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Sample records for quantitative temporal analysis

  1. Temporal kinetics and quantitative analysis of Cryptococcus neoformans nonlytic exocytosis.

    PubMed

    Stukes, Sabriya A; Cohen, Hillel W; Casadevall, Arturo

    2014-05-01

    Cryptococcus neoformans is a facultative intracellular pathogen and the causative agent of cryptococcosis, a disease that is often fatal to those with compromised immune systems. C. neoformans has the capacity to escape phagocytic cells through a process known as nonlytic exocytosis whereby the cryptococcal cell is released from the macrophage into the extracellular environment, leaving both the host and pathogen alive. Little is known about the mechanism behind nonlytic exocytosis, but there is evidence that both the fungal and host cells contribute to the process. In this study, we used time-lapse movies of C. neoformans-infected macrophages to delineate the kinetics and quantitative aspects of nonlytic exocytosis. We analyzed approximately 800 macrophages containing intracellular C. neoformans and identified 163 nonlytic exocytosis events that were further characterized into three subcategories: type I (complete emptying of macrophage), type II (partial emptying of macrophage), and type III (cell-to-cell transfer). The majority of type I and II events occurred after several hours of intracellular residence, whereas type III events occurred significantly (P < 0.001) earlier in the course of macrophage infection. Our results show that nonlytic exocytosis is a morphologically and temporally diverse process that occurs relatively rapidly in the course of macrophage infection. PMID:24595144

  2. Temporal Kinetics and Quantitative Analysis of Cryptococcus neoformans Nonlytic Exocytosis

    PubMed Central

    Stukes, Sabriya A.; Cohen, Hillel W.

    2014-01-01

    Cryptococcus neoformans is a facultative intracellular pathogen and the causative agent of cryptococcosis, a disease that is often fatal to those with compromised immune systems. C. neoformans has the capacity to escape phagocytic cells through a process known as nonlytic exocytosis whereby the cryptococcal cell is released from the macrophage into the extracellular environment, leaving both the host and pathogen alive. Little is known about the mechanism behind nonlytic exocytosis, but there is evidence that both the fungal and host cells contribute to the process. In this study, we used time-lapse movies of C. neoformans-infected macrophages to delineate the kinetics and quantitative aspects of nonlytic exocytosis. We analyzed approximately 800 macrophages containing intracellular C. neoformans and identified 163 nonlytic exocytosis events that were further characterized into three subcategories: type I (complete emptying of macrophage), type II (partial emptying of macrophage), and type III (cell-to-cell transfer). The majority of type I and II events occurred after several hours of intracellular residence, whereas type III events occurred significantly (P < 0.001) earlier in the course of macrophage infection. Our results show that nonlytic exocytosis is a morphologically and temporally diverse process that occurs relatively rapidly in the course of macrophage infection. PMID:24595144

  3. Microscopy environment for quantitative spatial and temporal analysis of multicellular interactions

    NASA Astrophysics Data System (ADS)

    Sudar, Damir; Parvin, Bahram; Callahan, Daniel E.; Schwarz, Richard I.; Knowles, David W.; Ortiz de Solorzano, Carlos; Barcellos-Hoff, Mary H.

    2002-05-01

    Quantitative analysis of spatial and temporal concurrent responses of multiple markers in 3-dimensional cell cultures is hampered by the routine mode of sequential image acquisition, measurement and analysis of specific targets. A system was developed for detailed analysis of multi-dimensional, time-sequence responses and in order to relate features in novel and meaningful ways that will further our understanding of basic biology. Optical sectioning of the 3-dimensional structures is achieved with structured light illumination using the Wilson grating as described by Lanni. The automated microscopy system can image multicellular structures and track dynamic events, and is equipped for simultaneous/ sequential imaging of multiple fluorescent markers. Computer-controlled perfusion of external stimuli into the culture system allows (i) real-time observations of multiple cellular responses and (ii) automatic and intelligent adjustment of experimental parameters. This creates a feedback loop in real-time that directs desired responses in a given experiment. On-line image analysis routines provide cell-by-cell measurement results through segmentation and feature extraction (i.e. intensity, localization, etc.), and quantitation of meta-features such as dynamic responses of cells or correlations between different cells. Off-line image and data analysis is used to derive models of the processes involved, which will deepen the understanding of the basic biology.

  4. Quantitative kinetic analysis of lung nodules by temporal subtraction technique in dynamic chest radiography with a flat panel detector

    NASA Astrophysics Data System (ADS)

    Tsuchiya, Yuichiro; Kodera, Yoshie; Tanaka, Rie; Sanada, Shigeru

    2007-03-01

    Early detection and treatment of lung cancer is one of the most effective means to reduce cancer mortality; chest X-ray radiography has been widely used as a screening examination or health checkup. The new examination method and the development of computer analysis system allow obtaining respiratory kinetics by the use of flat panel detector (FPD), which is the expanded method of chest X-ray radiography. Through such changes functional evaluation of respiratory kinetics in chest has become available. Its introduction into clinical practice is expected in the future. In this study, we developed the computer analysis algorithm for the purpose of detecting lung nodules and evaluating quantitative kinetics. Breathing chest radiograph obtained by modified FPD was converted into 4 static images drawing the feature, by sequential temporal subtraction processing, morphologic enhancement processing, kinetic visualization processing, and lung region detection processing, after the breath synchronization process utilizing the diaphragmatic analysis of the vector movement. The artificial neural network used to analyze the density patterns detected the true nodules by analyzing these static images, and drew their kinetic tracks. For the algorithm performance and the evaluation of clinical effectiveness with 7 normal patients and simulated nodules, both showed sufficient detecting capability and kinetic imaging function without statistically significant difference. Our technique can quantitatively evaluate the kinetic range of nodules, and is effective in detecting a nodule on a breathing chest radiograph. Moreover, the application of this technique is expected to extend computer-aided diagnosis systems and facilitate the development of an automatic planning system for radiation therapy.

  5. Quantitative Analysis of Spatial-Temporal Correlations during Germination of Spores of Bacillus Species ▿

    PubMed Central

    Zhang, Jinqiao; Garner, Will; Setlow, Peter; Yu, Ji

    2011-01-01

    Bacteria of Bacillus species sporulate upon starvation, and the resultant dormant spores germinate when the environment appears likely to allow the resumption of vegetative growth. Normally, the rates of germination of individual spores in populations are very heterogeneous, and the current work has investigated whether spore-to-spore communication enhances the synchronicity of germination. In order to do this work, time-lapse optical images of thousands of individual spores were captured during germination, and an image analysis algorithm was developed to do the following: (i) measure the positions and germination rates of many thousands of individual spores and (ii) compute pairwise correlations of their germination. This analysis showed that an individual spore's germination rate was dependent on its distance from other spores, especially at short distances. Thus, spores that were within a few micrometers exhibited an increased synchronicity in germination, suggesting that there is a mechanism for short-range communication between such spores during germination. However, two molecules known to be germinants that are released during germination, l-alanine and the 1:1 chelate of Ca2+ and dipicolinic acid, did not mediate spore-to-spore communication during germination. PMID:21622756

  6. Quantitative Proteome Analysis of Temporally Resolved Phagosomes Following Uptake Via Key Phagocytic Receptors*

    PubMed Central

    Dill, Brian D.; Gierlinski, Marek; Härtlova, Anetta; Arandilla, Alba González; Guo, Manman; Clarke, Rosemary G.; Trost, Matthias

    2015-01-01

    Macrophages operate at the forefront of innate immunity and their discrimination of foreign versus “self” particles is critical for a number of responses including efficient pathogen killing, antigen presentation, and cytokine induction. In order to efficiently destroy the particles and detect potential threats, macrophages express an array of receptors to sense and phagocytose prey particles. In this study, we accurately quantified a proteomic time-course of isolated phagosomes from murine bone marrow-derived macrophages induced by particles conjugated to seven different ligands representing pathogen-associated molecular patterns, immune opsonins or apoptotic cell markers. We identified a clear functional differentiation over the three timepoints and detected subtle differences between certain ligand-phagosomes, indicating that triggering of receptors through a single ligand type has mild, but distinct, effects on phagosome proteome and function. Moreover, our data shows that uptake of phosphatidylserine-coated beads induces an active repression of NF-κB immune responses upon Toll-like receptor (TLR)-activation by recruitment of anti-inflammatory regulators to the phagosome. This data shows for the first time a systematic time-course analysis of bone marrow-derived macrophages phagosomes and how phagosome fate is regulated by the receptors triggered for phagocytosis. PMID:25755298

  7. A semi-quantitative GeLC-MS analysis of temporal proteome expression in the emerging nosocomial pathogen Ochrobactrum anthropi

    PubMed Central

    Graham, Robert Leslie James; Sharma, Mohit K; Ternan, Nigel G; Weatherly, D Brent; Tarleton, Rick L; McMullan, Geoff

    2007-01-01

    Background The α-Proteobacteria are capable of interaction with eukaryotic cells, with some members, such as Ochrobactrum anthropi, capable of acting as human pathogens. O. anthropi has been the cause of a growing number of hospital-acquired infections; however, little is known about its growth, physiology and metabolism. We used proteomics to investigate how protein expression of this organism changes with time during growth. Results This first gel-based liquid chromatography-mass spectrometry (GeLC-MS) temporal proteomic analysis of O. anthropi led to the positive identification of 131 proteins. These were functionally classified and physiochemically characterized. Utilizing the emPAI protocol to estimate protein abundance, we assigned molar concentrations to all proteins, and thus were able to identify 19 with significant changes in their expression. Pathway reconstruction led to the identification of a variety of central metabolic pathways, including nucleotide biosynthesis, fatty acid anabolism, glycolysis, TCA cycle and amino acid metabolism. In late phase growth we identified a number of gene products under the control of the oxyR regulon, which is induced in response to oxidative stress and whose protein products have been linked with pathogen survival in response to host immunity reactions. Conclusion This study identified distinct proteomic profiles associated with specific growth points for O. anthropi, while the use of emPAI allowed semi-quantitative analyses of protein expression. It was possible to reconstruct central metabolic pathways and infer unique functional and adaptive processes associated with specific growth phases, thereby resulting in a deeper understanding of the physiology and metabolism of this emerging pathogenic bacterium. PMID:17567905

  8. Quantitative cerebral perfusion assessment using microscope-integrated analysis of intraoperative indocyanine green fluorescence angiography versus positron emission tomography in superficial temporal artery to middle cerebral artery anastomosis

    PubMed Central

    Kobayashi, Shinya; Ishikawa, Tatsuya; Tanabe, Jun; Moroi, Junta; Suzuki, Akifumi

    2014-01-01

    Background: Intraoperative qualitative indocyanine green (ICG) angiography has been used in cerebrovascular surgery. Hyperperfusion may lead to neurological complications after superficial temporal artery to middle cerebral artery (STA-MCA) anastomosis. The purpose of this study is to quantitatively evaluate intraoperative cerebral perfusion using microscope-integrated dynamic ICG fluorescence analysis, and to assess whether this value predicts hyperperfusion syndrome (HPS) after STA-MCA anastomosis. Methods: Ten patients undergoing STA-MCA anastomosis due to unilateral major cerebral artery occlusive disease were included. Ten patients with normal cerebral perfusion served as controls. The ICG transit curve from six regions of interest (ROIs) on the cortex, corresponding to ROIs on positron emission tomography (PET) study, was recorded. Maximum intensity (IMAX), cerebral blood flow index (CBFi), rise time (RT), and time to peak (TTP) were evaluated. Results: RT/TTP, but not IMAX or CBFi, could differentiate between control and study subjects. RT/TTP correlated (|r| = 0.534-0.807; P < 0.01) with mean transit time (MTT)/MTT ratio in the ipsilateral to contralateral hemisphere by PET study. Bland–Altman analysis showed a wide limit of agreement between RT and MTT and between TTP and MTT. The ratio of RT before and after bypass procedures was significantly lower in patients with postoperative HPS than in patients without postoperative HPS (0.60 ± 0.032 and 0.80 ± 0.056, respectively; P = 0.017). The ratio of TTP was also significantly lower in patients with postoperative HPS than in patients without postoperative HPS (0.64 ± 0.081 and 0.85 ± 0.095, respectively; P = 0.017). Conclusions: Time-dependent intraoperative parameters from the ICG transit curve provide quantitative information regarding cerebral circulation time with quality and utility comparable to information obtained by PET. These parameters may help predict the occurrence of postoperative HPS. PMID

  9. Effect of preservative addition on sensory and dynamic profile of Lucanian dry-sausages as assessed by quantitative descriptive analysis and temporal dominance of sensations.

    PubMed

    Braghieri, Ada; Piazzolla, Nicoletta; Galgano, Fernanda; Condelli, Nicola; De Rosa, Giuseppe; Napolitano, Fabio

    2016-12-01

    The quantitative descriptive analysis (QDA) was combined with temporal dominance of sensations (TDS) to assess the sensory properties of Lucanian dry-sausages either added with nitrate, nitrite and l-ascorbic acid (NS), or not (NNS). Both QDA and TDS differentiated the two groups of sausages. NNS products were perceived with higher intensity of hardness (P<0.05) and tended to be perceived with higher intensities of flavor (P<0.10), pepper (P<0.20), and oiliness (P<0.20), while resulting lower in chewiness (P<0.20). TDS showed that in all the sausages hardness was the first dominant attribute; then, in NNS products flavor remained dominant until the end of tasting, whereas in NS products oiliness prevailed. In conclusion, TDS showed that the perception of some textural parameters, such as oiliness, during mastication was more dominant in NS products, whereas using conventional QDA this attribute appeared higher in sausages manufactured without preservatives. Therefore, TDS provided additional information for the description and differentiation of Lucanian sausages. PMID:27486959

  10. Temporal mapping and analysis

    NASA Technical Reports Server (NTRS)

    O'Hara, Charles G. (Inventor); Shrestha, Bijay (Inventor); Vijayaraj, Veeraraghavan (Inventor); Mali, Preeti (Inventor)

    2011-01-01

    A compositing process for selecting spatial data collected over a period of time, creating temporal data cubes from the spatial data, and processing and/or analyzing the data using temporal mapping algebra functions. In some embodiments, the temporal data cube is creating a masked cube using the data cubes, and computing a composite from the masked cube by using temporal mapping algebra.

  11. Quantitative Hydrocarbon Surface Analysis

    NASA Technical Reports Server (NTRS)

    Douglas, Vonnie M.

    2000-01-01

    The elimination of ozone depleting substances, such as carbon tetrachloride, has resulted in the use of new analytical techniques for cleanliness verification and contamination sampling. The last remaining application at Rocketdyne which required a replacement technique was the quantitative analysis of hydrocarbons by infrared spectrometry. This application, which previously utilized carbon tetrachloride, was successfully modified using the SOC-400, a compact portable FTIR manufactured by Surface Optics Corporation. This instrument can quantitatively measure and identify hydrocarbons from solvent flush of hardware as well as directly analyze the surface of metallic components without the use of ozone depleting chemicals. Several sampling accessories are utilized to perform analysis for various applications.

  12. Effect of disconnecting the orbital prefrontal cortex from the nucleus accumbens core on inter-temporal choice behaviour: A quantitative analysis

    PubMed Central

    Bezzina, G.; Body, S.; Cheung, T.H.C.; Hampson, C.L.; Bradshaw, C.M.; Szabadi, E.; Anderson, I.M.; Deakin, J.F.W.

    2008-01-01

    Previous experiments showed that destruction of the orbital prefrontal cortex (OPFC) or the nucleus accumbens core (AcbC) in rats altered choice between two delayed food reinforcers. Application of a quantitative model of inter-temporal choice suggested that lesions of either structure increased the delay-dependent degradation of reinforcer value (delay discounting); destruction of the OPFC (but not the AcbC) also increased the relative value of the larger reinforcer. This experiment examined the effect of disconnecting the OPFC from the AcbC on inter-temporal choice. Rats received excitotoxin-induced contralateral lesions of the OPFC and AcbC (disconnection), severing of the anterior corpus callosum (callosotomy), a combined lesion (disconnection + callosotomy) or sham lesions. They were trained in a discrete-trials progressive delay schedule to press levers A and B for a sucrose solution. Responses on A delivered 50 μl of the solution after a delay dA; responses on B delivered 100 μl after a delay dB. dB increased across blocks of trials; dA was manipulated across phases of the experiment. Indifference delay, dB(50) (value of dB corresponding to 50% choice of B), was estimated for each rat in each phase, and linear indifference functions (dB(50)vs. dA) were derived. The disconnection + callosotomy group showed a lower intercept of the indifference function (implying a higher rate of delay discounting) than the sham-lesioned group; the disconnection group showed a similar but less robust effect, whereas the callosotomy group did not differ significantly from the sham-lesioned group. The results suggest that OPFC–AcbC connections are involved in delay discounting of food reinforcers, but provide no evidence for an involvement of OPFC–AcbC connections in regulating sensitivity to reinforcer size. PMID:18472170

  13. Quantitative environmental risk analysis

    SciTech Connect

    Klovning, J.; Nilsen, E.F.

    1995-12-31

    According to regulations relating to implementation and rise of risk analysis in the petroleum activities issued by the Norwegian Petroleum Directorate, it is mandatory for an operator on the Norwegian Continental Shelf to establish acceptance criteria for environmental risk in the activities and carry out environmental risk analysis. This paper presents a {open_quotes}new{close_quotes} method for environmental risk analysis developed by the company. The objective has been to assist the company to meet rules and regulations and to assess and describe the environmental risk in a systematic manner. In the environmental risk analysis the most sensitive biological resource in the affected area is used to assess the environmental damage. The analytical method is based on the methodology for quantitative risk analysis related to loss of life. In addition it incorporates the effect of seasonal fluctuations in the environmental risk evaluations. The paper is describing the function of the main analytical sequences exemplified through an analysis of environmental risk related to exploration drilling in an environmental sensitive area on the Norwegian Continental Shelf.

  14. A Temporal View of Soft Tissue Quantitative Ultrasound

    NASA Astrophysics Data System (ADS)

    O'Brien, William D.

    The objective of soft tissue quantitative ultrasound (QUS) is to improve diagnostic ultrasound imaging capabilities via quantitative outcomes. Over the past three or so decades, there have been an increasing number of QUS successes. A temporal view moves us back in history almost six decades when techniques and theoretical developments were in their earliest stages that impacted modern QUS successes. The earliest theoretical developments and techniques some six decades ago can be attributed to Lev Chernov, Philip Morse, Herman Feshbach, Uno Ingard, John Wild and Jack Reid. Later, Floyd Dunn developed important views as to how connective tissue affected the interaction between ultrasound and soft tissue. Then, as the theory of wave propagation in soft tissues with random inhomogeneities was extended and applied by Fred Lizzi, Jim Zagzebski and Mike Insana (and their colleagues), contemporary QUS successes started to emerge.

  15. Quantitative methods for stochastic high frequency spatio-temporal and non-linear analysis: Assessing health effects of exposure to extreme ambient temperature

    NASA Astrophysics Data System (ADS)

    Liss, Alexander

    Extreme weather events, such as heat waves and cold spells, cause substantial excess mortality and morbidity in the vulnerable elderly population, and cost billions of dollars. The accurate and reliable assessment of adverse effects of extreme weather events on human health is crucial for environmental scientists, economists, and public health officials to ensure proper protection of vulnerable populations and efficient allocation of scarce resources. However, the methodology for the analysis of large national databases is yet to be developed. The overarching objective of this dissertation is to examine the effect of extreme weather on the elderly population of the Conterminous US (ConUS) with respect to seasonality in temperature in different climatic regions by utilizing heterogeneous high frequency and spatio-temporal resolution data. To achieve these goals the author: 1) incorporated dissimilar stochastic high frequency big data streams and distinct data types into the integrated data base for use in analytical and decision support frameworks; 2) created an automated climate regionalization system based on remote sensing and machine learning to define climate regions for the Conterminous US; 3) systematically surveyed the current state of the art and identified existing gaps in the scientific knowledge; 4) assessed the dose-response relationship of exposure to temperature extremes on human health in relatively homogeneous climate regions using different statistical models, such as parametric and non-parametric, contemporaneous and asynchronous, applied to the same data; 5) assessed seasonal peak timing and synchronization delay of the exposure and the disease within the framework of contemporaneous high frequency harmonic time series analysis and modification of the effect by the regional climate; 6) modeled using hyperbolic functional form non-linear properties of the effect of exposure to extreme temperature on human health. The proposed climate

  16. A quantitative method for the evaluation of three-dimensional structure of temporal bone pneumatization.

    PubMed

    Hill, Cheryl A; Richtsmeier, Joan T

    2008-10-01

    Temporal bone pneumatization has been included in lists of characters used in phylogenetic analyses of human evolution. While studies suggest that the extent of pneumatization has decreased over the course of human evolution, little is known about the processes underlying these changes or their significance. In short, reasons for the observed reduction and the potential reorganization within pneumatized spaces are unknown. Technological limitations have limited previous analyses of pneumatization in extant and fossil species to qualitative observations of the extent of temporal bone pneumatization. In this paper, we introduce a novel application of quantitative methods developed for the study of trabecular bone to the analysis of pneumatized spaces of the temporal bone. This method utilizes high-resolution X-ray computed tomography (HRXCT) images and quantitative software to estimate three-dimensional parameters (bone volume fractions, anisotropy, and trabecular thickness) of bone structure within defined units of pneumatized spaces. We apply this approach in an analysis of temporal bones of diverse but related primate species, Gorilla gorilla, Pan troglodytes, Homo sapiens, and Papio hamadryas anubis, to illustrate the potential of these methods. In demonstrating the utility of these methods, we show that there are interspecific differences in the bone structure of pneumatized spaces, perhaps reflecting changes in the localized growth dynamics, location of muscle attachments, encephalization, or basicranial flexion. PMID:18715622

  17. Quantitative analysis of live-cell growth at the shoot apex of Arabidopsis thaliana: algorithms for feature measurement and temporal alignment.

    PubMed

    Tataw, Oben M; Reddy, G Venugopala; Keogh, Eamonn J; Roy-Chowdhury, Amit K

    2013-01-01

    Study of the molecular control of organ growth requires establishment of the causal relationship between gene expression and cell behaviors. We seek to understand this relationship at the shoot apical meristem (SAM) of model plant Arabidopsis thaliana. This requires the spatial mapping and temporal alignment of different functional domains into a single template. Live-cell imaging techniques allow us to observe real-time organ primordia growth and gene expression dynamics at cellular resolution. In this paper, we propose a framework for the measurement of growth features at the 3D reconstructed surface of organ primordia, as well as algorithms for robust time alignment of primordia. We computed areas and deformation values from reconstructed 3D surfaces of individual primordia from live-cell imaging data. Based on these growth measurements, we applied a multiple feature landscape matching (LAM-M) algorithm to ensure a reliable temporal alignment of multiple primordia. Although the original landscape matching (LAM) algorithm motivated our alignment approach, it sometimes fails to properly align growth curves in the presence of high noise/distortion. To overcome this shortcoming, we modified the cost function to consider the landscape of the corresponding growth features. We also present an alternate parameter-free growth alignment algorithm which performs as well as LAM-M for high-quality data, but is more robust to the presence of outliers or noise. Results on primordia and guppy evolutionary growth data show that the proposed alignment framework performs at least as well as the LAM algorithm in the general case, and significantly better in the case of increased noise. PMID:24384704

  18. Neurochemical phenotype of corticocortical connections in the macaque monkey: quantitative analysis of a subset of neurofilament protein-immunoreactive projection neurons in frontal, parietal, temporal, and cingulate cortices

    NASA Technical Reports Server (NTRS)

    Hof, P. R.; Nimchinsky, E. A.; Morrison, J. H.; Bloom, F. E. (Principal Investigator)

    1995-01-01

    The neurochemical characteristics of the neuronal subsets that furnish different types of corticocortical connections have been only partially determined. In recent years, several cytoskeletal proteins have emerged as reliable markers to distinguish subsets of pyramidal neurons in the cerebral cortex of primates. In particular, previous studies using an antibody to nonphosphorylated neurofilament protein (SMI-32) have revealed a consistent degree of regional and laminar specificity in the distribution of a subpopulation of pyramidal cells in the primate cerebral cortex. The density of neurofilament protein-immunoreactive neurons was shown to vary across corticocortical pathways in macaque monkeys. In the present study, we have used the antibody SMI-32 to examine further and to quantify the distribution of a subset of corticocortically projecting neurons in a series of long ipsilateral corticocortical pathways in comparison to short corticocortical, commissural, and limbic connections. The results demonstrate that the long association pathways interconnecting the frontal, parietal, and temporal neocortex have a high representation of neurofilament protein-enriched pyramidal neurons (45-90%), whereas short corticocortical, callosal, and limbic pathways are characterized by much lower numbers of such neurons (4-35%). These data suggest that different types of corticocortical connections have differential representation of highly specific neuronal subsets that share common neurochemical characteristics, thereby determining regional and laminar cortical patterns of morphological and molecular heterogeneity. These differences in neuronal neurochemical phenotype among corticocortical circuits may have considerable influence on cortical processing and may be directly related to the type of integrative function subserved by each cortical pathway. Finally, it is worth noting that neurofilament protein-immunoreactive neurons are dramatically affected in the course of

  19. Temporal Data Set Reduction Based on D-Optimality for Quantitative FLIM-FRET Imaging

    PubMed Central

    Omer, Travis; Intes, Xavier; Hahn, Juergen

    2015-01-01

    Fluorescence lifetime imaging (FLIM) when paired with Förster resonance energy transfer (FLIM-FRET) enables the monitoring of nanoscale interactions in living biological samples. FLIM-FRET model-based estimation methods allow the quantitative retrieval of parameters such as the quenched (interacting) and unquenched (non-interacting) fractional populations of the donor fluorophore and/or the distance of the interactions. The quantitative accuracy of such model-based approaches is dependent on multiple factors such as signal-to-noise ratio and number of temporal points acquired when sampling the fluorescence decays. For high-throughput or in vivo applications of FLIM-FRET, it is desirable to acquire a limited number of temporal points for fast acquisition times. Yet, it is critical to acquire temporal data sets with sufficient information content to allow for accurate FLIM-FRET parameter estimation. Herein, an optimal experimental design approach based upon sensitivity analysis is presented in order to identify the time points that provide the best quantitative estimates of the parameters for a determined number of temporal sampling points. More specifically, the D-optimality criterion is employed to identify, within a sparse temporal data set, the set of time points leading to optimal estimations of the quenched fractional population of the donor fluorophore. Overall, a reduced set of 10 time points (compared to a typical complete set of 90 time points) was identified to have minimal impact on parameter estimation accuracy (≈5%), with in silico and in vivo experiment validations. This reduction of the number of needed time points by almost an order of magnitude allows the use of FLIM-FRET for certain high-throughput applications which would be infeasible if the entire number of time sampling points were used. PMID:26658308

  20. Temporal Lobe Epilepsy: Quantitative MR Volumetry in Detection of Hippocampal Atrophy

    PubMed Central

    Farid, Nikdokht; Girard, Holly M.; Kemmotsu, Nobuko; Smith, Michael E.; Magda, Sebastian W.; Lim, Wei Y.; Lee, Roland R.

