISCT) for MSC identification. When the significant gene lists were analyzed through pathway analysis, these genes were involved in the top-scoring networks of cellular growth and proliferation and cellular development. A meta-analysis of the literature for significant genes revealed that the MSCs seem to be undergoing differentiation into a senescent cell type when cultured extensively. Consistent with the differences in gene expression at passage 3 and 7, MSCs exhibited a significantly greater potential for cell division at passage 3 in comparison to passage 7. Conclusions Our results identified specific gene markers that distinguish aging MSCs grown in cell culture. Confirmatory studies are needed to correlate these molecular markers with biologic attributes that may facilitate the development

  7. [Tumor markers for hepatocellular carcinoma].

    PubMed

    Tateishi, Ryosuke; Enooku, Kenichiro; Shiina, Shuichiro; Koike, Kazuhiko

    2012-05-01

    Three tumor markers for hepatocellular carcinoma (HCC) are available in Japan: alpha-fetoprotein (AFP), protein induced by vitamin K absence or antagonists-II (PIVKA-II), and Lens culinaris agglutinin-reactive fraction of alpha-fetoprotein (AFP-L3). Although AFP has drawbacks in its specificity, it is widely utilized in treatment evaluation and prognosis prediction. PIVKA-II is a unique marker that does not correlate with AFP value and can predict microvascular invasion. AFP-L3 is a highly specific marker and strong predictor of poor prognosis. These three markers are indispensable in every aspect of clinical practice of hepatocellular carcinoma including surveillance, diagnosis, treatment evaluation, and prognosis prediction.

  8. Beta-2 Microglobulin Tumor Marker

    MedlinePlus

    ... limited. Home Visit Global Sites Search Help? Beta-2 Microglobulin Tumor Marker Share this page: Was this page helpful? Also known as: B2M; B 2 M; β2-Microglobulin; Thymotaxin Formal name: Beta 2 ...

  9. Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats.

    PubMed

    Konovalov, Fedor A; Goncharov, Nikolay P; Goryunova, Svetlana; Shaturova, Aleksandra; Proshlyakova, Tatyana; Kudryavtsev, Alexander

    2010-06-01

    Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive. PMID:20407790

  10. Use of SSR markers for DNA fingerprinting and diversity analysis of Pakistani sugarcane (Saccharum spp. hybrids) cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years SSR markers have been used widely for genetic analysis. The objective of this study was to use an SSR-based marker system to develop the molecular fingerprints and analyze the genetic relationship of sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers wer...

  11. [Laboratory markers of melanoma progression].

    PubMed

    Bánfalvi, Teodóra; Edesné, Mariann B; Gergye, Mária; Udvarhelyi, Nóra; Orosz, Zsolt; Gilde, Katalin; Kremmer, Tibor; Ottó, Szabolcs; Tímár, József

    2003-01-01

    Extracellular tumour markers may have potential role in the follow-up of patients with malignant melanoma, in therapy monitoring and in prediction of prognosis. In our article circulating tumour markers in melanoma (melanoma inhibitory activity, lipid bound sialic acid, neuron specific enolase, TA90 immune complex, S-100B protein, 5-S-cysteinyldopa, tyrosinase, cytokines, metalloproteinases, LDH) were reviewed. Among laboratory melanoma markers the S-100B protein is the most investigated. S-100B protein has high specificity, appropriate sensitivity and proved to be significant prognostic factor independent from stages. High serum values are associated with shorter survival. However, before S-100B monitoring immunohistochemistry for the detection of S-100B is required. In the case of malignant melanomas with low expression serum S-100B monitoring may not be sensitive enough to follow disease progression. Although the serum concentration of 5-S-cysteinyldopa did not prove to be independent prognostic factor in our previous studies comprising the highest patient number in the literature, the marker was suggested for therapy monitoring. The survival analysis indicated that the elevated 5-S-cysteinyldopa level predicts shorter survival. In spite of the calculated low correlation between the two markers, parallel elevation of S-100B protein and 5-S-cysteinyldopa indicated shorter survival. On the basis of the literature LDH is the most appropriate tumour marker in stage IV to predict prognosis, but its sensitivity and specificity could not achieve that of S-100B protein. S-100B and LDH proved to be similarly reliable in respect to the clinical outcome. Determination of serum concentration of MIA and tyrosinase are also reliable markers in malignant melanoma. The other investigated markers are not well known yet or do not provide useful information to the clinicians. PMID:12704461

  12. Breast cancer statistics and markers.

    PubMed

    Donepudi, Mallika Siva; Kondapalli, Kasturi; Amos, Seelam Jeevan; Venkanteshan, Pavithra

    2014-01-01

    Breast cancer is one of the familiar diseases in women. Incidence and mortality due to cancer, particularly breast cancer has been increasing for last 50 years, even though there is a lacuna in the diagnosis of breast cancer at early stages. According to World Health Organization (WHO) 2012 reports, breast cancer is the leading cause of death in women, accounting 23% of all cancer deaths. In Asia, one in every three women faces the risk of breast cancer in their lifetime as per reports of WHO 2012. Here, the review is been focused on different breast cancer markers, that is, tissue markers (hormone receptors, human epidermal growth factor-2, urokinase plasminogen activator, plasminogen activator inhibitor, p53 and cathepsin D), genetic markers (BRAC1 and 2 and gene expression microarray technique, etc.), and serum markers (CA 15.3, BR 27.29, MCA, CA 549, carcinoembryonic antigen, oncoproteins, and cytokeratins) used in present diagnosis, but none of the mentioned markers can diagnose breast cancer at an early stage. There is a disquieting need for the identification of best diagnosing marker, which can be able to diagnose even in early stage of breast carcinogenesis.

  13. RP-HPLC method using one marker for quantification of four podophyllum lignans in medicinal plants.

    PubMed

    Lu, Ningwei; An, Qiong; Li, Ning; Dong, Yuming

    2014-07-01

    A high-performance liquid chromatographic method using a single standard has been established for the quantitative analysis of four podophyllum lignans in Dysosma versipellis (Hance) M. Cheng and Podophyllum emodi Wall. Var. chinesis Sprague. The method involved the quantitative analysis of multiple components by a single marker. The chromatographic method was validated for linearity and range, limit of detection and qualification, precision, stability, reproducibility and robustness. Relative correcting factors were calculated and examined by five concentrations of four podophyllum lignans, two high-performance liquid chromatographic systems and three chromatographic columns. The method was applied to analyze 10 batches of samples. The quantitative results were compared with the results by an external standard method through intra-class coefficient, which indicated that the established method was reliable for the determination of the four podophyllum lignans in the two medicinal plants.

  14. The Statistical Loop Analyzer (SLA)

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.

    1985-01-01

    The statistical loop analyzer (SLA) is designed to automatically measure the acquisition, tracking and frequency stability performance characteristics of symbol synchronizers, code synchronizers, carrier tracking loops, and coherent transponders. Automated phase lock and system level tests can also be made using the SLA. Standard baseband, carrier and spread spectrum modulation techniques can be accomodated. Through the SLA's phase error jitter and cycle slip measurements the acquisition and tracking thresholds of the unit under test are determined; any false phase and frequency lock events are statistically analyzed and reported in the SLA output in probabilistic terms. Automated signal drop out tests can be performed in order to trouble shoot algorithms and evaluate the reacquisition statistics of the unit under test. Cycle slip rates and cycle slip probabilities can be measured using the SLA. These measurements, combined with bit error probability measurements, are all that are needed to fully characterize the acquisition and tracking performance of a digital communication system.

  15. Portable imaging polarized light analyzer

    NASA Astrophysics Data System (ADS)

    Shashar, Nadav; Cronin, Thomas W.; Johnson, George; Wolff, Lawrence B.

    1995-06-01

    Many animals, both marine and terrestrial, are sensitive to the orientation of the e-vector of partially linearly polarized light (PLPL). This sensitivity is used for navigation, spatial orientation, and detection of large bodies of water. However, it is not clear what other information animals may receive from polarized light. Natural light fields, both in the sky and underwater, are known to be partially polarized. Additionally, natural objects reflect light that is polarized at specific orientations. Sensors capable of measuring the characteristics of PLPL, namely partial polarization and orientation, throughout an image are not yet available. By placing 2 twisted nematic liquid crystals (TNLCs) and a fixed polarizing filter in series in front of a video camera, and by controlling the angles of rotation of the orientation of polarization produced by the TNLCs, we are able to fully analyze PLPL throughout a full image on a single pixel basis. As a recording device we use a small camcorder. The sensor can be operated autonomously, with the images analyzed at a later stage, or it can be connected (in a future phase) via a frame grabber to a personal computer which analyzes the information online. The analyzed image can be presented as a false color image, where hue represents orientation of polarization and saturation represents partial polarization. Field measurements confirm that PLPL is a characteristic distributed both under water and on land. Marine background light is strongly horizontally polarized. Light reflected from leaves is polarized mainly according to their spatial orientation. Differences between PLPL reflected from objects or animals and their background can be used to enhance contrast and break color camouflage. Our sensor presents a new approach for answering questions related to the ecology of vision and is a new tool for remote sensing.

  16. Satellite-based interference analyzer

    NASA Technical Reports Server (NTRS)

    Varice, H.; Johannsen, K.; Sabaroff, S.

    1977-01-01

    System identifies terrestrial sources of radiofrequency interference and measures their frequency spectra and amplitudes. Designed to protect satellite communication networks, system measures entire noise spectrum over selected frequency band and can raster-scan geographical region to locate noise sources. Once interference is analyzed, realistic interference protection ratios are determined and mathematical models for predicting ratio-frequency noise spectra are established. This enhances signal-detection and locates optimum geographical positions and frequency bands for communication equipment.

  17. DEEP WATER ISOTOPIC CURRENT ANALYZER

    DOEpatents

    Johnston, W.H.

    1964-04-21

    A deepwater isotopic current analyzer, which employs radioactive isotopes for measurement of ocean currents at various levels beneath the sea, is described. The apparatus, which can determine the direction and velocity of liquid currents, comprises a shaft having a plurality of radiation detectors extending equidistant radially therefrom, means for releasing radioactive isotopes from the shaft, and means for determining the time required for the isotope to reach a particular detector. (AEC)

  18. Analyzing ion distributions around DNA.

    PubMed

    Lavery, Richard; Maddocks, John H; Pasi, Marco; Zakrzewska, Krystyna

    2014-07-01

    We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation. PMID:24906882

  19. Analyzing ion distributions around DNA

    PubMed Central

    Lavery, Richard; Maddocks, John H.; Pasi, Marco; Zakrzewska, Krystyna

    2014-01-01

    We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation. PMID:24906882

  20. Remote Laser Diffraction PSD Analyzer

    SciTech Connect

    T. A. Batcheller; G. M. Huestis; S. M. Bolton

    2000-06-01

    Particle size distribution (PSD) analysis of radioactive slurry samples were obtained using a modified off-the-shelf classical laser light scattering particle size analyzer. A Horiba Instruments Inc. Model La-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a hot cell (gamma radiation) environment. The general details of the modifications to this analyzer are presented in this paper. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not achievable - making this technology far superior than the traditional methods used previously. Remote deployment and utilization of this technology is in an exploratory stage. The risk of malfunction in this radiation environment is countered by gaining of this tremendously useful fundamental engineering data. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives.

  1. Remote Laser Diffraction PSD Analyzer

    SciTech Connect

    Batcheller, Thomas Aquinas; Huestis, Gary Michael; Bolton, Steven Michael

    2000-06-01

    Particle size distribution (PSD) analysis of radioactive slurry samples were obtained using a modified "off-the-shelf" classical laser light scattering particle size analyzer. A Horiba Instruments Inc. Model La-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a "hot cell" (gamma radiation) environment. The general details of the modifications to this analyzer are presented in this paper. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not achievable - making this technology far superior than the traditional methods used previously. Remote deployment and utilization of this technology is in an exploratory stage. The risk of malfunction in this radiation environment is countered by gaining of this tremendously useful fundamental engineering data. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives.

  2. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach.

    PubMed

    Cheung, Mike W-L; Jak, Suzanne

    2016-01-01

    Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists-and probably the most crucial one-is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study.

  3. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach.

    PubMed

    Cheung, Mike W-L; Jak, Suzanne

    2016-01-01

    Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists-and probably the most crucial one-is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study. PMID:27242639

  4. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach

    PubMed Central

    Cheung, Mike W.-L.; Jak, Suzanne

    2016-01-01

    Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists—and probably the most crucial one—is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study. PMID:27242639

  5. OmicsVis: an interactive tool for visually analyzing metabolomics data.

    PubMed

    Livengood, Philip; Maciejewski, Ross; Chen, Wei; Ebert, David S

    2012-01-01

    When analyzing metabolomics data, cancer care researchers are searching for differences between known healthy samples and unhealthy samples. By analyzing and understanding these differences, researchers hope to identify cancer biomarkers. Due to the size and complexity of the data produced, however, analysis can still be very slow and time consuming. This is further complicated by the fact that datasets obtained will exhibit incidental differences in intensity and retention time, not related to actual chemical differences in the samples being evaluated. Additionally, automated tools to correct these errors do not always produce reliable results. This work presents a new analytics system that enables interactive comparative visualization and analytics of metabolomics data obtained by two-dimensional gas chromatography-mass spectrometry (GC × GC-MS). The key features of this system are the ability to produce visualizations of multiple GC × GC-MS data sets, and to explore those data sets interactively, allowing a user to discover differences and features in real time. The system provides statistical support in the form of difference, standard deviation, and kernel density estimation calculations to aid users in identifying meaningful differences between samples. These are combined with novel transfer functions and multiform, linked visualizations in order to provide researchers with a powerful new tool for GC × GC-MS exploration and bio-marker discovery.

  6. Biochemical Markers of Myocardial Damage

    PubMed Central

    2016-01-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  7. Biochemical Markers of Myocardial Damage.

    PubMed

    Bodor, Geza S

    2016-04-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  8. The Aqueduct Global Flood Analyzer

    NASA Astrophysics Data System (ADS)

    Iceland, Charles

    2015-04-01

    As population growth and economic growth take place, and as climate change accelerates, many regions across the globe are finding themselves increasingly vulnerable to flooding. A recent OECD study of the exposure of the world's large port cities to coastal flooding found that 40 million people were exposed to a 1 in 100 year coastal flood event in 2005, and the total value of exposed assets was about US 3,000 billion, or 5% of global GDP. By the 2070s, those numbers were estimated to increase to 150 million people and US 35,000 billion, or roughly 9% of projected global GDP. Impoverished people in developing countries are particularly at risk because they often live in flood-prone areas and lack the resources to respond. WRI and its Dutch partners - Deltares, IVM-VU University Amsterdam, Utrecht University, and PBL Netherlands Environmental Assessment Agency - are in the initial stages of developing a robust set of river flood and coastal storm surge risk measures that show the extent of flooding under a variety of scenarios (both current and future), together with the projected human and economic impacts of these flood scenarios. These flood risk data and information will be accessible via an online, easy-to-use Aqueduct Global Flood Analyzer. We will also investigate the viability, benefits, and costs of a wide array of flood risk reduction measures that could be implemented in a variety of geographic and socio-economic settings. Together, the activities we propose have the potential for saving hundreds of thousands of lives and strengthening the resiliency and security of many millions more, especially those who are most vulnerable. Mr. Iceland will present Version 1.0 of the Aqueduct Global Flood Analyzer and provide a preview of additional elements of the Analyzer to be released in the coming years.

  9. Transient One-dimensional Pipe Flow Analyzer

    1986-04-08

    TOPAZ-SNLL, the Transient One- dimensional Pipe flow AnalyZer code, is a user-friendly computer program for modeling the heat transfer, fluid mechanics, and thermodynamics of multi-species gas transfer in arbitrary arrangements of pipes, valves, vessels, and flow branches. Although the flow conservation equations are assumed to be one-dimensional and transient, multidimensional features of internal fluid flow and heat transfer may be accounted for using the available quasi-steady flow correlations (e.g., Moody friction factor correlation and variousmore » form loss and heat transfer correlations). Users may also model the effects of moving system boundaries such as pistons, diaphragms, and bladders. The features of fully compressible flow are modeled, including the propagation of shocks and rarefaction waves, as well as the establishment of multiple choke points along the flow path.« less

  10. Method for network analyzation and apparatus

    DOEpatents

    Bracht, Roger B.; Pasquale, Regina V.

    2001-01-01

    A portable network analyzer and method having multiple channel transmit and receive capability for real-time monitoring of processes which maintains phase integrity, requires low power, is adapted to provide full vector analysis, provides output frequencies of up to 62.5 MHz and provides fine sensitivity frequency resolution. The present invention includes a multi-channel means for transmitting and a multi-channel means for receiving, both in electrical communication with a software means for controlling. The means for controlling is programmed to provide a signal to a system under investigation which steps consecutively over a range of predetermined frequencies. The resulting received signal from the system provides complete time domain response information by executing a frequency transform of the magnitude and phase information acquired at each frequency step.

  11. Transient One-dimensional Pipe Flow Analyzer

    SciTech Connect

    1986-04-08

    TOPAZ-SNLL, the Transient One- dimensional Pipe flow AnalyZer code, is a user-friendly computer program for modeling the heat transfer, fluid mechanics, and thermodynamics of multi-species gas transfer in arbitrary arrangements of pipes, valves, vessels, and flow branches. Although the flow conservation equations are assumed to be one-dimensional and transient, multidimensional features of internal fluid flow and heat transfer may be accounted for using the available quasi-steady flow correlations (e.g., Moody friction factor correlation and various form loss and heat transfer correlations). Users may also model the effects of moving system boundaries such as pistons, diaphragms, and bladders. The features of fully compressible flow are modeled, including the propagation of shocks and rarefaction waves, as well as the establishment of multiple choke points along the flow path.

  12. [Examination of the olfactory analyzer].

    PubMed

    Domrachev, A A; Afon'kin, V Iu

    2002-01-01

    A method of threshold olfactometry is proposed consisting in the use of three olfactive substances (tincture of valerian, acetic acid, liquid ammonia) in selected concentrations. This allows to investigate the thresholds of certain modality. Each concentration of the olfactive substance is placed into a glass bottle (100 ml) and stored at the temperature 18-20 degrees C. The examination of the state of the olfactory analyzer within a 24-h working day showed stability of threshold olfactometry when the organism is tired. Utilization of threshold olfactometry in some diagnostic areas is shown. PMID:12056163

  13. The OpenSHMEM Analyzer

    2014-07-30

    The OpenSHMEM Analyzer is a compiler-based tool that can help users detect errors and provide useful analyses about their OpenSHMEM applications. The tool is built on top of the OpenUH compiler (a branch of Open64 compiler) and presents OpenSHMEM information as feedback to the user. Some of the analyses it provides include checks for correct usage of symmetric variables in OpenSHMEM calls, out-of-bounds checks for symmetric data, checks for the correct initialization of pointers tomore » symmetric data, and symmetric data alias information.« less

  14. MULTICHANNEL PULSE-HEIGHT ANALYZER

    DOEpatents

    Russell, J.T.; Lefevre, H.W.

    1958-01-21

    This patent deals with electronic computing circuits and more particularly to pulse-height analyzers used for classifying variable amplitude pulses into groups of different amplitudes. The device accomplishes this pulse allocation by by converting the pulses into frequencies corresponding to the amplitudes of the pulses, which frequencies are filtered in channels individually pretuned to a particular frequency and then detected and recorded in the responsive channel. This circuit substantially overcomes the disadvantages of prior annlyzers incorporating discriminators pre-set to respond to certain voltage levels, since small variation in component values is not as critical to satisfactory circuit operation.

  15. Method for analyzing microbial communities

    SciTech Connect

    Zhou, Jizhong; Wu, Liyou

    2010-07-20

    The present invention provides a method for quantitatively analyzing microbial genes, species, or strains in a sample that contains at least two species or strains of microorganisms. The method involves using an isothermal DNA polymerase to randomly and representatively amplify genomic DNA of the microorganisms in the sample, hybridizing the resultant polynucleotide amplification product to a polynucleotide microarray that can differentiate different genes, species, or strains of microorganisms of interest, and measuring hybridization signals on the microarray to quantify the genes, species, or strains of interest.

  16. Truck acoustic data analyzer system

    DOEpatents

    Haynes, Howard D.; Akerman, Alfred; Ayers, Curtis W.

    2006-07-04

    A passive vehicle acoustic data analyzer system having at least one microphone disposed in the acoustic field of a moving vehicle and a computer in electronic communication the microphone(s). The computer detects and measures the frequency shift in the acoustic signature emitted by the vehicle as it approaches and passes the microphone(s). The acoustic signature of a truck driving by a microphone can provide enough information to estimate the truck speed in miles-per-hour (mph), engine speed in rotations-per-minute (RPM), turbocharger speed in RPM, and vehicle weight.

  17. Charged particle mobility refrigerant analyzer

    DOEpatents

    Allman, Steve L.; Chen, Chung-Hsuan; Chen, Fang C.

    1993-01-01

    A method for analyzing a gaseous electronegative species comprises the steps of providing an analysis chamber; providing an electric field of known potential within the analysis chamber; admitting into the analysis chamber a gaseous sample containing the gaseous electronegative species; providing a pulse of free electrons within the electric field so that the pulse of free electrons interacts with the gaseous electronegative species so that a swarm of electrically charged particles is produced within the electric field; and, measuring the mobility of the electrically charged particles within the electric field.

  18. Charged particle mobility refrigerant analyzer

    DOEpatents

    Allman, S.L.; Chunghsuan Chen; Chen, F.C.

    1993-02-02

    A method for analyzing a gaseous electronegative species comprises the steps of providing an analysis chamber; providing an electric field of known potential within the analysis chamber; admitting into the analysis chamber a gaseous sample containing the gaseous electronegative species; providing a pulse of free electrons within the electric field so that the pulse of free electrons interacts with the gaseous electronegative species so that a swarm of electrically charged particles is produced within the electric field; and, measuring the mobility of the electrically charged particles within the electric field.

  19. The OpenSHMEM Analyzer

    SciTech Connect

    Hernandez, Oscar

    2014-07-30

    The OpenSHMEM Analyzer is a compiler-based tool that can help users detect errors and provide useful analyses about their OpenSHMEM applications. The tool is built on top of the OpenUH compiler (a branch of Open64 compiler) and presents OpenSHMEM information as feedback to the user. Some of the analyses it provides include checks for correct usage of symmetric variables in OpenSHMEM calls, out-of-bounds checks for symmetric data, checks for the correct initialization of pointers to symmetric data, and symmetric data alias information.

  20. Automating a residual gas analyzer

    NASA Technical Reports Server (NTRS)

    Petrie, W. F.; Westfall, A. H.

    1982-01-01

    A residual gas analyzer (RGA), a device for measuring the amounts and species of various gases present in a vacuum system is discussed. In a recent update of the RGA, it was shown that the use of microprocessors could revolutionize data acquisition and data reduction. This revolution is exemplified by the Inficon 1Q200 RGA which was selected to meet the needs of this update. The Inficon RGA and the Zilog microcomputer were interfaced in order the receive and format the digital data from the RGA. This automated approach is discussed in detail.

  1. Trace Gas Analyzer (TGA) program

    NASA Technical Reports Server (NTRS)

    1977-01-01

    The design, fabrication, and test of a breadboard trace gas analyzer (TGA) is documented. The TGA is a gas chromatograph/mass spectrometer system. The gas chromatograph subsystem employs a recirculating hydrogen carrier gas. The recirculation feature minimizes the requirement for transport and storage of large volumes of carrier gas during a mission. The silver-palladium hydrogen separator which permits the removal of the carrier gas and its reuse also decreases vacuum requirements for the mass spectrometer since the mass spectrometer vacuum system need handle only the very low sample pressure, not sample plus carrier. System performance was evaluated with a representative group of compounds.

  2. Some easily analyzable convolutional codes

    NASA Technical Reports Server (NTRS)

    Mceliece, R.; Dolinar, S.; Pollara, F.; Vantilborg, H.

    1989-01-01

    Convolutional codes have played and will play a key role in the downlink telemetry systems on many NASA deep-space probes, including Voyager, Magellan, and Galileo. One of the chief difficulties associated with the use of convolutional codes, however, is the notorious difficulty of analyzing them. Given a convolutional code as specified, say, by its generator polynomials, it is no easy matter to say how well that code will perform on a given noisy channel. The usual first step in such an analysis is to computer the code's free distance; this can be done with an algorithm whose complexity is exponential in the code's constraint length. The second step is often to calculate the transfer function in one, two, or three variables, or at least a few terms in its power series expansion. This step is quite hard, and for many codes of relatively short constraint lengths, it can be intractable. However, a large class of convolutional codes were discovered for which the free distance can be computed by inspection, and for which there is a closed-form expression for the three-variable transfer function. Although for large constraint lengths, these codes have relatively low rates, they are nevertheless interesting and potentially useful. Furthermore, the ideas developed here to analyze these specialized codes may well extend to a much larger class.

  3. COBSTRAN - COMPOSITE BLADE STRUCTURAL ANALYZER

    NASA Technical Reports Server (NTRS)

    Aiello, R. A.

    1994-01-01

    The COBSTRAN (COmposite Blade STRuctural ANalyzer) program is a pre- and post-processor that facilitates the design and analysis of composite turbofan and turboprop blades, as well as composite wind turbine blades. COBSTRAN combines composite mechanics and laminate theory with a data base of fiber and matrix properties. As a preprocessor for NASTRAN or another Finite Element Method (FEM) program, COBSTRAN generates an FEM model with anisotropic homogeneous material properties. Stress output from the FEM program is provided as input to the COBSTRAN postprocessor. The postprocessor then uses the composite mechanics and laminate theory routines to calculate individual ply stresses, strains, interply stresses, thru-the-thickness stresses and failure margins. COBSTRAN is designed to carry out the many linear analyses required to efficiently model and analyze blade-like structural components made of multilayered angle-plied fiber composites. Components made from isotropic or anisotropic homogeneous materials can also be modeled as a special case of COBSTRAN. NASTRAN MAT1 or MAT2 material cards are generated according to user supplied properties. COBSTRAN is written in FORTRAN 77 and was implemented on a CRAY X-MP with a UNICOS 5.0.12 operating system. The program requires either COSMIC NASTRAN or MSC NASTRAN as a structural analysis package. COBSTRAN was developed in 1989, and has a memory requirement of 262,066 64 bit words.

  4. Thermal and evolved gas analyzer

    NASA Technical Reports Server (NTRS)

    Williams, M. S.; Boynton, W. V.; James, R. L.; Verts, W. T.; Bailey, S. H.; Hamara, D. K.

    1998-01-01

    The Thermal and Evolved Gas Analyzer (TEGA) instrument will perform calorimetry and evolved gas analysis on soil samples collected from the Martian surface. TEGA is one of three instruments, along with a robotic arm, that form the Mars Volatile and Climate Survey (MVACS) payload. The other instruments are a stereo surface imager, built by Peter Smith of the University of Arizona and a meteorological station, built by JPL. The MVACS lander will investigate a Martian landing site at approximately 70 deg south latitude. Launch will take place from Kennedy Space Center in January, 1999. The TEGA project started in February, 1996. In the intervening 24 months, a flight instrument concept has been designed, prototyped, built as an engineering model and flight model, and tested. The instrument performs laboratory-quality differential-scanning calorimetry (DSC) over the temperature range of Mars ambient to 1400K. Low-temperature volatiles (water and carbon dioxide ices) and the carbonates will be analyzed in this temperature range. Carbonates melt and evolve carbon dioxide at temperatures above 600 C. Evolved oxygen (down to a concentration of 1 ppm) is detected, and C02 and water vapor and the isotopic variations of C02 and water vapor are detected and their concentrations measured. The isotopic composition provides important tests of the theory of solar system formation.

  5. Managing healthcare information: analyzing trust.

    PubMed

    Söderström, Eva; Eriksson, Nomie; Åhlfeldt, Rose-Mharie

    2016-08-01

    Purpose - The purpose of this paper is to analyze two case studies with a trust matrix tool, to identify trust issues related to electronic health records. Design/methodology/approach - A qualitative research approach is applied using two case studies. The data analysis of these studies generated a problem list, which was mapped to a trust matrix. Findings - Results demonstrate flaws in current practices and point to achieving balance between organizational, person and technology trust perspectives. The analysis revealed three challenge areas, to: achieve higher trust in patient-focussed healthcare; improve communication between patients and healthcare professionals; and establish clear terminology. By taking trust into account, a more holistic perspective on healthcare can be achieved, where trust can be obtained and optimized. Research limitations/implications - A trust matrix is tested and shown to identify trust problems on different levels and relating to trusting beliefs. Future research should elaborate and more fully address issues within three identified challenge areas. Practical implications - The trust matrix's usefulness as a tool for organizations to analyze trust problems and issues is demonstrated. Originality/value - Healthcare trust issues are captured to a greater extent and from previously unchartered perspectives. PMID:27477934

  6. Evaluation of Potential Clinical Surrogate Markers of a Trauma Induced Alteration of Clotting Factor Activities

    PubMed Central

    Payas, Arzu; Schoeneberg, Carsten; Wegner, Alexander; Kauther, Max Daniel; Lendemans, Sven

    2016-01-01

    Objective. The aim of this study was to identify routinely available clinical surrogate markers for potential clotting factor alterations following multiple trauma. Methods. In 68 patients admitted directly from the scene of the accident, all soluble clotting factors were analyzed and clinical data was collected prospectively. Ten healthy subjects served as control group. Results. Patients showed reduced activities of clotting factors II, V, VII, and X and calcium levels (all P < 0.0001 to 0.01). Levels of hemoglobin and base deficit correlated moderately to highly with the activities of a number of clotting factors. Nonsurvivors and patients who needed preclinical intubation or hemostatic therapy showed significantly reduced factor activities at admission. In contrast, factor VIII activity was markedly elevated after injury in general (P < 0.0001), but reduced in nonsurvivors (P < 0.05). Conclusions. Multiple trauma causes an early reduction of the activities of nearly all soluble clotting factors in general. Initial hemoglobin and, with certain qualifications, base deficit levels demonstrated a potential value in detecting those underlying clotting factor deficiencies. Nevertheless, their role as triggers of a hemostatic therapy as well as the observed response of factor VIII to multiple trauma and also its potential prognostic value needs further evaluation. PMID:27433474

  7. Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

    PubMed

    Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

    2016-01-01

    In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea. PMID:26909914

  8. Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

    PubMed

    Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

    2016-01-01

    In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea.