    2012-01-01

    Purpose: To determine the ability of fully automated volumetric magnetic resonance (MR) imaging to depict hippocampal atrophy (HA) and to help correctly lateralize the seizure focus in patients with temporal lobe epilepsy (TLE). Materials and Methods: This study was conducted with institutional review board approval and in compliance with HIPAA regulations. Volumetric MR imaging data were analyzed for 34 patients with TLE and 116 control subjects. Structural volumes were calculated by using U.S. Food and Drug Administration–cleared software for automated quantitative MR imaging analysis (NeuroQuant). Results of quantitative MR imaging were compared with visual detection of atrophy, and, when available, with histologic specimens. Receiver operating characteristic analyses were performed to determine the optimal sensitivity and specificity of quantitative MR imaging for detecting HA and asymmetry. A linear classifier with cross validation was used to estimate the ability of quantitative MR imaging to help lateralize the seizure focus. Results: Quantitative MR imaging–derived hippocampal asymmetries discriminated patients with TLE from control subjects with high sensitivity (86.7%–89.5%) and specificity (92.2%–94.1%). When a linear classifier was used to discriminate left versus right TLE, hippocampal asymmetry achieved 94% classification accuracy. Volumetric asymmetries of other subcortical structures did not improve classification. Compared with invasive video electroencephalographic recordings, lateralization accuracy was 88% with quantitative MR imaging and 85% with visual inspection of volumetric MR imaging studies but only 76% with visual inspection of clinical MR imaging studies. Conclusion: Quantitative MR imaging can depict the presence and laterality of HA in TLE with accuracy rates that may exceed those achieved with visual inspection of clinical MR imaging studies. Thus, quantitative MR imaging may enhance standard visual analysis, providing a

  1. 3D-catFISH: a system for automated quantitative three-dimensional compartmental analysis of temporal gene transcription activity imaged by fluorescence in situ hybridization.

    PubMed

    Chawla, Monica K; Lin, Gang; Olson, Kathy; Vazdarjanova, Almira; Burke, Sara N; McNaughton, Bruce L; Worley, Paul F; Guzowski, John F; Roysam, Badrinath; Barnes, Carol A

    2004-10-15

    Fluorescence in situ hybridization (FISH) of neural activity-regulated, immediate-early gene (IEG) expression provides a method of functional brain imaging with cellular resolution. This enables the identification, in one brain, of which specific principal neurons were active during each of two distinct behavioral epochs. The unprecedented potential of this differential method for large-scale analysis of functional neural circuits is limited, however, by the time-intensive nature of manual image analysis. A comprehensive software tool for processing three-dimensional, multi-spectral confocal image stacks is described which supports the automation of this analysis. Nuclei counterstained with conventional DNA dyes and FISH signals indicating the sub-cellular distribution of specific, IEG RNA species are imaged using different spectral channels. The DNA channel data are segmented into individual nuclei by a three-dimensional multi-step algorithm that corrects for depth-dependent attenuation, non-isotropic voxels, and imaging noise. Intra-nuclear and cytoplasmic FISH signals are associated spatially with the nuclear segmentation results to generate a detailed tabular/database and graphic representation. Here we present a comprehensive validation of data generated by the automated software against manual quantification by human experts on hippocampal and parietal cortical regions (96.5% concordance with multi-expert consensus). The high degree of reliability and accuracy suggests that the software will generalize well to multiple brain areas and eventually to large-scale brain analysis. PMID:15351517

  2. Quantitative intracerebral brain hemorrhage analysis

    NASA Astrophysics Data System (ADS)

    Loncaric, Sven; Dhawan, Atam P.; Cosic, Dubravko; Kovacevic, Domagoj; Broderick, Joseph; Brott, Thomas

    1999-05-01

    In this paper a system for 3-D quantitative analysis of human spontaneous intracerebral brain hemorrhage (ICH) is described. The purpose of the developed system is to perform quantitative 3-D measurements of the parameters of ICH region and from computed tomography (CT) images. The measured parameter in this phase of the system development is volume of the hemorrhage region. The goal of the project is to measure parameters for a large number of patients having ICH and to correlate measured parameters to patient morbidity and mortality.

  3. Software for quantitative trait analysis

    PubMed Central

    2005-01-01

    This paper provides a brief overview of software currently available for the genetic analysis of quantitative traits in humans. Programs that implement variance components, Markov Chain Monte Carlo (MCMC), Haseman-Elston (H-E) and penetrance model-based linkage analyses are discussed, as are programs for measured genotype association analyses and quantitative trait transmission disequilibrium tests. The software compared includes LINKAGE, FASTLINK, PAP, SOLAR, SEGPATH, ACT, Mx, MERLIN, GENEHUNTER, Loki, Mendel, SAGE, QTDT and FBAT. Where possible, the paper provides URLs for acquiring these programs through the internet, details of the platforms for which the software is available and the types of analyses performed. PMID:16197737

  4. Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction

    PubMed Central

    Weekes, Michael P.; Tomasec, Peter; Huttlin, Edward L.; Fielding, Ceri A.; Nusinow, David; Stanton, Richard J.; Wang, Eddie C.Y.; Aicheler, Rebecca; Murrell, Isa; Wilkinson, Gavin W.G.; Lehner, Paul J.; Gygi, Steven P.

    2014-01-01

    Summary A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model. PaperClip PMID:24906157

  5. A Novel Method of Quantitative Anterior Chamber Depth Estimation Using Temporal Perpendicular Digital Photography

    PubMed Central

    Zamir, Ehud; Kong, George Y.X.; Kowalski, Tanya; Coote, Michael; Ang, Ghee Soon

    2016-01-01

    Purpose We hypothesize that: (1) Anterior chamber depth (ACD) is correlated with the relative anteroposterior position of the pupillary image, as viewed from the temporal side. (2) Such a correlation may be used as a simple quantitative tool for estimation of ACD. Methods Two hundred sixty-six phakic eyes had lateral digital photographs taken from the temporal side, perpendicular to the visual axis, and underwent optical biometry (Nidek AL scanner). The relative anteroposterior position of the pupillary image was expressed using the ratio between: (1) lateral photographic temporal limbus to pupil distance (“E”) and (2) lateral photographic temporal limbus to cornea distance (“Z”). In the first chronological half of patients (Correlation Series), E:Z ratio (EZR) was correlated with optical biometric ACD. The correlation equation was then used to predict ACD in the second half of patients (Prediction Series) and compared to their biometric ACD for agreement analysis. Results A strong linear correlation was found between EZR and ACD, R = −0.91, R2 = 0.81. Bland-Altman analysis showed good agreement between predicted ACD using this method and the optical biometric ACD. The mean error was −0.013 mm (range −0.377 to 0.336 mm), standard deviation 0.166 mm. The 95% limits of agreement were ±0.33 mm. Conclusions Lateral digital photography and EZR calculation is a novel method to quantitatively estimate ACD, requiring minimal equipment and training. Translational Relevance EZ ratio may be employed in screening for angle closure glaucoma. It may also be helpful in outpatient medical clinic settings, where doctors need to judge the safety of topical or systemic pupil-dilating medications versus their risk of triggering acute angle closure glaucoma. Similarly, non ophthalmologists may use it to estimate the likelihood of acute angle closure glaucoma in emergency presentations. PMID:27540496

  6. Temporal Instabilities in Amblyopic Perception: A Quantitative Approach.

    PubMed

    Thiel, Aylin; Iftime, Adrian

    2016-04-01

    The purpose of this study is to quantify the temporal characteristics of spatial misperceptions in human amblyopia. Twenty-two adult participants with strabismus, strabismic, anisometropic, or mixed amblyopia were asked to describe their subjective percept of static geometrical patterns with different spatial frequencies and shapes, as seen with their non-dominant eye. We generated digital reconstructions of their perception (static images or movies) that were subsequently validated by the subjects using consecutive matching sessions. We calculated the Shannon entropy variation in time for each recorded movie, as a measure of temporal instability. Nineteen of the 22 subjects perceived temporal instabilities that can be broadly classified in two categories. We found that the average frequency of the perceived temporal instabilities is ∼1 Hz. The stimuli with higher spatial frequencies yielded more often temporally unstable perceptions with higher frequencies. We suggest that type and amount of temporal instabilities in amblyopic vision are correlated with the etiology and spatial frequency of the stimulus. PMID:26786394

  7. Image analysis and quantitative morphology.

    PubMed

    Mandarim-de-Lacerda, Carlos Alberto; Fernandes-Santos, Caroline; Aguila, Marcia Barbosa

    2010-01-01

    Quantitative studies are increasingly found in the literature, particularly in the fields of development/evolution, pathology, and neurosciences. Image digitalization converts tissue images into a numeric form by dividing them into very small regions termed picture elements or pixels. Image analysis allows automatic morphometry of digitalized images, and stereology aims to understand the structural inner three-dimensional arrangement based on the analysis of slices showing two-dimensional information. To quantify morphological structures in an unbiased and reproducible manner, appropriate isotropic and uniform random sampling of sections, and updated stereological tools are needed. Through the correct use of stereology, a quantitative study can be performed with little effort; efficiency in stereology means as little counting as possible (little work), low cost (section preparation), but still good accuracy. This short text provides a background guide for non-expert morphologists. PMID:19960334

  8. Temporal Expression-based Analysis of Metabolism

    PubMed Central

    Segrè, Daniel

    2012-01-01

    Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress in this regard has been made by integrating high-throughput gene expression data into genome-scale stoichiometric models of metabolism. Here, we extend previous approaches to perform a Temporal Expression-based Analysis of Metabolism (TEAM). We apply TEAM to understanding the complex metabolic dynamics of the respiratorily versatile bacterium Shewanella oneidensis grown under aerobic, lactate-limited conditions. TEAM predicts temporal metabolic flux distributions using time-series gene expression data. Increased predictive power is achieved by supplementing these data with a large reference compendium of gene expression, which allows us to take into account the unique character of the distribution of expression of each individual gene. We further propose a straightforward method for studying the sensitivity of TEAM to changes in its fundamental free threshold parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed. By comparing the qualitative characteristics of these zones to additional experimental data, we are able to constrain the range of θ to a small, well-defined interval. In parallel, the sensitivity analysis reveals the inherently difficult nature of dynamic metabolic flux modeling: small errors early in the simulation propagate to relatively large changes later in the simulation. We expect that handling such “history-dependent” sensitivities will be a major challenge in the future development of dynamic metabolic-modeling techniques. PMID:23209390

  9. Bioimaging for quantitative phenotype analysis.

    PubMed

    Chen, Weiyang; Xia, Xian; Huang, Yi; Chen, Xingwei; Han, Jing-Dong J

    2016-06-01

    With the development of bio-imaging techniques, an increasing number of studies apply these techniques to generate a myriad of image data. Its applications range from quantification of cellular, tissue, organismal and behavioral phenotypes of model organisms, to human facial phenotypes. The bio-imaging approaches to automatically detect, quantify, and profile phenotypic changes related to specific biological questions open new doors to studying phenotype-genotype associations and to precisely evaluating molecular changes associated with quantitative phenotypes. Here, we review major applications of bioimage-based quantitative phenotype analysis. Specifically, we describe the biological questions and experimental needs addressable by these analyses, computational techniques and tools that are available in these contexts, and the new perspectives on phenotype-genotype association uncovered by such analyses. PMID:26850283

  10. Optimization of quantitative infrared analysis

    NASA Astrophysics Data System (ADS)

    Duerst, Richard W.; Breneman, W. E.; Dittmar, Rebecca M.; Drugge, Richard E.; Gagnon, Jim E.; Pranis, Robert A.; Spicer, Colleen K.; Stebbings, William L.; Westberg, J. W.; Duerst, Marilyn D.

    1994-01-01

    A number of industrial processes, especially quality assurance procedures, accept information on relative quantities of components in mixtures, whenever absolute values for the quantitative analysis are unavailable. These relative quantities may be determined from infrared intensity ratios even though known standards are unavailable. Repeatability [vs precisionhl in quantitative analysis is a critical parameter for meaningful results. In any given analysis, multiple runs provide "answers" with a certain standard deviation. Obviously, the lower the standard deviation, the better the precision. In attempting to minimize the standard deviation and thus improve precision, we need to delineate which contributing factors we have control over (such as sample preparation techniques, data analysis methodology) and which factors we have little control over (environmental and instrument noise, for example). For a given set of conditions, the best instrumental precision achievable on an IR instrument should be determinable. Traditionally, the term "signal-to-noise" (S/N) has been used for a single spectrum, realizing that S/N improves with an increase in number of scans coadded for generation of that single spectrum. However, the S/N ratio does not directly reflect the precision achievable for an absorbing band. We prefer to use the phrase "maximum achievable instrument precision" (MAIP), which is equivalent to the minimum relative standard deviation for a given peak (either height or area) in spectra. For a specific analysis, the analyst should have in mind the desired precision. Only if the desired precision is less than the MA1P will the analysis be feasible. Once the MAIP is established, other experimental procedures may be modified to improve the analytical precision, if it is below that which is expected (the MAIP).

  11. Quantitative transverse flow measurement using OCT speckle decorrelation analysis

    PubMed Central

    Liu, Xuan; Huang, Yong; Ramella-Roman, Jessica C.; Mathews, Scott A.; Kang, Jin U.

    2014-01-01

    We propose an inter-Ascan speckle decorrelation based method that can quantitatively assess blood flow normal to the direction of the OCT imaging beam. To validate this method, we performed a systematic study using both phantom and in vivo animal models. Results show that our speckle analysis method can accurately extract transverse flow speed with high spatial and temporal resolution. PMID:23455305

  12. Upper limb automatisms differ quantitatively in temporal and frontal lobe epilepsies.

    PubMed

    Silva Cunha, João P; Rémi, Jan; Vollmar, Christian; Fernandes, José M; Gonzalez-Victores, Jose A; Noachtar, Soheyl

    2013-05-01

    We quantitatively evaluated the localizing and lateralizing characteristics of ictal upper limb automatisms (ULAs) in patients with temporal lobe epilepsy (TLE; n=38) and frontal lobe epilepsy (FLE; n=20). Movement speed, extent, length, and duration of ULAs were quantitatively analyzed with motion capturing techniques. Upper limb automatisms had a larger extent (p<0.001), covered more distance (p<0.05), and were faster (p<0.001) in FLE than in TLE. In TLE, the maximum speed of ULAs was higher ipsilaterally than contralaterally (173 vs. 84pixels/s; p=0.02), with no significant difference in FLE (511 vs. 428). The duration of ictal automatisms in relation to the total seizure duration was shorter in TLE than in FLE (median 36% vs. 63%; p<0.001), with no difference in the absolute duration (26s vs. 27s). These results demonstrate that quantitative movement analysis of ULAs differentiates FLE from TLE, which may aid in the localization of the epileptogenic zone. PMID:23545438

  13. Automated quantitative analysis for pneumoconiosis

    NASA Astrophysics Data System (ADS)

    Kondo, Hiroshi; Zhao, Bin; Mino, Masako

    1998-09-01

    Automated quantitative analysis for pneumoconiosis is presented. In this paper Japanese standard radiographs of pneumoconiosis are categorized by measuring the area density and the number density of small rounded opacities. And furthermore the classification of the size and shape of the opacities is made from the measuring of the equivalent radiuses of each opacity. The proposed method includes a bi- level unsharp masking filter with a 1D uniform impulse response in order to eliminate the undesired parts such as the images of blood vessels and ribs in the chest x-ray photo. The fuzzy contrast enhancement is also introduced in this method for easy and exact detection of small rounded opacities. Many simulation examples show that the proposed method is more reliable than the former method.

  14. A quantitative fitness analysis workflow.

    PubMed

    Banks, A P; Lawless, C; Lydall, D A

    2012-01-01

    Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel(1,2,3,4). QFA can be applied to focused observations of single cultures but is most useful for genome-wide genetic interaction or drug screens investigating up to thousands of independent cultures. The central experimental method is the inoculation of independent, dilute liquid microbial cultures onto solid agar plates which are incubated and regularly photographed. Photographs from each time-point are analyzed, producing quantitative cell density estimates, which are used to construct growth curves, allowing quantitative fitness measures to be derived. Culture fitnesses can be compared to quantify and rank genetic interaction strengths or drug sensitivities. The effect on culture fitness of any treatments added into substrate agar (e.g. small molecules, antibiotics or nutrients) or applied to plates externally (e.g. UV irradiation, temperature) can be quantified by QFA. The QFA workflow produces growth rate estimates analogous to those obtained by spectrophotometric measurement of parallel liquid cultures in 96-well or 200-well plate readers. Importantly, QFA has significantly higher throughput compared with such methods. QFA cultures grow on a solid agar surface and are therefore well aerated during growth without the need for stirring or shaking. QFA throughput is not as high as that of some Synthetic Genetic Array (SGA) screening methods(5,6). However, since QFA cultures are heavily diluted before being inoculated onto agar, QFA can capture more complete growth curves, including exponential and saturation phases(3). For example, growth curve observations allow culture doubling times to be estimated directly with high precision, as discussed previously(1). Here we present a specific QFA protocol applied to thousands of S. cerevisiae cultures which are automatically handled by robots during inoculation, incubation and

  15. A Quantitative Fitness Analysis Workflow

    PubMed Central

    Lydall, D.A.

    2012-01-01

    Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel1,2,3,4. QFA can be applied to focused observations of single cultures but is most useful for genome-wide genetic interaction or drug screens investigating up to thousands of independent cultures. The central experimental method is the inoculation of independent, dilute liquid microbial cultures onto solid agar plates which are incubated and regularly photographed. Photographs from each time-point are analyzed, producing quantitative cell density estimates, which are used to construct growth curves, allowing quantitative fitness measures to be derived. Culture fitnesses can be compared to quantify and rank genetic interaction strengths or drug sensitivities. The effect on culture fitness of any treatments added into substrate agar (e.g. small molecules, antibiotics or nutrients) or applied to plates externally (e.g. UV irradiation, temperature) can be quantified by QFA. The QFA workflow produces growth rate estimates analogous to those obtained by spectrophotometric measurement of parallel liquid cultures in 96-well or 200-well plate readers. Importantly, QFA has significantly higher throughput compared with such methods. QFA cultures grow on a solid agar surface and are therefore well aerated during growth without the need for stirring or shaking. QFA throughput is not as high as that of some Synthetic Genetic Array (SGA) screening methods5,6. However, since QFA cultures are heavily diluted before being inoculated onto agar, QFA can capture more complete growth curves, including exponential and saturation phases3. For example, growth curve observations allow culture doubling times to be estimated directly with high precision, as discussed previously1. Here we present a specific QFA protocol applied to thousands of S. cerevisiae cultures which are automatically handled by robots during inoculation, incubation and imaging

  16. Quantitative analysis of endogenous compounds.

    PubMed

    Thakare, Rhishikesh; Chhonker, Yashpal S; Gautam, Nagsen; Alamoudi, Jawaher Abdullah; Alnouti, Yazen

    2016-09-01

    Accurate quantitative analysis of endogenous analytes is essential for several clinical and non-clinical applications. LC-MS/MS is the technique of choice for quantitative analyses. Absolute quantification by LC/MS requires preparing standard curves in the same matrix as the study samples so that the matrix effect and the extraction efficiency for analytes are the same in both the standard and study samples. However, by definition, analyte-free biological matrices do not exist for endogenous compounds. To address the lack of blank matrices for the quantification of endogenous compounds by LC-MS/MS, four approaches are used including the standard addition, the background subtraction, the surrogate matrix, and the surrogate analyte methods. This review article presents an overview these approaches, cite and summarize their applications, and compare their advantages and disadvantages. In addition, we discuss in details, validation requirements and compatibility with FDA guidelines to ensure method reliability in quantifying endogenous compounds. The standard addition, background subtraction, and the surrogate analyte approaches allow the use of the same matrix for the calibration curve as the one to be analyzed in the test samples. However, in the surrogate matrix approach, various matrices such as artificial, stripped, and neat matrices are used as surrogate matrices for the actual matrix of study samples. For the surrogate analyte approach, it is required to demonstrate similarity in matrix effect and recovery between surrogate and authentic endogenous analytes. Similarly, for the surrogate matrix approach, it is required to demonstrate similar matrix effect and extraction recovery in both the surrogate and original matrices. All these methods represent indirect approaches to quantify endogenous compounds and regardless of what approach is followed, it has to be shown that none of the validation criteria have been compromised due to the indirect analyses. PMID

  17. Quantitative analysis of sandstone porosity

    SciTech Connect

    Ferrell, R.E. Jr.; Carpenter, P.K.

    1988-01-01

    A quantitative analysis of changes in porosity associated with sandstone diagenesis was accomplished with digital back-scattered electron image analysis techniques. The volume percent (vol. %) of macroporosity, quartz, clay minerals, feldspar, and other constituents combined with stereological parameters, such as the size and shape of the analyzed features, permitted the determination of cement volumes, the ratio of primary to secondary porosity, and the relative abundance of detrital and authigenic clay minerals. The analyses were produced with a JEOL 733 Superprobe and a TRACOR/NORTHERN 5700 Image Analyzer System. The results provided a numerical evaluation of sedimentological facies controls and diagenetic effects on the permeabilities of potential reservoirs. In a typical application, subtle differences in the diagnetic development of porosity were detected in Wilcox sandstones from central Louisiana. Mechanical compaction of these shoreface sandstones has reduced the porosity to approximately 20%. In most samples with permeabilities greater than 10 md, the measured ratio of macroporosity to microporosity associated with pore-filling kaolinite was 3:1. In other sandstones with lower permeabilities, the measured ratio was higher, but the volume of pore-filling clay was essentially the same. An analysis of the frequency distribution of pore diameters and shapes revealed that the latter samples contained 2-3 vol% of grain-dissolution or moldic porosity. Fluid entry to these large pores was restricted and the clays produced from the grain dissolution products reduced the observed permeability. The image analysis technique provided valuable data for the distinction of productive and nonproductive intervals in this reservoir.

  18. Quantitative peri-ictal electrocorticography and long-term seizure outcomes in temporal lobe epilepsy.

    PubMed

    Park, Seong-Cheol; Lee, Sang Kun; Chung, Chun Kee

    2015-01-01

    We analyzed peri-ictal electrocorticography below 70 Hz by a semiautomatic quantitative method. Thirty-four patients with medically intractable temporal lobe epilepsy underwent chronic electrocorticography using subdural electrodes. The resection extent of cortices with maximum amplitude activities were compared between seizure outcome groups. In detected activity significantly related to seizure outcome, we analyzed waveforms with automated waveform amplitude analysis. Mann-Whitney U tests were used. Mean follow-up duration was 49.7 ± 18.2 months. The resection extents of maximum amplitude activities in theta bands during the period between -10 and -5s from the ictal onset were significantly different between seizure outcome groups (adjusted p=0.01, the Benjamini-Hochberg correction). Delta, alpha and beta bands were related to seizure outcome only without multiple comparison corrections (unadjusted p=0.02, 0.03 and 0.04). Waveform peak amplitudes greater than 200 μV tended to be more common in the seizure free group than in the non-seizure-free group (unadjusted p=0.06). Waveform peak amplitudes greater than 350 μV were significantly more common in the cortical dysplasia type I group than in the hippocampal sclerosis group (unadjusted p=0.03). The resection of theta band activities during the preictal period was most important for good seizure outcome in temporal lobe epilepsy. PMID:25524857

  19. Visual Constraints for the Perception of Quantitative Depth from Temporal Interocular Unmatched Features

    PubMed Central

    Ni, Rui; Chen, Lin; Andersen, George J.

    2010-01-01

    Previous research (Brooks & Gillam, 2006) has found that temporal interocular unmatched (IOUM) features generate a perception of subjective contours and can result in a perception of quantitative depth. In the present study we examine in detail the factors important for quantitative depth perception from IOUM features. In Experiments 1 and 2 observers were shown temporal IOUM features based on three dots that disappeared behind an implicit surface. Subjects reported a perception of a subjective surface and were able to perceive qualitative depth. In Experiments 3 and 4 metrical depth was perceived when binocular disparity features were added to the display. These results suggest that quantitative depth from IOUM information is perceived when binocular matched information is present in regions adjacent to the surface. In addition, the perceived depth of the subjective surface decreased with an increase in the width of the subjective surface suggesting a limitation in the propagation of quantitative depth to surface regions where qualitative depth information is available. PMID:20493899

  20. Quantitative Analysis of Glaciated Landscapes

    NASA Astrophysics Data System (ADS)

    Huerta, A. D.

    2005-12-01

    The evolution of glaciated mountains is at the heart of the debate over Late Cenozoic linkages between climate and tectonics. Traditionally, the development of high summit elevations is attributed to tectonic processes. However, much of the high elevation of the Transantarctic Mountains can be attributed solely to uplift in response to glacial erosion (Stern et al., 2005). The Transantarctic Mountains (TAM) provide an unparalleled opportunity to study glacial erosion. The mountain range has experienced glacial conditions since Oligocene time. In the higher and dryer regions of the TAM there is only a thin veneer of ice and snow draping the topography. In these regions landforms that were shaped during earlier climatic conditions are preserved. In fact, both glacial and fluvial landforms dating as far back as 18 Ma are preserved locally. In addition, the TAM are ideal for studying glacial erosion since the range has experienced minimal tectonic uplift since late Oligocene time, thus isolating the erosion signal from any tectonic signal. With the advent of digital data sets and GIS methodologies, quantitative analysis can identify key aspects of glaciated landscape morphology, and thus develop powerful analytical techniques for objective study of glaciation. Inspection of USGS topographic maps of the TAM reveals that mountain tops display an extreme range of glacial modification. For example, in the Mt. Rabot region (83°-84° S), mountain peaks are strongly affected by glaciation; cirque development is advanced with cirque diameters on the range of several kilometers, and cirque confluence has resulted in the formation of ``knife-edge'' arêtes up to 10 km long. In contrast, in the Mt. Murchison area (73°-74° S) cirque development is youthful, and there is minimal development of arêtes. Preliminary work indicates that analysis of DEM's and contour lines can be used to distinguish degree of glaciation. In particular, slope, curvature, and power spectrum analysis

  1. Quantitative phase imaging of biological cells using spatially low and temporally high coherent light source.

    PubMed

    Ahmad, Azeem; Dubey, Vishesh; Singh, Gyanendra; Singh, Veena; Mehta, Dalip Singh

    2016-04-01

    In this Letter, we demonstrate quantitative phase imaging of biological samples, such as human red blood cells (RBCs) and onion cells using narrow temporal frequency and wide angular frequency spectrum light source. This type of light source was synthesized by the combined effect of spatial, angular, and temporal diversity of speckle reduction technique. The importance of using low spatial and high temporal coherence light source over the broad band and narrow band light source is that it does not require any dispersion compensation mechanism for biological samples. Further, it avoids the formation of speckle or spurious fringes which arises while using narrow band light source. PMID:27192285

  2. Temporal fringe pattern analysis with parallel computing

    SciTech Connect

    Tuck Wah Ng; Kar Tien Ang; Argentini, Gianluca

    2005-11-20

    Temporal fringe pattern analysis is invaluable in transient phenomena studies but necessitates long processing times. Here we describe a parallel computing strategy based on the single-program multiple-data model and hyperthreading processor technology to reduce the execution time. In a two-node cluster workstation configuration we found that execution periods were reduced by 1.6 times when four virtual processors were used. To allow even lower execution times with an increasing number of processors, the time allocated for data transfer, data read, and waiting should be minimized. Parallel computing is found here to present a feasible approach to reduce execution times in temporal fringe pattern analysis.