  9. Salivary markers of oxidative stress in oral diseases

    PubMed Central

    Tóthová, L'ubomíra; Kamodyová, Natália; Červenka, Tomáš; Celec, Peter

    2015-01-01

    Saliva is an interesting alternative diagnostic body fluid with several specific advantages over blood. These include non-invasive and easy collection and related possibility to do repeated sampling. One of the obstacles that hinders the wider use of saliva for diagnosis and monitoring of systemic diseases is its composition, which is affected by local oral status. However, this issue makes saliva very interesting for clinical biochemistry of oral diseases. Periodontitis, caries, oral precancerosis, and other local oral pathologies are associated with oxidative stress. Several markers of lipid peroxidation, protein oxidation and DNA damage induced by reactive oxygen species can be measured in saliva. Clinical studies have shown an association with oral pathologies at least for some of the established salivary markers of oxidative stress. This association is currently limited to the population level and none of the widely used markers can be applied for individual diagnostics. Oxidative stress seems to be of local oral origin, but it is currently unclear whether it is caused by an overproduction of reactive oxygen species due to inflammation or by the lack of antioxidants. Interventional studies, both, in experimental animals as well as humans indicate that antioxidant treatment could prevent or slow-down the progress of periodontitis. This makes the potential clinical use of salivary markers of oxidative stress even more attractive. This review summarizes basic information on the most commonly used salivary markers of oxidative damage, antioxidant status, and carbonyl stress and the studies analyzing these markers in patients with caries or periodontitis. PMID:26539412

  10. Analyzing Schizophrenia by DNA Microarrays

    PubMed Central

    Horváth, Szatmár; Janka, Zoltán; Mirnics, Károly

    2010-01-01

    To understand the pathological processes of schizophrenia we must embrace the analysis of the diseased human brain: we will never be able to recapitulate the pathology of uniquely human disorders in an animal model. Based on the outcome of the transcriptome profiling experiments performed to date it appears that schizophrenia is associated with a global gene expression disturbance across many cortical regions. In addition, transcriptome changes are present in multiple cell types, including specific subclasses of principal neurons, interneurons and oligodendrocytes. Furthermore, transcripts related to synaptic transmission, energy metabolism and inhibitory neurotransmission are routinely found underexpressed in the postmortem brain tissue of subjects with schizophrenia. To put these transcriptome data in biological context we must make our data publicly available and report our findings in a proper, expanded MIAME format. Cell type specific expression profiling and sequencing-based transcripts assessments should be expanded, with particular attention to understanding splice-variant changes in various mental disorders. Deciphering the pathophysiology of mental disorders depends on integrating data from across many research fields and techniques. Leads from postmortem transcriptome profiling will be essential to generate model animals, perform tissue culture experiments and develop or evaluate novel drugs to treat this devastating disorder. PMID:20801428

  11. Analyzing Dynamics of Cooperating Spacecraft

    NASA Technical Reports Server (NTRS)

    Hughes, Stephen P.; Folta, David C.; Conway, Darrel J.

    2004-01-01

    A software library has been developed to enable high-fidelity computational simulation of the dynamics of multiple spacecraft distributed over a region of outer space and acting with a common purpose. All of the modeling capabilities afforded by this software are available independently in other, separate software systems, but have not previously been brought together in a single system. A user can choose among several dynamical models, many high-fidelity environment models, and several numerical-integration schemes. The user can select whether to use models that assume weak coupling between spacecraft, or strong coupling in the case of feedback control or tethering of spacecraft to each other. For weak coupling, spacecraft orbits are propagated independently, and are synchronized in time by controlling the step size of the integration. For strong coupling, the orbits are integrated simultaneously. Among the integration schemes that the user can choose are Runge-Kutta Verner, Prince-Dormand, Adams-Bashforth-Moulton, and Bulirsh- Stoer. Comparisons of performance are included for both the weak- and strongcoupling dynamical models for all of the numerical integrators.

  12. Marker imputation in barley association studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping requires higher marker density than linkage mapping, potentially leading to more missing marker data and to higher genotyping costs. In human genetics, methods exist to impute missing marker data and whole markers that were typed in a reference panel but not in the experimental d...

  13. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 1 2011-01-01 2011-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  14. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  15. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 1 2013-01-01 2013-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  16. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 1 2014-01-01 2014-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  17. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 1 2012-01-01 2012-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  18. Nonlinear Single Spin Spectrum Analyzer

    NASA Astrophysics Data System (ADS)

    Kotler, Shlomi; Akerman, Nitzan; Glickman, Yinnon; Ozeri, Roee

    2014-03-01

    Qubits have been used as linear spectrum analyzers of their environments, through the use of decoherence spectroscopy. Here we solve the problem of nonlinear spectral analysis, required for discrete noise induced by a strongly coupled environment. Our nonperturbative analytical model shows a nonlinear signal dependence on noise power, resulting in a spectral resolution beyond the Fourier limit as well as frequency mixing. We develop a noise characterization scheme adapted to this nonlinearity. We then apply it using a single trapped ion as a sensitive probe of strong, non-Gaussian, discrete magnetic field noise. Finally, we experimentally compared the performance of equidistant vs Uhrig modulation schemes for spectral analysis. Phys. Rev. Lett. 110, 110503 (2013). Synopsis at http://physics.aps.org/synopsis-for/10.1103/PhysRevLett.110.110503 Current position: NIST, Boulder, CO.

  19. Analyze distillation columns with thermodynamics

    SciTech Connect

    Ognisty, T.P. )

    1995-02-01

    In a distillation column, heat supplies the work for separating the components of a feed stream into products. Distillation columns consume some 95% of the total energy used in separations. This amounts to roughly 3% of the energy consumed in the US. Since distillation is so energy intensive and requires significant capital outlays, an endless quest to improve the economics has continued since the beginning of the industry. By analyzing the thermodynamics of a distillation column, an engineer can quantify the thermodynamic efficiency of the process, identify the regions where energy can be better utilized, and define the minimum targets for energy consumption. This article reviews the principles of distillation column thermodynamics and outlines the analysis of lost work profiles and column heat profiles. It then illustrates these concepts through three examples.

  20. Compact Microwave Fourier Spectrum Analyzer

    NASA Technical Reports Server (NTRS)

    Savchenkov, Anatoliy; Matsko, Andrey; Strekalov, Dmitry

    2009-01-01

    A compact photonic microwave Fourier spectrum analyzer [a Fourier-transform microwave spectrometer, (FTMWS)] with no moving parts has been proposed for use in remote sensing of weak, natural microwave emissions from the surfaces and atmospheres of planets to enable remote analysis and determination of chemical composition and abundances of critical molecular constituents in space. The instrument is based on a Bessel beam (light modes with non-zero angular momenta) fiber-optic elements. It features low power consumption, low mass, and high resolution, without a need for any cryogenics, beyond what is achievable by the current state-of-the-art in space instruments. The instrument can also be used in a wide-band scatterometer mode in active radar systems.

  1. Markers of bile duct tumors

    PubMed Central

    Malaguarnera, Giulia; Giordano, Maria; Paladina, Isabella; Rando, Alessandra; Uccello, Mario; Basile, Francesco; Biondi, Antonio; Carnazzo, Santo; Alessandria, Innocenza; Mazzarino, Clorinda

    2011-01-01

    Biliary tract carcinomas are relatively rare, representing less than 1% of cancers. However, their incidence has increased in Japan and in industrialized countries like the USA. Biliary tract tumors have a poor prognosis and a high mortality rate because they are usually detected late in the course of the disease; therapeutic treatment options are often limited and of minimal utility. Recent studies have shown the importance of serum and molecular markers in the diagnosis and follow up of biliary tract tumors. This review aims to introduce the main features of the most important serum and molecular markers of biliary tree tumors. Some considerable tumor markers are cancer antigen 125, carbohydrate antigen 19-9, carcinoembryonic antigen, chromogranin A, mucin 1, mucin 5, alpha-fetoprotein, claudins and cytokeratins. PMID:21528090

  2. Multiple Sclerosis.

    ERIC Educational Resources Information Center

    Plummer, Nancy; Michael, Nancy, Ed.

    This module on multiple sclerosis is intended for use in inservice or continuing education programs for persons who administer medications in long-term care facilities. Instructor information, including teaching suggestions, and a listing of recommended audiovisual materials and their sources appear first. The module goal and objectives are then…

  3. Granulocyte-Macrophage Colony-Stimulating Factor Auto-Antibodies: A Marker of Aggressive Crohn’s Disease

    PubMed Central

    Gathungu, Grace; Kim, Mi-Ok; Ferguson, John P.; Sharma, Yashoda; Zhang, Wei; Ng, Sok Meng E.; Bonkowski, Erin; Ning, Kaida; Simms, Lisa A.; Croft, Anthony R.; Stempak, Joanne M.; Walker, Nicole; Huang, Ning; Xiao, Yang; Silverberg, Mark S.; Trapnell, Bruce C.; Cho, Judy H.; Radford-Smith, Graham L.; Denson, Lee A.

    2013-01-01

    Background & Aims Neutralizing auto-antibodies (Ab) against granulocyte-macrophage colony-stimulating factor (GM-CSF Ab) have been associated with stricturing ileal Crohn’s disease (CD) in a largely pediatric patient cohort (total 394, adult CD 57). The aim of this study was to examine this association in two independent predominantly adult inflammatory bowel disease patient cohorts. Methods Serum samples from 745 subjects from the NIDDK IBD Genetics Consortium and 737 patients from Australia were analyzed for GM-CSF Ab and genetic markers. We conducted multiple regression analysis with backwards elimination to assess the contribution of GM-CSF Ab levels, established CD risk alleles and smoking on ileal disease location in the 477 combined CD subjects from both cohorts. We also determined associations of GM-CSF Ab levels with complications requiring surgical intervention in combined CD subjects in both cohorts. Results Serum samples from CD patients expressed significantly higher concentrations of GM-CSF Ab when compared to Ulcerative Colitis or controls in each cohort. Non-smokers with ileal CD expressed significantly higher GM-CSF Ab concentrations in the Australian cohort (p= 0.002). Elevated GM-CSF Ab, ileal disease location and disease duration greater than 3 years were independently associated with stricturing/penetrating behavior and intestinal resection for CD. Conclusions The expression of high GM-CSF Ab is a risk marker for aggressive CD behavior and complications including surgery. Modifying factors include environmental exposure to smoking and genetic risk markers. PMID:23749272

  4. Analyzing endocrine system conservation and evolution.

    PubMed

    Bonett, Ronald M

    2016-08-01

    Analyzing variation in rates of evolution can provide important insights into the factors that constrain trait evolution, as well as those that promote diversification. Metazoan endocrine systems exhibit apparent variation in evolutionary rates of their constituent components at multiple levels, yet relatively few studies have quantified these patterns and analyzed them in a phylogenetic context. This may be in part due to historical and current data limitations for many endocrine components and taxonomic groups. However, recent technological advancements such as high-throughput sequencing provide the opportunity to collect large-scale comparative data sets for even non-model species. Such ventures will produce a fertile data landscape for evolutionary analyses of nucleic acid and amino acid based endocrine components. Here I summarize evolutionary rate analyses that can be applied to categorical and continuous endocrine traits, and also those for nucleic acid and protein-based components. I emphasize analyses that could be used to test whether other variables (e.g., ecology, ontogenetic timing of expression, etc.) are related to patterns of rate variation and endocrine component diversification. The application of phylogenetic-based rate analyses to comparative endocrine data will greatly enhance our understanding of the factors that have shaped endocrine system evolution.

  5. Urine markers of interstitial cystitis.

    PubMed

    Erickson, D R

    2001-06-01

    This article describes the current state of the art with regard to urine markers of interstitial cystitis (IC), and describes the areas that need continuing research. Articles referenced in MEDLINE that describe urine alterations in IC were reviewed. Additional articles were identified by cross-referencing. The different marker alterations were tabulated. The relevant articles were discussed, considering different purposes for urine markers including: (1) diagnosing IC; (2) confirming a specific pathophysiology for IC; and (3) predicting or following response to a specific treatment. Currently, 2 markers (glycoprotein-51 and antiproliferative factor [APF]) clearly separate IC and control subjects, with minimal overlap. Markers that correlate with specific bladder biopsy features include 1,4-methylimidazole acetic acid and eosinophil cationic protein (ECP), which correlate with mast cell density, and interleukin (IL)-6, which correlates with mononuclear inflammation. Markers that changed after treatment were as follows: (1) nitric oxide synthase and cyclic guanosine monophosphate increased with oral L-arginine; (2) ECP decreased with subcutaneous heparin; (3) prostaglandin E(2) and kallikrein decreased after bladder distention; (4) neutrophil chemotactic activity decreased after dimethyl sulfoxide; (5) IL-2 inhibitor decreased after oral nifedipine; (6) IL-2, IL-6, and IL-8 decreased after bacille Calmette-Guérin (BCG) vaccine; and (7) APF and heparin-binding epidermal growth factor changed to or toward normal levels after bladder distention or sacral nerve stimulation. A larger number of urine alterations have been reported, and a few are being pursued further by correlating with bladder biopsy findings or treatment responses. Further research is needed.

  6. Comparison of two different methods of preoperative marking for toric intraocular lens implantation: bubble marker versus pendulum marker

    PubMed Central

    Farooqui, Javed Hussain; Koul, Archana; Dutta, Ranjan; Shroff, Noshir Minoo

    2016-01-01

    AIM To compare the accuracy of two different methods of preoperative marking for toric intraocular lens (IOL) implantation, bubble marker versus pendulum marker, as a means of establishing the reference point for the final alignment of the toric IOL to achieve an outcome as close as possible to emmetropia. METHODS Toric IOLs were implanted in 180 eyes of 110 patients. One group (55 patients) had preoperative marking of both eyes done with bubble marker (ASICO AE-2791TBL) and the other group (55 patients) with pendulum marker (Rumex®3-193). Reference marks were placed at 3-, 6-, and 9-o'clock positions on the limbus. Slit-lamp photographs were analyzed using Adobe Photoshop (version 7.0). Amount of alignment error (in degrees) induced in each group was measured. RESULTS Mean absolute rotation error in the preoperative marking in the horizontal axis was 2.42±1.71 in the bubble marker group and 2.83±2.31in the pendulum marker group (P=0.501). Sixty percent of the pendulum group and 70% of the bubble group had rotation error ≤3 (P=0.589), and 90% eyes of the pendulum group and 96.7% of the bubble group had rotation error ≤5 (P=0.612). CONCLUSION Both preoperative marking techniques result in approximately 3 of alignment error. Both marking techniques are simple, predictable, reproducible and easy to perform. PMID:27275425

  7. A Comparative Study of Intensity Markers in Engineering and Applied Linguistics

    ERIC Educational Resources Information Center

    Behnam, Biook; Mirzapour, Fatemeh

    2012-01-01

    Writers use intensity markers as one of strategies in order to negotiate their claims and to make their writings persuasive and credible. This study is an attempt to examine the type, frequency, and functions of intensity markers in research articles of two disciplines of Applied Linguistics and Electrical Engineering by analyzing surface…

  8. Integrating objective gene-brain-behavior markers of psychiatric disorders.

    PubMed

    Gordon, Evian; Liddell, Belinda J; Brown, Kerri J; Bryant, Richard; Clark, C Richard; DAS, Pritha; Dobson-Stone, Carol; Falconer, Erin; Felmingham, Kim; Flynn, Gary; Gatt, Justine M; Harris, Anthony; Hermens, Daniel F; Hopkinson, Patrick J; Kemp, Andrew H; Kuan, Stacey A; Lazzaro, Illario; Moyle, Jonson; Paul, Robert H; Rennie, Chris J; Schofield, Peter; Whitford, Thomas; Williams, Leanne M

    2007-03-01

    There is little consensus about which objective markers should be used to assess major psychiatric disorders, and predict/evaluate treatment response for these disorders. Clinical practice relies instead on subjective signs and symptoms, such that there is a "translational gap" between research findings and clinical practice. This gap arises from: a) a lack of integrative theoretical models which provide a basis for understanding links between gene-brain-behavior mechanisms and clinical entities; b) the reliance on studying one measure at a time so that linkages between markers are their specificity are not established; and c) the lack of a definitive understanding of what constitutes normative function. Here, we draw on a standardized methodology for acquiring multiple sources of genomic, brain and behavioral data in the same subjects, to propose candidate markers of selected psychiatric disorders: depression, post-traumatic stress disorder, schizophrenia, attention-deficit/hyperactivity disorder and dementia disorders. This methodology has been used to establish a standardized international database which provides a comprehensive framework and the basis for testing hypotheses derived from an integrative theoretical model of the brain. Using this normative base, we present preliminary findings for a number of disorders in relation to the proposed markers. Establishing these objective markers will be the first step towards determining their sensitivity, specificity and treatment prediction in individual patients.