  3. Quantitative analysis of retinal OCT.

    PubMed

    Sonka, Milan; Abràmoff, Michael D

    2016-10-01

    Clinical acceptance of 3-D OCT retinal imaging brought rapid development of quantitative 3-D analysis of retinal layers, vasculature, retinal lesions as well as facilitated new research in retinal diseases. One of the cornerstones of many such analyses is segmentation and thickness quantification of retinal layers and the choroid, with an inherently 3-D simultaneous multi-layer LOGISMOS (Layered Optimal Graph Image Segmentation for Multiple Objects and Surfaces) segmentation approach being extremely well suited for the task. Once retinal layers are segmented, regional thickness, brightness, or texture-based indices of individual layers can be easily determined and thus contribute to our understanding of retinal or optic nerve head (ONH) disease processes and can be employed for determination of disease status, treatment responses, visual function, etc. Out of many applications, examples provided in this paper focus on image-guided therapy and outcome prediction in age-related macular degeneration and on assessing visual function from retinal layer structure in glaucoma. PMID:27503080

  4. Detection of temporal lobe epilepsy using support vector machines in multi-parametric quantitative MR imaging.

    PubMed

    Cantor-Rivera, Diego; Khan, Ali R; Goubran, Maged; Mirsattari, Seyed M; Peters, Terry M

    2015-04-01

    The detection of MRI abnormalities that can be associated to seizures in the study of temporal lobe epilepsy (TLE) is a challenging task. In many cases, patients with a record of epileptic activity do not present any discernible MRI findings. In this domain, we propose a method that combines quantitative relaxometry and diffusion tensor imaging (DTI) with support vector machines (SVM) aiming to improve TLE detection. The main contribution of this work is two-fold: on one hand, the feature selection process, principal component analysis (PCA) transformations of the feature space, and SVM parameterization are analyzed as factors constituting a classification model and influencing its quality. On the other hand, several of these classification models are studied to determine the optimal strategy for the identification of TLE patients using data collected from multi-parametric quantitative MRI. A total of 17 TLE patients and 19 control volunteers were analyzed. Four images were considered for each subject (T1 map, T2 map, fractional anisotropy, and mean diffusivity) generating 936 regions of interest per subject, then 8 different classification models were studied, each one comprised by a distinct set of factors. Subjects were correctly classified with an accuracy of 88.9%. Further analysis revealed that the heterogeneous nature of the disease impeded an optimal outcome. After dividing patients into cohesive groups (9 left-sided seizure onset, 8 right-sided seizure onset) perfect classification for the left group was achieved (100% accuracy) whereas the accuracy for the right group remained the same (88.9%). We conclude that a linear SVM combined with an ANOVA-based feature selection+PCA method is a good alternative in scenarios like ours where feature spaces are high dimensional, and the sample size is limited. The good accuracy results and the localization of the respective features in the temporal lobe suggest that a multi-parametric quantitative MRI, ROI-based, SVM

  5. Quantitative representation of nonrepetitive temporal behavior. [solar flares in soft x-ray flux application

    NASA Technical Reports Server (NTRS)

    Nakagawa, Y.; Teuber, D. L.

    1980-01-01

    Analytical representations suitable to analyze the nonrepetitive pulse-like temporal behavior of physical quantities are derived. The representation utilizes solutions of a linear model equation in which the temporal variation is subject to time-dependent driving and dissipative forces. The property of solutions is described, and it is shown that such representations can provide a basis for quantitative comparisons of behaviors and a basis for physically meaningful interpretations of the results. Observations of solar flares in the soft X-ray flux have been analyzed with this method.

  6. Quantitative Analysis of Face Symmetry.

    PubMed

    Tamir, Abraham

    2015-06-01

    The major objective of this article was to report quantitatively the degree of human face symmetry for reported images taken from the Internet. From the original image of a certain person that appears in the center of each triplet, 2 symmetric combinations were constructed that are based on the left part of the image and its mirror image (left-left) and on the right part of the image and its mirror image (right-right). By applying a computer software that enables to determine length, surface area, and perimeter of any geometric shape, the following measurements were obtained for each triplet: face perimeter and area; distance between the pupils; mouth length; its perimeter and area; nose length and face length, usually below the ears; as well as the area and perimeter of the pupils. Then, for each of the above measurements, the value C, which characterizes the degree of symmetry of the real image with respect to the combinations right-right and left-left, was calculated. C appears on the right-hand side below each image. A high value of C indicates a low symmetry, and as the value is decreasing, the symmetry is increasing. The magnitude on the left relates to the pupils and compares the difference between the area and perimeter of the 2 pupils. The major conclusion arrived at here is that the human face is asymmetric to some degree; the degree of asymmetry is reported quantitatively under each portrait. PMID:26080172

  7. Quantitative analysis of digital microscope images.

    PubMed

    Wolf, David E; Samarasekera, Champika; Swedlow, Jason R

    2013-01-01

    This chapter discusses quantitative analysis of digital microscope images and presents several exercises to provide examples to explain the concept. This chapter also presents the basic concepts in quantitative analysis for imaging, but these concepts rest on a well-established foundation of signal theory and quantitative data analysis. This chapter presents several examples for understanding the imaging process as a transformation from sample to image and the limits and considerations of quantitative analysis. This chapter introduces to the concept of digitally correcting the images and also focuses on some of the more critical types of data transformation and some of the frequently encountered issues in quantization. Image processing represents a form of data processing. There are many examples of data processing such as fitting the data to a theoretical curve. In all these cases, it is critical that care is taken during all steps of transformation, processing, and quantization. PMID:23931513

  8. Quantitative analysis of qualitative images

    NASA Astrophysics Data System (ADS)

    Hockney, David; Falco, Charles M.

    2005-03-01

    We show optical evidence that demonstrates artists as early as Jan van Eyck and Robert Campin (c1425) used optical projections as aids for producing their paintings. We also have found optical evidence within works by later artists, including Bermejo (c1475), Lotto (c1525), Caravaggio (c1600), de la Tour (c1650), Chardin (c1750) and Ingres (c1825), demonstrating a continuum in the use of optical projections by artists, along with an evolution in the sophistication of that use. However, even for paintings where we have been able to extract unambiguous, quantitative evidence of the direct use of optical projections for producing certain of the features, this does not mean that paintings are effectively photographs. Because the hand and mind of the artist are intimately involved in the creation process, understanding these complex images requires more than can be obtained from only applying the equations of geometrical optics.

  9. Time series analysis of temporal networks

    NASA Astrophysics Data System (ADS)

    Sikdar, Sandipan; Ganguly, Niloy; Mukherjee, Animesh

    2016-01-01

    A common but an important feature of all real-world networks is that they are temporal in nature, i.e., the network structure changes over time. Due to this dynamic nature, it becomes difficult to propose suitable growth models that can explain the various important characteristic properties of these networks. In fact, in many application oriented studies only knowing these properties is sufficient. For instance, if one wishes to launch a targeted attack on a network, this can be done even without the knowledge of the full network structure; rather an estimate of some of the properties is sufficient enough to launch the attack. We, in this paper show that even if the network structure at a future time point is not available one can still manage to estimate its properties. We propose a novel method to map a temporal network to a set of time series instances, analyze them and using a standard forecast model of time series, try to predict the properties of a temporal network at a later time instance. To our aim, we consider eight properties such as number of active nodes, average degree, clustering coefficient etc. and apply our prediction framework on them. We mainly focus on the temporal network of human face-to-face contacts and observe that it represents a stochastic process with memory that can be modeled as Auto-Regressive-Integrated-Moving-Average (ARIMA). We use cross validation techniques to find the percentage accuracy of our predictions. An important observation is that the frequency domain properties of the time series obtained from spectrogram analysis could be used to refine the prediction framework by identifying beforehand the cases where the error in prediction is likely to be high. This leads to an improvement of 7.96% (for error level ≤20%) in prediction accuracy on an average across all datasets. As an application we show how such prediction scheme can be used to launch targeted attacks on temporal networks. Contribution to the Topical Issue

  10. Runtime Analysis of Linear Temporal Logic Specifications

    NASA Technical Reports Server (NTRS)

    Giannakopoulou, Dimitra; Havelund, Klaus

    2001-01-01

    This report presents an approach to checking a running program against its Linear Temporal Logic (LTL) specifications. LTL is a widely used logic for expressing properties of programs viewed as sets of executions. Our approach consists of translating LTL formulae to finite-state automata, which are used as observers of the program behavior. The translation algorithm we propose modifies standard LTL to B chi automata conversion techniques to generate automata that check finite program traces. The algorithm has been implemented in a tool, which has been integrated with the generic JPaX framework for runtime analysis of Java programs.

  11. Qualitative and Quantitative Analysis: Interpretation of Electropherograms

    NASA Astrophysics Data System (ADS)

    Szumski, Michał; Buszewski, Bogusław

    In this chapter the basic information on qualitative and quantitative analysis in CE is provided. Migration time and spectral data are described as the most important parameters used for identification of compounds. The parameters that negatively influence qualitative analysis are briefly mentioned. In the quantitative analysis section the external standard and internal standard calibration methods are described. Variables influencing peak height and peak area in capillary electrophoresis are briefly summarized. Also, a discussion on electrodisperssion and its influence on a observed peak shape is provided.

  12. Quantitative histogram analysis of images

    NASA Astrophysics Data System (ADS)

    Holub, Oliver; Ferreira, Sérgio T.

    2006-11-01

    A routine for histogram analysis of images has been written in the object-oriented, graphical development environment LabVIEW. The program converts an RGB bitmap image into an intensity-linear greyscale image according to selectable conversion coefficients. This greyscale image is subsequently analysed by plots of the intensity histogram and probability distribution of brightness, and by calculation of various parameters, including average brightness, standard deviation, variance, minimal and maximal brightness, mode, skewness and kurtosis of the histogram and the median of the probability distribution. The program allows interactive selection of specific regions of interest (ROI) in the image and definition of lower and upper threshold levels (e.g., to permit the removal of a constant background signal). The results of the analysis of multiple images can be conveniently saved and exported for plotting in other programs, which allows fast analysis of relatively large sets of image data. The program file accompanies this manuscript together with a detailed description of two application examples: The analysis of fluorescence microscopy images, specifically of tau-immunofluorescence in primary cultures of rat cortical and hippocampal neurons, and the quantification of protein bands by Western-blot. The possibilities and limitations of this kind of analysis are discussed. Program summaryTitle of program: HAWGC Catalogue identifier: ADXG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXG_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers: Mobile Intel Pentium III, AMD Duron Installations: No installation necessary—Executable file together with necessary files for LabVIEW Run-time engine Operating systems or monitors under which the program has been tested: WindowsME/2000/XP Programming language used: LabVIEW 7.0 Memory required to execute with typical data:˜16MB for starting and ˜160MB used for

  13. Quantitative analysis of surface electromyography: Biomarkers for convulsive seizures.

    PubMed

    Beniczky, Sándor; Conradsen, Isa; Pressler, Ronit; Wolf, Peter

    2016-08-01

    Muscle activity during seizures is in electroencephalographical (EEG) praxis often considered an irritating artefact. This article discusses ways by surface electromyography (EMG) to turn it into a valuable tool of epileptology. Muscles are in direct synaptic contact with motor neurons. Therefore, EMG signals provide direct information about the electric activity in the motor cortex. Qualitative analysis of EMG has traditionally been a part of the long-term video-EEG recordings. Recent development in quantitative analysis of EMG signals yielded valuable information on the pathomechanisms of convulsive seizures, demonstrating that it was different from maximal voluntary contraction, and different from convulsive psychogenic non-epileptic seizures. Furthermore, the tonic phase of the generalised tonic-clonic seizures (GTCS) proved to have different quantitative features than tonic seizures. The high temporal resolution of EMG allowed detailed characterisation of temporal dynamics of the GTCS, suggesting that the same inhibitory mechanisms that try to prevent the build-up of the seizure activity, contribute to ending the seizure. These findings have clinical implications: the quantitative EMG features provided the pathophysiologic substrate for developing neurophysiologic biomarkers that accurately identify GTCS. This proved to be efficient both for seizure detection and for objective, automated distinction between convulsive and non-convulsive epileptic seizures. PMID:27212115

  14. Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories.

    PubMed

    White, Douglas E; Sylvester, Jonathan B; Levario, Thomas J; Lu, Hang; Streelman, J Todd; McDevitt, Todd C; Kemp, Melissa L

    2015-07-01

    Interrogating fundamental cell biology principles that govern tissue morphogenesis is critical to better understanding of developmental biology and engineering novel multicellular systems. Recently, functional micro-tissues derived from pluripotent embryonic stem cell (ESC) aggregates have provided novel platforms for experimental investigation; however elucidating the factors directing emergent spatial phenotypic patterns remains a significant challenge. Computational modelling techniques offer a unique complementary approach to probe mechanisms regulating morphogenic processes and provide a wealth of spatio-temporal data, but quantitative analysis of simulations and comparison to experimental data is extremely difficult. Quantitative descriptions of spatial phenomena across multiple systems and scales would enable unprecedented comparisons of computational simulations with experimental systems, thereby leveraging the inherent power of computational methods to interrogate the mechanisms governing emergent properties of multicellular biology. To address these challenges, we developed a portable pattern recognition pipeline consisting of: the conversion of cellular images into networks, extraction of novel features via network analysis, and generation of morphogenic trajectories. This novel methodology enabled the quantitative description of morphogenic pattern trajectories that could be compared across diverse systems: computational modelling of multicellular structures, differentiation of stem cell aggregates, and gastrulation of cichlid fish. Moreover, this method identified novel spatio-temporal features associated with different stages of embryo gastrulation, and elucidated a complex paracrine mechanism capable of explaining spatiotemporal pattern kinetic differences in ESC aggregates of different sizes. PMID:26095427

  15. Temporal analysis of multispectral scanner data.

    NASA Technical Reports Server (NTRS)

    Richardson, A. J.; Wiegand, C. L.; Torline, R. J.

    1973-01-01

    Multispectral scanner reflectance data were sampled for bare soil, cotton, sorghum, corn, and citrus at four dates during a growing season (April, May, June, and July 1969) to develop a time-dependent signature for crop and soil discrimination. Discrimination tests were conducted for single-date and multidate formats using training and test data sets. For classifications containing several crops, the multidate or temporal approach improved discrimination compared with the single-date approach. The multidate approach also preserved recognition accuracy better in going from training fields to test fields than the single-date analysis. The spectral distinctiveness of bare soil versus vegetation resulted in essentially equal discrimination using single-date versus multidate data for those two categories.

  16. Mobile app-based quantitative scanometric analysis.

    PubMed

    Wong, Jessica X H; Liu, Frank S F; Yu, Hua-Zhong

    2014-12-16

    The feasibility of using smartphones and other mobile devices as the detection platform for quantitative scanometric assays is demonstrated. The different scanning modes (color, grayscale, black/white) and grayscale converting protocols (average, weighted average/luminosity, and software specific) have been compared in determining the optical darkness ratio (ODR) values, a conventional quantitation measure for scanometric assays. A mobile app was developed to image and analyze scanometric assays, as demonstrated by paper-printed tests and a biotin-streptavidin assay on a plastic substrate. Primarily for ODR analysis, the app has been shown to perform as well as a traditional desktop scanner, augmenting that smartphones (and other mobile devices) promise to be a practical platform for accurate, quantitative chemical analysis and medical diagnostics. PMID:25420202

  17. Quantitative WDS analysis using electron probe microanalyzer

    SciTech Connect

    Ul-Hamid, Anwar . E-mail: anwar@kfupm.edu.sa; Tawancy, Hani M.; Mohammed, Abdul-Rashid I.; Al-Jaroudi, Said S.; Abbas, Nureddin M.

    2006-04-15

    In this paper, the procedure for conducting quantitative elemental analysis by ZAF correction method using wavelength dispersive X-ray spectroscopy (WDS) in an electron probe microanalyzer (EPMA) is elaborated. Analysis of a thermal barrier coating (TBC) system formed on a Ni-based single crystal superalloy is presented as an example to illustrate the analysis of samples consisting of a large number of major and minor elements. The analysis was performed by known standards and measured peak-to-background intensity ratios. The procedure for using separate set of acquisition conditions for major and minor element analysis is explained and its importance is stressed.

  18. Seniors' Online Communities: A Quantitative Content Analysis

    ERIC Educational Resources Information Center

    Nimrod, Galit

    2010-01-01

    Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was…

  19. Biomechanical cell analysis using quantitative phase imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wax, Adam; Park, Han Sang; Eldridge, William J.

    2016-03-01

    Quantitative phase imaging provides nanometer scale sensitivity and has been previously used to study spectral and temporal characteristics of individual cells in vitro, especially red blood cells. Here we extend this work to study the mechanical responses of individual cells due to the influence of external stimuli. Cell stiffness may be characterized by analyzing the inherent thermal fluctuations of cells but by applying external stimuli, additional information can be obtained. The time dependent response of cells due to external shear stress is examined with high speed quantitative phase imaging and found to exhibit characteristics that relate to their stiffness. However, analysis beyond the cellular scale also reveals internal organization of the cell and its modulation due to pathologic processes such as carcinogenesis. Further studies with microfluidic platforms point the way for using this approach in high throughput assays.

  20. Quantitative Proteomics Analysis of Leukemia Cells.

    PubMed

    Halbach, Sebastian; Dengjel, Jörn; Brummer, Tilman

    2016-01-01

    Chronic myeloid leukemia (CML) is driven by the oncogenic fusion kinase Bcr-Abl, which organizes its own signaling network with various proteins. These proteins, their interactions, and their role in relevant signaling pathways can be analyzed by quantitative mass spectrometry (MS) approaches in various models systems, e.g., in cell culture models. In this chapter, we describe in detail immunoprecipitations and quantitative proteomics analysis using stable isotope labeling by amino acids in cell culture (SILAC) of components of the Bcr-Abl signaling pathway in the human CML cell line K562. PMID:27581145

  1. Method and apparatus for chromatographic quantitative analysis

    DOEpatents

    Fritz, James S.; Gjerde, Douglas T.; Schmuckler, Gabriella

    1981-06-09

    An improved apparatus and method for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single eluent and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.

  2. Quantitative analysis of blood vessel geometry

    NASA Astrophysics Data System (ADS)

    Fuhrman, Michael G.; Abdul-Karim, Othman; Shah, Sujal; Gilbert, Steven G.; Van Bibber, Richard

    2001-07-01

    Re-narrowing or restenosis of a human coronary artery occurs within six months in one third of balloon angioplasty procedures. Accurate and repeatable quantitative analysis of vessel shape is important to characterize the progression and type of restenosis, and to evaluate effects new therapies might have. A combination of complicated geometry and image variability, and the need for high resolution and large image size makes visual/manual analysis slow, difficult, and prone to error. The image processing and analysis described here was developed to automate feature extraction of the lumen, internal elastic lamina, neointima, external elastic lamina, and tunica adventitia and to enable an objective, quantitative definition of blood vessel geometry. The quantitative geometrical analysis enables the measurement of several features including perimeter, area, and other metrics of vessel damage. Automation of feature extraction creates a high throughput capability that enables analysis of serial sections for more accurate measurement of restenosis dimensions. Measurement results are input into a relational database where they can be statistically analyzed compared across studies. As part of the integrated process, results are also imprinted on the images themselves to facilitate auditing of the results. The analysis is fast, repeatable and accurate while allowing the pathologist to control the measurement process.

  3. Comprehensive Quantitative Analysis on Privacy Leak Behavior

    PubMed Central

    Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

    2013-01-01

    Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

  4. Comprehensive quantitative analysis on privacy leak behavior.

    PubMed

    Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

    2013-01-01

    Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

  5. Quantitative Proteomic Analysis of the Human Nucleolus.

    PubMed

    Bensaddek, Dalila; Nicolas, Armel; Lamond, Angus I

    2016-01-01

    Recent years have witnessed spectacular progress in the field of mass spectrometry (MS)-based quantitative proteomics, including advances in instrumentation, chromatography, sample preparation methods, and experimental design for multidimensional analyses. It is now possible not only to identify most of the protein components of a cell proteome in a single experiment, but also to describe additional proteome dimensions, such as protein turnover rates, posttranslational modifications, and subcellular localization. Furthermore, by comparing the proteome at different time points, it is possible to create a "time-lapse" view of proteome dynamics. By combining high-throughput quantitative proteomics with detailed subcellular fractionation protocols and data analysis techniques it is also now possible to characterize in detail the proteomes of specific subcellular organelles, providing important insights into cell regulatory mechanisms and physiological responses. In this chapter we present a reliable workflow and protocol for MS-based analysis and quantitation of the proteome of nucleoli isolated from human cells. The protocol presented is based on a SILAC analysis of human MCF10A-Src-ER cells with analysis performed on a Q-Exactive Plus Orbitrap MS instrument (Thermo Fisher Scientific). The subsequent chapter describes how to process the resulting raw MS files from this experiment using MaxQuant software and data analysis procedures to evaluate the nucleolar proteome using customized R scripts. PMID:27576725

  6. Quantitative image analysis of celiac disease

    PubMed Central

    Ciaccio, Edward J; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

    2015-01-01

    We outline the use of quantitative techniques that are currently used for analysis of celiac disease. Image processing techniques can be useful to statistically analyze the pixular data of endoscopic images that is acquired with standard or videocapsule endoscopy. It is shown how current techniques have evolved to become more useful for gastroenterologists who seek to understand celiac disease and to screen for it in suspected patients. New directions for focus in the development of methodology for diagnosis and treatment of this disease are suggested. It is evident that there are yet broad areas where there is potential to expand the use of quantitative techniques for improved analysis in suspected or known celiac disease patients. PMID:25759524

  7. Phase noise optimization in temporal phase-shifting digital holography with partial coherence light sources and its application in quantitative cell imaging.

    PubMed

    Remmersmann, Christian; Stürwald, Stephan; Kemper, Björn; Langehanenberg, Patrik; von Bally, Gert

    2009-03-10

    In temporal phase-shifting-based digital holographic microscopy, high-resolution phase contrast imaging requires optimized conditions for hologram recording and phase retrieval. To optimize the phase resolution, for the example of a variable three-step algorithm, a theoretical analysis on statistical errors, digitalization errors, uncorrelated errors, and errors due to a misaligned temporal phase shift is carried out. In a second step the theoretically predicted results are compared to the measured phase noise obtained from comparative experimental investigations with several coherent and partially coherent light sources. Finally, the applicability for noise reduction is demonstrated by quantitative phase contrast imaging of pancreas tumor cells. PMID:19277078

  8. Spatial and temporal epidemiological analysis in the Big Data era.

    PubMed

    Pfeiffer, Dirk U; Stevens, Kim B

    2015-11-01

    Concurrent with global economic development in the last 50 years, the opportunities for the spread of existing diseases and emergence of new infectious pathogens, have increased substantially. The activities associated with the enormously intensified global connectivity have resulted in large amounts of data being generated, which in turn provides opportunities for generating knowledge that will allow more effective management of animal and human health risks. This so-called Big Data has, more recently, been accompanied by the Internet of Things which highlights the increasing presence of a wide range of sensors, interconnected via the Internet. Analysis of this data needs to exploit its complexity, accommodate variation in data quality and should take advantage of its spatial and temporal dimensions, where available. Apart from the development of hardware technologies and networking/communication infrastructure, it is necessary to develop appropriate data management tools that make this data accessible for analysis. This includes relational databases, geographical information systems and most recently, cloud-based data storage such as Hadoop distributed file systems. While the development in analytical methodologies has not quite caught up with the data deluge, important advances have been made in a number of areas, including spatial and temporal data analysis where the spectrum of analytical methods ranges from visualisation and exploratory analysis, to modelling. While there used to be a primary focus on statistical science in terms of methodological development for data analysis, the newly emerged discipline of data science is a reflection of the challenges presented by the need to integrate diverse data sources and exploit them using novel data- and knowledge-driven modelling methods while simultaneously recognising the value of quantitative as well as qualitative analytical approaches. Machine learning regression methods, which are more robust and can handle

  9. Using Qualitative Hazard Analysis to Guide Quantitative Safety Analysis

    NASA Technical Reports Server (NTRS)

    Shortle, J. F.; Allocco, M.

    2005-01-01

    Quantitative methods can be beneficial in many types of safety investigations. However, there are many difficulties in using quantitative m ethods. Far example, there may be little relevant data available. This paper proposes a framework for using quantitative hazard analysis to prioritize hazard scenarios most suitable for quantitative mziysis. The framework first categorizes hazard scenarios by severity and likelihood. We then propose another metric "modeling difficulty" that desc ribes the complexity in modeling a given hazard scenario quantitatively. The combined metrics of severity, likelihood, and modeling difficu lty help to prioritize hazard scenarios for which quantitative analys is should be applied. We have applied this methodology to proposed concepts of operations for reduced wake separation for airplane operatio ns at closely spaced parallel runways.

  10. Decoding brain cancer dynamics: a quantitative histogram-based approach using temporal MRI

    NASA Astrophysics Data System (ADS)

    Zhou, Mu; Hall, Lawrence O.; Goldgof, Dmitry B.; Russo, Robin; Gillies, Robert J.; Gatenby, Robert A.

    2015-03-01

    Brain tumor heterogeneity remains a challenge for probing brain cancer evolutionary dynamics. In light of evolution, it is a priority to inspect the cancer system from a time-domain perspective since it explicitly tracks the dynamics of cancer variations. In this paper, we study the problem of exploring brain tumor heterogeneity from temporal clinical magnetic resonance imaging (MRI) data. Our goal is to discover evidence-based knowledge from such temporal imaging data, where multiple clinical MRI scans from Glioblastoma multiforme (GBM) patients are generated during therapy. In particular, we propose a quantitative histogram-based approach that builds a prediction model to measure the difference in histograms obtained from pre- and post-treatment. The study could significantly assist radiologists by providing a metric to identify distinctive patterns within each tumor, which is crucial for the goal of providing patient-specific treatments. We examine the proposed approach for a practical application - clinical survival group prediction. Experimental results show that our approach achieved 90.91% accuracy.

  11. Quantitative phase microscopy: automated background leveling techniques and smart temporal phase unwrapping.

    PubMed

    Goldstein, Goldie; Creath, Katherine

    2015-06-01

    In order for time-dynamic quantitative phase microscopy to yield meaningful data to scientists, raw phase measurements must be converted to sequential time series that are consistently phase unwrapped with minimal residual background shape. Beyond the initial phase unwrapping, additional steps must be taken to convert the phase to time-meaningful data sequences. This consists of two major operations both outlined in this paper and shown to operate robustly on biological datasets. An automated background leveling procedure is introduced that consistently removes background shape and minimizes mean background phase value fluctuations. By creating a background phase value that is stable over time, the phase values of features of interest can be examined as a function of time to draw biologically meaningful conclusions. Residual differences between sequential frames of data can be present due to inconsistent phase unwrapping, causing localized regions to have phase values at similar object locations inconsistently changed by large values between frames, not corresponding to physical changes in the sample being observed. This is overcome by introducing a new method, referred to as smart temporal unwrapping that temporally unwraps and filters the phase data such that small motion between frames is accounted for and phase data are unwrapped consistently between frames. The combination of these methods results in the creation of phase data that is stable over time by minimizing errors introduced within the processing of the raw data. PMID:26192681

  12. Temporal Mixture Analysis of Hypertemporal Antarctic Sea Ice Data in the Sense of Machine Learning

    NASA Astrophysics Data System (ADS)

    Chi, J.; Kim, H. C.

    2015-12-01

    Hypertemporal data, or time series acquired at high temporal frequencies, are often used to determine seasonal characteristics of environmental phenomena such as sea ice concentration. However, it is difficult to analyze long-term hypertemporal remote sensing data over extensive areas without prior information. Most pixels of hypertemporal data are highly mixed and contain several distinct temporal signals that represent seasonal characteristics of substances. This study performed temporal mixture analysis, which is algebraically similar to spectral mixture analysis, but occurs in the time domain instead of the spectral domain. Temporal mixture analysis was used to investigate the temporal characteristics of Antarctic sea ice. Two general steps were used to address mixing problems: 1) finding temporally unique signatures of pure components, which are referred to as temporal endmembers, and 2) unmixing each pixel in the time series data as a linear combination of the endmember fractional abundances. Because endmember selection is critical to the success of both spectral and temporal mixture analysis, it is important to select proper endmembers from large quantities of hypertemporal data. A machine learning algorithm was introduced to successfully identify endmembers without prior knowledge. A fully linear mixing model was then implemented in an attempt to produce more robust and physically meaningful abundance estimates. Experiments that quantitatively and qualitatively evaluated the proposed approaches were conducted. A temporal mixture analysis of high-temporal-dimensional data provides a unique summary of long-term Antarctic sea ice and noise-whitened reconstruction images via inverse processing. Further, comparisons of regional sea-ice fractions provide a better understanding of the overall Antarctic sea ice changes.