  9. Markers of early disease and prognosis in COPD

    PubMed Central

    Dahl, Morten; Nordestgaard, Børge G

    2009-01-01

    COPD is a complex disease with multiple pathological components, which we unfortunately tend to ignore when spirometry is used as the only method to evaluate the disorder. Additional measures are needed to allow a more complete and clinically relevant assessment of COPD. The earliest potential risk factors of disease in COPD are variations in the genetic background. Genetic variations are present from conception and can determine lifelong changes in enzyme activities and protein concentrations. In contrast, measurements in blood, sputum, exhaled breath, broncho-alveolar lavage, and lung biopsies may vary substantially over time. This review explores potential markers of early disease and prognosis in COPD by examining genetic markers in the α1-antitrypsin, cystic fibrosis transmembrane conductance regulator (CFTR), and MBL-2 genes, and by examining the biochemical markers fibrinogen and C-reactive protein (CRP), which correlate with degree of pulmonary inflammation during stable conditions of COPD. Chronic lung inflammation appears to contribute to the pathogenesis of COPD, and markers of this process have promising predictive value in COPD. To implement markers for COPD in clinical practice, besides those already established for the α1-antitrypsin gene, further research and validation studies are needed. PMID:19436688

  10. Hyperprolactinemia during antipsychotics treatment increases the level of coagulation markers

    PubMed Central

    Ishioka, Masamichi; Yasui-Furukori, Norio; Sugawara, Norio; Furukori, Hanako; Kudo, Shuhei; Nakamura, Kazuhiko

    2015-01-01

    Objective The strong association between psychiatric patients who receive antipsychotics and the incidence of venous thromboembolism (VTE) is known. Although previous reports suggest that hyperprolactinemia often increases markers of activated coagulation, few studies have examined the direct relationship between the prolactin level elevated by antipsychotics and activated markers of activated coagulation. Method The participants included 182 patients with schizophrenia (male =89, female =93) who received antipsychotic treatments for at least 3 months. Markers of VTE (D-dimer, fibrin/fibrinogen degradation products, and thrombin–antithrombin complex) and serum prolactin concentrations were measured. Results Prolactin levels were significantly correlated with the logarithmic transformation of the D-dimer (r=0.320, P=0.002) and fibrin/fibrinogen degradation product levels (r=0.236, P=0.026) but not of the thrombin–antithrombin complex level (r=0.117, ns) among men. However, no correlations were found between the VTE markers and prolactin levels among women. These results were confirmed using multiple regression analyses that included demographic factors and antipsychotic dosages. Conclusion The current study indicates that hyperprolactinemia is associated with an increase in markers of activated coagulation among men receiving antipsychotics. This finding clinically implies that monitoring and modulating prolactin levels among men are important to decrease the risk of VTE. PMID:25750528

  11. Prevalence of celiac disease in multiple sclerosis

    PubMed Central

    2011-01-01

    Background Celiac disease (CD) is a common systemic disease related to a permanent intolerance to gluten and is often associated with different autoimmune and neurological diseases. Its mean prevalence in the general population is 1-2% worldwide. Our aim was to study the prevalence of celiac disease in a prospective series of Multiple Sclerosis (MS) patients and their first-degree relatives. Methods We analyzed the prevalence of serological, histological and genetic CD markers in a series of 72 MS patients and in their 126 first-degree relatives, compared to 123 healthy controls. Results Tissue IgA-anti-transglutaminase-2 antibodies were positive in 7 MS patients (10%), compared to 3 healthy controls (2.4%) (p < 0.05). OR: 5.33 (CI-95%: 1.074-26.425). No differences were found in HLA-DQ2 markers between MS patients (29%) and controls (26%) (NS). We detected mild or moderate villous atrophy (Marsh III type) in duodenal biopsies, in 8 MS patients (11.1%). We also found a high proportion of CD among first-degree relatives: 23/126 (32%). Several associated diseases were detected, mainly dermatitis 41 (57%) and iron deficiency anemia in 28 (39%) MS patients. We also found in them, an increased frequency of circulating auto-antibodies such as anti-TPO in 19 (26%), ANA in 11 (15%) and AMA in 2 (3%). Conclusions We have found an increased prevalence of CD in 8 of the 72 MS patients (11.1%) and also in their first-degree relatives (23/126 [32%]). Therefore, increased efforts aimed at the early detection and dietary treatment of CD, among antibody-positive MS patients, are advisable. PMID:21385364

  12. Preparing and Analyzing Iced Airfoils

    NASA Technical Reports Server (NTRS)

    Vickerman, Mary B.; Baez, Marivell; Braun, Donald C.; Cotton, Barbara J.; Choo, Yung K.; Coroneos, Rula M.; Pennline, James A.; Hackenberg, Anthony W.; Schilling, Herbert W.; Slater, John W.; Burke, Kevin M.; Nolan, Gerald J.; Brown, Dennis

    2004-01-01

    SmaggIce version 1.2 is a computer program for preparing and analyzing iced airfoils. It includes interactive tools for (1) measuring ice-shape characteristics, (2) controlled smoothing of ice shapes, (3) curve discretization, (4) generation of artificial ice shapes, and (5) detection and correction of input errors. Measurements of ice shapes are essential for establishing relationships between characteristics of ice and effects of ice on airfoil performance. The shape-smoothing tool helps prepare ice shapes for use with already available grid-generation and computational-fluid-dynamics software for studying the aerodynamic effects of smoothed ice on airfoils. The artificial ice-shape generation tool supports parametric studies since ice-shape parameters can easily be controlled with the artificial ice. In such studies, artificial shapes generated by this program can supplement simulated ice obtained from icing research tunnels and real ice obtained from flight test under icing weather condition. SmaggIce also automatically detects geometry errors such as tangles or duplicate points in the boundary which may be introduced by digitization and provides tools to correct these. By use of interactive tools included in SmaggIce version 1.2, one can easily characterize ice shapes and prepare iced airfoils for grid generation and flow simulations.

  13. Thomson parabola ion energy analyzer

    SciTech Connect

    Cobble, James A; Flippo, Kirk A; Letzring, Samuel A; Lopez, Frank E; Offermann, Dustin T; Oertel, John A; Mastrosimone, Dino

    2010-01-01

    A new, versatile Thomson parabola ion energy (TPIE) analyzer has been designed and constructed for use at the OMEGA-EP facility. Multi-MeV ions from EP targets are transmitted through a W pinhole into a (5- or 8-kG) magnetic field and subsequently through a parallel electric field of up to 30 kV/cm. The ion drift region may have a user-selected length of 10, 50, or 80 cm. With the highest fields, 500-Me V C{sup 6+} and C{sup 5+} may be resolved. TPIE is TIM-mounted at OMEGA-EP and is qualified in all existing TIMs. The instrument runs on pressure-interlocked 15-VDC power available in EP TIM carts. It may be inserted to within several inches of the target to attain sufficient flux for a measurement. For additional flux control, the user may select a square-aperture W pinhole of 0.004-inch or 0.010-inch. The detector consists of CR-39 backed by an image plate. The fully relativistic design code and design features are discussed. Ion spectral results from first use at OMEGA-EP are expected.

  14. Analyzing and modeling heterogeneous behavior

    NASA Astrophysics Data System (ADS)

    Lin, Zhiting; Wu, Xiaoqing; He, Dongyue; Zhu, Qiang; Ni, Jixiang

    2016-05-01

    Recently, it was pointed out that the non-Poisson statistics with heavy tail existed in many scenarios of human behaviors. But most of these studies claimed that power-law characterized diverse aspects of human mobility patterns. In this paper, we suggest that human behavior may not be driven by identical mechanisms and can be modeled as a Semi-Markov Modulated Process. To verify our suggestion and model, we analyzed a total of 1,619,934 records of library visitations (including undergraduate and graduate students). It is found that the distribution of visitation intervals is well fitted with three sections of lines instead of the traditional power law distribution in log-log scale. The results confirm that some human behaviors cannot be simply expressed as power law or any other simple functions. At the same time, we divided the data into groups and extracted period bursty events. Through careful analysis in different groups, we drew a conclusion that aggregate behavior might be composed of heterogeneous behaviors, and even the behaviors of the same type tended to be different in different period. The aggregate behavior is supposed to be formed by "heterogeneous groups". We performed a series of experiments. Simulation results showed that we just needed to set up two states Semi-Markov Modulated Process to construct proper representation of heterogeneous behavior.

  15. Myeloma (multiple)

    PubMed Central

    2006-01-01

    Introduction Multiple myeloma is the most common primary cancer of the bones in adults, representing about 1% of all cancers diagnosed in the US in 2004, and 14% of all haematological malignancies. In the UK, multiple myeloma accounts for 1% of all new cases of cancer diagnosed each year. Methods and outcomes We conducted a systematic review and aimed to answer the following clinical questions: What are the effects of treatment in people with asymptomatic early stage multiple myeloma (stage I)? What are the effects of first-line treatments in people with advanced stage multiple myeloma (stages II and III)? What are the effect of salvage treatments, or supportive therapy, in people with advanced stage multiple myeloma (stages II and III)? We searched: Medline, Embase, The Cochrane Library and other important databases up to November 2004 (Clinical Evidence reviews are updated periodically, please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). Results We found 71 systematic reviews, RCTs, or observational studies that met our inclusion criteria. Conclusions In this systematic review we present information relating to the effectiveness and safety of the following interventions: allogenic transplant (non-myeloablative), autologous stem cell transplant (early or late transplantation, double or single, purging of), bisphosphonates, bone marrow stem cells, bortezomib, chemotherapy (combination, conventional dose, intermediate dose plus stem cell rescue, high-dose plus stem cell rescue), combination chemotherapy plus corticosteroids, deferred treatment (in stage I disease), early chemotherapy plus corticosteroids (in stage I disease), epoetin alpha, first-line treatments, infection prophylaxis, interferon, maintenance therapy (in advanced multiple myeloma), melphalan (normal dose

  16. A biological marker model for predicting disease transitions.

    PubMed

    Klein, J P; Klotz, J H; Grever, M R

    1984-12-01

    For patients with chronic myelogenous leukemia (CML), the effect of elevated blood levels of adenosine deaminase (ADA) is studied as a marker for transitions from stable disease to blast crisis and then to death. Data in the form of snapshots over time, with day, state of disease, and ADA level, are analyzed for 55 patients. A simple three-state Markov model with one-way transition probabilities dependent on ADA is used to determine if the marker has a significant effect on the prediction of changes from stable disease to blast crisis. PMID:6598390

  17. Association mapping in multiple segregating populations of sugar beet (Beta vulgaris L.).

    PubMed

    Stich, Benjamin; Melchinger, Albrecht E; Heckenberger, Martin; Möhring, Jens; Schechert, Axel; Piepho, Hans-Peter

    2008-11-01

    Association mapping in multiple segregating populations (AMMSP) combines high power to detect QTL in genome-wide approaches of linkage mapping with high mapping resolution of association mapping. The main objectives of this study were to (1) examine the applicability of AMMSP in a plant breeding context based on segregating populations of various size of sugar beet (Beta vulgaris L.), (2) compare different biometric approaches for AMMSP, and (3) detect markers with significant main effect across locations for nine traits in sugar beet. We used 768 F(n) (n = 2, 3, 4) sugar beet genotypes which were randomly derived from 19 crosses among diploid elite sugar beet clones. For all nine traits, the genotypic and genotype x location interaction variances were highly significant (P < 0.01). Using a one-step AMMSP approach, the total number of significant (P < 0.05) marker-phenotype associations was 44. The identification of genome regions associated with the traits under consideration indicated that not only segregating populations derived from crosses of parental genotypes in a systematic manner could be used for AMMSP but also populations routinely derived in plant breeding programs from multiple, related crosses. Furthermore, our results suggest that data sets, whose size does not permit analysis by the one-step AMMSP approach, might be analyzed using the two-step approach based on adjusted entry means for each location without losing too much power for detection of marker-phenotype associations.

  18. Bitter taste markers explain variability in vegetable sweetness, bitterness, and intake.

    PubMed

    Dinehart, M E; Hayes, J E; Bartoshuk, L M; Lanier, S L; Duffy, V B

    2006-02-28

    Intake of vegetables falls short of recommendations to lower risk of chronic diseases. Most research addresses bitterness as a sensory deterrent to consuming vegetables. We examined bitter and sweet sensations from vegetables as mediators of vegetable preference and intake as well as how these tastes vary with markers of genetic variation in taste (3.2 mM 6-n-propylthiouracil bitterness) and taste pathology (1.0 mM quinine bitterness, chorda tympani nerve relative to whole mouth). Seventy-one females and 39 males (18-60 years) reported prototypical tastes from and preference for Brussels sprouts, kale and asparagus as well as servings of vegetables consumed, excluding salad and potatoes. Intensity and hedonic ratings were made with the general Labeled Magnitude Scale. Data were analyzed with multiple linear regression and structural equation modeling. Vegetable sweetness and bitterness were independent predictors of more or less preference for sampled vegetables and vegetable intake, respectively. Those who taste PROP as most bitter also tasted the vegetables as most bitter and least sweet. The spatial pattern of quinine bitterness, suggestive of insult to chorda tympani taste fibers, was associated with less bitterness and sweetness from vegetables. Via structural equation modeling, PROP best explained variability in vegetable preference and intake via vegetable bitterness whereas the quinine marker explained variability in vegetable preference and intake via vegetable bitterness and sweetness. In summary, bitterness and sweetness of sampled vegetables varied by taste genetic and taste function markers, which explained differences in preference for vegetables tasted in the laboratory as well as overall vegetable intake outside the laboratory.

  19. [CA 125--a tumor marker?].

    PubMed

    Pabst, T; Ludwig, C

    1995-06-17

    Tumor markers are useful tools in monitoring malignancies postoperatively or under hormone-/chemotherapy. In contrast, they usually lack diagnostic relevance and uncritical use may result in confusing situations. We describe three cases of diagnostic determinations of the tumor marker CA 125 resulting in subsequent partially invasive procedures. Based on these three cases, serum CA 125 levels were examined in 49 patients with abdominal diseases. We found CA 125 to be less a tumor product than an unspecific expression of stimulated mesothelial cells of the peritoneum. CA 125 was a marker for ascites (16 of 16 patients) and an indicator of infra-diaphragmatic involvement in non-Hodgkin's lymphoma (11 of 12 patients). Furthermore, 5 of 6 patients with inflammatory abdominal diseases showed elevated CA 125 levels, as did 13 of 15 patients with solid abdominal tumors of different histology (all non-ovarian cancer, no ascites). In conclusion, CA 125 remains a good marker for follow-up of ovarian cancer, but should not be used for diagnosis of abdominal processes.

  20. Validation of a combined autosomal/Y-chromosomal STR approach for analyzing typical biological stains in sexual-assault cases.