  13. Quantitative resilience analysis through control design.

    SciTech Connect

    Sunderland, Daniel; Vugrin, Eric D.; Camphouse, Russell Chris

    2009-09-01

    Critical infrastructure resilience has become a national priority for the U. S. Department of Homeland Security. System resilience has been studied for several decades in many different disciplines, but no standards or unifying methods exist for critical infrastructure resilience analysis. Few quantitative resilience methods exist, and those existing approaches tend to be rather simplistic and, hence, not capable of sufficiently assessing all aspects of critical infrastructure resilience. This report documents the results of a late-start Laboratory Directed Research and Development (LDRD) project that investigated the development of quantitative resilience through application of control design methods. Specifically, we conducted a survey of infrastructure models to assess what types of control design might be applicable for critical infrastructure resilience assessment. As a result of this survey, we developed a decision process that directs the resilience analyst to the control method that is most likely applicable to the system under consideration. Furthermore, we developed optimal control strategies for two sets of representative infrastructure systems to demonstrate how control methods could be used to assess the resilience of the systems to catastrophic disruptions. We present recommendations for future work to continue the development of quantitative resilience analysis methods.

  14. Spatio-temporal analysis of environmental radiation in Korea

    SciTech Connect

    Kim, J.Y.; Lee, B.C.; Shin, H.K.

    2007-07-01

    Geostatistical visualization of environmental radiation is a very powerful approach to explore and understand spatio-temporal variabilities of environmental radiation data. Spatial patterns of environmental radiation can be described quantitatively in terms of variogram and kriging, which are based on the idea that statistical variation of data are functions of distance. (authors)

  15. Quantitative Bias Analysis in Regulatory Settings.

    PubMed

    Lash, Timothy L; Fox, Matthew P; Cooney, Darryl; Lu, Yun; Forshee, Richard A

    2016-07-01

    Nonrandomized studies are essential in the postmarket activities of the US Food and Drug Administration, which, however, must often act on the basis of imperfect data. Systematic errors can lead to inaccurate inferences, so it is critical to develop analytic methods that quantify uncertainty and bias and ensure that these methods are implemented when needed. "Quantitative bias analysis" is an overarching term for methods that estimate quantitatively the direction, magnitude, and uncertainty associated with systematic errors influencing measures of associations. The Food and Drug Administration sponsored a collaborative project to develop tools to better quantify the uncertainties associated with postmarket surveillance studies used in regulatory decision making. We have described the rationale, progress, and future directions of this project. PMID:27196652

  16. Accuracy in Quantitative 3D Image Analysis

    PubMed Central

    Bassel, George W.

    2015-01-01

    Quantitative 3D imaging is becoming an increasingly popular and powerful approach to investigate plant growth and development. With the increased use of 3D image analysis, standards to ensure the accuracy and reproducibility of these data are required. This commentary highlights how image acquisition and postprocessing can introduce artifacts into 3D image data and proposes steps to increase both the accuracy and reproducibility of these analyses. It is intended to aid researchers entering the field of 3D image processing of plant cells and tissues and to help general readers in understanding and evaluating such data. PMID:25804539

  17. Quantitative architectural analysis of bronchial intraepithelial neoplasia

    NASA Astrophysics Data System (ADS)

    Guillaud, Martial; MacAulay, Calum E.; Le Riche, Jean C.; Dawe, Chris; Korbelik, Jagoda; Lam, Stephen

    2000-04-01

    Considerable variation exists among pathologist in the interpretation of intraepithelial neoplasia making it difficult to determine the natural history of these lesion and to establish management guidelines for chemoprevention. The aim of the study is to evaluate architectural features of pre-neoplastic progression in lung cancer, and to search for a correlation between architectural index and conventional pathology. Quantitative architectural analysis was performed on a series of normal lung biopsies and Carcinoma In Situ (CIS). Centers of gravity of the nuclei within a pre-defined region of interest were used as seeds to generate a Voronoi Diagram. About 30 features derived from the Voronoi diagram, its dual the Delaunay tessellation, and the Minimum Spanning Tree were extracted. A discriminant analysis was performed to separate between the two groups. The architectural Index was calculated for each of the bronchial biopsies that were interpreted as hyperplasia, metaplasia, mild, moderate or severe dysplasia by conventional histopathology criteria. As a group, lesions classified as CIS by conventional histopathology criteria could be distinguished from dysplasia using the architectural Index. Metaplasia was distinct from hyperplasia and hyperplasia from normal. There was overlap between severe and moderate dysplasia but mild dysplasia could be distinguished form moderate dysplasia. Bronchial intraepithelial neoplastic lesions can be degraded objectively by architectural features. Combination of architectural features and nuclear morphometric features may improve the quantitation of the changes occurring during the intra-epithelial neoplastic process.

  18. Quantitative interactome analysis reveals a chemoresistant edgotype

    PubMed Central

    Chavez, Juan D.; Schweppe, Devin K.; Eng, Jimmy K.; Zheng, Chunxiang; Taipale, Alex; Zhang, Yiyi; Takara, Kohji; Bruce, James E.

    2015-01-01

    Chemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for ‘edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype. PMID:26235782

  19. Quantitative interactome analysis reveals a chemoresistant edgotype.

    PubMed

    Chavez, Juan D; Schweppe, Devin K; Eng, Jimmy K; Zheng, Chunxiang; Taipale, Alex; Zhang, Yiyi; Takara, Kohji; Bruce, James E

    2015-01-01

    Chemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for 'edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype. PMID:26235782

  20. Quantitative analysis of NMR spectra with chemometrics

    NASA Astrophysics Data System (ADS)

    Winning, H.; Larsen, F. H.; Bro, R.; Engelsen, S. B.

    2008-01-01

    The number of applications of chemometrics to series of NMR spectra is rapidly increasing due to an emerging interest for quantitative NMR spectroscopy e.g. in the pharmaceutical and food industries. This paper gives an analysis of advantages and limitations of applying the two most common chemometric procedures, Principal Component Analysis (PCA) and Multivariate Curve Resolution (MCR), to a designed set of 231 simple alcohol mixture (propanol, butanol and pentanol) 1H 400 MHz spectra. The study clearly demonstrates that the major advantage of chemometrics is the visualisation of larger data structures which adds a new exploratory dimension to NMR research. While robustness and powerful data visualisation and exploration are the main qualities of the PCA method, the study demonstrates that the bilinear MCR method is an even more powerful method for resolving pure component NMR spectra from mixtures when certain conditions are met.

  1. Spectral and Temporal Laser Fluorescence Analysis Such as for Natural Aquatic Environments

    NASA Technical Reports Server (NTRS)

    Chekalyuk, Alexander (Inventor)

    2015-01-01

    An Advanced Laser Fluorometer (ALF) can combine spectrally and temporally resolved measurements of laser-stimulated emission (LSE) for characterization of dissolved and particulate matter, including fluorescence constituents, in liquids. Spectral deconvolution (SDC) analysis of LSE spectral measurements can accurately retrieve information about individual fluorescent bands, such as can be attributed to chlorophyll-a (Chl-a), phycobiliprotein (PBP) pigments, or chromophoric dissolved organic matter (CDOM), among others. Improved physiological assessments of photosynthesizing organisms can use SDC analysis and temporal LSE measurements to assess variable fluorescence corrected for SDC-retrieved background fluorescence. Fluorescence assessments of Chl-a concentration based on LSE spectral measurements can be improved using photo-physiological information from temporal measurements. Quantitative assessments of PBP pigments, CDOM, and other fluorescent constituents, as well as basic structural characterizations of photosynthesizing populations, can be performed using SDC analysis of LSE spectral measurements.

  2. Materials characterization through quantitative digital image analysis

    SciTech Connect

    J. Philliber; B. Antoun; B. Somerday; N. Yang

    2000-07-01

    A digital image analysis system has been developed to allow advanced quantitative measurement of microstructural features. This capability is maintained as part of the microscopy facility at Sandia, Livermore. The system records images digitally, eliminating the use of film. Images obtained from other sources may also be imported into the system. Subsequent digital image processing enhances image appearance through the contrast and brightness adjustments. The system measures a variety of user-defined microstructural features--including area fraction, particle size and spatial distributions, grain sizes and orientations of elongated particles. These measurements are made in a semi-automatic mode through the use of macro programs and a computer controlled translation stage. A routine has been developed to create large montages of 50+ separate images. Individual image frames are matched to the nearest pixel to create seamless montages. Results from three different studies are presented to illustrate the capabilities of the system.

  3. Forecasting Antarctic Sea Ice Concentrations Using Results of Temporal Mixture Analysis

    NASA Astrophysics Data System (ADS)

    Chi, Junhwa; Kim, Hyun-Cheol

    2016-06-01

    Sea ice concentration (SIC) data acquired by passive microwave sensors at daily temporal frequencies over extended areas provide seasonal characteristics of sea ice dynamics and play a key role as an indicator of global climate trends; however, it is typically challenging to study long-term time series. Of the various advanced remote sensing techniques that address this issue, temporal mixture analysis (TMA) methods are often used to investigate the temporal characteristics of environmental factors, including SICs in the case of the present study. This study aims to forecast daily SICs for one year using a combination of TMA and time series modeling in two stages. First, we identify temporally meaningful sea ice signatures, referred to as temporal endmembers, using machine learning algorithms, and then we decompose each pixel into a linear combination of temporal endmembers. Using these corresponding fractional abundances of endmembers, we apply a autoregressive model that generally fits all Antarctic SIC data for 1979 to 2013 to forecast SIC values for 2014. We compare our results using the proposed approach based on daily SIC data reconstructed from real fractional abundances derived from a pixel unmixing method and temporal endmember signatures. The proposed method successfully forecasts new fractional abundance values, and the resulting images are qualitatively and quantitatively similar to the reference data.

  4. Quantitative proteomic analysis of single pancreatic islets

    PubMed Central

    Waanders, Leonie F.; Chwalek, Karolina; Monetti, Mara; Kumar, Chanchal; Lammert, Eckhard; Mann, Matthias

    2009-01-01

    Technological developments make mass spectrometry (MS)-based proteomics a central pillar of biochemical research. MS has been very successful in cell culture systems, where sample amounts are not limiting. To extend its capabilities to extremely small, physiologically distinct cell types isolated from tissue, we developed a high sensitivity chromatographic system that measures nanogram protein mixtures for 8 h with very high resolution. This technology is based on splitting gradient effluents into a capture capillary and provides an inherent technical replicate. In a single analysis, this allowed us to characterize kidney glomeruli isolated by laser capture microdissection to a depth of more than 2,400 proteins. From pooled pancreatic islets of Langerhans, another type of “miniorgan,” we obtained an in-depth proteome of 6,873 proteins, many of them involved in diabetes. We quantitatively compared the proteome of single islets, containing 2,000–4,000 cells, treated with high or low glucose levels, and covered most of the characteristic functions of beta cells. Our ultrasensitive analysis recapitulated known hyperglycemic changes but we also find components up-regulated such as the mitochondrial stress regulator Park7. Direct proteomic analysis of functionally distinct cellular structures opens up perspectives in physiology and pathology. PMID:19846766

  5. Analysis of brain patterns using temporal measures

    DOEpatents

    Georgopoulos, Apostolos

    2015-08-11

    A set of brain data representing a time series of neurophysiologic activity acquired by spatially distributed sensors arranged to detect neural signaling of a brain (such as by the use of magnetoencephalography) is obtained. The set of brain data is processed to obtain a dynamic brain model based on a set of statistically-independent temporal measures, such as partial cross correlations, among groupings of different time series within the set of brain data. The dynamic brain model represents interactions between neural populations of the brain occurring close in time, such as with zero lag, for example. The dynamic brain model can be analyzed to obtain the neurophysiologic assessment of the brain. Data processing techniques may be used to assess structural or neurochemical brain pathologies.

  6. Temporal shape analysis via the spectral signature.

    PubMed

    Bernardis, Elena; Konukoglu, Ender; Ou, Yangming; Metaxas, Dimitris N; Desjardins, Benoit; Pohl, Kilian M

    2012-01-01

    In this paper, we adapt spectral signatures for capturing morphological changes over time. Advanced techniques for capturing temporal shape changes frequently rely on first registering the sequence of shapes and then analyzing the corresponding set of high dimensional deformation maps. Instead, we propose a simple encoding motivated by the observation that small shape deformations lead to minor refinements in the spectral signature composed of the eigenvalues of the Laplace operator. The proposed encoding does not require registration, since spectral signatures are invariant to pose changes. We apply our representation to the shapes of the ventricles extracted from 22 cine MR scans of healthy controls and Tetralogy of Fallot patients. We then measure the accuracy score of our encoding by training a linear classifier, which outperforms the same classifier based on volumetric measurements. PMID:23286031

  7. Applying temporal network analysis to the venture capital market

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Feng, Ling; Zhu, Rongqian; Stanley, H. Eugene

    2015-10-01

    Using complex network theory to study the investment relationships of venture capital firms has produced a number of significant results. However, previous studies have often neglected the temporal properties of those relationships, which in real-world scenarios play a pivotal role. Here we examine the time-evolving dynamics of venture capital investment in China by constructing temporal networks to represent (i) investment relationships between venture capital firms and portfolio companies and (ii) the syndication ties between venture capital investors. The evolution of the networks exhibits rich variations in centrality, connectivity and local topology. We demonstrate that a temporal network approach provides a dynamic and comprehensive analysis of real-world networks.

  8. Combining qualitative and quantitative spatial and temporal information in a hierarchical structure: Approximate reasoning for plan execution monitoring

    NASA Technical Reports Server (NTRS)

    Hoebel, Louis J.

    1993-01-01

    The problem of plan generation (PG) and the problem of plan execution monitoring (PEM), including updating, queries, and resource-bounded replanning, have different reasoning and representation requirements. PEM requires the integration of qualitative and quantitative information. PEM is the receiving of data about the world in which a plan or agent is executing. The problem is to quickly determine the relevance of the data, the consistency of the data with respect to the expected effects, and if execution should continue. Only spatial and temporal aspects of the plan are addressed for relevance in this work. Current temporal reasoning systems are deficient in computational aspects or expressiveness. This work presents a hybrid qualitative and quantitative system that is fully expressive in its assertion language while offering certain computational efficiencies. In order to proceed, methods incorporating approximate reasoning using hierarchies, notions of locality, constraint expansion, and absolute parameters need be used and are shown to be useful for the anytime nature of PEM.

  9. Applying Knowledge of Quantitative Design and Analysis

    ERIC Educational Resources Information Center

    Baskas, Richard S.

    2011-01-01

    This study compared and contrasted two quantitative scholarly articles in relation to their research designs. Their designs were analyzed by the comparison of research references and research specific vocabulary to describe how various research methods were used. When researching and analyzing quantitative scholarly articles, it is imperative to…

  10. Error Propagation Analysis for Quantitative Intracellular Metabolomics

    PubMed Central

    Tillack, Jana; Paczia, Nicole; Nöh, Katharina; Wiechert, Wolfgang; Noack, Stephan

    2012-01-01

    Model-based analyses have become an integral part of modern metabolic engineering and systems biology in order to gain knowledge about complex and not directly observable cellular processes. For quantitative analyses, not only experimental data, but also measurement errors, play a crucial role. The total measurement error of any analytical protocol is the result of an accumulation of single errors introduced by several processing steps. Here, we present a framework for the quantification of intracellular metabolites, including error propagation during metabolome sample processing. Focusing on one specific protocol, we comprehensively investigate all currently known and accessible factors that ultimately impact the accuracy of intracellular metabolite concentration data. All intermediate steps are modeled, and their uncertainty with respect to the final concentration data is rigorously quantified. Finally, on the basis of a comprehensive metabolome dataset of Corynebacterium glutamicum, an integrated error propagation analysis for all parts of the model is conducted, and the most critical steps for intracellular metabolite quantification are detected. PMID:24957773

  11. Quantitative methods for ecological network analysis.

    PubMed

    Ulanowicz, Robert E

    2004-12-01

    The analysis of networks of ecological trophic transfers is a useful complement to simulation modeling in the quest for understanding whole-ecosystem dynamics. Trophic networks can be studied in quantitative and systematic fashion at several levels. Indirect relationships between any two individual taxa in an ecosystem, which often differ in either nature or magnitude from their direct influences, can be assayed using techniques from linear algebra. The same mathematics can also be employed to ascertain where along the trophic continuum any individual taxon is operating, or to map the web of connections into a virtual linear chain that summarizes trophodynamic performance by the system. Backtracking algorithms with pruning have been written which identify pathways for the recycle of materials and energy within the system. The pattern of such cycling often reveals modes of control or types of functions exhibited by various groups of taxa. The performance of the system as a whole at processing material and energy can be quantified using information theory. In particular, the complexity of process interactions can be parsed into separate terms that distinguish organized, efficient performance from the capacity for further development and recovery from disturbance. Finally, the sensitivities of the information-theoretic system indices appear to identify the dynamical bottlenecks in ecosystem functioning. PMID:15556474

  12. Data compression for speckle correlation interferometry temporal fringe pattern analysis

    SciTech Connect

    Tuck Wah Ng; Kar Tien Ang

    2005-05-01

    Temporal fringe pattern analysis is gaining prominence in speckle correlation interferometry, in particular for transient phenomena studies. This form of analysis, nevertheless, necessitates large data storage. Current compression schemes do not facilitate efficient data retrieval and may even result in important data loss. We describe a novel compression scheme that does not result in crucial data loss and allows for the efficient retrieval of data for temporal fringe analysis. In sample tests with digital speckle interferometry on fringe patterns of a plate and of a cantilever beam subjected to temporal phase and load evolution, respectively, we achieved a compression ratio of 1.6 without filtering out any data from discontinuous and low fringe modulation spatial points. By eliminating 38% of the data from discontinuous and low fringe modulation spatial points, we attained a significant compression ratio of 2.4.

  13. Qualitative, quantitative and temporal study of cutting agents for cocaine and heroin over 9 years.

    PubMed

    Broséus, Julian; Gentile, Natacha; Bonadio Pont, Federica; Garcia Gongora, Juan Manuel; Gasté, Laëtitia; Esseiva, Pierre

    2015-12-01

    Forensic laboratories mainly focus on the qualification and the quantitation of the illicit drug under analysis as both aspects are used for judiciary purposes. Therefore, information related to cutting agents (adulterants and diluents) detected in illicit drugs is limited in the forensic literature. This article discusses the type and frequency of adulterants and diluents detected in more than 6000 cocaine specimens and 3000 heroin specimens, confiscated in western Switzerland from 2006 to 2014. The results show a homogeneous and quite unchanging adulteration for heroin, while for cocaine it could be characterised as heterogeneous and relatively dynamic. Furthermore, the results indicate that dilution affects more cocaine than heroin. Therefore, the results provided by this study tend to reveal differences between the respective structures of production or distribution of cocaine and heroin. This research seeks to promote the systematic analysis of cutting agents by forensic laboratories. Collecting and processing data related to the presence of cutting agents in illicit drug specimens produces relevant information to understand and to compare the structure of illicit drug markets. PMID:26448535

  14. Using repeated sources to quantitatively determine temporal change of medium properties: Theory and an example

    NASA Astrophysics Data System (ADS)

    Long, Hui; Wen, Lianxing

    2012-09-01

    We develop a theory of using difference wavefields of repeated sources to locate and quantify temporal medium change and apply the theory to locate temporal change of seismic properties beneath the Japan subduction zone using repeated earthquakes. Our theory states the difference wavefields of two repeated sources in a temporally changed medium can be equivalently treated as wavefields propagating from conceptual sources, with their location at the place of temporal change and their strengths equal to the product of magnitude of medium property change and magnitude of the initial wavefields from the repeated sources. When the medium change extends to a finite region, the conceptual sources become volumetric sources distributed over the region of the medium change and propagating in the direction of the initial wave. The conceptualization establishes a theoretical framework for possible applications of using difference wavefields to locate and quantify temporal medium changes in geological sciences, ultrasonic experiments, civil engineering and medical imaging. We search repeating earthquakes occurring in the Japan subduction zone, formulate an empirical procedure to extract the difference wavefields between repeating earthquakes and determine temporal change of seismic properties using a back-projection method. We locate the temporal change of seismic properties beneath the Japan subduction zone to be at (37.2°N, 142°E), and estimate the magnitude of the conceptual body force associated with the temporal change to be 1.15 × 1010N, or as a reference, a 0.87% density change for an assumed volume of temporal change of 103 km3.

  15. Geostatistical Analysis of Spatio-Temporal Forest Fire Data

    NASA Astrophysics Data System (ADS)

    Vega Orozco, Carmen D.; Kanevski, Mikhail; Tonini, Marj; Conedera, Marc

    2010-05-01

    Forest fire is one of the major phenomena causing degradation of environment, landscape, natural ecosystems, human health and economy. One of the main topic in forest fire data studies deals with the detection, analysis and modelling of spatio-temporal patterns of clustering. Spatial patterns of forest fire locations, their sizes and their sequence in time are of great interest for fire prediction and for forest fire management planning and distribution in optimal way necessary resources. Currently, fires can be analyzed and monitored by using different statistical tools, for example, Ripley's k-function, fractals, Allan factor, scan statistics, etc. Some of them are adapted to temporal or spatial data and are either local or global. In the present study the main attention is paid to the application of geostatistical tools - variography and methods for the analysis of monitoring networks (MN) clustering techniques (topological, statistical and fractal measures), in order to detect and to characterize spatio-temporal forest fire patterns. The main studies performed include: a) analysis of forest fires temporal sequences; b) spatial clustering of forest fires; c) geostatistical spatial analysis of burnt areas. Variography was carried out both for temporal and spatial data. Real case study is based on the forest-fire event data from Canton of Ticino (Switzerland) for a period of 1969 to 2008. The results from temporal analysis show the presence of clustering and seasonal periodicities. Comprehensive analysis of the variograms shows an anisotropy in the direction 30° East-North where smooth changes are detected, while on the direction 30° North-West a greater variability was identified. The research was completed with an application of different MN analysis techniques including, analysis of distributions of distances between events, Morisita Index (MI), fractal dimensions (sandbox counting and box counting methods) and functional fractal dimensions, adapted and

  16. Variability of Soil Temperature: A Spatial and Temporal Analysis.

    ERIC Educational Resources Information Center

    Walsh, Stephen J.; And Others

    1991-01-01

    Discusses an analysis of the relationship of soil temperatures at 3 depths to various climatic variables along a 200-kilometer transect in west-central Oklahoma. Reports that temperature readings increased from east to west. Concludes that temperature variations were explained by a combination of spatial, temporal, and biophysical factors. (SG)

  17. Some Epistemological Considerations Concerning Quantitative Analysis

    ERIC Educational Resources Information Center

    Dobrescu, Emilian

    2008-01-01

    This article presents the author's address at the 2007 "Journal of Applied Quantitative Methods" ("JAQM") prize awarding festivity. The festivity was included in the opening of the 4th International Conference on Applied Statistics, November 22, 2008, Bucharest, Romania. In the address, the author reflects on three theses that question the…

  18. Quantitative Analysis of Radar Returns from Insects

    NASA Technical Reports Server (NTRS)

    Riley, J. R.

    1979-01-01

    When a number of flying insects is low enough to permit their resolution as individual radar targets, quantitative estimates of their aerial density are developed. Accurate measurements of heading distribution using a rotating polarization radar to enhance the wingbeat frequency method of identification are presented.

  19. Quantitative analysis of comparative genomic hybridization

    SciTech Connect

    Manoir, S. du; Bentz, M.; Joos, S. |

    1995-01-01

    Comparative genomic hybridization (CGH) is a new molecular cytogenetic method for the detection of chromosomal imbalances. Following cohybridization of DNA prepared from a sample to be studied and control DNA to normal metaphase spreads, probes are detected via different fluorochromes. The ratio of the test and control fluorescence intensities along a chromosome reflects the relative copy number of segments of a chromosome in the test genome. Quantitative evaluation of CGH experiments is required for the determination of low copy changes, e.g., monosomy or trisomy, and for the definition of the breakpoints involved in unbalanced rearrangements. In this study, a program for quantitation of CGH preparations is presented. This program is based on the extraction of the fluorescence ratio profile along each chromosome, followed by averaging of individual profiles from several metaphase spreads. Objective parameters critical for quantitative evaluations were tested, and the criteria for selection of suitable CGH preparations are described. The granularity of the chromosome painting and the regional inhomogeneity of fluorescence intensities in metaphase spreads proved to be crucial parameters. The coefficient of variation of the ratio value for chromosomes in balanced state (CVBS) provides a general quality criterion for CGH experiments. Different cutoff levels (thresholds) of average fluorescence ratio values were compared for their specificity and sensitivity with regard to the detection of chromosomal imbalances. 27 refs., 15 figs., 1 tab.

  20. Quantitative analysis of diffusion tensor imaging (DTI) using statistical parametric mapping (SPM) for brain disorders

    NASA Astrophysics Data System (ADS)

    Lee, Jae-Seung; Im, In-Chul; Kang, Su-Man; Goo, Eun-Hoe; Kwak, Byung-Joon

    2013-07-01

    This study aimed to quantitatively analyze data from diffusion tensor imaging (DTI) using statistical parametric mapping (SPM) in patients with brain disorders and to assess its potential utility for analyzing brain function. DTI was obtained by performing 3.0-T magnetic resonance imaging for patients with Alzheimer's disease (AD) and vascular dementia (VD), and the data were analyzed using Matlab-based SPM software. The two-sample t-test was used for error analysis of the location of the activated pixels. We compared regions of white matter where the fractional anisotropy (FA) values were low and the apparent diffusion coefficients (ADCs) were increased. In the AD group, the FA values were low in the right superior temporal gyrus, right inferior temporal gyrus, right sub-lobar insula, and right occipital lingual gyrus whereas the ADCs were significantly increased in the right inferior frontal gyrus and right middle frontal gyrus. In the VD group, the FA values were low in the right superior temporal gyrus, right inferior temporal gyrus, right limbic cingulate gyrus, and right sub-lobar caudate tail whereas the ADCs were significantly increased in the left lateral globus pallidus and left medial globus pallidus. In conclusion by using DTI and SPM analysis, we were able to not only determine the structural state of the regions affected by brain disorders but also quantitatively analyze and assess brain function.

  1. Advancing sensitivity analysis to precisely characterize temporal parameter dominance

    NASA Astrophysics Data System (ADS)

    Guse, Björn; Pfannerstill, Matthias; Strauch, Michael; Reusser, Dominik; Lüdtke, Stefan; Volk, Martin; Gupta, Hoshin; Fohrer, Nicola

    2016-04-01

    Parameter sensitivity analysis is a strategy for detecting dominant model parameters. A temporal sensitivity analysis calculates daily sensitivities of model parameters. This allows a precise characterization of temporal patterns of parameter dominance and an identification of the related discharge conditions. To achieve this goal, the diagnostic information as derived from the temporal parameter sensitivity is advanced by including discharge information in three steps. In a first step, the temporal dynamics are analyzed by means of daily time series of parameter sensitivities. As sensitivity analysis method, we used the Fourier Amplitude Sensitivity Test (FAST) applied directly onto the modelled discharge. Next, the daily sensitivities are analyzed in combination with the flow duration curve (FDC). Through this step, we determine whether high sensitivities of model parameters are related to specific discharges. Finally, parameter sensitivities are separately analyzed for five segments of the FDC and presented as monthly averaged sensitivities. In this way, seasonal patterns of dominant model parameter are provided for each FDC segment. For this methodical approach, we used two contrasting catchments (upland and lowland catchment) to illustrate how parameter dominances change seasonally in different catchments. For all of the FDC segments, the groundwater parameters are dominant in the lowland catchment, while in the upland catchment the controlling parameters change seasonally between parameters from different runoff components. The three methodical steps lead to clear temporal patterns, which represent the typical characteristics of the study catchments. Our methodical approach thus provides a clear idea of how the hydrological dynamics are controlled by model parameters for certain discharge magnitudes during the year. Overall, these three methodical steps precisely characterize model parameters and improve the understanding of process dynamics in hydrological

  2. Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size

    SciTech Connect

    Zhang, Haizhen; Burnum, Kristin E.; Luna, Maria L.; Petritis, Brianne O.; Kim, Jong Seo; Qian, Weijun; Moore, Ronald J.; Heredia-Langner, Alejandro; Webb-Robertson, Bobbie-Jo M.; Thrall, Brian D.; Camp, David G.; Smith, Richard D.; Pounds, Joel G.; Liu, Tao

    2011-12-01

    In biofluids (e.g., blood plasma) nanoparticles are readily embedded in layers of proteins that can affect their biological activity and biocompatibility. Herein, we report a study on the interactions between human plasma proteins and nanoparticles with a controlled systematic variation of properties using stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS) based quantitative proteomics. Novel protocol has been developed to simplify the isolation of nanoparticle bound proteins and improve the reproducibility. Plasma proteins associated with polystyrene nanoparticles with three different surface chemistries and two sizes as well as for four different exposure times (for a total of 24 different samples) were identified and quantified by LC-MS analysis. Quantitative comparison of relative protein abundances were achieved by spiking an 18 O-labeled 'universal reference' into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantitation across the sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive pattern that classifies the nanoparticles based on their surface properties and size. In addition, data on the temporal study indicated that the stable protein 'corona' that was isolated for the quantitative analysis appeared to be formed in less than 5 minutes. The comprehensive results obtained herein using quantitative proteomics have potential implications towards predicting nanoparticle biocompatibility.