    PubMed

    Purps, Josephine; Geppert, Maria; Nagy, Marion; Roewer, Lutz

    2015-11-01

    DNA testing is an established part of the investigation and prosecution of sexual assault. The primary purpose of DNA evidence is to identify a suspect and/or to demonstrate sexual contact. However, due to highly uneven proportions of female and male DNA in typical stains, routine autosomal analysis often fails to detect the DNA of the assailant. To evaluate the forensic efficiency of the combined application of autosomal and Y-chromosomal short tandem repeat (STR) markers, we present a large retrospective casework study of probative evidence collected in sexual-assault cases. We investigated up to 39 STR markers by testing combinations of the 16-locus NGMSElect kit with both the 23-locus PowerPlex Y23 and the 17-locus Yfiler kit. Using this dual approach we analyzed DNA extracts from 2077 biological stains collected in 287 cases over 30 months. To assess the outcome of the combined approach in comparison to stand-alone autosomal analysis we evaluated informative DNA profiles. Our investigation revealed that Y-STR analysis added up to 21% additional, highly informative (complete, single-source) profiles to the set of reportable autosomal STR profiles for typical stains collected in sexual-assault cases. Detection of multiple male contributors was approximately three times more likely with Y-chromosomal profiling than with autosomal STR profiling. In summary, 1/10 cases would have remained inconclusive (and could have been dismissed) if Y-STR analysis had been omitted from DNA profiling in sexual-assault cases.

  1. Motion capture for human motion measuring by using single camera with triangle markers

    NASA Astrophysics Data System (ADS)

    Takahashi, Hidenori; Tanaka, Takayuki; Kaneko, Shun'ichi

    2005-12-01

    This study aims to realize a motion capture for measuring 3D human motions by using single camera. Although motion capture by using multiple cameras is widely used in sports field, medical field, engineering field and so on, optical motion capture method with one camera is not established. In this paper, the authors achieved a 3D motion capture by using one camera, named as Mono-MoCap (MMC), on the basis of two calibration methods and triangle markers which each length of side is given. The camera calibration methods made 3D coordinates transformation parameter and a lens distortion parameter with Modified DLT method. The triangle markers enabled to calculate a coordinate value of a depth direction on a camera coordinate. Experiments of 3D position measurement by using the MMC on a measurement space of cubic 2 m on each side show an average error of measurement of a center of gravity of a triangle marker was less than 2 mm. As compared with conventional motion capture method by using multiple cameras, the MMC has enough accuracy for 3D measurement. Also, by putting a triangle marker on each human joint, the MMC was able to capture a walking motion, a standing-up motion and a bending and stretching motion. In addition, a method using a triangle marker together with conventional spherical markers was proposed. Finally, a method to estimate a position of a marker by measuring the velocity of the marker was proposed in order to improve the accuracy of MMC.

  2. Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality.

    PubMed

    Li, Li; Tacke, Eckhard; Hofferbert, Hans-Reinhardt; Lübeck, Jens; Strahwald, Josef; Draffehn, Astrid M; Walkemeier, Birgit; Gebhardt, Christiane

    2013-04-01

    Tuber yield, starch content, starch yield and chip color are complex traits that are important for industrial uses and food processing of potato. Chip color depends on the quantity of reducing sugars glucose and fructose in the tubers, which are generated by starch degradation. Reducing sugars accumulate when tubers are stored at low temperatures. Early and efficient selection of cultivars with superior yield, starch yield and chip color is hampered by the fact that reliable phenotypic selection requires multiple year and location trials. Application of DNA-based markers early in the breeding cycle, which are diagnostic for superior alleles of genes that control natural variation of tuber quality, will reduce the number of clones to be evaluated in field trials. Association mapping using genes functional in carbohydrate metabolism as markers has discovered alleles of invertases and starch phosphorylases that are associated with tuber quality traits. Here, we report on new DNA variants at loci encoding ADP-glucose pyrophosphorylase and the invertase Pain-1, which are associated with positive or negative effect with chip color, tuber starch content and starch yield. Marker-assisted selection (MAS) and marker validation were performed in tetraploid breeding populations, using various combinations of 11 allele-specific markers associated with tuber quality traits. To facilitate MAS, user-friendly PCR assays were developed for specific candidate gene alleles. In a multi-parental population of advanced breeding clones, genotypes were selected for having different combinations of five positive and the corresponding negative marker alleles. Genotypes combining five positive marker alleles performed on average better than genotypes with four negative alleles and one positive allele. When tested individually, seven of eight markers showed an effect on at least one quality trait. The direction of effect was as expected. Combinations of two to three marker alleles were

  3. Uniparental genetic markers in South Amerindians

    PubMed Central

    Bisso-Machado, Rafael; Bortolini, Maria Cátira; Salzano, Francisco Mauro

    2012-01-01

    A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data. PMID:22888284

  4. Uniparental genetic markers in South Amerindians.

    PubMed

    Bisso-Machado, Rafael; Bortolini, Maria Cátira; Salzano, Francisco Mauro

    2012-04-01

    A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data. PMID:22888284

  5. Circulating Adipokines and Inflammatory Markers and Postmenopausal Breast Cancer Risk

    PubMed Central

    Wang, Tao; Cushman, Mary; Xue, Xiaonan; Wassertheil-Smoller, Sylvia; Strickler, Howard D.; Rohan, Thomas E.; Manson, JoAnn E.; McTiernan, Anne; Kaplan, Robert C.; Scherer, Philipp E.; Chlebowski, Rowan T.; Snetselaar, Linda; Wang, Dan; Ho, Gloria Y. F.

    2015-01-01

    Background: Adipokines and inflammation may provide a mechanistic link between obesity and postmenopausal breast cancer, yet epidemiologic data on their associations with breast cancer risk are limited. Methods: In a case-cohort analysis nested within the Women’s Health Initiative Observational Study, a prospective cohort of postmenopausal women, baseline plasma samples from 875 incident breast cancer case patients and 839 subcohort participants were tested for levels of seven adipokines, namely leptin, adiponectin, resistin, interleukin-6, tumor necrosis factor-α, hepatocyte growth factor, and plasminogen activator inhibitor-1, and for C-reactive protein (CRP), an inflammatory marker. Data were analyzed by multivariable Cox modeling that included established breast cancer risk factors and previously measured estradiol and insulin levels. All statistical tests were two-sided. Results: The association between plasma CRP levels and breast cancer risk was dependent on hormone therapy (HT) use at baseline (P interaction = .003). In a model that controlled for multiple breast cancer risk factors including body mass index (BMI), estradiol, and insulin, CRP level was positively associated with breast cancer risk among HT nonusers (hazard ratio for high vs low CRP levels = 1.67, 95% confidence interval = 1.04 to 2.68, P trend = .029). None of the other adipokines were statistically significantly associated with breast cancer risk. Following inclusion of CRP, insulin, and estradiol in a multivariable model, the association of BMI with breast cancer was attenuated by 115%. Conclusion: These data indicate that CRP is a risk factor for postmenopausal breast cancer among HT nonusers. Inflammatory mediators, together with insulin and estrogen, may play a role in the obesity–breast cancer relation. PMID:26185195

  6. Molecular markers in oral lichen planus: A systematic review

    PubMed Central

    Sagari, Shitalkumar; Sanadhya, Sudhanshu; Doddamani, Mallikarjun; Rajput, Rajan

    2016-01-01

    Oral lichen planus (OLP) is a chronic inflammatory mucosal disease that is usually detected in 0.5–2.2% of the human population. Among these, only 0.5–2.9% of the lesions progress to carcinoma. However, there are no prognostic markers available presently to recognize the increased risk in malignant transformation of the lesions. Selected markers for cell proliferation, adhesion, apoptosis and lymphocytic infiltration were analyzed by immunohistochemistry in addition to static cytometry for DNA content. The concept linking OLP and oral squamous cell carcinoma states that chronic inflammation results in crucial DNA damage, which further progresses to development of carcinoma. Even though in the past decade, enormous information has been accumulated on malignant potential of OLP, its transformation still remains unclear. Hence, the purpose of this article was to review cellular and molecular markers to understand the pathogenesis of OLP and its progression toward malignancy. PMID:27194873

  7. Plant tissue culture and molecular markers.

    PubMed

    Tamayo-Ordoñez, María; Huijara-Vasconselos, Javier; Quiroz-Moreno, Adriana; Ortíz-García, Matilde; Sánchez-Teyer, Lorenzo Felipe

    2012-01-01

    Tissue culture can be used to propagate elite material or to generate new variability by employing somaclonal variation. Genetic stability of the process must be evaluated analyzing DNA profiles by the use of molecular markers. Several techniques have been reported for the screening of genetic variation on tissue culture derived material; however, a highly informative and good relation among the time-cost-information is obtained using Amplified Fragment Length Polymorphism (AFLP) in automatic sequencer. This technique involves a double-digestion of DNA with restriction enzymes, ligation of adapters at both extremities of the restriction fragments, and finally, selective polymerase chain reaction (PCR) amplification of the fragments. A semiautomatic process for the analysis could be used, but several considerations must be taken into account before such a use. PMID:22610640

  8. Multiple Sclerosis

    PubMed Central

    2013-01-01

    Multiple sclerosis (MS) is a chronic progressive demyelinating disease of the central nervous system. Common manifestations include paresthesias, diplopia, loss of vision, numbness or weakness of the limbs, bowel or bladder dysfunction, spasticity, ataxia, fatigue, and mental changes. Four main patterns of MS are recognized: relapsing remitting, primary progressive, secondary progressive, and progressive relapsing. The cause of MS is unknown, although it appears to be an autoimmune disease. Much of what is known about MS has been learned from an animal model of the disease, experimental allergic encephalomyelitis. PMID:24381825

  9. Multiple Sclerosis.

    PubMed

    Schiess, Nicoline; Calabresi, Peter A

    2016-08-01

    It is estimated that there are 300,000 people with multiple sclerosis (MS) in the United States and 2.3 million worldwide. Each MS attack can affect function in cognitive, emotional, motoric, sensory, or visual domains. Patients are often struck in the prime of their lives as they attempt to move forward with career, and family. Since the previous 2010 Seminars in Neurology Pearls and Pitfalls issue, the world of MS has drastically changed and advanced. Here the authors address the ever-changing MS world in both treatment options and diagnostics, covering easily missed differential diagnoses, newly available immunomodulatory therapy, and the challenges of safely treating patients. PMID:27643903

  10. Multiple myeloma

    PubMed Central

    Rajkumar, S. Vincent

    2008-01-01

    Multiple myeloma is a clonal plasma cell malignancy that accounts for slightly more than 10% of all hematologic cancers. In this paper, we present a historically focused review of the disease, from the description of the first case in 1844 to the present. The evolution of drug therapy and stem-cell transplantation for the treatment of myeloma, as well as the development of new agents, is discussed. We also provide an update on current concepts of diagnosis and therapy, with an emphasis on how treatments have emerged from a historical perspective after certain important discoveries and the results of experimental studies. PMID:18332230

  11. The correlation between internal and external markers for abdominal tumors: Implications for respiratory gating

    SciTech Connect

    Gierga, David P. . E-mail: dgierga@partners.org; Brewer, Johanna; Sharp, Gregory C.; Betke, Margrit; Willett, Christopher G.; Chen, George T.Y.

    2005-04-01

    Purpose: The correlation of the respiratory motion of external patient markers and abdominal tumors was examined. Data of this type are important for image-guided therapy techniques, such as respiratory gating, that monitor the movement of external fiducials. Methods and Materials: Fluoroscopy sessions for 4 patients with internal, radiopaque tumor fiducial clips were analyzed by computer vision techniques. The motion of the internal clips and the external markers placed on the patient's abdominal skin surface were quantified and correlated. Results: In general, the motion of the tumor and external markers were well correlated. The maximum amount of peak-to-peak craniocaudal tumor motion was 2.5 cm. The ratio of tumor motion to external-marker motion ranged from 0.85 to 7.1. The variation in tumor position for a given external-marker position ranged from 2 to 9 mm. The period of the breathing cycle ranged from 2.7 to 4.5 seconds, and the frequency patterns for both the tumor and the external markers were similar. Conclusions: Although tumor motion generally correlated well with external fiducial marker motion, relatively large underlying tumor motion can occur compared with external-marker motion and variations in the tumor position for a given marker position. Treatment margins should be determined on the basis of a detailed understanding of tumor motion, as opposed to relying only on external-marker information.

  12. 40 CFR 1065.309 - Continuous gas analyzer system-response and updating-recording verification-for gas analyzers...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calibrations and Verifications § 1065.309 Continuous... ambient air drawn into the probe. Select span gases for the species being continuously combined, other... air. You may use a multi-gas span gas, such as NO-CO-CO2-C3H8-CH4, to verify multiple analyzers at...

  13. 40 CFR 1065.309 - Continuous gas analyzer system-response and updating-recording verification-for gas analyzers...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calibrations and Verifications § 1065.309 Continuous... ambient air drawn into the probe. Select span gases for the species being continuously combined, other... air. You may use a multi-gas span gas, such as NO-CO-CO2-C3H8-CH4, to verify multiple analyzers at...

  14. 40 CFR 1065.309 - Continuous gas analyzer system-response and updating-recording verification-for gas analyzers...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calibrations and Verifications § 1065.309 Continuous... ambient air drawn into the probe. Select span gases for the species being continuously combined, other... air. You may use a multi-gas span gas, such as NO-CO-CO2-C3H8-CH4, to verify multiple analyzers at...

  15. 40 CFR 1065.309 - Continuous gas analyzer system-response and updating-recording verification-for gas analyzers...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calibrations and Verifications § 1065.309 Continuous... ambient air drawn into the probe. Select span gases for the species being continuously combined, other... air. You may use a multi-gas span gas, such as NO-CO-CO2-C3H8-CH4, to verify multiple analyzers at...

  16. [Multiple myeloma].

    PubMed

    Abe, Masahiro; Miki, Hirokazu; Nakamura, Shingen

    2016-03-01

    Owing to the positive clinical benefits obtained with new agents, complete remission (CR) can be used as a surrogate for overall survival, and should be achieved. Although multiple myeloma is a heterogeneous disease in terms of myeloma cell- and patient-related risk factors, patients should receive the most effective combination therapy based on proteasome inhibitors and/or immunomodulatory drugs (IMiDs) as backbone medication irrespective of the risks encountered in the setting of induction therapy ("one-size-fits-all" therapy), followed by consolidation/maintenance therapy to achieve CR with the ultimate goal of extended survival. Myeloma-defining biomarkers have been established to identify high-risk smoldering myeloma requiring treatment. The development of salvage treatments yielding better outcomes for relapsed/refractory myeloma is urgently needed. Upcoming novel molecular targeting agents with different modes of action and immunotherapeutic agents will be integrated into myeloma treatment regimens with a great therapeutic impact, and further evolution of the treatment paradigm for multiple myeloma is eagerly anticipated. PMID:27076236

  17. Analyzing Receptor Assemblies in the Cell Membrane Using Fluorescence Anisotropy Imaging with TIRF Microscopy

    PubMed Central

    Erdelyi, Miklos; Simon, Joseph; Barnard, Eric A.; Kaminski, Clemens F.

    2014-01-01

    Signaling within and between animal cells is controlled by the many receptor proteins in their membrane. They variously operate as trans-membrane monomers and homo- or hetero-dimers, and may assemble with ion-channels: analyses thereof are needed in studies of receptor actions in tissue physiology and pathology. Interactions between membrane proteins are detectable when pre-labeled with fluorophores, but a much fuller analysis is achievable via advanced optical techniques on living cells. In this context, the measurement of polarization anisotropy in the emitted fluorescence has been the least exploited. Here we demonstrate its methodology and particular advantages in the study of receptor protein assembly. Through excitation in both TIRF and EPI fluorescence illumination modes we are able to quantify and suppress contributions to the signal from extraneous intra-cellular fluorescence, and we show that the loss of fluorescence-polarization measured in membrane proteins reports on receptor protein assembly in real time. Receptor monomers and homo-dimers in the cell membrane can be analyzed quantitatively and for homo-dimers only a single fluorescent marker is needed, thus suppressing ambiguities that arise in alternative assays, which require multiple label moieties and which are thus subject to stoichiometric uncertainty. PMID:24945870

  18. Biochemical markers of acute pancreatitis.

    PubMed

    Matull, W R; Pereira, S P; O'Donohue, J W

    2006-04-01

    Serum amylase remains the most commonly used biochemical marker for the diagnosis of acute pancreatitis, but its sensitivity can be reduced by late presentation, hypertriglyceridaemia, and chronic alcoholism. Urinary trypsinogen-2 is convenient, of comparable diagnostic accuracy, and provides greater (99%) negative predictive value. Early prediction of the severity of acute pancreatitis can be made by well validated scoring systems at 48 hours, but the novel serum markers procalcitonin and interleukin 6 allow earlier prediction (12 to 24 hours after admission). Serum alanine transaminase >150 IU/l and jaundice suggest a gallstone aetiology, requiring endoscopic retrograde cholangiopancreatography. For obscure aetiologies, serum calcium and triglycerides should be measured. Genetic polymorphisms may play an important role in "idiopathic" acute recurrent pancreatitis.

  19. Allelic association between marker loci.

    PubMed

    Lonjou, C; Collins, A; Morton, N E

    1999-02-16

    Allelic association has proven useful to refine the location of major genes prior to positional cloning, but it is of uncertain value for genome scans in complex inheritance. We have extended kinship theory to give information content for linkage and allelic association. Application to pairs of closely linked markers as a surrogate for marker x oligogene pairs indicates that association is largely determined by regional founders, with little effect of subsequent demography. Sub-Saharan Africa has the least allelic association, consistent with settlement of other regions by small numbers of founders. Recent speculation about substantial advantages of isolates over large populations, of constant size over expansion, and of F1 hybrids over incrosses is not supported by theory or data. On the contrary, fewer affected cases, less opportunity for replication, and more stochastic variation tend to make isolates less informative for allelic association, as they are for linkage.

  20. Tumor markers for hepatocellular carcinoma

    PubMed Central

    ZHAO, YAN-JIE; JU, QIANG; LI, GUAN-CHENG

    2013-01-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with a high rate of morbidity and mortality. HCC affects approximately one million individuals annually worldwide, with the incidence equal to the mortality rate. In 2008, HCC was listed as the third most lethal cancer. Thus, early diagnosis is crucial for improving the survival rate for patients. α-fetoprotein (AFP) together with iconography and pathology detection are commonly used in the clinical early diagnosis of liver cancer. However, the specificity and sensitivity of AFP used in screening for liver cancer are not satisfactory. Athough the development of molecular biology has led to the identification of new tumor markers, including proteantigens, cytokines, enzymes and isoenzymes, as well as related genes that can be used in the treatment and prognosis of liver cancer, more tumor markers are required for effective early diagnosis of diseases and monitoring of the curative effect. PMID:24649215

  1. Lessons from mouse chimaera experiments with a reiterated transgene marker: revised marker criteria and a review of chimaera markers.

    PubMed

    Keighren, Margaret A; Flockhart, Jean; Hodson, Benjamin A; Shen, Guan-Yi; Birtley, James R; Notarnicola-Harwood, Antonio; West, John D

    2015-08-01

    Recent reports of a new generation of ubiquitous transgenic chimaera markers prompted us to consider the criteria used to evaluate new chimaera markers and develop more objective assessment methods. To investigate this experimentally we used several series of fetal and adult chimaeras, carrying an older, multi-copy transgenic marker. We used two additional independent markers and objective, quantitative criteria for cell selection and cell mixing to investigate quantitative and spatial aspects of developmental neutrality. We also suggest how the quantitative analysis we used could be simplified for future use with other markers. As a result, we recommend a five-step procedure for investigators to evaluate new chimaera markers based partly on criteria proposed previously but with a greater emphasis on examining the developmental neutrality of prospective new markers. These five steps comprise (1) review of published information, (2) evaluation of marker detection, (3) genetic crosses to check for effects on viability and growth, (4) comparisons of chimaeras with and without the marker and (5) analysis of chimaeras with both cell populations labelled. Finally, we review a number of different chimaera markers and evaluate them using the extended set of criteria. These comparisons indicate that, although the new generation of ubiquitous fluorescent markers are the best of those currently available and fulfil most of the criteria required of a chimaera marker, further work is required to determine whether they are developmentally neutral.

  2. Update on Integrated Optical Design Analyzer

    NASA Technical Reports Server (NTRS)

    Moore, James D., Jr.; Troy, Ed

    2003-01-01

    Updated information on the Integrated Optical Design Analyzer (IODA) computer program has become available. IODA was described in Software for Multidisciplinary Concurrent Optical Design (MFS-31452), NASA Tech Briefs, Vol. 25, No. 10 (October 2001), page 8a. To recapitulate: IODA facilitates multidisciplinary concurrent engineering of highly precise optical instruments. The architecture of IODA was developed by reviewing design processes and software in an effort to automate design procedures. IODA significantly reduces design iteration cycle time and eliminates many potential sources of error. IODA integrates the modeling efforts of a team of experts in different disciplines (e.g., optics, structural analysis, and heat transfer) working at different locations and provides seamless fusion of data among thermal, structural, and optical models used to design an instrument. IODA is compatible with data files generated by the NASTRAN structural-analysis program and the Code V (Registered Trademark) optical-analysis program, and can be used to couple analyses performed by these two programs. IODA supports multiple-load-case analysis for quickly accomplishing trade studies. IODA can also model the transient response of an instrument under the influence of dynamic loads and disturbances.

  3. Cutaneous Markers of Internal Disease

    PubMed Central

    Forsey, R. R.; Reardon, P. Michael

    1982-01-01

    Cutaneous markers of internal disease are legion. This article discusses the pigmentary disorders, acanthosis nigricans, pruritus, the xanthomas and problems of photosensitivity, outlining the appropriate procedures to establish a definite diagnosis, and in some cases the management of such patients. ImagesFig. 1Fig. 2Fig. 3Fig. 4Fig. 5Fig. 6Fig. 7Fig. 8Fig. 9Fig. 10Fig. 11 PMID:21286147

  4. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this... the following: (1) Markers must be located at each public road crossing, at each railroad...

  5. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this... the following: (1) Markers must be located at each public road crossing, at each railroad...

  6. A thiostrepton resistance gene and its mutants serve as selectable markers in Geobacillus kaustophilus HTA426.

    PubMed

    Wada, Keisuke; Kobayashi, Jyumpei; Furukawa, Megumi; Doi, Katsumi; Ohshiro, Takashi; Suzuki, Hirokazu

    2016-01-01

    Effective utilization of microbes often requires complex genetic modification using multiple antibiotic resistance markers. Because a few markers have been used in Geobacillus spp., the present study was designed to identify a new marker for these thermophiles. We explored antibiotic resistance genes functional in Geobacillus kaustophilus HTA426 and identified a thiostrepton resistance gene (tsr) effective at 50 °C. The tsr gene was further used to generate the mutant tsr(H258Y) functional at 55 °C. Higher functional temperature of the mutant was attributable to the increase in thermostability of the gene product because recombinant protein produced from tsr(H258Y) was more thermostable than that from tsr. In fact, the tsr(H258Y) gene served as a selectable marker for plasmid transformation of G. kaustophilus. This new marker could facilitate complex genetic modification of G. kaustophilus and potentially other Geobacillus spp.

  7. [Multiple apheresis].

    PubMed

    Coffe, C

    2007-05-01

    Multiple apheresis makes it possible to obtain at least two labile blood components from a single donor using a cell separator. It can be either multicomponent apheresis leading to the preparation of at least two different blood component types or red blood cell apheresis providing two identical red blood cell concentrates. These techniques available in addition to whole blood donation, are modifying collection strategies in many Etablissements Français du Sang and will contribute to improve stock logistics in the future. In areas with insufficient stock, these procedures will help achieve blood component self-sufficiency. The author first describes the principle underlying different--current or future--techniques as well as their advantages and drawbacks. He finally addresses the potential impact of these processes on the evolution of blood collection and the advantages to be gained. PMID:17521944

  8. Proteomic Investigation of Falciparum and Vivax Malaria for Identification of Surrogate Protein Markers

    PubMed Central

    Ray, Sandipan; Renu, Durairaj; Srivastava, Rajneesh; Gollapalli, Kishore; Taur, Santosh; Jhaveri, Tulip; Dhali, Snigdha; Chennareddy, Srinivasarao; Potla, Ankit; Dikshit, Jyoti Bajpai; Srikanth, Rapole; Gogtay, Nithya; Thatte, Urmila; Patankar, Swati; Srivastava, Sanjeeva

    2012-01-01

    This study was conducted to analyze alterations in the human serum proteome as a consequence of infection by malaria parasites Plasmodium falciparum and P. vivax to obtain mechanistic insights about disease pathogenesis, host immune response, and identification of potential protein markers. Serum samples from patients diagnosed with falciparum malaria (FM) (n = 20), vivax malaria (VM) (n = 17) and healthy controls (HC) (n = 20) were investigated using multiple proteomic techniques and results were validated by employing immunoassay-based approaches. Specificity of the identified malaria related serum markers was evaluated by means of analysis of leptospirosis as a febrile control (FC). Compared to HC, 30 and 31 differentially expressed and statistically significant (p<0.05) serum proteins were identified in FM and VM respectively, and almost half (46.2%) of these proteins were commonly modulated due to both of the plasmodial infections. 13 proteins were found to be differentially expressed in FM compared to VM. Functional pathway analysis involving the identified proteins revealed the modulation of different vital physiological pathways, including acute phase response signaling, chemokine and cytokine signaling, complement cascades and blood coagulation in malaria. A panel of identified proteins consists of six candidates; serum amyloid A, hemopexin, apolipoprotein E, haptoglobin, retinol-binding protein and apolipoprotein A-I was used to build statistical sample class prediction models. By employing PLS-DA and other classification methods the clinical phenotypic classes (FM, VM, FC and HC) were predicted with over 95% prediction accuracy. Individual performance of three classifier proteins; haptoglobin, apolipoprotein A-I and retinol-binding protein in diagnosis of malaria was analyzed using receiver operating characteristic (ROC) curves. The discrimination of FM, VM, FC and HC groups on the basis of differentially expressed serum proteins demonstrates

  9. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 3 2011-10-01 2011-10-01 false Line markers. 195.410 Section 195.410... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this section, each operator shall place and maintain line markers over each buried pipeline in accordance...

  10. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 3 2012-10-01 2012-10-01 false Line markers. 195.410 Section 195.410... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this section, each operator shall place and maintain line markers over each buried pipeline in accordance...

  11. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 3 2014-10-01 2014-10-01 false Line markers. 195.410 Section 195.410... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this section, each operator shall place and maintain line markers over each buried pipeline in accordance...

  12. Mixtures with relatives and linked markers.

    PubMed

    Dørum, Guro; Kling, Daniel; Tillmar, Andreas; Vigeland, Magnus Dehli; Egeland, Thore

    2016-05-01

    Mixture DNA profiles commonly appear in forensic genetics, and a large number of statistical methods and software are available for such cases. However, most of the literature concerns mixtures where the contributors are assumed unrelated and the genetic markers are unlinked. In this paper, we consider mixtures of linked markers and related contributors. If no relationships are involved, linkage can be ignored. While unlinked markers can be treated independently, linkage introduces dependencies. The use of linked markers presents statistical and computational challenges, but may also lead to a considerable increase in power since the number of markers available is much larger if we do not require the markers to be unlinked. In addition, some cases that cannot be solved with an unlimited number of unlinked autosomal markers can be solved with linked markers. We focus on two special cases of linked markers: pairs of linked autosomal markers and X-chromosomal markers. A framework is presented for calculation of likelihood ratios for mixtures with general relationships and with linkage between any number of markers. Finally, we explore the effect of linkage disequilibrium, also called allelic association, on the likelihood ratio.

  13. Selectively active markers for solving of the partial occlusion problem in matchmoving and chromakeying workflow

    NASA Astrophysics Data System (ADS)

    Mazurek, Przemysław

    2013-09-01

    Matchmoving (Match Moving) is the process used for the estimation of camera movements for further integration of acquired video image with computer graphics. The estimation of movements is possible using pattern recognition, 2D and 3D tracking algorithms. The main problem for the workflow is the partial occlusion of markers by the actor, because manual rotoscoping is necessary for fixing of the chroma-keyed footage. In the paper, the partial occlusion problem is solved using the invented, selectively active electronic markers. The sensor network with multiple infrared links detects occlusion state (no-occlusion, partial, full) and switch LED's based markers.

  14. Identification of molecular markers associated with mite resistance in coconut (Cocos nucifera L.).

    PubMed

    Shalini, K V; Manjunatha, S; Lebrun, P; Berger, A; Baudouin, L; Pirany, N; Ranganath, R M; Prasad, D Theertha

    2007-01-01

    Coconut mite (Aceria guerreronis 'Keifer') has become a major threat to Indian coconut (Coçcos nucifera L.) cultivators and the processing industry. Chemical and biological control measures have proved to be costly, ineffective, and ecologically undesirable. Planting mite-resistant coconut cultivars is the most effective method of preventing yield loss and should form a major component of any integrated pest management stratagem. Coconut genotypes, and mite-resistant and -susceptible accessions were collected from different parts of South India. Thirty-two simple sequence repeat (SSR) and 7 RAPD primers were used for molecular analyses. In single-marker analysis, 9 SSR and 4 RAPD markers associated with mite resistance were identified. In stepwise multiple regression analysis of SSRs, a combination of 6 markers showed 100% association with mite infestation. Stepwise multiple regression analysis for RAPD data revealed that a combination of 3 markers accounted for 83.86% of mite resistance in the selected materials. Combined stepwise multiple regression analysis of RAPD and SSR data showed that a combination of 5 markers explained 100% of the association with mite resistance in coconut. Markers associated with mite resistance are important in coconut breeding programs and will facilitate the selection of mite-resistant plants at an early stage as well as mother plants for breeding programs. PMID:17546069

  15. Stem cells, colorectal cancer and cancer stem cell markers correlations.

    PubMed

    Cherciu, Irina; Bărbălan, A; Pirici, D; Mărgăritescu, C; Săftoiu, A

    2014-01-01

    : The idea of stem cells as being progenitors of cancer was initially controversial, but later supported by research in the field of leukemia and solid tumors. Afterwards, it was established that genetic abnormalities can affect the stem and progenitor cells, leading to uncontrolled replication and deregulated differentiation. These alterations will cause the changeover to cancerous stem cells (CSC) having two main characteristics: tumor initiation and maintenance. This review will focus on the colorectal cancer stem cell (CR-CSCs) theory which provides a better understanding of different tumor processes: initiation, aggressive growth, recurrence, treatment resistance and metastasis. A search in PubMed/Medline was performed using the following keywords: colorectal cancer stem cells (CR-CSCs), colorectal neoplasms stem cells, colorectal cancer stem cell (CR-CSCs) markers, etc. Electronic searches were supplemented by hand searching reference lists, abstracts and proceedings from meetings. Isolation of CR-CSCs can be achieved by targeting and selecting subpopulation of tumor cells based on expression of one or multiple cell surface markers associated with cancer self-renewal, markers as: CD133, CD166, CD44, CD24, beta1 integrin-CD29, Lgr5, EpCAM (ESA), ALDH-1, Msi-1, DCAMLK1 or EphB receptors. The identification and localization of CR-CSCs through different markers will hopefully lead to a better stratification of prognosis and treatment response, as well as the development of new effective strategies for cancer management.