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  4. Structural and quantitative analysis of Equisetum alkaloids.

    PubMed

    Cramer, Luise; Ernst, Ludger; Lubienski, Marcus; Papke, Uli; Schiebel, Hans-Martin; Jerz, Gerold; Beuerle, Till

    2015-08-01

    Equisetum palustre L. is known for its toxicity for livestock. Several studies in the past addressed the isolation and identification of the responsible alkaloids. So far, palustrine (1) and N(5)-formylpalustrine (2) are known alkaloids of E. palustre. A HPLC-ESI-MS/MS method in combination with simple sample work-up was developed to identify and quantitate Equisetum alkaloids. Besides the two known alkaloids six related alkaloids were detected in different Equisetum samples. The structure of the alkaloid palustridiene (3) was derived by comprehensive 1D and 2D NMR experiments. N(5)-Acetylpalustrine (4) was also thoroughly characterized by NMR for the first time. The structure of N(5)-formylpalustridiene (5) is proposed based on mass spectrometry results. Twenty-two E. palustre samples were screened by a HPLC-ESI-MS/MS method after development of a simple sample work-up and in most cases the set of all eight alkaloids were detected in all parts of the plant. A high variability of the alkaloid content and distribution was found depending on plant organ, plant origin and season ranging from 88 to 597mg/kg dried weight. However, palustrine (1) and the alkaloid palustridiene (3) always represented the main alkaloids. For the first time, a comprehensive identification, quantitation and distribution of Equisetum alkaloids was achieved. PMID:25823584

  5. Quantitative measurement of zinc secretion from pancreatic islets with high temporal resolution using droplet-based microfluidics

    PubMed Central

    Easley, Christopher J.; Rocheleau, Jonathan V.; Head, W. Steven; Piston, David W.

    2009-01-01

    We assayed glucose-stimulated insulin secretion (GSIS) from live, murine islets of Langerhans in microfluidic devices by the downstream formation of aqueous droplets. Zinc ions, which are co-secreted with insulin from β-cells, were quantitatively measured from single islets with high temporal resolution using a fluorescent indicator, FluoZin-3. Real-time storage of secretions into droplets (volume of 0.470 ± 0.009 nL) effectively preserves the temporal chemical information, allowing reconstruction of the secretory time record. The use of passive flow control within the device removes the need for syringe pumps, requiring only a single handheld syringe. Under stimulatory glucose levels (11 mM), bursts of zinc as high as ~800 fg islet−1 min−1 were measured. Treatment with diazoxide effectively blocked zinc secretion, as expected. High temporal resolution reveals two major classes of oscillations in secreted zinc, with predominate periods at ~20-40 s and ~ 5-10 min. The more rapid oscillation periods match closely with those of intraislet calcium oscillations, while the slower oscillations are consistent with insulin pulses typically measured in bulk islet experiments or in the bloodstream. This droplet sampling technique should be widely applicable to time-resolved cellular secretion measurements, either in real-time or for post-processing. PMID:19874061

  6. Joint association analysis of bivariate quantitative and qualitative traits.

    PubMed

    Yuan, Mengdie; Diao, Guoqing

    2011-01-01

    Univariate genome-wide association analysis of quantitative and qualitative traits has been investigated extensively in the literature. In the presence of correlated phenotypes, it is more intuitive to analyze all phenotypes simultaneously. We describe an efficient likelihood-based approach for the joint association analysis of quantitative and qualitative traits in unrelated individuals. We assume a probit model for the qualitative trait, under which an unobserved latent variable and a prespecified threshold determine the value of the qualitative trait. To jointly model the quantitative and qualitative traits, we assume that the quantitative trait and the latent variable follow a bivariate normal distribution. The latent variable is allowed to be correlated with the quantitative phenotype. Simultaneous modeling of the quantitative and qualitative traits allows us to make more precise inference on the pleiotropic genetic effects. We derive likelihood ratio tests for the testing of genetic effects. An application to the Genetic Analysis Workshop 17 data is provided. The new method yields reasonable power and meaningful results for the joint association analysis of the quantitative trait Q1 and the qualitative trait disease status at SNPs with not too small MAF. PMID:22373162

  7. Quantitative data analysis of ESAR data

    NASA Astrophysics Data System (ADS)

    Phruksahiran, N.; Chandra, M.

    2013-07-01

    A synthetic aperture radar (SAR) data processing uses the backscattered electromagnetic wave to map radar reflectivity of the ground surface. The polarization property in radar remote sensing was used successfully in many applications, especially in target decomposition. This paper presents a case study to the experiments which are performed on ESAR L-Band full polarized data sets from German Aerospace Center (DLR) to demonstrate the potential of coherent target decomposition and the possibility of using the weather radar measurement parameter, such as the differential reflectivity and the linear depolarization ratio to obtain the quantitative information of the ground surface. The raw data of ESAR has been processed by the SAR simulator developed using MATLAB program code with Range-Doppler algorithm.

  8. Qualitative and quantitative analysis of endocytic recycling.

    PubMed

    Reineke, James B; Xie, Shuwei; Naslavsky, Naava; Caplan, Steve

    2015-01-01

    Endocytosis, which encompasses the internalization and sorting of plasma membrane (PM) lipids and proteins to distinct membrane-bound intracellular compartments, is a highly regulated and fundamental cellular process by which eukaryotic cells dynamically regulate their PM composition. Indeed, endocytosis is implicated in crucial cellular processes that include proliferation, migration, and cell division as well as maintenance of tissue homeostasis such as apical-basal polarity. Once PM constituents have been taken up into the cell, either via clathrin-dependent endocytosis (CDE) or clathrin-independent endocytosis (CIE), they typically have two fates: degradation through the late-endosomal/lysosomal pathway or returning to the PM via endocytic recycling pathways. In this review, we will detail experimental procedures that allow for both qualitative and quantitative assessment of endocytic recycling of transmembrane proteins internalized by CDE and CIE, using the HeLa cervical cancer cell line as a model system. PMID:26360033

  9. Towards a Quantitative OCT Image Analysis

    PubMed Central

    Garcia Garrido, Marina; Beck, Susanne C.; Mühlfriedel, Regine; Julien, Sylvie; Schraermeyer, Ulrich; Seeliger, Mathias W.

    2014-01-01

    Background Optical coherence tomography (OCT) is an invaluable diagnostic tool for the detection and follow-up of retinal pathology in patients and experimental disease models. However, as morphological structures and layering in health as well as their alterations in disease are complex, segmentation procedures have not yet reached a satisfactory level of performance. Therefore, raw images and qualitative data are commonly used in clinical and scientific reports. Here, we assess the value of OCT reflectivity profiles as a basis for a quantitative characterization of the retinal status in a cross-species comparative study. Methods Spectral-Domain Optical Coherence Tomography (OCT), confocal Scanning-La­ser Ophthalmoscopy (SLO), and Fluorescein Angiography (FA) were performed in mice (Mus musculus), gerbils (Gerbillus perpadillus), and cynomolgus monkeys (Macaca fascicularis) using the Heidelberg Engineering Spectralis system, and additional SLOs and FAs were obtained with the HRA I (same manufacturer). Reflectivity profiles were extracted from 8-bit greyscale OCT images using the ImageJ software package (http://rsb.info.nih.gov/ij/). Results Reflectivity profiles obtained from OCT scans of all three animal species correlated well with ex vivo histomorphometric data. Each of the retinal layers showed a typical pattern that varied in relative size and degree of reflectivity across species. In general, plexiform layers showed a higher level of reflectivity than nuclear layers. A comparison of reflectivity profiles from specialized retinal regions (e.g. visual streak in gerbils, fovea in non-human primates) with respective regions of human retina revealed multiple similarities. In a model of Retinitis Pigmentosa (RP), the value of reflectivity profiles for the follow-up of therapeutic interventions was demonstrated. Conclusions OCT reflectivity profiles provide a detailed, quantitative description of retinal layers and structures including specialized retinal regions

  10. Proxy-to-proxy calibration: Increasing the temporal resolution of quantitative climate reconstructions

    PubMed Central

    von Gunten, Lucien; D'Andrea, William J.; Bradley, Raymond S.; Huang, Yongsong

    2012-01-01

    High-resolution paleoclimate reconstructions are often restricted by the difficulties of sampling geologic archives in great detail and the analytical costs of processing large numbers of samples. Using sediments from Lake Braya Sø, Greenland, we introduce a new method that provides a quantitative high-resolution paleoclimate record by combining measurements of the alkenone unsaturation index () with non-destructive scanning reflectance spectroscopic measurements in the visible range (VIS-RS). The proxy-to-proxy (PTP) method exploits two distinct calibrations: the in situ calibration of to lake water temperature and the calibration of scanning VIS-RS data to down core data. Using this approach, we produced a quantitative temperature record that is longer and has 5 times higher sampling resolution than the original time series, thereby allowing detection of temperature variability in frequency bands characteristic of the AMO over the past 7,000 years. PMID:22934132

  11. Temporal lobe in human aging: A quantitative protein profiling study of samples from Chinese Human Brain Bank.

    PubMed

    Xu, Benhong; Xiong, Feng; Tian, Rui; Zhan, Shaohua; Gao, Yanpan; Qiu, Wenying; Wang, Renzhi; Ge, Wei; Ma, Chao

    2016-01-01

    The temporal lobe is a portion of the cerebral cortex with critical functionality. The age-related protein profile changes in the human temporal lobe have not been previously studied. This 4-plex tandem mass tag labeled proteomic study was performed on samples of temporal lobe from Chinese donors. Tissue samples were assigned to four age groups: Group A (the young, age: 34±13 years); Group B (the elderly, 62±5 years); Group C (the aged, 84±4 years) and Group D (the old, 95±1 years). Pooled samples from the different groups were subjected to proteomics and bioinformatics analysis to identify age-related changes in protein expression and associated pathways. We isolated 5072 proteins, and found that 67 proteins were downregulated and 109 proteins were upregulated in one or more groups during the aging process. Western blotting assays were performed to verify the proteomic results. Bioinformatic analysis identified proteins involved in neuronal degeneration, including proteins involved in neuronal firing, myelin sheath damage, and cell structure stability. We also observed the accumulation of extracellular matrix and lysosomal proteins which imply the occurrence of fibrosis and autophagy. Our results suggest a series of changes across a wide range of proteins in the human temporal lobe that may relate to aging and age-related neurodegenerative disorders. PMID:26631761

  12. Statistical Analysis on Temporal Properties of BL Lacertae

    NASA Astrophysics Data System (ADS)

    Guo, Yu Cheng; Hu, Shao Ming; Li, Yu Tong; Chen, Xu

    2016-04-01

    A comprehensive temporal analysis has been performed on optical light curves of BL Lacertae in B, V and R bands. The light curves were denoised by Gaussian smoothing and decomposed into individual flares using an exponential profile. Asymmetry, duration, peak flux and equivalent energy output of flares were measured and the frequency distributions are presented. Most optical flares of BL Lacertae are highly symmetric, with a weak tendency towards gradual rises and rapid decays. The distribution of flare durations is not random but consistent with a gamma distribution. Peak fluxes and energy outputs of flares all follow lognormal distribution. A positive correlation is detected between flare durations and peak fluxes. The temporal properties of BL Lacertae provide evidence of the stochastic magnetohydrodynamic process in accretion disk and jet. Results presented here can serve as constraints on physical models attempting to interpreting blazar variations.

  13. Statistical analysis of the temporal properties of BL Lacertae

    NASA Astrophysics Data System (ADS)

    Guo, Yu Cheng; Hu, Shao Ming; Li, Yu Tong; Chen, Xu

    2016-08-01

    A comprehensive temporal analysis has been performed on optical light curves of BL Lacertae in the B, V and R bands. The light curves were denoised by Gaussian smoothing and decomposed into individual flares using an exponential profile. The asymmetry, duration, peak flux and equivalent energy output of flares were measured and the frequency distributions presented. Most optical flares of BL Lacertae are highly symmetric, with a weak tendency towards gradual rises and rapid decays. The distribution of flare durations is not random, but consistent with a gamma distribution. Peak fluxes and energy outputs of flares all follow a log-normal distribution. A positive correlation is detected between flare durations and peak fluxes. The temporal properties of BL Lacertae provide evidence of the stochastic magnetohydrodynamic process in the accretion disc and jet.The results presented here can serve as constraints on physical models attempting to interpret blazar variations.

  14. Multiple quantitative trait analysis using bayesian networks.

    PubMed

    Scutari, Marco; Howell, Phil; Balding, David J; Mackay, Ian

    2014-09-01

    Models for genome-wide prediction and association studies usually target a single phenotypic trait. However, in animal and plant genetics it is common to record information on multiple phenotypes for each individual that will be genotyped. Modeling traits individually disregards the fact that they are most likely associated due to pleiotropy and shared biological basis, thus providing only a partial, confounded view of genetic effects and phenotypic interactions. In this article we use data from a Multiparent Advanced Generation Inter-Cross (MAGIC) winter wheat population to explore Bayesian networks as a convenient and interpretable framework for the simultaneous modeling of multiple quantitative traits. We show that they are equivalent to multivariate genetic best linear unbiased prediction (GBLUP) and that they are competitive with single-trait elastic net and single-trait GBLUP in predictive performance. Finally, we discuss their relationship with other additive-effects models and their advantages in inference and interpretation. MAGIC populations provide an ideal setting for this kind of investigation because the very low population structure and large sample size result in predictive models with good power and limited confounding due to relatedness. PMID:25236454

  15. Quantitative infrared analysis of hydrogen fluoride

    SciTech Connect

    Manuta, D.M.

    1997-04-01

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

  16. Quantitative multi-modal NDT data analysis

    SciTech Connect

    Heideklang, René; Shokouhi, Parisa

    2014-02-18

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

  17. Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

    PubMed Central

    Jensen, Thomas; Holten-Rossing, Henrik; Svendsen, Ida M H; Jacobsen, Christina; Vainer, Ben

    2016-01-01

    Background: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including staining may benefit. Methods: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm are presented. Results: It is shown that the autofluorescence intensity of unstained microsections at two different wavelengths is a suitable starting point for automated digital analysis of myocytes, fibrous tissue, lipofuscin, and the extracellular compartment. The output of the method is absolute quantitation along with accurate outlines of above-mentioned components. The digital quantitations are verified by comparison to point grid quantitations performed on the microsections after Van Gieson staining. Conclusion: The presented method is amply described as a prestain multicomponent quantitation and outlining tool for histological sections of cardiac tissue. The main perspective is the opportunity for combination with digital analysis of stained microsections, for which the method may provide an accurate digital framework. PMID:27141321

  18. The quantitative failure of human reliability analysis

    SciTech Connect

    Bennett, C.T.

    1995-07-01

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

  19. A Quantitative Analysis of Countries' Research Strengths

    ERIC Educational Resources Information Center

    Saxena, Anurag; Brazer, S. David; Gupta, B. M.

    2009-01-01

    This study employed a multidimensional analysis to evaluate transnational patterns of scientific research to determine relative research strengths among widely varying nations. Findings from this study may inform national policy with regard to the most efficient use of scarce national research resources, including government and private funding.…

  20. Multiscale recurrence analysis of spatio-temporal data

    NASA Astrophysics Data System (ADS)

    Riedl, M.; Marwan, N.; Kurths, J.

    2015-12-01

    The description and analysis of spatio-temporal dynamics is a crucial task in many scientific disciplines. In this work, we propose a method which uses the mapogram as a similarity measure between spatially distributed data instances at different time points. The resulting similarity values of the pairwise comparison are used to construct a recurrence plot in order to benefit from established tools of recurrence quantification analysis and recurrence network analysis. In contrast to other recurrence tools for this purpose, the mapogram approach allows the specific focus on different spatial scales that can be used in a multi-scale analysis of spatio-temporal dynamics. We illustrate this approach by application on mixed dynamics, such as traveling parallel wave fronts with additive noise, as well as more complicate examples, pseudo-random numbers and coupled map lattices with a semi-logistic mapping rule. Especially the complicate examples show the usefulness of the multi-scale consideration in order to take spatial pattern of different scales and with different rhythms into account. So, this mapogram approach promises new insights in problems of climatology, ecology, or medicine.

  1. Temporal Analysis of Atmospheric Data Using Open Standards

    NASA Astrophysics Data System (ADS)

    Campalani, P.; Beccati, A.; Mantovani, S.; Baumann, P.

    2014-04-01

    The continuous growth of remotely sensed data raises the need for efficient ways of accessing data archives. The classical model of accessing remote sensing (satellite) archives via distribution of large files is increasingly making way for a more dynamic and interactive data service. A challenge, though, is interoperability of such services, in particular when multi-dimensional data and advanced processing are involved. Individually crafted service interfaces typically do not allow substitution and combination of services. Open standards can provide a way forward if they are powerful enough to address both data and processing model. The OGC Web Coverage Service (WCS) is a modular service suite which provides high-level interface definitions for data access, subsetting, filtering, and processing of spatio-temporal raster data. WCS based service interfaces to data archives deliver data in their original semantics useful for further client-side processing, as opposed to the Web Map Service (WMS) (de la Beaujardière, 2006) which performs a pre-rendering into images only useful for display to humans. In this paper we present a case study where the OGC coverage data and service model defines the client/server interface for a climate data service. In particular, we show how flexible temporal analysis can be performed efficiently on massive spatio-temporal coverage objects. This service, which is operational on a several Terabyte data holding, has been established as part of the EarthServer initiative focusing on Big Data in the Earth and Planetary sciences.

  2. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    ERIC Educational Resources Information Center

    Katharaki, Maria; Katharakis, George

    2010-01-01

    In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

  3. High frequency localised "hot spots" in temporal lobes of patients with intractable tinnitus: a quantitative electroencephalographic (QEEG) study.

    PubMed

    Ashton, Heather; Reid, Keith; Marsh, Richard; Johnson, Ian; Alter, Kai; Griffiths, Tim

    2007-10-01

    Tinnitus, the perception of noise in the absence of an external auditory stimulus, is common, frequently distressing and often intractable. It is associated with a number of conditions including deafness but may arise spontaneously. Brain imaging studies indicate increased neuronal excitability and decreased density of benzodiazepine receptors in temporal (auditory) cortex but the source and mechanism of such changes are unknown. Various electroencephalographic (EEG) abnormalities involving temporal lobe and other brain areas have been described but recordings have been limited to standard EEG wave bands up to frequencies of 22Hz. This clinical study of otherwise healthy patients with intractable unilateral tinnitus, using quantitative EEG power spectral mapping (QEEG), identified discrete localised unilateral foci of high frequency activity in the gamma range (>40-80Hz) over the auditory cortex in eight patients experiencing tinnitus during recording. These high frequency "hot spots" were not present in 25 subjects without tinnitus. The results suggest that further EEG investigations should include recordings in the gamma frequency range since such high frequency oscillations are believed to be necessary for perception. Identification of "hot spots" in tinnitus patients would provide a means for monitoring the effects of new treatments. These findings may also provide a model for exploration of more complex phenomena such as verbal and musical hallucinations. PMID:17888572

  4. Influence of corrosion layers on quantitative analysis

    NASA Astrophysics Data System (ADS)

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

    2005-09-01

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

  5. Quantitative transcriptome analysis using RNA-seq.

    PubMed

    Külahoglu, Canan; Bräutigam, Andrea

    2014-01-01

    RNA-seq has emerged as the technology of choice to quantify gene expression. This technology is a convenient accurate tool to quantify diurnal changes in gene expression, gene discovery, differential use of promoters, and splice variants for all genes expressed in a single tissue. Thus, RNA-seq experiments provide sequence information and absolute expression values about transcripts in addition to relative quantification available with microarrays or qRT-PCR. The depth of information by sequencing requires careful assessment of RNA intactness and DNA contamination. Although the RNA-seq is comparatively recent, a standard analysis framework has emerged with the packages of Bowtie2, TopHat, and Cufflinks. With rising popularity of RNA-seq tools have become manageable for researchers without much bioinformatical knowledge or programming skills. Here, we present a workflow for a RNA-seq experiment from experimental planning to biological data extraction. PMID:24792045

  6. Quantitative and temporal relationships of egg production and sound production by black drum Pogonias cromis.

    PubMed

    Locascio, J V; Burghart, S; Mann, D A

    2012-09-01

    The timing and levels of black drum Pogonias cromis sound production and egg production were compared in an estuarine canal basin of Cape Coral in south-west Florida. Surface plankton samples were collected hourly from 1800 to 0400 on two consecutive nights while continuous acoustic recordings were made simultaneously at five locations in the canal basin. Five pairs of nights were sampled during a part of the spawning season from late January to early April 2006. Pogonias cromis sound production and egg production occurred on all evenings that samples were collected; however, both the timing and levels of sound production were negatively associated with those of egg production. Egg production estimates ranged from a low of 4·8 eggs m(-3) in February to a high of 2889·2 eggs m(-3) in April. Conversely, maximum nightly sound pressure levels (SPL) ranged from a low of 89·5 dB in April to a high of 131·9 dB (re: 1 µPa) in February. The temporal centre of sound production was relatively stable among all nights sampled but spawning occurred earlier in the day as the season progressed and exhibited a strong, positive association with increased water temperature. The negative relationship between the levels of sound production and egg production was unexpected given the usefulness of sound production as a proxy for reproduction on a seasonal basis and may possibly be explained by differences in the spawning potential of the female population in the study area on nights sampled. Egg mortality rates increased throughout the season and were positively associated with densities of hydrozoans and ctenophores. PMID:22957862

  7. Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

    PubMed

    Gunar, O V; Sakhno, N G

    2015-12-30

    The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. PMID:26456251

  8. Quantitative surface spectroscopic analysis of multicomponent polymers

    NASA Astrophysics Data System (ADS)

    Zhuang, Hengzhong

    Angle-dependent electron spectroscopy for chemical analysis (ESCA) has been successfully used to examine the surface compositional gradient of a multicomponent polymer. However, photoelectron intensities detected at each take-off angle of ESCA measurements are convoluted signals. The convoluted nature of the signal distorts depth profiles for samples having compositional gradients. To recover the true concentration profiles for the samples, a deconvolution program has been described in Chapter 2. The compositional profiles of two classes of important multicomponent polymers, i.e., poly(dimethysiloxane urethane) (PU-DMS) segmented copolymers and fluorinated poly(amide urethane) block copolymers, are achieved using this program. The effects of the polymer molecular structure and the processing variation on its surface compositional profile have been studied. Besides surface composition, it is desirable to know whether the distribution of segment or block lengths at the surface is different than in the bulk, because this aspect of surface structure may lead to properties different than that predicted simply by knowledge of the surface composition and the bulk structure. In Chapter 3, we pioneered the direct determination of the distribution of polydimethylsiloxane (PDMS) segment lengths at the surface of PU-DMS using time-of-flight secondary ion mass spectrometry (SUMS). Exciting preliminary results are provided: for the thick film of PU-DMS with nominal MW of PDMS = 1000, the distribution of the PDMS segment lengths at the surface is nearly identical to that in the bulk, whereas in the case of the thick films of PU-DMS with nominal MW of PDMS = 2400, only those PDMS segments with MW of ca. 1000 preferentially segregated at the surface. As a potential minimal fouling coating or biocompatible cardio-vascular materials, PU-DMS copolymers eventually come into contact with water once in use. Could such an environmental change (from air to aqueous) induce any undesirable

  9. Quantitative analysis of in vivo cell proliferation.

    PubMed

    Cameron, Heather A

    2006-11-01

    Injection and immunohistochemical detection of 5-bromo-2'-deoxyuridine (BrdU) has become the standard method for studying the birth and survival of neurons, glia, and other cell types in the nervous system. BrdU, a thymidine analog, becomes stably incorporated into DNA during the S-phase of mitosis. Because DNA containing BrdU can be specifically recognized by antibodies, this method allows dividing cells to be marked at any given time and then identified at time points from a few minutes to several years later. BrdU immunohistochemistry is suitable for cell counting to examine the regulation of cell proliferation and cell fate. It can be combined with labeling by other antibodies, allowing confocal analysis of cell phenotype or expression of other proteins. The potential for nonspecific labeling and toxicity are discussed. Although BrdU immunohistochemistry has almost completely replaced tritiated thymidine autoradiography for labeling dividing cells, this method and situations in which it is still useful are also described. PMID:18428635

  10. [Qualitative and quantitative gamma-hydroxybutyrate analysis].

    PubMed

    Petek, Maja Jelena; Vrdoljak, Ana Lucić

    2006-12-01

    Gamma-hydroxybutyrate (GHB) is a naturally occurring compound present in the brain and peripheral tissues of mammals. It is a minor metabolite and precursor of gamma-aminobutyric acid (GABA). Just as GABA, GHB is believed to play a role in neurotransmission. GHB was first synthesized in vitro in 1960, when it revealed depressive and hypnotic effects on the central nervous system. In 1960s it was used as an anaesthetic and later as an alternative to anabolic steroids, in order to enhance muscle growth. However, after it was shown that it caused strong physical dependence and severe side effects, GHB was banned. For the last fifteen years, GHB has been abused for its intoxicating effects such as euphoria, reduced inhibitions and sedation. Illicitly it is available as white powder or as clear liquid. Paradoxically GHB can easily be manufactured from its precursor gamma-butyrolactone (GBL), which has not yet been banned. Because of many car accidents and criminal acts in which it is involved, GHB has become an important object of forensic laboratory analysis. This paper describes gas and liquid chromatography, infrared spectroscopy, microscopy, colourimetry and nuclear magnetic resonance as methods for detection and quantification of GHB in urine and illicit products. PMID:17265679

  11. Control of separation and quantitative analysis by GC-FTIR

    NASA Astrophysics Data System (ADS)

    Semmoud, A.; Huvenne, Jean P.; Legrand, P.

    1992-03-01

    Software for 3-D representations of the 'Absorbance-Wavenumber-Retention time' is used to control the quality of the GC separation. Spectral information given by the FTIR detection allows the user to be sure that a chromatographic peak is 'pure.' The analysis of peppermint essential oil is presented as an example. This assurance is absolutely required for quantitative applications. In these conditions, we have worked out a quantitative analysis of caffeine. Correlation coefficients between integrated absorbance measurements and concentration of caffeine are discussed at two steps of the data treatment.