  16. Intermediate filament genes as differentiation markers in the leech Helobdella

    PubMed Central

    Kuo, Dian-Han

    2011-01-01

    The intermediate filament (IF) cytoskeleton is a general feature of differentiated cells. Its molecular components, IF proteins, constitute a large family including the evolutionarily conserved nuclear lamins and the more diverse collection of cytoplasmic intermediate filament (CIF) proteins. In vertebrates, genes encoding CIFs exhibit cell/tissue type-specific expression profiles and are thus useful as differentiation markers. The expression of invertebrate CIFs, however, is not well documented. Here, we report a whole-genome survey of IF genes and their developmental expression patterns in the leech Helobdella, a lophotrochozoan model for developmental biology research. We found that, as in vertebrates, each of the leech CIF genes is expressed in a specific set of cell/tissue types. This allows us to detect earliest points of differentiation for multiple cell types in leech development and to use CIFs as molecular markers for studying cell fate specification in leech embryos. In addition, to determine the feasibility of using CIFs as universal metazoan differentiation markers, we examined phylogenetic relationships of IF genes from various species. Our results suggest that CIFs, and thus their cell/tissue-specific expression patterns, have expanded several times independently during metazoan evolution. Moreover, comparing the expression patterns of CIF orthologs between two leech species suggests that rapid evolutionary changes in the cell or tissue specificity of CIFs have occurred among leeches. Hence, CIFs are not suitable for identifying cell or tissue homology except among very closely related species, but they are nevertheless useful species-specific differentiation markers. PMID:21938507

  17. Ion trap array mass analyzer: structure and performance.

    PubMed

    Li, Xiaoxu; Jiang, Gongyu; Luo, Chan; Xu, Fuxing; Wang, Yuanyuan; Ding, Li; Ding, Chuan-Fan

    2009-06-15

    An ion trap array (ITA) mass analyzer--a novel ion trap mass analyzer with multiple ion trapping and analyzing channels--was designed and constructed. Its property and performance were investigated and reported in this paper. The ITA was built with several planar electrodes including two parallel printed circuit board (PCB) plates. Each PCB plate was fabricated to several identical rectangular electric strips based on normal PCB fabrication technology and was placed symmetrically to those on the opposite plate. There is no electrode between any two adjacent strips. Every strip was supplied with an rf voltage while the polarity of the voltage applied to the adjacent two strips was opposite. So the electric potential at the central plane between two adjacent strips is zero. Multiple identical electric field regions that contain the dominant quadrupole plus some other high-order fields were produced between the two PCB plates. The multiple identical electric field regions will have the property of ion trapping, ion storage, and mass analysis functions. So an ITA could work as multiple ion trap mass analyzers. It could perform multiple sample ion storage, mass-selected ion isolation, ion ejection, and mass analysis simultaneously. The ITA was operated at both "digital ion trap mode" and "conventional rf mode" experimentally. A preliminary mass spectrum has been carried out in one of the ion trap channels, and it shows a mass resolution of over 1000. Additional functions such as mass-selected ion isolation and mass-selected ion ejection have also been tested. Furthermore, the ITA has a small size and very low cost. An ITA with four channels is less than 30 cm(3) in total volume, and it shows a great promise for the miniaturization of the whole mass spectrometer instrument and high-throughput mass analysis. PMID:19441854

  18. Role of apolipoprotein E polymorphism as a prognostic marker in traumatic brain injury and neurodegenerative disease: a critical review.

    PubMed

    Maiti, Tanmoy Kumar; Konar, Subhas; Bir, Shyamal; Kalakoti, Piyush; Bollam, Papireddy; Nanda, Anil

    2015-11-01

    OBJECT The difference in course and outcome of several neurodegenerative conditions and traumatic injuries of the nervous system points toward a possible role of genetic and environmental factors as prognostic markers. Apolipoprotein E (Apo-E), a key player in lipid metabolism, is recognized as one of the most powerful genetic risk factors for dementia and other neurodegenerative diseases. In this article, the current understanding of APOE polymorphism in various neurological disorders is discussed. METHODS The English literature was searched for various studies describing the role of APOE polymorphism as a prognostic marker in neurodegenerative diseases and traumatic brain injury. The wide ethnic distribution of APOE polymorphism was discussed, and the recent meta-analyses of role of APOE polymorphism in multiple diseases were analyzed and summarized in tabular form. RESULTS Results from the review of literature revealed that the distribution of APOE is varied in different ethnic populations. APOE polymorphism plays a significant role in pathogenesis of neurodegeneration, particularly in Alzheimer's disease. APOE ε4 is considered a marker for poor prognosis in various diseases, but APOE ε2 rather than APOE ε4 has been associated with cerebral amyloid angiopathy-related bleeding and sporadic Parkinson's disease. The role of APOE polymorphism in various neurological diseases has not been conclusively elucidated. CONCLUSIONS Apo-E is a biomarker for various neurological and systemic diseases. Therefore, while analyzing the role of APOE polymorphism in neurological diseases, the interpretation should be done after adjusting all the confounding factors. A continuous quest to look for associations with various neurological diseases and wide knowledge of available literature are required to improve the understanding of the role of APOE polymorphism in these conditions and identify potential therapeutic targets.

  19. Multiple roles for HOXA3 in regulating thymus and parathyroid differentiation and morphogenesis in mouse

    PubMed Central

    Chojnowski, Jena L.; Masuda, Kyoko; Trau, Heidi A.; Thomas, Kirk; Capecchi, Mario; Manley, Nancy R.

    2014-01-01

    Hoxa3 was the first Hox gene to be mutated by gene targeting in mice and is required for the development of multiple endoderm and neural crest cell (NCC)-derived structures in the pharyngeal region. Previous studies have shown that the Hoxa3 null mutant lacks third pharyngeal pouch derivatives, the thymus and parathyroids by E18.5, and organ-specific markers are absent or downregulated during initial organogenesis. Our current analysis of the Hoxa3 null mutant shows that organ-specific domains did undergo initial patterning, but the location and timing of key regional markers within the pouch, including Tbx1, Bmp4 and Fgf8, were altered. Expression of the parathyroid marker Gcm2 was initiated but was quickly downregulated and differentiation failed; by contrast, thymus markers were delayed but achieved normal levels, concurrent with complete loss through apoptosis. To determine the cell type-specific roles of Hoxa3 in third pharyngeal pouch development, we analyzed tissue-specific mutants using endoderm and/or NCC-specific Cre drivers. Simultaneous deletion with both drivers resulted in athymia at E18.5, similar to the null. By contrast, the individual tissue-specific Hoxa3 deletions resulted in small, ectopic thymi, although each had a unique phenotype. Hoxa3 was primarily required in NCCs for morphogenesis. In endoderm, Hoxa3 temporally regulated initiation of the thymus program and was required in a cell-autonomous manner for parathyroid differentiation. Furthermore, Hoxa3 was required for survival of third pharyngeal pouch-derived organs, but expression in either tissue was sufficient for this function. These data show that Hoxa3 has multiple complex and tissue-specific functions during patterning, differentiation and morphogenesis of the thymus and parathyroids. PMID:25249461

  20. Neutron multiplicity analysis tool

    SciTech Connect

    Stewart, Scott L

    2010-01-01

    I describe the capabilities of the EXCOM (EXcel based COincidence and Multiplicity) calculation tool which is used to analyze experimental data or simulated neutron multiplicity data. The input to the program is the count-rate data (including the multiplicity distribution) for a measurement, the isotopic composition of the sample and relevant dates. The program carries out deadtime correction and background subtraction and then performs a number of analyses. These are: passive calibration curve, known alpha and multiplicity analysis. The latter is done with both the point model and with the weighted point model. In the current application EXCOM carries out the rapid analysis of Monte Carlo calculated quantities and allows the user to determine the magnitude of sample perturbations that lead to systematic errors. Neutron multiplicity counting is an assay method used in the analysis of plutonium for safeguards applications. It is widely used in nuclear material accountancy by international (IAEA) and national inspectors. The method uses the measurement of the correlations in a pulse train to extract information on the spontaneous fission rate in the presence of neutrons from ({alpha},n) reactions and induced fission. The measurement is relatively simple to perform and gives results very quickly ({le} 1 hour). By contrast, destructive analysis techniques are extremely costly and time consuming (several days). By improving the achievable accuracy of neutron multiplicity counting, a nondestructive analysis technique, it could be possible to reduce the use of destructive analysis measurements required in safeguards applications. The accuracy of a neutron multiplicity measurement can be affected by a number of variables such as density, isotopic composition, chemical composition and moisture in the material. In order to determine the magnitude of these effects on the measured plutonium mass a calculational tool, EXCOM, has been produced using VBA within Excel. This

  1. Microsatellite marker development and Mendelian analysis in the Matschie's tree kangaroo (Dendrolagus matschiei).

    PubMed

    McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

    2010-01-01

    Matschie's tree kangaroo (Dendrolagus matschiei) is an endangered arboreal macropodid endemic to the Huon Peninsula, Papua New Guinea (PNG). We developed 5 microsatellite markers for D. matschiei, which are the first markers developed for Dendrolagus. We screened 17 additional markers that were developed for other marsupial taxa and identified 3 that were polymorphic in D. matschiei. We estimated allelic and genetic diversity with the set of 8 markers by analyzing 22 D. matschiei from Wasaunon on the Huon Peninsula, PNG. The number of alleles ranged from 2 to 9 and expected heterozygosity ranged from 0.440 to 0.794. We tested for null alleles and Mendelian inheritance by analyzing 19 pairs of D. matschiei parents and offspring from Association of Zoos and Aquariums institutions. Null alleles were not detected and Mendelian inheritance was followed for all 8 markers. We also evaluated the reliability of using the markers to amplify DNA extracted from D. matschiei fecal samples and the ability of the markers to amplify DNA samples from Goodfellow's tree kangaroo (Dendrolagus goodfellowi ssp.), Doria's tree kangaroo (Dendrolagus dorianus ssp.), and Grizzled tree kangaroo (Dendrolagus inustus ssp.). Microsatellite markers can be used to inform management decisions to conserve D. matschiei in captivity and the wild.

  2. A Rapid and Simple LC-MS Method Using Collagen Marker Peptides for Identification of the Animal Source of Leather.

    PubMed

    Kumazawa, Yuki; Taga, Yuki; Iwai, Kenji; Koyama, Yoh-Ichi

    2016-08-01

    Identification of the animal source of leather is difficult using traditional methods, including microscopic observation and PCR. In the present study, a LC-MS method was developed for detecting interspecies differences in the amino acid sequence of type I collagen, which is a major component of leather, among six animals (cattle, horse, pig, sheep, goat, and deer). After a dechroming procedure and trypsin digestion, six tryptic peptides of type I collagen were monitored by LC-MS in multiple reaction monitoring mode for the animal source identification using the patterns of the presence or absence of the marker peptides. We analyzed commercial leathers from various production areas using this method, and found some leathers in which the commercial label disagreed with the identified animal source. Our method enabled rapid and simple leather certification and could be applied to other animals whether or not their collagen sequences are available in public databases.

  3. A Rapid and Simple LC-MS Method Using Collagen Marker Peptides for Identification of the Animal Source of Leather.

    PubMed

    Kumazawa, Yuki; Taga, Yuki; Iwai, Kenji; Koyama, Yoh-Ichi

    2016-08-01

    Identification of the animal source of leather is difficult using traditional methods, including microscopic observation and PCR. In the present study, a LC-MS method was developed for detecting interspecies differences in the amino acid sequence of type I collagen, which is a major component of leather, among six animals (cattle, horse, pig, sheep, goat, and deer). After a dechroming procedure and trypsin digestion, six tryptic peptides of type I collagen were monitored by LC-MS in multiple reaction monitoring mode for the animal source identification using the patterns of the presence or absence of the marker peptides. We analyzed commercial leathers from various production areas using this method, and found some leathers in which the commercial label disagreed with the identified animal source. Our method enabled rapid and simple leather certification and could be applied to other animals whether or not their collagen sequences are available in public databases. PMID:27397145

  4. Neutral loss of isocyanic acid in peptide CID spectra: a novel diagnostic marker for mass spectrometric identification of protein citrullination.

    PubMed

    Hao, Gang; Wang, Danchen; Gu, Jane; Shen, Qiuying; Gross, Steven S; Wang, Yanming

    2009-04-01

    Protein citrullination is emerging as an important signaling mechanism that modulates a variety of biological processes. This protein modification constitutes only a 1 Da mass shift, and can be readily confused with other common protein modifications that yield an identical mass shift. In an attempt to develop a robust methodology for detection of protein citrullination sites, we analyzed synthetic citrulline-containing peptides by electrospray ionization tandem mass spectrometry. Collision-induced dissociation (CID) spectra revealed abundant neutral loss of 43 Da from citrullinated peptide precursor ions, which was reconciled by elimination of the HNCO moiety (isocyanic acid) from the citrulline ureido group. The elimination occurs readily in multiple charge states of precursor ions and also in b and y ions. HNCO loss in CID spectra provides a novel diagnostic marker for citrullination, and its utility was demonstrated by the discovery of Arg197 as the specific site of citrullination on nucleophosmin upon peptidylarginine deiminase 4 treatment. PMID:19200748

  5. Multiple sclerosis

    PubMed Central

    Boster, Aaron L.; Racke, Michael K.

    2013-01-01

    Summary Preliminary studies have suggested that a high salt diet may play a role in the development of autoimmune disease and possibly multiple sclerosis (MS). Promising clinical trial results for 2 new therapies for MS have been reported. Dimethyl fumarate, also known by its investigational name BG-12, became the third oral disease-modifying therapy for MS to be Food and Drug Administration (FDA)–approved in March 2013. Interestingly, dimethyl fumarate served as the active compound used for the treatment of psoriasis for decades. Alemtuzumab remains under investigation and is not currently FDA-approved for treatment of MS. Other drugs currently approved for alternative indications are being investigated for use in MS. Additionally, an investigation of alternative dosing strategies for glatiramer acetate suggests that patients may benefit from a higher dose formulation and less frequent medication administration. Advances in basic science research have identified another potential autoantigenic target in MS, KIR4.1, which may provide further insight into MS pathophysiology. PMID:24175156

  6. Multiple sclerosis.

    PubMed

    Filippi, Massimo; Preziosa, Paolo; Rocca, Maria A

    2016-01-01

    Due to its sensitivity to the different multiple sclerosis (MS)-related abnormalities, magnetic resonance imaging (MRI) has become an established tool to diagnose MS and to monitor its evolution. MRI has been included in the diagnostic workup of patients with clinically isolated syndromes suggestive of MS, and ad hoc criteria have been proposed and are regularly updated. In patients with definite MS, the ability of conventional MRI techniques to explain patients' clinical status and progression of disability is still suboptimal. Several advanced MRI-based technologies have been applied to estimate overall MS burden in the different phases of the disease. Their use has allowed the heterogeneity of MS pathology in focal lesions, normal-appearing white matter and gray matter to be graded in vivo. Recently, additional features of MS pathology, including macrophage infiltration and abnormal iron deposition, have become quantifiable. All of this, combined with functional imaging techniques, is improving our understanding of the mechanisms associated with MS evolution. In the near future, the use of ultrahigh-field systems is likely to provide additional insight into disease pathophysiology. However, the utility of advanced MRI techniques in clinical trial monitoring and in assessing individual patients' response to treatment still needs to be assessed. PMID:27432676

  7. The effectiveness of indigestible markers for identifying individual animal feces and their prevalence of use in North American zoos.

    PubMed

    Fuller, Grace; Margulis, Susan W; Santymire, Rachel

    2011-01-01

    Techniques for analyzing hormone metabolites in animal excreta have created many opportunities for noninvasive monitoring of health, reproduction, and welfare in zoo animals, but can be difficult to implement when individual samples are not readily identifiable in animal groups. A common approach to this problem is to feed animals an indigestible marker that subsequently appears in feces, but there has been little systematic research on the use of such "fecal markers." First, we used an online survey to assess the prevalence of fecal marker use in North American zoological institutions. Second, we conducted a series of experimental tests utilizing commonly employed fecal markers in a variety of typical zoo taxa to determine the: (1) effectiveness of several markers to accurately distinguish samples in a variety of species, (2) minimum quantity of marker needed for detection, and (3) length of time between ingestion and detection in the feces. The majority of the 45 institutions that completed the survey reported using fecal markers with their collections. The survey also revealed that the most frequently used markers are seeds/grains and food colorants, with the former generally used in Carnivora and the latter in Primates. Our experimental data confirmed the success of these taxa/marker combinations and also revealed that food colorants function as markers in a variety of avian, reptilian, and mammalian species. Our data describe successful fecal markers for a wide variety of zoo taxa and should, therefore, be useful for zoological managers and researchers needing to employ fecal markers in future investigations.

  8. [Neuropathologic markers in degenerative dementias].

    PubMed

    Hauw, J J; Seilhean, D; Colle, M A; Hogenhuys, J; Duyckaerts, C

    1998-01-01

    The number of neuropathological markers used for the diagnosis of degenerative dementias is rapidly increasing, and this is somewhat confusing: some lesions described a long time ago, such as ballooned cells, proved to be less specific than they were supposed to be; this is also the case for Lewy bodies, that have been recognised in a larger spectrum of disorders than thought a few years ago. On the contrary, for an increasing number of neuropathologists, Pick bodies are now mandatory for the diagnosis of Pick disease, and this contrasts with the prevalent opinions of the late sixties or seventies. There are a number of reasons for the changing significance of neuropathological markers. Three of them can be easily identified: 1) the burst of immunohistochemistry into neuropathology allowed an easier recognition, a better delineation and new pathophysiological approaches to old lesions, and a dramatic increase in the description of new markers, especially in glial cells; 2) in some conditions characterized by the number and distribution of some lesions rather than by their mere presence, such as aging and Alzheimer disease, a better neuroanatomical point of view permitted new insights into the concept of disease versus age-related changes; 3) more accurate clinicopathologic correlations showed clearly the need of grouping or lumping together some entities: for example, obvious relationship aroused between progressive supranuclear palsy and corticobasal degeneration; in contrast, distinguishing different disorders in the frontal lobe dementias grouped together into "Pick disease" was felt necessary. This review summarizes the main criteria for identification, and the presumed meaning of the chief markers indicating the presence of abnormally phosphorylated tau proteins, A beta peptides, and PrP proteins. Abnormally phosphorylated tau proteins can be stored in the neurons, and participate in the constitution of many lesions (neurofibrillary tangles, neuropil threads

  9. [Immunological markers of rheumatoid arthritis].

    PubMed

    Matuszewska, Agnieszka; Madej, Marta; Wiland, Piotr

    2016-03-25

    Rheumatoid arthritis (RA) is the most common connective tissue disease of autoimmune origin. The disease is characterized by chronic inflammation leading to bone erosions and organ involvement. RA is a progressive disease. It affects the quality of life, leading to disability and death mainly due to premature cardiovascular disease. Early diagnosis and appropriate treatment are essential for prognosis and quality of life improvement. In 2010 the American College of Rheumatology (ACR) and The European League Against Rheumatism (EULAR) established new RA classification criteria. Besides clinical symptoms it includes two immunologic criteria: rheumatoid factor (RF) and anti-citrullinated protein antibodies (anti-CCP antibodies). RF is the first well-known RA immunologic marker. It is observed in 80-85% of patients with RA. Elevated serum level of RF has been associated with increased disease activity, radiographic progression, and the presence of extraarticular manifestations. The sensitivity of RF is 50-90%, and specificity is 50-95%. Anti-CCP antibodies appear to be a more specific marker than RF. They are often present at the very beginning of the disease, or even years before the first symptoms. The prognostic value of anti-CCP antibodies is well established. High serum level of anti-CCP correlates with poor prognosis and early erosions of the joints. The sensitivity of anti-CCP2 is 48-80%, and specificity is 96-98%. New immunologic markers include anti-carbamylated protein antibodies (anti-CarP) and antibodies against heterogeneous nuclear ribonucleoproteins (anti-hnRNP A2/B1, RA33). Scientists aim to identify a highly sensitive and specific biomarker of the disease that not only has diagnostic and prognostic value but also may predict the response to treatment.

  10. Autonomic dysfunction in multiple sclerosis.

    PubMed

    Racosta, Juan Manuel; Kimpinski, Kurt; Morrow, Sarah Anne; Kremenchutzky, Marcelo

    2015-12-01

    Autonomic dysfunction is a prevalent and significant cause of disability among patients with multiple sclerosis. Autonomic dysfunction in multiple sclerosis is usually explained by lesions within central nervous system regions responsible for autonomic regulation, but novel evidence suggests that other factors may be involved as well. Additionally, the interactions between the autonomic nervous system and the immune system have generated increased interest about the role of autonomic dysfunction in the pathogenesis of multiple sclerosis. In this paper we analyze systematically the most relevant signs and symptoms of autonomic dysfunction in MS, considering separately their potential causes and implications.

  11. Determination of optimal placements of markers on the thigh during walking and landing

    NASA Astrophysics Data System (ADS)

    Thouzé, A.; Monnet, T.; Begon, M.; Pain, M. T. G.

    2010-06-01

    Kinematics of skin markers are affected by skin tissue artefact with respect to the bone during sports activities or locomotion. The purpose of this study is to determine the less disturbed marker’s location for walking and landing. Twenty-six markers were put on the thigh of nine male subjects. Each subject performed a static trial, a setup movement for determining a functional hip joint centre and five walking and landing trials. The marker displacements were obtained by comparing recorded marker positions and solidified marker positions based on the geometry of the static acquisition. The markers were subsequently ranked from the worst to the least deformed. The ranking of each trial for each subject was analyzed with the concordance coefficient of Kendall and descriptive statistics were used to determine the most and the least disturbed markers. The results show reproducibility between trials for each subject for the two movements. Statistical analysis shows that the most deformed markers during walking were located close to the hip and knee joints whereas the least disturbed were on the mid-thigh. The landing analysis does not permit to determine the best markers from the worst.

  12. A multi-marker assay to distinguish malignant melanomas from benign nevi

    PubMed Central

    Kashani-Sabet, Mohammed; Rangel, Javier; Torabian, Sima; Nosrati, Mehdi; Simko, Jeff; Jablons, David M.; Moore, Dan H.; Haqq, Chris; Miller, James R.; Sagebiel, Richard W.

    2009-01-01

    The histopathological diagnosis of melanoma can be challenging. No currently used molecular markers accurately distinguish between nevus and melanoma. Recent transcriptome analyses have shown the differential expression of several genes in melanoma progression. Here, we describe a multi-marker diagnostic assay using 5 markers (ARPC2, FN1, RGS1, SPP1, and WNT2) overexpressed in melanomas. Immunohistochemical marker expression was analyzed in 693 melanocytic neoplasms comprising a training set (tissue microarray of 534 melanomas and nevi), and 4 independent validation sets: tissue sections of melanoma arising in a nevus; dysplastic nevi; Spitz nevi; and misdiagnosed melanocytic neoplasms. Both intensity and pattern of expression were scored for each marker. Based on the differential expression of these 5 markers between nevi and melanomas in the training set, a diagnostic algorithm was obtained. Using this algorithm, the lesions in the validation sets were diagnosed as nevus or melanoma, and the results were compared with the known histological diagnoses. Both the intensity and pattern of expression of each marker were significantly different in melanomas compared to nevi. The diagnostic algorithm exploiting these differences achieved a specificity of 95% and a sensitivity of 91% in the training set. In the validation sets, the multi-marker assay correctly diagnosed a high percentage of melanomas arising in a nevus, Spitz nevi, dysplastic nevi, and misdiagnosed lesions. The multi-marker assay described here can aid in the diagnosis of melanoma. PMID:19332774

  13. Genetic markers as instrumental variables

    PubMed Central

    von Hinke, Stephanie; Davey Smith, George; Lawlor, Debbie A.; Propper, Carol; Windmeijer, Frank

    2016-01-01

    The use of genetic markers as instrumental variables (IV) is receiving increasing attention from economists, statisticians, epidemiologists and social scientists. Although IV is commonly used in economics, the appropriate conditions for the use of genetic variants as instruments have not been well defined. The increasing availability of biomedical data, however, makes understanding of these conditions crucial to the successful use of genotypes as instruments. We combine the econometric IV literature with that from genetic epidemiology, and discuss the biological conditions and IV assumptions within the statistical potential outcomes framework. We review this in the context of two illustrative applications. PMID:26614692

  14. Unitary personality source traits analyzed for heritability.

    PubMed

    Cattell, R B; Rao, D C; Schuerger, J M; Vaughan, D S

    1981-01-01

    1,768 12- to 18-year-old boys, in pairs from five constellations (identical and fraternal twins, brothers, unrelated boys raised together and a random general population sample) were measured by the O-A (performance) personality battery on source traits UI 16, 17 and 19. Corrections were made for ages and test validities in computing observed variances. Nine equations were set up in the multiple abstract variance (MAVA) model giving expectancies from seven unknown abstract variances (genetic, threptic, and genothreptic covariances) with respect to observed variances. Maximum likelihood analysis showed that genetic or threptic contribution alone was unable to fit the data, and the best fit was given by a parsimonious form of MAVA dropping genothreptic correlations. Population heritabilities calculated on this basis were 0.46 for UI 16 (ego assertion), 0.21 for UI 17 (control, upbringing), and 0.50 for UI 19 (independence). When compared with an earlier study by the O-A, but by a different analysis, and with the same data analyzed by tho other methods, a reasonably consistent conclusion emerges that UI 17 is little inherited, while UI 16 and UI 19 are rather strongly inherited. The contribution of the behavior-genetic evidence to the theories about these source traits is discussed. It is concluded that UI 16 is initially in development a temperament factor, probably with physiological associations in metabolic rate, etc.; that UI 19 is a strong and sex-related temperament factor, and that UI 17 is a sentiment pattern of cultured inhibition almost wholly dependent on family and social upbringing.

  15. Identification and validation of functional markers in a global rice collection by association mapping.

    PubMed

    Jahani, Mojtaba; Nematzadeh, Ghorbanali; Dolatabadi, Behnaz; Hashemi, Sayyed Hamidreza; Mohammadi-Nejad, Ghasem

    2014-06-01

    Recent results indicate that marker-assisted selection is an effective approach to reduce the cost and to improve the efficacy and accuracy of selection in plant breeding. This study was conducted to identify and validate molecular markers linked to important breeding traits by association mapping. The association was evaluated between 81 molecular markers (STS, SSR, Indel, CAPS, and PCR-based SNP) and 15 morphological traits in a global panel of 100 rice (Oryza sativa) accessions. The population structure analysis identified three main subpopulations. Obvious kinship relationships were also detected between the rice accessions. Association analysis was performed based on the mixed linear model by considering population structure and family relatedness. In addition, the false discovery rate method was used to correct the multiple testing. A total of 47 marker-trait associations were identified, including 22 markers for 14 traits. Among all, the polymorphism at the loci DDR-GL was highly associated with grain characters (grain length, grain width, and length/width ratio). In addition, marker RM3148 was responsible for five important traits simultaneously. Results demonstrated that such informative markers can be very useful for rice breeding programs using marker-assisted selection. Moreover, the diverse populations of rice accessions are a valuable resource for association mapping of morphological traits.

  16. Cranial muscle markers: a preliminary examination of size, sex, and age effects.

    PubMed

    Weiss, Elizabeth

    2010-02-01

    Most muscle marker research consists of post-cranial analyses, but some researchers examine crania to reconstruct activities. Regardless of bones examined, anthropologists know of some of the complexities surrounding muscle marker development. Here, posterior cranial muscle markers are analyzed to determine whether they are useful in reconstructing activities by examining effects that may hinder reconstructions. Additionally, upper limb muscle markers and humeral cross-sectional robusticity variables are correlated with cranial muscle markers to determine if robust individuals are generally robust due to the synergistic effects of muscle use. Cranial muscle markers of 65 prehistoric California Amerinds are scored using a five-point observer rating scale. Body mass is calculated from femoral head size; maximum cranial length and breadth are measured with a spreading caliper; and age and sex are determined through standard procedures. Upper limb muscle markers are scored on seven sites using two dimensions within a seven-point scale. Cross-sectional properties are calculated from biplanar humeral radiographs. Aggregates are created for cranial muscle markers, upper limb muscle markers, and cross-sectional robusticity. Cranial muscle markers correlate significantly with cranial length, r=0.25 and cross-sectional robusticity of humerus, r=0.29; P's<0.05. All variables differed between sexes (Mann-Whitney=31.00-307.50, P's<0.01). Results imply that some differences in cranial muscle markers are related to size; however, individuals with well-developed cranial muscle markers have greater upper limb robusticity possibly due to activity patterns. Sex differences remained after size controls and may relate to activity differences.

  17. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    PubMed

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

  18. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    PubMed

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property. PMID:27504250

  19. Expert system for analyzing eddy current measurements

    DOEpatents

    Levy, Arthur J.; Oppenlander, Jane E.; Brudnoy, David M.; Englund, James M.; Loomis, Kent C.

    1994-01-01

    A method and apparatus (called DODGER) analyzes eddy current data for heat exchanger tubes or any other metallic object. DODGER uses an expert system to analyze eddy current data by reasoning with uncertainty and pattern recognition. The expert system permits DODGER to analyze eddy current data intelligently, and obviate operator uncertainty by analyzing the data in a uniform and consistent manner.

  20. Early B-cell Factor gene association with multiple sclerosis in the Spanish population

    PubMed Central

    Martínez, Alfonso; Mas, Ana; de las Heras, Virginia; Arroyo, Rafael; Fernández-Arquero, Miguel; de la Concha, Emilio G; Urcelay, Elena

    2005-01-01

    Background The etiology of multiple sclerosis (MS) is at present not fully elucidated, although it is considered to result from the interaction of environmental and genetic susceptibility factors. In this work we aimed at testing the Early B-cell Factor (EBF1) gene as a functional and positional candidate risk factor for this neurological disease. Axonal damage is a hallmark for multiple sclerosis clinical disability and EBF plays an evolutionarily conserved role in the expression of proteins essential for axonal pathfinding. Failure of B-cell differentiation was found in EBF-deficient mice and involvement of B-lymphocytes in MS has been suggested from their presence in cerebrospinal fluid and lesions of patients. Methods The role of the EBF1 gene in multiple sclerosis susceptibility was analyzed by performing a case-control study with 356 multiple sclerosis patients and 540 ethnically matched controls comparing the EBF1 polymorphism rs1368297 and the microsatellite D5S2038. Results Significant association of an EBF1-intronic polymorphism (rs1368297, A vs. T: p = 0.02; OR = 1.26 and AA vs. [TA+TT]: p = 0.02; OR = 1.39) was discovered. This association was even stronger after stratification for the well-established risk factor of multiple sclerosis in the Major Histocompatibility Complex, DRB1*1501 (AA vs. [TA+TT]: p = 0.005; OR = 1.78). A trend for association in the case-control study of another EBF1 marker, the allele 5 of the very informative microsatellite D5S2038, was corroborated by Transmission Disequilibrium Test of 53 trios (p = 0.03). Conclusion Our data support EBF1 gene association with MS pathogenesis in the Spanish white population. Two genetic markers within the EBF1 gene have been found associated with this neurological disease, indicative either of their causative role or that of some other polymorphism in linkage disequilibrium with them. PMID:16255771