  12. A quantitative analysis of the F18 flight control system

    NASA Technical Reports Server (NTRS)

    Doyle, Stacy A.; Dugan, Joanne B.; Patterson-Hine, Ann

    1993-01-01

    This paper presents an informal quantitative analysis of the F18 flight control system (FCS). The analysis technique combines a coverage model with a fault tree model. To demonstrate the method's extensive capabilities, we replace the fault tree with a digraph model of the F18 FCS, the only model available to us. The substitution shows that while digraphs have primarily been used for qualitative analysis, they can also be used for quantitative analysis. Based on our assumptions and the particular failure rates assigned to the F18 FCS components, we show that coverage does have a significant effect on the system's reliability and thus it is important to include coverage in the reliability analysis.

  13. Early Child Grammars: Qualitative and Quantitative Analysis of Morphosyntactic Production

    ERIC Educational Resources Information Center

    Legendre, Geraldine

    2006-01-01

    This article reports on a series of 5 analyses of spontaneous production of verbal inflection (tense and person-number agreement) by 2-year-olds acquiring French as a native language. A formal analysis of the qualitative and quantitative results is developed using the unique resources of Optimality Theory (OT; Prince & Smolensky, 2004). It is…

  14. Quantitating the subtleties of microglial morphology with fractal analysis

    PubMed Central

    Karperien, Audrey; Ahammer, Helmut; Jelinek, Herbert F.

    2013-01-01

    It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between “ramified resting” and “activated amoeboid” has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells). Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology. PMID:23386810

  15. Development of a quantitative autoradiography image analysis system

    SciTech Connect

    Hoffman, T.J.; Volkert, W.A.; Holmes R.A.

    1986-03-01

    A low cost image analysis system suitable for quantitative autoradiography (QAR) analysis has been developed. Autoradiographs can be digitized using a conventional Newvicon television camera interfaced to an IBM-XT microcomputer. Software routines for image digitization and capture permit the acquisition of thresholded or windowed images with graphic overlays that can be stored on storage devices. Image analysis software performs all background and non-linearity corrections prior to display as black/white or pseudocolor images. The relationship of pixel intensity to a standard radionuclide concentration allows the production of quantitative maps of tissue radiotracer concentrations. An easily modified subroutine is provided for adaptation to use appropriate operational equations when parameters such as regional cerebral blood flow or regional cerebral glucose metabolism are under investigation. This system could provide smaller research laboratories with the capability of QAR analysis at relatively low cost.

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

  17. Improved method and apparatus for chromatographic quantitative analysis

    DOEpatents

    Fritz, J.S.; Gjerde, D.T.; Schmuckler, G.

    An improved apparatus and method are described for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single element and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.

  18. Quantitative numerical analysis of transient IR-experiments on buildings

    NASA Astrophysics Data System (ADS)

    Maierhofer, Ch.; Wiggenhauser, H.; Brink, A.; Röllig, M.

    2004-12-01

    Impulse-thermography has been established as a fast and reliable tool in many areas of non-destructive testing. In recent years several investigations have been done to apply active thermography to civil engineering. For quantitative investigations in this area of application, finite difference calculations have been performed for systematic studies on the influence of environmental conditions, heating power and time, defect depth and size and thermal properties of the bulk material (concrete). The comparison of simulated and experimental data enables the quantitative analysis of defects.

  19. Scanning tunneling microscopy on rough surfaces-quantitative image analysis

    NASA Astrophysics Data System (ADS)

    Reiss, G.; Brückl, H.; Vancea, J.; Lecheler, R.; Hastreiter, E.

    1991-07-01

    In this communication, the application of scanning tunneling microscopy (STM) for a quantitative evaluation of roughnesses and mean island sizes of polycrystalline thin films is discussed. Provided strong conditions concerning the resolution are satisfied, the results are in good agreement with standard techniques as, for example, transmission electron microscopy. Owing to its high resolution, STM can supply a better characterization of surfaces than established methods, especially concerning the roughness. Microscopic interpretations of surface dependent physical properties thus can be considerably improved by a quantitative analysis of STM images.

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

    PubMed

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

    2011-01-14

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

  1. Quantitative analysis of culture using millions of digitized books

    PubMed Central

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

    2011-01-01

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

  2. Looking for complexity in quantitative semiology of frontal and temporal lobe seizures using neuroethology and graph theory.

    PubMed

    Bertti, Poliana; Tejada, Julian; Martins, Ana Paula Pinheiro; Dal-Cól, Maria Luiza Cleto; Terra, Vera Cristina; de Oliveira, José Antônio Cortes; Velasco, Tonicarlo Rodrigues; Sakamoto, Américo Ceiki; Garcia-Cairasco, Norberto

    2014-09-01

    Epileptic syndromes and seizures are the expression of complex brain systems. Because no analysis of complexity has been applied to epileptic seizure semiology, our goal was to apply neuroethology and graph analysis to the study of the complexity of behavioral manifestations of epileptic seizures in human frontal lobe epilepsy (FLE) and temporal lobe epilepsy (TLE). We analyzed the video recordings of 120 seizures of 18 patients with FLE and 28 seizures of 28 patients with TLE. All patients were seizure-free >1 year after surgery (Engel Class I). All patients' behavioral sequences were analyzed by means of a glossary containing all behaviors and analyzed for neuroethology (Ethomatic software). The same series were used for graph analysis (CYTOSCAPE). Behaviors, displayed as nodes, were connected by edges to other nodes according to their temporal sequence of appearance. Using neuroethology analysis, we confirmed data in the literature such as in FLE: brief/frequent seizures, complex motor behaviors, head and eye version, unilateral/bilateral tonic posturing, speech arrest, vocalization, and rapid postictal recovery and in the case of TLE: presence of epigastric aura, lateralized dystonias, impairment of consciousness/speech during ictal and postictal periods, and development of secondary generalization. Using graph analysis metrics of FLE and TLE confirmed data from flowcharts. However, because of the algorithms we used, they highlighted more powerfully the connectivity and complex associations among behaviors in a quite selective manner, depending on the origin of the seizures. The algorithms we used are commonly employed to track brain connectivity from EEG and MRI sources, which makes our study very promising for future studies of complexity in this field. PMID:25216767

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

    PubMed

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

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. PMID:24889823

  4. Temporal analysis of acoustic emission from a plunged granular bed

    NASA Astrophysics Data System (ADS)

    Tsuji, Daisuke; Katsuragi, Hiroaki

    2015-10-01

    The statistical property of acoustic emission (AE) events from a plunged granular bed is analyzed by means of actual-time and natural-time analyses. These temporal analysis methods allow us to investigate the details of AE events that follow a power-law distribution. In the actual-time analysis, the calm-time distribution, and the decay of the event-occurrence density after the largest event (i.e., the Omori-Utsu law) are measured. Although the former always shows a power-law form, the latter does not always obey a power law. Markovianity of the event-occurrence process is also verified using a scaling law by assuming that both of them exhibit power laws. We find that the effective shear strain rate is a key parameter to classify the emergence rate of power-law nature and Markovianity in granular AE events. For the natural-time analysis, the existence of self-organized critical states is revealed by calculating the variance of natural time χk, where k th natural time of N events is defined as χk=k /N . In addition, the energy difference distribution can be fitted by a q -Gaussian form, which is also consistent with the criticality of the system.

  5. Urban expansion analysis based on spatial variables derived from multi-temporal remote sensing imagery

    NASA Astrophysics Data System (ADS)

    Yang, Yetao; Wang, Yingying; Zhou, Qiming; Gong, Jianya

    2008-10-01

    In this research, we focus on the spatial pattern of the urban expansion. The spatial pattern of the urban area can be quantitatively delineated by many spatial variables. Numerous spatial variables have been examined to evaluate their applicability to the urban change. These metrics include road network accessibility, built-up density and some landscape metrics. Remote sensing technology was used for monitoring dynamic urban change. Multi-temporal Landsat TM images (1988, 1991, 1994, 1997, 2000, and 2002) were used for the change detection using post-classification comparison method. The road network and its change were extracted from multitemporal images using the GDPA algorithm. Contagion, one of the landscape metrics, was selected, because it it can describe the heterogeneity of the suburban area, where the landuse change is most likely to happen. Analysis has also been conducted to identify the relationship between urban change and these spatial variables.

  6. New insight in quantitative analysis of vascular permeability during immune reaction (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Kalchenko, Vyacheslav; Molodij, Guillaume; Kuznetsov, Yuri; Smolyakov, Yuri; Israeli, David; Meglinski, Igor; Harmelin, Alon

    2016-03-01

    The use of fluorescence imaging of vascular permeability becomes a golden standard for assessing the inflammation process during experimental immune response in vivo. The use of the optical fluorescence imaging provides a very useful and simple tool to reach this purpose. The motivation comes from the necessity of a robust and simple quantification and data presentation of inflammation based on a vascular permeability. Changes of the fluorescent intensity, as a function of time is a widely accepted method to assess the vascular permeability during inflammation related to the immune response. In the present study we propose to bring a new dimension by applying a more sophisticated approach to the analysis of vascular reaction by using a quantitative analysis based on methods derived from astronomical observations, in particular by using a space-time Fourier filtering analysis followed by a polynomial orthogonal modes decomposition. We demonstrate that temporal evolution of the fluorescent intensity observed at certain pixels correlates quantitatively to the blood flow circulation at normal conditions. The approach allows to determine the regions of permeability and monitor both the fast kinetics related to the contrast material distribution in the circulatory system and slow kinetics associated with extravasation of the contrast material. Thus, we introduce a simple and convenient method for fast quantitative visualization of the leakage related to the inflammatory (immune) reaction in vivo.

  7. Temporal radiographic texture analysis in the detection of periprosthetic osteolysis

    SciTech Connect

    Wilkie, Joel R.; Giger, Maryellen L.; Chinander, Michael R.; Engh, Charles A. Sr.; Hopper, Robert H. Jr.; Martell, John M.

    2008-01-15

    Periprosthetic osteolysis is one of the most serious long-term problems in total hip arthroplasty. It has been primarily attributed to the body's inflammatory response to submicron polyethylene particles worn from the hip implant, and it leads to bone loss and structural deterioration in the surrounding bone. It was previously demonstrated that radiographic texture analysis (RTA) has the ability to distinguish between osteolysis and normal cases at the time of clinical detection of the disease; however, that analysis did not take into account the changes in texture over time. The goal of this preliminary analysis, however, is to assess the ability of temporal radiographic texture analysis (tRTA) to distinguish between patients who develop osteolysis and normal cases. Two tRTA methods were used in the study: the RTA feature change from baseline at various follow-up intervals and the slope of the best-fit line to the RTA data series. These tRTA methods included Fourier-based and fractal-based features calculated from digitized images of 202 total hip replacement cases, including 70 that developed osteolysis. Results show that separation between the osteolysis and normal groups increased over time for the feature difference method, as the disease progressed, with area under the curve (AUC) values from receiver operating characteristic analysis of 0.65 to 0.72 at 15 years postsurgery. Separation for the slope method was also evident, with AUC values ranging from 0.65 to 0.76 for the task of distinguishing between osteolysis and normal cases. The results suggest that tRTA methods have the ability to measure changes in trabecular structure, and may be useful in the early detection of periprosthetic osteolysis.

  8. Quantitative analysis of Si/SiGeC superlattices using atom probe tomography.

    PubMed

    Estivill, Robert; Grenier, Adeline; Duguay, Sébastien; Vurpillot, François; Terlier, Tanguy; Barnes, Jean-Paul; Hartmann, Jean-Michel; Blavette, Didier

    2015-12-01

    SiGe and its alloys are used as key materials in innovative electronic devices. The analysis of these materials together with the localisation of dopants and impurities on a very fine scale is of crucial importance for better understanding their electronic properties. The quantification of carbon and germanium in an as-grown Si/SiGeC superlattice has been investigated using Atom Probe Tomography as a function of analysis conditions and sample anneal temperature. The mass spectrum is heavily influenced by the analysis conditions and chemical identification is needed. It was found that quantitative results are obtained using a intermediate electric field. The evaporation of carbon ions shows a strong spatial and temporal correlation. A series of annealed samples have been analysed, presenting an inhomogeneous carbon distribution, appearing in the shape of small clusters. These findings confirm previous results and give a better understanding of the processes occurring in these technologically important materials. PMID:25814020

  9. Clifford algebra-based spatio-temporal modelling and analysis for complex geo-simulation data

    NASA Astrophysics Data System (ADS)

    Luo, Wen; Yu, Zhaoyuan; Hu, Yong; Yuan, Linwang

    2013-10-01

    The spatio-temporal data simulating Ice-Land-Ocean interaction of Antarctic are used to demonstrate the Clifford algebra-based data model construction, spatio-temporal query and data analysis. The results suggest that Clifford algebra provides a powerful mathematical tool for the whole modelling and analysis chains for complex geo-simulation data. It can also help implement spatio-temporal analysis algorithms more clearly and simply.

  10. An Analysis of Critical Factors for Quantitative Immunoblotting

    PubMed Central

    Janes, Kevin A.

    2015-01-01

    Immunoblotting (also known as Western blotting) combined with digital image analysis can be a reliable method for analyzing the abundance of proteins and protein modifications, but not every immunoblot-analysis combination produces an accurate result. Here, I illustrate how sample preparation, protocol implementation, detection scheme, and normalization approach profoundly affect the quantitative performance of immunoblotting. This study implemented diagnostic experiments that assess an immunoblot-analysis workflow for accuracy and precision. The results showed that ignoring such diagnostics can lead to pseudoquantitative immunoblot data that dramatically overestimate or underestimate true differences in protein abundance. PMID:25852189

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

    PubMed

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image. PMID:26556680

  12. An Improved Quantitative Analysis Method for Plant Cortical Microtubules

    PubMed Central

    Lu, Yi; Huang, Chenyang; Wang, Jia; Shang, Peng

    2014-01-01

    The arrangement of plant cortical microtubules can reflect the physiological state of cells. However, little attention has been paid to the image quantitative analysis of plant cortical microtubules so far. In this paper, Bidimensional Empirical Mode Decomposition (BEMD) algorithm was applied in the image preprocessing of the original microtubule image. And then Intrinsic Mode Function 1 (IMF1) image obtained by decomposition was selected to do the texture analysis based on Grey-Level Cooccurrence Matrix (GLCM) algorithm. Meanwhile, in order to further verify its reliability, the proposed texture analysis method was utilized to distinguish different images of Arabidopsis microtubules. The results showed that the effect of BEMD algorithm on edge preserving accompanied with noise reduction was positive, and the geometrical characteristic of the texture was obvious. Four texture parameters extracted by GLCM perfectly reflected the different arrangements between the two images of cortical microtubules. In summary, the results indicate that this method is feasible and effective for the image quantitative analysis of plant cortical microtubules. It not only provides a new quantitative approach for the comprehensive study of the role played by microtubules in cell life activities but also supplies references for other similar studies. PMID:24744684

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

    PubMed

    Dudekula, Khadar; Le Bihan, Thierry

    2016-09-01

    The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis. PMID:27358910

  14. Quantitative risk analysis of oil storage facilities in seismic areas.

    PubMed

    Fabbrocino, Giovanni; Iervolino, Iunio; Orlando, Francesca; Salzano, Ernesto

    2005-08-31

    Quantitative risk analysis (QRA) of industrial facilities has to take into account multiple hazards threatening critical equipment. Nevertheless, engineering procedures able to evaluate quantitatively the effect of seismic action are not well established. Indeed, relevant industrial accidents may be triggered by loss of containment following ground shaking or other relevant natural hazards, either directly or through cascade effects ('domino effects'). The issue of integrating structural seismic risk into quantitative probabilistic seismic risk analysis (QpsRA) is addressed in this paper by a representative study case regarding an oil storage plant with a number of atmospheric steel tanks containing flammable substances. Empirical seismic fragility curves and probit functions, properly defined both for building-like and non building-like industrial components, have been crossed with outcomes of probabilistic seismic hazard analysis (PSHA) for a test site located in south Italy. Once the seismic failure probabilities have been quantified, consequence analysis has been performed for those events which may be triggered by the loss of containment following seismic action. Results are combined by means of a specific developed code in terms of local risk contour plots, i.e. the contour line for the probability of fatal injures at any point (x, y) in the analysed area. Finally, a comparison with QRA obtained by considering only process-related top events is reported for reference. PMID:15908107

  15. Temporal instability analysis of inviscid compound jets falling under gravity

    NASA Astrophysics Data System (ADS)

    Mohsin, Muhammad; Uddin, Jamal; Decent, Stephen P.; Afzaal, Muhammad F.

    2013-01-01

    Compound liquid jets can be used in a variety of industrial applications ranging from capsule production in pharmaceutics to enhance printing methods in ink-jet printing. An appreciation of how instability along compound jets can lead to breakup and droplet formation is thus critical in many fields in science and engineering. In this paper, we perform a theoretical analysis to examine the instability of an axisymmetric inviscid compound liquid jet which falls vertically under the influence of gravity. We use a long-wavelength, slender-jet asymptotic expansion to reduce the governing equations of the problem into a set of one-dimensional partial differential equations, which describe the evolution of the leading-order axial velocity of the jet as well as the radii of both the inner and the outer interfaces. We first determine the steady-state solutions of the one-dimensional model equations and then we perform a linear temporal instability analysis to obtain a dispersion relation, which gives us useful information about the maximum growth rate and the maximum wavenumber of the imposed wave-like disturbance. We use our results to estimate the location and qualitative nature of breakup and then compare our results with numerical simulations.

  16. Analysis of global ionospheric TEC temporal-spatial characteristics

    NASA Astrophysics Data System (ADS)

    Jiang, Maofang; Huang, Liangke; Wu, Pituan; Cai, Chenghui; Liu, Lilong

    2015-12-01

    The formation of the ionosphere is mainly the interaction of solar radiation and the earth's atmosphere, in different temporal-spatial environment, the characteristics of the ionosphere is more complex, and the Total Electron Content (TEC) is one of the important parameters of the ionospheric morphology and structure. Therefore, in this paper, using the high-precision TEC time series provided by the International GNSS Service (IGS) as experimental data, by Fast Fourier Transform (FFT) to detect its periodic changes, and then focus on analysis the characteristics of diurnal variation, seasonal variation and annual variation and winter anomaly, simultaneous analysis of the ionospheric characteristics vary with latitude and longitude. The result show that: (1) TEC changes more intense during the day, but the night is quiet, and in different latitudes, the TEC reached peak value at different moment; (2) Winter anomaly exists only during the day, night does not exist; (3) In the same time domain, TEC value decreases gradually with the increase of latitude, and it has different spatial variation features in different hemispheres.

  17. A Quantitative 3D Motility Analysis of Trypanosoma brucei by Use of Digital In-line Holographic Microscopy

    PubMed Central

    Weiße, Sebastian; Heddergott, Niko; Heydt, Matthias; Pflästerer, Daniel; Maier, Timo; Haraszti, Tamás; Grunze, Michael; Engstler, Markus; Rosenhahn, Axel

    2012-01-01

    We present a quantitative 3D analysis of the motility of the blood parasite Trypanosoma brucei. Digital in-line holographic microscopy has been used to track single cells with high temporal and spatial accuracy to obtain quantitative data on their behavior. Comparing bloodstream form and insect form trypanosomes as well as mutant and wildtype cells under varying external conditions we were able to derive a general two-state-run-and-tumble-model for trypanosome motility. Differences in the motility of distinct strains indicate that adaption of the trypanosomes to their natural environments involves a change in their mode of swimming. PMID:22629379

  18. Single-Molecule Sensors: Challenges and Opportunities for Quantitative Analysis.

    PubMed

    Gooding, J Justin; Gaus, Katharina

    2016-09-12

    Measurement science has been converging to smaller and smaller samples, such that it is now possible to detect single molecules. This Review focuses on the next generation of analytical tools that combine single-molecule detection with the ability to measure many single molecules simultaneously and/or process larger and more complex samples. Such single-molecule sensors constitute a new type of quantitative analytical tool, as they perform analysis by molecular counting and thus potentially capture the heterogeneity of the sample. This Review outlines the advantages and potential of these new, quantitative single-molecule sensors, the measurement challenges in making single-molecule devices suitable for analysis, the inspiration biology provides for overcoming these challenges, and some of the solutions currently being explored. PMID:27444661

  19. The 'when' and 'where' of semantic coding in the anterior temporal lobe: Temporal representational similarity analysis of electrocorticogram data.

    PubMed

    Chen, Y; Shimotake, A; Matsumoto, R; Kunieda, T; Kikuchi, T; Miyamoto, S; Fukuyama, H; Takahashi, R; Ikeda, A; Lambon Ralph, M A

    2016-06-01

    Electrocorticograms (ECoG) provide a unique opportunity to monitor neural activity directly at the cortical surface. Ten patients with subdural electrodes covering ventral and lateral anterior temporal regions (ATL) performed a picture naming task. Temporal representational similarity analysis (RSA) was used, for the first time, to compare spatio-temporal neural patterns from the ATL surface with pre-defined theoretical models. The results indicate that the neural activity in the ventral subregion of the ATL codes semantic representations from 250 msec after picture onset. The observed activation similarity was not related to the visual similarity of the pictures or the phonological similarity of their names. In keeping with convergent evidence for the importance of the ATL in semantic processing, these results provide the first direct evidence of semantic coding from the surface of the ventral ATL and its time-course. PMID:27085891

  20. Quantitative NMR Analysis of Partially Substituted Biodiesel Glycerols

    SciTech Connect

    Nagy, M.; Alleman, T. L.; Dyer, T.; Ragauskas, A. J.

    2009-01-01

    Phosphitylation of hydroxyl groups in biodiesel samples with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane followed by 31P-NMR analysis provides a rapid quantitative analytical technique for the determination of substitution patterns on partially esterified glycerols. The unique 31P-NMR chemical shift data was established with a series mono and di-substituted fatty acid esters of glycerol and then utilized to characterize an industrial sample of partially processed biodiesel.

  1. Quantitative analysis of chaotic synchronization by means of coherence

    NASA Astrophysics Data System (ADS)

    Shabunin, A.; Astakhov, V.; Kurths, J.

    2005-07-01

    We use an index of chaotic synchronization based on the averaged coherence function for the quantitative analysis of the process of the complete synchronization loss in unidirectionally coupled oscillators and maps. We demonstrate that this value manifests different stages of the synchronization breaking. It is invariant to time delay and insensitive to small noise and distortions, which can influence the accessible signals at measurements. Peculiarities of the synchronization destruction in maps and oscillators are investigated.

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  3. Quantitation of glycerophosphorylcholine by flow injection analysis using immobilized enzymes.

    PubMed

    Mancini, A; Del Rosso, F; Roberti, R; Caligiana, P; Vecchini, A; Binaglia, L

    1996-09-20

    A method for quantitating glycerophosphorylcholine by flow injection analysis is reported in the present paper. Glycerophosphorylcholine phosphodiesterase and choline oxidase, immobilized on controlled porosity glass beads, are packed in a small reactor inserted in a flow injection manifold. When samples containing glycerophosphorylcholine are injected, glycerophosphorylcholine is hydrolyzed into choline and sn-glycerol-3-phosphate. The free choline produced in this reaction is oxidized to betain and hydrogen peroxide. Hydrogen peroxide is detected amperometrically. Quantitation of glycerophosphorylcholine in samples containing choline and phosphorylcholine is obtained inserting ahead of the reactor a small column packed with a mixed bed ion exchange resin. The time needed for each determination does not exceed one minute. The present method, applied to quantitate glycerophosphorylcholine in samples of seminal plasma, gave results comparable with those obtained using the standard enzymatic-spectrophotometric procedure. An alternative procedure, making use of co-immobilized glycerophosphorylcholine phosphodiesterase and glycerol-3-phosphate oxidase for quantitating glycerophosphorylcholine, glycerophosphorylethanolamine and glycerophosphorylserine is also described. PMID:8905629

  4. Quantitative Motion Analysis in Two and Three Dimensions.

    PubMed

    Wessels, Deborah J; Lusche, Daniel F; Kuhl, Spencer; Scherer, Amanda; Voss, Edward; Soll, David R

    2016-01-01

    This chapter describes 2D quantitative methods for motion analysis as well as 3D motion analysis and reconstruction methods. Emphasis is placed on the analysis of dynamic cell shape changes that occur through extension and retraction of force generating structures such as pseudopodia and lamellipodia. Quantitative analysis of these structures is an underutilized tool in the field of cell migration. Our intent, therefore, is to present methods that we developed in an effort to elucidate mechanisms of basic cell motility, directed cell motion during chemotaxis, and metastasis. We hope to demonstrate how application of these methods can more clearly define alterations in motility that arise due to specific mutations or disease and hence, suggest mechanisms or pathways involved in normal cell crawling and treatment strategies in the case of disease. In addition, we present a 4D tumorigenesis model for high-resolution analysis of cancer cells from cell lines and human cancer tissue in a 3D matrix. Use of this model led to the discovery of the coalescence of cancer cell aggregates and unique cell behaviors not seen in normal cells or normal tissue. Graphic illustrations to visually display and quantify cell shape are presented along with algorithms and formulae for calculating select 2D and 3D motion analysis parameters. PMID:26498790

  5. a Temporal and Spatial Analysis of Urban Heat Island in Basin City Utilizing Remote Sensing Techniques

    NASA Astrophysics Data System (ADS)

    Chang, Hsiao-Tung

    2016-06-01

    Urban Heat Island (UHI) has been becoming a key factor in deteriorating the urban ecological environment. Spatial-temporal analysis on its prototype of basin city's UHI and quantitatively evaluating effect from rapid urbanization will provide theoretical foundation for relieving UHI effect. Based on Landsat 8, ETM+ and TM images of Taipei basin areas from 1900 to 2015, this article has retrieved the land surface temperature (LST) at summer solstice of each year, and then analysed spatial-temporal pattern and evolution characters of UHI in Taipei basin in this decade. The results showed that the expansion built district, UHI area constantly expanded from centre city to the suburb areas. The prototype of UHI in Taipei basin that showed in addition to higher temperatures in the centre city also were relatively high temperatures gathered boundaries surrounded by foot of mountains side. It calls "sinking heat island". From 1900 to 2000, the higher UHI areas were different land use type change had obvious difference by public infrastructure works. And then, in next 15 years till 2015, building density of urban area has been increasing gradually. It has the trend that UHI flooding raises follow urban land use density. Hot spot of UHI in Taipei basin also has the same characteristics. The results suggest that anthropogenic heat release probably plays a significant role in the UHI effect, and must be considered in urban planning adaptation strategies.

  6. Quantitative Analysis of Calcium Spikes in Noisy Fluorescent Background

    PubMed Central

    Janicek, Radoslav; Hotka, Matej; Zahradníková, Alexandra; Zahradníková, Alexandra; Zahradník, Ivan

    2013-01-01

    Intracellular calcium signals are studied by laser-scanning confocal fluorescence microscopy. The required spatio-temporal resolution makes description of calcium signals difficult because of the low signal-to-noise ratio. We designed a new procedure of calcium spike analysis based on their fitting with a model. The accuracy and precision of calcium spike description were tested on synthetic datasets generated either with randomly varied spike parameters and Gaussian noise of constant amplitude, or with constant spike parameters and Gaussian noise of various amplitudes. Statistical analysis was used to evaluate the performance of spike fitting algorithms. The procedure was optimized for reliable estimation of calcium spike parameters and for dismissal of false events. A new algorithm was introduced that corrects the acquisition time of pixels in line-scan images that is in error due to sequential acquisition of individual pixels along the space coordinate. New software was developed in Matlab and provided for general use. It allows interactive dissection of temporal profiles of calcium spikes from x-t images, their fitting with predefined function(s) and acceptance of results on statistical grounds, thus allowing efficient analysis and reliable description of calcium signaling in cardiac myocytes down to the in situ function of ryanodine receptors. PMID:23741324

  7. Multi-Temporal Analysis of WWII Reconnaissance Photos

    NASA Astrophysics Data System (ADS)

    Meixner, P.; Eckstein, M.

    2016-06-01

    There are millions of aerial photographs from the period of the Second Wold War available in the Allied archives, obtained by aerial photo reconnaissance, covering most of today's European countries. They are spanning the time from 1938 until the end of the war and even beyond. Photo reconnaissance provided intelligence information for the Allied headquarters and accompanied the bombing offensive against the German homeland and the occupied territories. One of the initial principal targets in Bohemia were the synthetized fuel works STW AG (Sudetenländische Treibstoffwerke AG) in Zaluzi (formerly Maltheuren) near Most (formerly Brück), Czech Republic. The STW AG synthetized fuel plant was not only subject to bombing raids, but a subject to quite intensive photo reconnaissance, too - long before the start of the bombing campaign. With a multi-temporal analysis of the available imagery from international archives we will demonstrate the factory build-up during 1942 and 1943, the effects of the bombing raids in 1944 and the struggle to keep the plant working in the last year of the war. Furthermore we would like to show the impact the bombings have today, in form of potential unexploded ordnance in the adjacent area of the open cast mines.

  8. [Analysis of fusion waves created with temporal pacing].

    PubMed

    Ueda, M; Shigemi, K; Hayashi, K; Kakihara, K; Nakajima, Y; Fukushima, H; Tanaka, Y

    1998-08-01

    Fifty-five beats of fusion waves were recorded continuously with an audio digital tape and the tape was re-played for analysis. A 45-year-old male (56 kg, 175 cm) with cervical spondylosis was scheduled to undergo laminoplasty of the cervical vertebral (C2-C6). A temporal ventricular (VVI mode) pacing lead was inserted from the right cubital vein to the right ventricular apex for preventing bradycardia while manipulating the medulla. The height of the R wave decreased gradually and the depth of S wave increased in the earlier period of fusion beats and it was reversed later. The narrow QRS width indicated that the electrode was placed near the cardiac conducting system. The gradually increasing intervals between P waves activated the pacing, and the P wave intervals recovered inhibiting the pacing. During the recovery phase, some beats were still activated by pacing instead of depressing the rate below the original rate. These beats suggest the importance of considering the atrial-ventricular conducting time. Arterial pressure fluctuated only slightly during the 'fusion beats, suggesting that despite the abnormality in the cardiac conduction system due to pacing, contraction of the ventricular muscles was only slightly affected in this case. PMID:9753972

  9. Right ventricular strain analysis from three-dimensional echocardiography by using temporally diffeomorphic motion estimation

    PubMed Central

    Zhu, Meihua; Ashraf, Muhammad; Broberg, Craig S.; Sahn, David J.; Song, Xubo

    2014-01-01

    Purpose: Quantitative analysis of right ventricle (RV) motion is important for study of the mechanism of congenital and acquired diseases. Unlike left ventricle (LV), motion estimation of RV is more difficult because of its complex shape and thin myocardium. Although attempts of finite element models on MR images and speckle tracking on echocardiography have shown promising results on RV strain analysis, these methods can be improved since the temporal smoothness of the motion is not considered. Methods: The authors have proposed a temporally diffeomorphic motion estimation method in which a spatiotemporal transformation is estimated by optimization of a registration energy functional of the velocity field in their earlier work. The proposed motion estimation method is a fully automatic process for general image sequences. The authors apply the method by combining with a semiautomatic myocardium segmentation method to the RV strain analysis of three-dimensional (3D) echocardiographic sequences of five open-chest pigs under different steady states. Results: The authors compare the peak two-point strains derived by their method with those estimated from the sonomicrometry, the results show that they have high correlation. The motion of the right ventricular free wall is studied by using segmental strains. The baseline sequence results show that the segmental strains in their methods are consistent with results obtained by other image modalities such as MRI. The image sequences of pacing steady states show that segments with the largest strain variation coincide with the pacing sites. Conclusions: The high correlation of the peak two-point strains of their method and sonomicrometry under different steady states demonstrates that their RV motion estimation has high accuracy. The closeness of the segmental strain of their method to those from MRI shows the feasibility of their method in the study of RV function by using 3D echocardiography. The strain analysis of the

  10. Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.

    ERIC Educational Resources Information Center

    Anderson, James L.; And Others

    1980-01-01

    Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)

  11. Label-Free Technologies for Quantitative Multiparameter Biological Analysis

    PubMed Central

    Qavi, Abraham J.; Washburn, Adam L.; Byeon, Ji-Yeon; Bailey, Ryan C.

    2009-01-01

    In the post-genomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We will describe the fundamental principles of these different methodologies and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application. PMID:19221722

  12. Microcomputer-based digital image analysis system for quantitative autoradiography

    SciTech Connect

    Hoffman, T.J.; Volkert, W.A.; Holmes, R.A.

    1988-01-01

    A computerized image processing system utilizing an IBM-XT personal microcomputer with the capability of performing quantitative cerebral autoradiography is described. All of the system components are standard computer and optical hardware that can be easily assembled. The system has 512 horizontal by 512 vertical axis resolution with 8 bits per pixel (256 gray levels). Unlike other dedicated image processing systems, the IBM-XT permits the assembly of an efficient, low-cost image analysis system without sacrificing other capabilities of the IBM personal computer. The application of this system in both qualitative and quantitative autoradiography has been the principal factor in developing a new radiopharmaceutical to measure regional cerebral blood flow.

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

    PubMed

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

    2015-01-01

    Leaf pavement cells are shaped like a jigsaw puzzle in most dicotyledon species. Molecular genetic studies have identified several genes required for pavement cells morphogenesis and proposed that microtubules play crucial roles in the interdigitation of pavement cells. In this study, we performed quantitative analysis of cortical microtubule orientation in leaf pavement cells in Arabidopsis thaliana. We captured confocal images of cortical microtubules in cotyledon leaf epidermis expressing GFP-tubulinβ and quantitatively evaluated the microtubule orientations relative to the pavement cell growth axis using original image processing techniques. Our results showed that microtubules kept parallel orientations to the growth axis during pavement cell growth. In addition, we showed that immersion treatment of seed cotyledons in solutions containing tubulin polymerization and depolymerization inhibitors decreased pavement cell complexity. Treatment with oryzalin and colchicine inhibited the symmetric division of guard mother cells. PMID:26039484

  14. Common and distinct neural correlates of personal and vicarious reward: A quantitative meta-analysis

    PubMed Central

    Morelli, Sylvia A.; Sacchet, Matthew D.; Zaki, Jamil

    2015-01-01

    Individuals experience reward not only when directly receiving positive outcomes (e.g., food or money), but also when observing others receive such outcomes. This latter phenomenon, known as vicarious reward, is a perennial topic of interest among psychologists and economists. More recently, neuroscientists have begun exploring the neuroanatomy underlying vicarious reward. Here we present a quantitative whole-brain meta-analysis of this emerging literature. We identified 25 functional neuroimaging studies that included contrasts between vicarious reward and a neutral control, and subjected these contrasts to an activation likelihood estimate (ALE) meta-analysis. This analysis revealed a consistent pattern of activation across studies, spanning structures typically associated with the computation of value (especially ventromedial prefrontal cortex) and mentalizing (including dorsomedial prefrontal cortex and superior temporal sulcus). We further quantitatively compared this activation pattern to activation foci from a previous meta-analysis of personal reward. Conjunction analyses yielded overlapping VMPFC activity in response to personal and vicarious reward. Contrast analyses identified preferential engagement of the nucleus accumbens in response to personal as compared to vicarious reward, and in mentalizing-related structures in response to vicarious as compared to personal reward. These data shed light on the common and unique components of the reward that individuals experience directly and through their social connections. PMID:25554428

  15. Quantitative analysis of astrogliosis in drug-dependent humans.

    PubMed

    Weber, Marco; Scherf, Nico; Kahl, Thomas; Braumann, Ulf-Dietrich; Scheibe, Patrick; Kuska, Jens-Peer; Bayer, Ronny; Büttner, Andreas; Franke, Heike

    2013-03-15

    Drug addiction is a chronic, relapsing disease caused by neurochemical and molecular changes in the brain. In this human autopsy study qualitative and quantitative changes of glial fibrillary acidic protein (GFAP)-positive astrocytes in the hippocampus of 26 lethally intoxicated drug addicts and 35 matched controls are described. The morphological characterization of these cells reflected alterations representative for astrogliosis. But, neither quantification of GFAP-positive cells nor the Western blot analysis indicated statistical significant differences between drug fatalities versus controls. However, by semi-quantitative scoring a significant shift towards higher numbers of activated astrocytes in the drug group was detected. To assess morphological changes quantitatively, graph-based representations of astrocyte morphology were obtained from single cell images captured by confocal laser scanning microscopy. Their underlying structures were used to quantify changes in astroglial fibers in an automated fashion. This morphometric analysis yielded significant differences between the investigated groups for four different measures of fiber characteristics (Euclidean distance, graph distance, number of graph elements, fiber skeleton distance), indicating that, e.g., astrocytes in drug addicts on average exhibit significant elongation of fiber structures as well as two-fold increase in GFAP-positive fibers as compared with those in controls. In conclusion, the present data show characteristic differences in morphology of hippocampal astrocytes in drug addicts versus controls and further supports the involvement of astrocytes in human pathophysiology of drug addiction. The automated quantification of astrocyte morphologies provides a novel, testable way to assess the fiber structures in a quantitative manner as opposed to standard, qualitative descriptions. PMID:23337617

  16. Quantitative Assessment of Spatio-Temporal Desertification Rates in Azerbaijan during Using Timeseries Landsat-8 Satellite Images

    NASA Astrophysics Data System (ADS)

    Bayramov, Emil; Mammadov, Ramiz

    2016-07-01

    The main goals of this research are the object-based landcover classification of LANDSAT-8 multi-spectral satellite images in 2014 and 2015, quantification of Normalized Difference Vegetation Indices (NDVI) rates within the land-cover classes, change detection analysis between the NDVIs derived from multi-temporal LANDSAT-8 satellite images and the quantification of those changes within the land-cover classes and detection of changes between land-cover classes. The object-based classification accuracy of the land-cover classes was validated through the standard confusion matrix which revealed 80 % of land-cover classification accuracy for both years. The analysis revealed that the area of agricultural lands increased from 30911 sq. km. in 2014 to 31999 sq. km. in 2015. The area of barelands increased from 3933 sq. km. in 2014 to 4187 sq. km. in 2015. The area of forests increased from 8211 sq. km. in 2014 to 9175 sq. km. in 2015. The area of grasslands decreased from 27176 sq. km. in 2014 to 23294 sq. km. in 2015. The area of urban areas increased from 12479 sq. km. in 2014 to 12956 sq. km. in 2015. The decrease in the area of grasslands was mainly explained by the landuse shifts of grasslands to agricultural and urban lands. The quantification of low and medium NDVI rates revealed the increase within the agricultural, urban and forest land-cover classes in 2015. However, the high NDVI rates within agricultural, urban and forest land-cover classes in 2015 revealed to be lower relative to 2014. The change detection analysis between landscover types of 2014 and 2015 allowed to determine that 7740 sq. km. of grasslands shifted to agricultural landcover type whereas 5442sq. km. of agricultural lands shifted to rangelands. This means that the spatio-temporal patters of agricultural activities occurred in Azerbaijan because some of the areas reduced agricultural activities whereas some of them changed their landuse type to agricultural. Based on the achieved results, it

  17. Bayesian Shrinkage Analysis of Quantitative Trait Loci for Dynamic Traits

    PubMed Central

    Yang, Runqing; Xu, Shizhong

    2007-01-01

    Many quantitative traits are measured repeatedly during the life of an organism. Such traits are called dynamic traits. The pattern of the changes of a dynamic trait is called the growth trajectory. Studying the growth trajectory may enhance our understanding of the genetic architecture of the growth trajectory. Recently, we developed an interval-mapping procedure to map QTL for dynamic traits under the maximum-likelihood framework. We fit the growth trajectory by Legendre polynomials. The method intended to map one QTL at a time and the entire QTL analysis involved scanning the entire genome by fitting multiple single-QTL models. In this study, we propose a Bayesian shrinkage analysis for estimating and mapping multiple QTL in a single model. The method is a combination between the shrinkage mapping for individual quantitative traits and the Legendre polynomial analysis for dynamic traits. The multiple-QTL model is implemented in two ways: (1) a fixed-interval approach where a QTL is placed in each marker interval and (2) a moving-interval approach where the position of a QTL can be searched in a range that covers many marker intervals. Simulation study shows that the Bayesian shrinkage method generates much better signals for QTL than the interval-mapping approach. We propose several alternative methods to present the results of the Bayesian shrinkage analysis. In particular, we found that the Wald test-statistic profile can serve as a mechanism to test the significance of a putative QTL. PMID:17435239

  18. Qualitative and temporal reasoning in engine behavior analysis

    NASA Technical Reports Server (NTRS)

    Dietz, W. E.; Stamps, M. E.; Ali, M.

    1987-01-01

    Numerical simulation models, engine experts, and experimental data are used to generate qualitative and temporal representations of abnormal engine behavior. Engine parameters monitored during operation are used to generate qualitative and temporal representations of actual engine behavior. Similarities between the representations of failure scenarios and the actual engine behavior are used to diagnose fault conditions which have already occurred, or are about to occur; to increase the surveillance by the monitoring system of relevant engine parameters; and to predict likely future engine behavior.

  19. Quantitative dual-probe microdialysis: mathematical model and analysis.

    PubMed

    Chen, Kevin C; Höistad, Malin; Kehr, Jan; Fuxe, Kjell; Nicholson, Charles

    2002-04-01

    Steady-state microdialysis is a widely used technique to monitor the concentration changes and distributions of substances in tissues. To obtain more information about brain tissue properties from microdialysis, a dual-probe approach was applied to infuse and sample the radiotracer, [3H]mannitol, simultaneously both in agar gel and in the rat striatum. Because the molecules released by one probe and collected by the other must diffuse through the interstitial space, the concentration profile exhibits dynamic behavior that permits the assessment of the diffusion characteristics in the brain extracellular space and the clearance characteristics. In this paper a mathematical model for dual-probe microdialysis was developed to study brain interstitial diffusion and clearance processes. Theoretical expressions for the spatial distribution of the infused tracer in the brain extracellular space and the temporal concentration at the probe outlet were derived. A fitting program was developed using the simplex algorithm, which finds local minima of the standard deviations between experiments and theory by adjusting the relevant parameters. The theoretical curves accurately fitted the experimental data and generated realistic diffusion parameters, implying that the mathematical model is capable of predicting the interstitial diffusion behavior of [3H]mannitol and that it will be a valuable quantitative tool in dual-probe microdialysis. PMID:12067242

  20. Drought analysis in Switzerland: spatial and temporal features

    NASA Astrophysics Data System (ADS)

    Di Franca, Gaetano; Molnar, Peter; Burlando, Paolo; Bonaccorso, Brunella; Cancelliere, Antonino

    2015-04-01

    Drought as a natural hazard may have negative impacts even in regions characterized by a general abundance of water resources. The Swiss Alpine region has experienced several extreme meteorological events (heat waves, droughts) during the last fifty years that have caused human and economic losses. Though Swiss climate is far from arid or semi-arid, natural climatic variability, exacerbated by climate change, could lead to more severe impacts from naturally occurring meteorological droughts (i.e. lack or significant reduction of precipitation) in the future. In this work, spatial and temporal features of meteorological droughts in Switzerland have been explored by the identification and probabilistic characterization of historic drought events on gridded precipitation data during the period 1961-2012. The run method has been applied to both monthly and annual precipitation time series to probabilistically characterize drought occurrences as well as to analyze their spatial variability. Spatial features have also been investigated by means of Principal Components Analysis (PCA) applied to Standardized Precipitation Index (SPI) series at 3, 6, and 12-month aggregated time scale, in order to detect areas with distinct precipitation patterns, accounting for seasonality throughout year and including both wet and dry conditions. Furthermore, a probabilistic analysis of drought areal extent has been carried out by applying an SPI-based procedure to derive Severity-Area-Frequency (SAF) curves. The application of run method reveals that Ticino and Valais are the most potentially drought-prone Swiss regions, since accumulated deficit precipitation is significantly higher (up to two times) than in the rest of the country. Inspection of SPI series reveals many events in which precipitation has shown significant anomalies from the average in the period 1961-2012 at the investigated time scales. Anomalies in rainfall seem to exhibit high spatial correlation, showing uniform sub

  1. Match analysis and temporal patterns of fatigue in rugby sevens.

    PubMed

    Granatelli, Giampietro; Gabbett, Tim J; Briotti, Gianluca; Padulo, Johnny; Buglione, Antonio; D'Ottavio, Stefano; Ruscello, Bruno M

    2014-03-01

    Rugby sevens is a rapidly growing sport. Match analysis is increasingly being used by sport scientists and coaches to improve the understanding of the physical demands of this sport. This study investigated the physical and physiological demands of elite men's rugby sevens, with special reference to the temporal patterns of fatigue during match play. Nine players, 4 backs and 5 forwards (age 25.1 ± 3.1 years) participated during 2 "Roma 7" international tournaments (2010 and 2011). All the players were at the professional level in the highest Italian rugby union, and 5 of these players also competed at the international level. During the matches (n = 15), the players were filmed to assess game performance. Global positioning system, heart rate (HR), and blood lactate (BLa) concentration data were measured and analyzed. The mean total distance covered throughout matches was 1,221 ± 118 m (first half = 643 ± 70 m and second half = 578 ± 77 m; with a decrease of 11.2%, p > 0.05, Effect Size [ES] = 0.29). The players achieved 88.3 ± 4.2 and 87.7 ± 3.4% of the HRmax during the first and second halves, respectively. The BLa for the first and second halves was 3.9 ± 0.9 and 11.2 ± 1.4 mmol·L, respectively. The decreases in performance occurred consistently in the final 3 minutes of the matches (-40.5% in the distance covered per minute). The difference found in relation to the playing position, although not statistically significant (p = 0.11), showed a large ES (η = 0.20), suggesting possible practical implications. These results demonstrate that rugby sevens is a demanding sport that places stress on both the anaerobic glycolytic and aerobic oxidative energy systems. Strength and conditioning programs designed to train these energy pathways may prevent fatigue-induced reductions in physical performance. PMID:23722109

  2. Quantitative option analysis for implementation and management of landfills.

    PubMed

    Kerestecioğlu, Merih

    2016-09-01

    The selection of the most feasible strategy for implementation of landfills is a challenging step. Potential implementation options of landfills cover a wide range, from conventional construction contracts to the concessions. Montenegro, seeking to improve the efficiency of the public services while maintaining affordability, was considering privatisation as a way to reduce public spending on service provision. In this study, to determine the most feasible model for construction and operation of a regional landfill, a quantitative risk analysis was implemented with four steps: (i) development of a global risk matrix; (ii) assignment of qualitative probabilities of occurrences and magnitude of impacts; (iii) determination of the risks to be mitigated, monitored, controlled or ignored; (iv) reduction of the main risk elements; and (v) incorporation of quantitative estimates of probability of occurrence and expected impact for each risk element in the reduced risk matrix. The evaluated scenarios were: (i) construction and operation of the regional landfill by the public sector; (ii) construction and operation of the landfill by private sector and transfer of the ownership to the public sector after a pre-defined period; and (iii) operation of the landfill by the private sector, without ownership. The quantitative risk assessment concluded that introduction of a public private partnership is not the most feasible option, unlike the common belief in several public institutions in developing countries. A management contract for the first years of operation was advised to be implemented, after which, a long term operating contract may follow. PMID:27354014

  3. Facegram - Objective quantitative analysis in facial reconstructive surgery.

    PubMed

    Gerós, Ana; Horta, Ricardo; Aguiar, Paulo

    2016-06-01

    Evaluation of effectiveness in reconstructive plastic surgery has become an increasingly important asset in comparing and choosing the most suitable medical procedure to handle facial disfigurement. Unfortunately, traditional methods to assess the results of surgical interventions are mostly qualitative and lack information about movement dynamics. Along with this, the few existing methodologies tailored to objectively quantify surgery results are not practical in the medical field due to constraints in terms of cost, complexity and poor suitability to clinical environment. These limitations enforce an urgent need for the creation of a new system to quantify facial movement and allow for an easy interpretation by medical experts. With this in mind, we present here a novel method capable of quantitatively and objectively assess complex facial movements, using a set of morphological, static and dynamic measurements. For this purpose, RGB-D cameras are used to acquire both color and depth images, and a modified block matching algorithm, combining depth and color information, was developed to track the position of anatomical landmarks of interest. The algorithms are integrated into a user-friendly graphical interface and the analysis outcomes are organized into an innovative medical tool, named facegram. This system was developed in close collaboration with plastic surgeons and the methods were validated using control subjects and patients with facial paralysis. The system was shown to provide useful and detailed quantitative information (static and dynamic) making it an appropriate solution for objective quantitative characterization of facial movement in a clinical environment. PMID:26994664

  4. Binary Imaging Analysis for Comprehensive Quantitative Assessment of Peripheral Nerve

    PubMed Central

    Hunter, Daniel A.; Moradzadeh, Arash; Whitlock, Elizabeth L.; Brenner, Michael J.; Myckatyn, Terence M.; Wei, Cindy H.; Tung, Thomas H.H.; Mackinnon, Susan E.

    2007-01-01

    Quantitative histomorphometry is the current gold standard for objective measurement of nerve architecture and its components. Many methods still in use rely heavily upon manual techniques that are prohibitively time consuming, predisposing to operator fatigue, sampling error, and overall limited reproducibility. More recently, investigators have attempted to combine the speed of automated morphometry with the accuracy of manual and semi-automated methods. Systematic refinements in binary imaging analysis techniques combined with an algorithmic approach allow for more exhaustive characterization of nerve parameters in the surgically relevant injury paradigms of regeneration following crush, transection, and nerve gap injuries. The binary imaging method introduced here uses multiple bitplanes to achieve reproducible, high throughput quantitative assessment of peripheral nerve. Number of myelinated axons, myelinated fiber diameter, myelin thickness, fiber distributions, myelinated fiber density, and neural debris can be quantitatively evaluated with stratification of raw data by nerve component. Results of this semi-automated method are validated by comparing values against those obtained with manual techniques. The use of this approach results in more rapid, accurate, and complete assessment of myelinated axons than manual techniques. PMID:17675163

  5. A quantitative analysis of IRAS maps of molecular clouds

    NASA Technical Reports Server (NTRS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  6. A quantitative analysis of IRAS maps of molecular clouds

    NASA Astrophysics Data System (ADS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-11-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  7. Simulating realistic predator signatures in quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.

    2015-01-01

    Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

  8. Lipid biomarker analysis for the quantitative analysis of airborne microorganisms

    SciTech Connect

    Macnaughton, S.J.; Jenkins, T.L.; Cormier, M.R.

    1997-08-01

    There is an ever increasing concern regarding the presence of airborne microbial contaminants within indoor air environments. Exposure to such biocontaminants can give rise to large numbers of different health effects including infectious diseases, allergenic responses and respiratory problems, Biocontaminants typically round in indoor air environments include bacteria, fungi, algae, protozoa and dust mites. Mycotoxins, endotoxins, pollens and residues of organisms are also known to cause adverse health effects. A quantitative detection/identification technique independent of culturability that assays both culturable and non culturable biomass including endotoxin is critical in defining risks from indoor air biocontamination. Traditionally, methods employed for the monitoring of microorganism numbers in indoor air environments involve classical culture based techniques and/or direct microscopic counting. It has been repeatedly documented that viable microorganism counts only account for between 0.1-10% of the total community detectable by direct counting. The classic viable microbiologic approach doe`s not provide accurate estimates of microbial fragments or other indoor air components that can act as antigens and induce or potentiate allergic responses. Although bioaerosol samplers are designed to damage the microbes as little as possible, microbial stress has been shown to result from air sampling, aerosolization and microbial collection. Higher collection efficiency results in greater cell damage while less cell damage often results in lower collection efficiency. Filtration can collect particulates at almost 100% efficiency, but captured microorganisms may become dehydrated and damaged resulting in non-culturability, however, the lipid biomarker assays described herein do not rely on cell culture. Lipids are components that are universally distributed throughout cells providing a means to assess independent of culturability.

  9. Quantitative Northern Blot Analysis of Mammalian rRNA Processing.

    PubMed

    Wang, Minshi; Pestov, Dimitri G

    2016-01-01

    Assembly of eukaryotic ribosomes is an elaborate biosynthetic process that begins in the nucleolus and requires hundreds of cellular factors. Analysis of rRNA processing has been instrumental for studying the mechanisms of ribosome biogenesis and effects of stress conditions on the molecular milieu of the nucleolus. Here, we describe the quantitative analysis of the steady-state levels of rRNA precursors, applicable to studies in mammalian cells and other organisms. We include protocols for gel electrophoresis and northern blotting of rRNA precursors using procedures optimized for the large size of these RNAs. We also describe the ratio analysis of multiple precursors, a technique that facilitates the accurate assessment of changes in the efficiency of individual pre-rRNA processing steps. PMID:27576717

  10. QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

    PubMed Central

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

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

  11. Altered resting-state functional activity in posttraumatic stress disorder: A quantitative meta-analysis

    PubMed Central

    Wang, Ting; Liu, Jia; Zhang, Junran; Zhan, Wang; Li, Lei; Wu, Min; Huang, Hua; Zhu, Hongyan; Kemp, Graham J.; Gong, Qiyong

    2016-01-01

    Many functional neuroimaging studies have reported differential patterns of spontaneous brain activity in posttraumatic stress disorder (PTSD), but the findings are inconsistent and have not so far been quantitatively reviewed. The present study set out to determine consistent, specific regional brain activity alterations in PTSD, using the Effect Size Signed Differential Mapping technique to conduct a quantitative meta-analysis of resting-state functional neuroimaging studies of PTSD that used either a non-trauma (NTC) or a trauma-exposed (TEC) comparison control group. Fifteen functional neuroimaging studies were included, comparing 286 PTSDs, 203 TECs and 155 NTCs. Compared with NTC, PTSD patients showed hyperactivity in the right anterior insula and bilateral cerebellum, and hypoactivity in the dorsal medial prefrontal cortex (mPFC); compared with TEC, PTSD showed hyperactivity in the ventral mPFC. The pooled meta-analysis showed hypoactivity in the posterior insula, superior temporal, and Heschl’s gyrus in PTSD. Additionally, subgroup meta-analysis (non-medicated subjects vs. NTC) identified abnormal activation in the prefrontal-limbic system. In meta-regression analyses, mean illness duration was positively associated with activity in the right cerebellum (PTSD vs. NTC), and illness severity was negatively associated with activity in the right lingual gyrus (PTSD vs. TEC). PMID:27251865

  12. Altered resting-state functional activity in posttraumatic stress disorder: A quantitative meta-analysis.

    PubMed

    Wang, Ting; Liu, Jia; Zhang, Junran; Zhan, Wang; Li, Lei; Wu, Min; Huang, Hua; Zhu, Hongyan; Kemp, Graham J; Gong, Qiyong

    2016-01-01

    Many functional neuroimaging studies have reported differential patterns of spontaneous brain activity in posttraumatic stress disorder (PTSD), but the findings are inconsistent and have not so far been quantitatively reviewed. The present study set out to determine consistent, specific regional brain activity alterations in PTSD, using the Effect Size Signed Differential Mapping technique to conduct a quantitative meta-analysis of resting-state functional neuroimaging studies of PTSD that used either a non-trauma (NTC) or a trauma-exposed (TEC) comparison control group. Fifteen functional neuroimaging studies were included, comparing 286 PTSDs, 203 TECs and 155 NTCs. Compared with NTC, PTSD patients showed hyperactivity in the right anterior insula and bilateral cerebellum, and hypoactivity in the dorsal medial prefrontal cortex (mPFC); compared with TEC, PTSD showed hyperactivity in the ventral mPFC. The pooled meta-analysis showed hypoactivity in the posterior insula, superior temporal, and Heschl's gyrus in PTSD. Additionally, subgroup meta-analysis (non-medicated subjects vs. NTC) identified abnormal activation in the prefrontal-limbic system. In meta-regression analyses, mean illness duration was positively associated with activity in the right cerebellum (PTSD vs. NTC), and illness severity was negatively associated with activity in the right lingual gyrus (PTSD vs. TEC). PMID:27251865

  13. Quantitative Analysis Of Cristobalite In The Presence Of Quartz

    NASA Astrophysics Data System (ADS)

    Totten, Gary A.

    1985-12-01

    The detection and quantitation of-cristobalite in quartz is necessary to calculate threshold value limits (TVL) for free crystalline silica (FCS) as proposed by the American Conference of Governmental Industrial Hygienists (ACGIH). The cristobalite standard used in this study was made by heating diatomaceous earth to the transition temperature for cristobalite. The potassium bromide (KBR) pellet method was used for the analysis. Potassium cyanide (KCN) was used as an internal standard. Samples ranged from 5% to 30% cris-tobalite in quartz. Precision for this method is within 2%.

  14. Quantitative proteomic analysis of drug-induced changes in mycobacteria.

    PubMed

    Hughes, Minerva A; Silva, Jeffrey C; Geromanos, Scott J; Townsend, Craig A

    2006-01-01

    A new approach for qualitative and quantitative proteomic analysis using capillary liquid chromatography and mass spectrometry to study the protein expression response in mycobacteria following isoniazid treatment is discussed. In keeping with known effects on the fatty acid synthase II pathway, proteins encoded by the kas operon (AcpM, KasA, KasB, Accd6) were significantly overexpressed, as were those involved in iron metabolism and cell division suggesting a complex interplay of metabolic events leading to cell death. PMID:16396495

  15. Application of a Temporal Reasoning Framework Tool in Analysis of Medical Device Adverse Events

    PubMed Central

    Clark, Kimberly K.; Sharma, Deepak K.; Chute, Christopher G.; Tao, Cui

    2011-01-01

    The Clinical Narrative Temporal Relation Ontology (CNTRO)1 project offers a semantic-web based reasoning framework, which represents temporal events and relationships within clinical narrative texts, and infer new knowledge over them. In this paper, the CNTRO reasoning framework is applied to temporal analysis of medical device adverse event files. One specific adverse event was used as a test case: late stent thrombosis. Adverse event narratives were obtained from the Food and Drug Administration’s (FDA) Manufacturing and User Facility Device Experience (MAUDE) database2. 15 adverse event files in which late stent thrombosis was confirmed were randomly selected across multiple drug eluting stent devices. From these files, 81 events and 72 temporal relations were annotated. 73 temporal questions were generated, of which 65 were correctly answered by the CNTRO system. This results in an overall accuracy of 89%. This system should be pursued further to continue assessing its potential benefits in temporal analysis of medical device adverse events. PMID:22195199

  16. Temporal analysis of remotely sensed turbidity in a coastal archipelago

    NASA Astrophysics Data System (ADS)

    Suominen, Tapio; Tolvanen, Harri

    2016-07-01

    A topographically fragmental archipelago with dynamic waters set the preconditions for assessing coherent remotely sensed information. We generated a turbidity dataset for an archipelago coast in the Baltic Sea from MERIS data (FSG L1b), using CoastColour L1P, L2R and L2W processors. We excluded land and mixed pixels by masking the imagery with accurate (1:10 000) shoreline data. Using temporal linear averaging (TLA), we produced satellite-imagery datasets applicable to temporal composites for the summer seasons of three years. The turbidity assessments and temporally averaged data were compared to in situ observations obtained with coastal monitoring programs. The ability of TLA to estimate missing pixel values was further assessed by cross-validation with the leave-one-out method. The correspondence between L2W turbidity and in situ observations was good (r = 0.89), and even after applying TLA the correspondence remained acceptable (r = 0.78). The datasets revealed spatially divergent temporal water characteristics, which may be relevant to the management, design of monitoring and habitat models. Monitoring observations may be spatially biased if the temporal succession of water properties is not taken into account in coastal areas with anisotropic dispersion of waters and asynchronous annual cycles. Accordingly, areas of varying turbidity may offer a different habitat for aquatic biota than areas of static turbidity, even though they may appear similar if water properties are measured for short annual periods.

  17. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

    PubMed

    Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-04-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes. PMID:27104857

  18. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits

    PubMed Central

    Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-01-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI’s Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes. PMID:27104857

  19. The spatial and temporal analysis of forest resources and institutions

    NASA Astrophysics Data System (ADS)

    Schweik, Charles M.

    This study addresses a central puzzle facing the Human Dimensions of Global Change research community: How can we understand the influence of environmental policies on human behavior when little or no information is available on the condition of forest resources? This dissertation capitalizes on new research tools, methods and approaches to overcome the "no information about the resource" problem. Specifically, I combine (1) forest mensuration techniques, (2) Global Positioning Systems, (3) Geographic Information Systems (GIS), (4) spatial statistics, (5) remote sensing, and (6) institutional analysis to analyze forest vegetation patterns. I provide explanation of these patterns by considering the incentive structures driving human decision-making and activity and do this through two studies in very different empirical settings. Both studies apply applicable theory related to human behavior and action. Both examine the incentive structures individuals face as they undertake daily activities related to forest resources. The first study, set in East Chitwan, Nepal, identifies spatial patterns in georeferenced forest inventory data and links these to patterns predicted by optimal foraging subject to institutional constraints. The second study compares forest management in one state and one national forest in Indiana, U.S.A. In this effort, I identify spatio-temporal patterns in the forest vegetation captured by a time series of Landsat multispectral images. The combination of natural forest regrowth and property manager actions in response to incentives and constraints explain these patterns. Substantively, both studies identify change in forest resources associated with combinations of the physical, human community and institutional "landscapes" in their regions. In both cases, geographic attributes of institutions (e.g., laws, rules) are found to influence the type and location of human actions. Methodologically, the two studies provide examples of how to control

  20. Temporal and multiple quantitative trait loci analyses of resistance to bacterial wilt in tomato permit the resolution of linked loci.

    PubMed

    Mangin, B; Thoquet, P; Olivier, J; Grimsley, N H

    1999-03-01

    Ralstonia solanacearum is a soil-borne bacterium that causes the serious disease known as bacterial wilt in many plant species. In tomato, several QTL controlling resistance have been found, but in different studies, markers spanning a large region of chromosome 6 showed strong association with the resistance. By using two different approaches to analyze the data from a field test F3 population, we show that at least two separate loci approximately 30 cM apart on this chromosome are most likely involved in the resistance. First, a temporal analysis of the progression of symptoms reveals a distal locus early in the development of the disease. As the disease progresses, the maximum LOD peak observed shifts toward the proximal end of the chromosome, obscuring the distal locus. Second, although classical interval mapping could only detect the presence of one locus, a statistical "two-QTL model" test, specifically adapted for the resolution of linked QTL, strongly supported the hypothesis for the presence of two loci. These results are discussed in the context of current molecular knowledge about disease resistance genes on chromosome 6 and observations made by tomato breeders during the production of bacterial wilt-resistant varieties. PMID:10049932

  1. Temporal and multiple quantitative trait loci analyses of resistance to bacterial wilt in tomato permit the resolution of linked loci.

    PubMed Central

    Mangin, B; Thoquet, P; Olivier, J; Grimsley, N H

    1999-01-01

    Ralstonia solanacearum is a soil-borne bacterium that causes the serious disease known as bacterial wilt in many plant species. In tomato, several QTL controlling resistance have been found, but in different studies, markers spanning a large region of chromosome 6 showed strong association with the resistance. By using two different approaches to analyze the data from a field test F3 population, we show that at least two separate loci approximately 30 cM apart on this chromosome are most likely involved in the resistance. First, a temporal analysis of the progression of symptoms reveals a distal locus early in the development of the disease. As the disease progresses, the maximum LOD peak observed shifts toward the proximal end of the chromosome, obscuring the distal locus. Second, although classical interval mapping could only detect the presence of one locus, a statistical "two-QTL model" test, specifically adapted for the resolution of linked QTL, strongly supported the hypothesis for the presence of two loci. These results are discussed in the context of current molecular knowledge about disease resistance genes on chromosome 6 and observations made by tomato breeders during the production of bacterial wilt-resistant varieties. PMID:10049932

  2. Spatial and Temporal Variation in Selection of Genes Associated with Pearl Millet Varietal Quantitative Traits In situ.

    PubMed

    Mariac, Cédric; Ousseini, Issaka S; Alio, Abdel-Kader; Jugdé, Hélène; Pham, Jean-Louis; Bezançon, Gilles; Ronfort, Joelle; Descroix, Luc; Vigouroux, Yves

    2016-01-01

    Ongoing global climate changes imply new challenges for agriculture. Whether plants and crops can adapt to such rapid changes is still a widely debated question. We previously showed adaptation in the form of earlier flowering in pearl millet at the scale of a whole country over three decades. However, this analysis did not deal with variability of year to year selection. To understand and possibly manage plant and crop adaptation, we need more knowledge of how selection acts in situ. Is selection gradual, abrupt, and does it vary in space and over time? In the present study, we tracked the evolution of allele frequency in two genes associated with pearl millet phenotypic variation in situ. We sampled 17 populations of cultivated pearl millet over a period of 2 years. We tracked changes in allele frequencies in these populations by genotyping more than seven thousand individuals. We demonstrate that several allele frequencies changes are compatible with selection, by correcting allele frequency changes associated with genetic drift. We found marked variation in allele frequencies from year to year, suggesting a variable selection effect in space and over time. We estimated the strength of selection associated with variations in allele frequency. Our results suggest that the polymorphism maintained at the genes we studied is partially explained by the spatial and temporal variability of selection. In response to environmental changes, traditional pearl millet varieties could rapidly adapt thanks to this available functional variability. PMID:27507986

  3. Spatial and Temporal Variation in Selection of Genes Associated with Pearl Millet Varietal Quantitative Traits In situ

    PubMed Central

    Mariac, Cédric; Ousseini, Issaka S.; Alio, Abdel-Kader; Jugdé, Hélène; Pham, Jean-Louis; Bezançon, Gilles; Ronfort, Joelle; Descroix, Luc; Vigouroux, Yves

    2016-01-01

    Ongoing global climate changes imply new challenges for agriculture. Whether plants and crops can adapt to such rapid changes is still a widely debated question. We previously showed adaptation in the form of earlier flowering in pearl millet at the scale of a whole country over three decades. However, this analysis did not deal with variability of year to year selection. To understand and possibly manage plant and crop adaptation, we need more knowledge of how selection acts in situ. Is selection gradual, abrupt, and does it vary in space and over time? In the present study, we tracked the evolution of allele frequency in two genes associated with pearl millet phenotypic variation in situ. We sampled 17 populations of cultivated pearl millet over a period of 2 years. We tracked changes in allele frequencies in these populations by genotyping more than seven thousand individuals. We demonstrate that several allele frequencies changes are compatible with selection, by correcting allele frequency changes associated with genetic drift. We found marked variation in allele frequencies from year to year, suggesting a variable selection effect in space and over time. We estimated the strength of selection associated with variations in allele frequency. Our results suggest that the polymorphism maintained at the genes we studied is partially explained by the spatial and temporal variability of selection. In response to environmental changes, traditional pearl millet varieties could rapidly adapt thanks to this available functional variability. PMID:27507986

  4. Pattern recognition of Landsat data based upon temporal trend analysis

    NASA Technical Reports Server (NTRS)

    Engvall, J. L.; Tubbs, J. D.; Holmes, Q. A.

    1977-01-01

    The Delta Classifier defined as an agricultural crop classification scheme employing a temporal trend procedure is applied to more than 100 different Landsat data sets collected during the 1974-1975 growing season throughout the major wheat-producing regions of the United States. The classification approach stresses examination of temporal trends of the Landsat mean vectors of crops in the absence of corresponding ground truth information. It is shown that the resulting classifications compare favorably to ground truth estimates for wheat proportion in those cases where ground truth is available, and that the temporal trend procedure yields estimates of the wheat proportion that are comparable to the best results from maximum likelihood classification with photointerpreter-defined training fields.

  5. Temporal scaling behavior of sea-level change in Hong Kong - Multifractal temporally weighted detrended fluctuation analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Yuanzhi; Ge, Erjia

    2013-01-01

    The rise in global sea levels has been recognized by many scientists as an important global research issue. The process of sea-level change has demonstrated a complex scaling behavior in space and time. Large numbers of tide gauge stations have been built to measure sea-level change in the North Pacific Ocean, Indian Ocean, North Atlantic Ocean, and Antarctic Ocean. Extensive studies have been devoted to exploring sea-level variation in Asia concerning the Bohai Gulf (China), the Yellow Sea (China), the Mekong Delta (Thailand), and Singapore. Hong Kong, however, a mega city with a population of over 7 million situated in the mouth of the Pear River Estuary in the west and the South China Sea in the east, has yet to be studied, particularly in terms of the temporal scaling behavior of sea-level change. This article presents an approach to studying the temporal scaling behavior of sea-level change over multiple time scales by analyzing the time series of sea-level change in Tai Po Kou, Tsim Bei Tsui, and Quarry Bay from the periods of 1964-2010, 1974-2010, and 1986-2010, respectively. The detection of long-range correlation and multi-fractality of sea-level change seeks answers to the following questions: (1) Is the current sea-level rise associated with and responsible for the next rise over time? (2) Does the sea-level rise have specific temporal patterns manifested by multi-scaling behaviors? and (3) Is the sea-level rise is temporally heterogeneous in the different parts of Hong Kong? Multi-fractal temporally weighted de-trended fluctuation analysis (MF-TWDFA), an extension of multi-fractal de-trended fluctuation analysis (MF-DFA), has been applied in this study to identify long-range correlation and multi-scaling behavior of the sea-level rise in Hong Kong. The experimental results show that the sea-level rise is long-range correlated and multi-fractal. The temporal patterns are heterogeneous over space. This finding implies that mechanisms associated with the

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

    NASA Astrophysics Data System (ADS)

    Haaland, David M.

    1992-03-01

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

  7. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    SciTech Connect

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-08-14

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

  8. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGESBeta

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-08-14

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

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

    SciTech Connect

    Haaland, D.M.

    1991-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-11-01

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

  11. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    PubMed Central

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-01-01

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ⋯Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations. PMID:26306198

  12. Automated monitoring and quantitative analysis of feeding behaviour in Drosophila

    PubMed Central

    Itskov, Pavel M.; Moreira, José-Maria; Vinnik, Ekaterina; Lopes, Gonçalo; Safarik, Steve; Dickinson, Michael H.; Ribeiro, Carlos

    2014-01-01

    Food ingestion is one of the defining behaviours of all animals, but its quantification and analysis remain challenging. This is especially the case for feeding behaviour in small, genetically tractable animals such as Drosophila melanogaster. Here, we present a method based on capacitive measurements, which allows the detailed, automated and high-throughput quantification of feeding behaviour. Using this method, we were able to measure the volume ingested in single sips of an individual, and monitor the absorption of food with high temporal resolution. We demonstrate that flies ingest food by rhythmically extending their proboscis with a frequency that is not modulated by the internal state of the animal. Instead, hunger and satiety homeostatically modulate the microstructure of feeding. These results highlight similarities of food intake regulation between insects, rodents, and humans, pointing to a common strategy in how the nervous systems of different animals control food intake. PMID:25087594

  13. A method for quantitative wet chemical analysis of urinary calculi.

    PubMed

    Larsson, L; Sörbo, B; Tiselius, H G; Ohman, S

    1984-06-27

    We describe a simple method for quantitative chemical analysis of urinary calculi requiring no specialized equipment. Pulverized calculi are dried over silica gel at room temperature and dissolved in nitric acid, which was the only effective agent for complete dissolution. Calcium, magnesium, ammonium, and phosphate are then determined by conventional methods. Oxalate is determined by a method based on the quenching action of oxalate on the fluorescence of a zirconium-flavonol complex. Uric acid, when treated with nitric acid, is stoichiometrically converted to alloxan, which is determined fluorimetrically with 1,2-phenylenediamine. Similarly, cystine is oxidized by nitric acid to sulfate, which is determined turbidimetrically as barium sulfate. Protein is determined spectrophotometrically as xanthoprotein. The total mass recovery of authentic calculi was 92.2 +/- 6.7 (SD) per cent. The method permits analysis of calculi as small as 1.0 mg. Internal quality control is performed with specially designed control samples. PMID:6086179

  14. [Quantitative analysis of transformer oil dissolved gases using FTIR].

    PubMed

    Zhao, An-xin; Tang, Xiao-jun; Wang, Er-zhen; Zhang, Zhong-hua; Liu, Jun-hua

    2013-09-01

    For the defects of requiring carrier gas and regular calibration, and low safety using chromatography to on line monitor transformer dissolved gases, it was attempted to establish a dissolved gas analysis system based on Fourier transform infrared spectroscopy. Taking into account the small amount of characteristic gases, many components, detection limit and safety requirements and the difficulty of degasser to put an end to the presence of interference gas, the quantitative analysis model was established based on sparse partial least squares, piecewise section correction and feature variable extraction algorithm using improvement TR regularization. With the characteristic gas of CH4, C2H6, C2H6, and CO2, the results show that using FTIR meets DGA requirements with the spectrum wave number resolution of 1 cm(-1) and optical path of 10 cm. PMID:24369641

  15. Quantitative Analysis of the Interdisciplinarity of Applied Mathematics.

    PubMed

    Xie, Zheng; Duan, Xiaojun; Ouyang, Zhenzheng; Zhang, Pengyuan

    2015-01-01

    The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999-2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics. PMID:26352604

  16. Segmentation and quantitative analysis of individual cells in developmental tissues.

    PubMed

    Nandy, Kaustav; Kim, Jusub; McCullough, Dean P; McAuliffe, Matthew; Meaburn, Karen J; Yamaguchi, Terry P; Gudla, Prabhakar R; Lockett, Stephen J

    2014-01-01

    Image analysis is vital for extracting quantitative information from biological images and is used extensively, including investigations in developmental biology. The technique commences with the segmentation (delineation) of objects of interest from 2D images or 3D image stacks and is usually followed by the measurement and classification of the segmented objects. This chapter focuses on the segmentation task and here we explain the use of ImageJ, MIPAV (Medical Image Processing, Analysis, and Visualization), and VisSeg, three freely available software packages for this purpose. ImageJ and MIPAV are extremely versatile and can be used in diverse applications. VisSeg is a specialized tool for performing highly accurate and reliable 2D and 3D segmentation of objects such as cells and cell nuclei in images and stacks. PMID:24318825

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

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

  18. Quantitative Analysis of the Interdisciplinarity of Applied Mathematics

    PubMed Central

    Zhang, Pengyuan

    2015-01-01

    The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999–2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics. PMID:26352604

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  20. Final Report for Dynamic Models for Causal Analysis of Panel Data. Methods for Temporal Analysis. Part I, Chapter 1.

    ERIC Educational Resources Information Center

    Hannan, Michael T.; Tuma, Nancy Brandon

    This document is part of a series of chapters described in SO 011 759. Working from the premise that temporal analysis is indispensable for the study of change, the document examines major alternatives in research design of this nature. Five sections focus on the features, advantages, and limitations of temporal analysis. Four designs which…

  1. Advances in Temporal Analysis in Learning and Instruction

    ERIC Educational Resources Information Center

    Molenaar, Inge

    2014-01-01

    This paper focuses on a trend to analyse temporal characteristics of constructs important to learning and instruction. Different researchers have indicated that we should pay more attention to time in our research to enhance explanatory power and increase validity. Constructs formerly viewed as personal traits, such as self-regulated learning and…

  2. Cubic map algebra functions for spatio-temporal analysis

    USGS Publications Warehouse

    Mennis, J.; Viger, R.; Tomlin, C.D.

    2005-01-01

    We propose an extension of map algebra to three dimensions for spatio-temporal data handling. This approach yields a new class of map algebra functions that we call "cube functions." Whereas conventional map algebra functions operate on data layers representing two-dimensional space, cube functions operate on data cubes representing two-dimensional space over a third-dimensional period of time. We describe the prototype implementation of a spatio-temporal data structure and selected cube function versions of conventional local, focal, and zonal map algebra functions. The utility of cube functions is demonstrated through a case study analyzing the spatio-temporal variability of remotely sensed, southeastern U.S. vegetation character over various land covers and during different El Nin??o/Southern Oscillation (ENSO) phases. Like conventional map algebra, the application of cube functions may demand significant data preprocessing when integrating diverse data sets, and are subject to limitations related to data storage and algorithm performance. Solutions to these issues include extending data compression and computing strategies for calculations on very large data volumes to spatio-temporal data handling.

  3. Quantitative analysis of lead in aqueous solutions by ultrasonic nebulizer assisted laser induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhong, Shi-Lei; Lu, Yuan; Kong, Wei-Jin; Cheng, Kai; Zheng, Ronger

    2016-08-01

    In this study, an ultrasonic nebulizer unit was established to improve the quantitative analysis ability of laser-induced breakdown spectroscopy (LIBS) for liquid samples detection, using solutions of the heavy metal element Pb as an example. An analytical procedure was designed to guarantee the stability and repeatability of the LIBS signal. A series of experiments were carried out strictly according to the procedure. The experimental parameters were optimized based on studies of the pulse energy influence and temporal evolution of the emission features. The plasma temperature and electron density were calculated to confirm the LTE state of the plasma. Normalizing the intensities by background was demonstrated to be an appropriate method in this work. The linear range of this system for Pb analysis was confirmed over a concentration range of 0-4,150ppm by measuring 12 samples with different concentrations. The correlation coefficient of the fitted calibration curve was as high as 99.94% in the linear range, and the LOD of Pb was confirmed as 2.93ppm. Concentration prediction experiments were performed on a further six samples. The excellent quantitative ability of the system was demonstrated by comparison of the real and predicted concentrations of the samples. The lowest relative error was 0.043% and the highest was no more than 7.1%.

  4. Digital Holographic Microscopy: Quantitative Phase Imaging and Applications in Live Cell Analysis

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Langehanenberg, Patrik; Kosmeier, Sebastian; Schlichthaber, Frank; Remmersmann, Christian; von Bally, Gert; Rommel, Christina; Dierker, Christian; Schnekenburger, Jürgen

    The analysis of complex processes in living cells creates a high demand for fast and label-free methods for online monitoring. Widely used fluorescence methods require specific labeling and are often restricted to chemically fixated samples. Thus, methods that offer label-free and minimally invasive detection of live cell processes and cell state alterations are of particular interest. In combination with light microscopy, digital holography provides label-free, multi-focus quantitative phase imaging of living cells. In overview, several methods for digital holographic microscopy (DHM) are presented. First, different experimental setups for the recording of digital holograms and the modular integration of DHM into common microscopes are described. Then the numerical processing of digitally captured holograms is explained. This includes the description of spatial and temporal phase shifting techniques, spatial filtering based reconstruction, holographic autofocusing, and the evaluation of self-interference holograms. Furthermore, the usage of partial coherent light and multi-wavelength approaches is discussed. Finally, potentials of digital holographic microscopy for quantitative cell imaging are illustrated by results from selected applications. It is shown that DHM can be used for automated tracking of migrating cells and cell thickness monitoring as well as for refractive index determination of cells and particles. Moreover, the use of DHM for label-free analysis in fluidics and micro-injection monitoring is demonstrated. The results show that DHM is a highly relevant method that allows novel insights in dynamic cell biology, with applications in cancer research and for drugs and toxicity testing.

  5. Quantitative image analysis in sonograms of the thyroid gland

    NASA Astrophysics Data System (ADS)

    Catherine, Skouroliakou; Maria, Lyra; Aristides, Antoniou; Lambros, Vlahos

    2006-12-01

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

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

    PubMed

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

    2015-08-01

    Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is not incorporated into the differential expression (DE) analysis. Here, we propose a novel probabilistic framework EBprot that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. To illustrate the wide applicability of EBprot in different experimental designs, we applied EBprot to a dataset for lung cancer subtype analysis with biological replicates and another dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells with multiplexed labeling. Through these examples, we show that the peptide-level analysis of EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets. The software suite is freely available on the Sourceforge website http://ebprot.sourceforge.net/. All MS data have been deposited in the ProteomeXchange with identifier PXD001426 (http://proteomecentral.proteomexchange.org/dataset/PXD001426/). PMID:25913743

  7. The Quantitative Analysis of Chennai Automotive Industry Cluster

    NASA Astrophysics Data System (ADS)

    Bhaskaran, Ethirajan

    2016-05-01

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

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

    PubMed

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

    2013-11-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. PMID:24130119

  9. The Quantitative Analysis of Chennai Automotive Industry Cluster

    NASA Astrophysics Data System (ADS)

    Bhaskaran, Ethirajan

    2016-07-01

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

  10. Geovisualization Approaches for Spatio-temporal Crime Scene Analysis - Towards 4D Crime Mapping

    NASA Astrophysics Data System (ADS)

    Wolff, Markus; Asche, Hartmut

    This paper presents a set of methods and techniques for analysis and multidimensional visualisation of crime scenes in a German city. As a first step the approach implies spatio-temporal analysis of crime scenes. Against this background a GIS-based application is developed that facilitates discovering initial trends in spatio-temporal crime scene distributions even for a GIS untrained user. Based on these results further spatio-temporal analysis is conducted to detect variations of certain hotspots in space and time. In a next step these findings of crime scene analysis are integrated into a geovirtual environment. Behind this background the concept of the space-time cube is adopted to allow for visual analysis of repeat burglary victimisation. Since these procedures require incorporating temporal elements into virtual 3D environments, basic methods for 4D crime scene visualisation are outlined in this paper.

  11. EDXRF quantitative analysis of chromophore chemical elements in corundum samples.

    PubMed

    Bonizzoni, L; Galli, A; Spinolo, G; Palanza, V

    2009-12-01

    Corundum is a crystalline form of aluminum oxide (Al(2)O(3)) and is one of the rock-forming minerals. When aluminum oxide is pure, the mineral is colorless, but the presence of trace amounts of other elements such as iron, titanium, and chromium in the crystal lattice gives the typical colors (including blue, red, violet, pink, green, yellow, orange, gray, white, colorless, and black) of gemstone varieties. The starting point for our work is the quantitative evaluation of the concentration of chromophore chemical elements with a precision as good as possible to match the data obtained by different techniques as such as optical absorption photoluminescence. The aim is to give an interpretation of the absorption bands present in the NIR and visible ranges which do not involve intervalence charge transfer transitions (Fe(2+) --> Fe(3+) and Fe(2+) --> Ti(4+)), commonly considered responsible of the important features of the blue sapphire absorption spectra. So, we developed a method to evaluate as accurately as possible the autoabsorption effects and the secondary excitation effects which frequently are sources of relevant errors in the quantitative EDXRF analysis. PMID:19821113

  12. Quantitative analysis of gene function in the Drosophila embryo.

    PubMed Central

    Tracey, W D; Ning, X; Klingler, M; Kramer, S G; Gergen, J P

    2000-01-01

    The specific functions of gene products frequently depend on the developmental context in which they are expressed. Thus, studies on gene function will benefit from systems that allow for manipulation of gene expression within model systems where the developmental context is well defined. Here we describe a system that allows for genetically controlled overexpression of any gene of interest under normal physiological conditions in the early Drosophila embryo. This regulated expression is achieved through the use of Drosophila lines that express a maternal mRNA for the yeast transcription factor GAL4. Embryos derived from females that express GAL4 maternally activate GAL4-dependent UAS transgenes at uniform levels throughout the embryo during the blastoderm stage of embryogenesis. The expression levels can be quantitatively manipulated through the use of lines that have different levels of maternal GAL4 activity. Specific phenotypes are produced by expression of a number of different developmental regulators with this system, including genes that normally do not function during Drosophila embryogenesis. Analysis of the response to overexpression of runt provides evidence that this pair-rule segmentation gene has a direct role in repressing transcription of the segment-polarity gene engrailed. The maternal GAL4 system will have applications both for the measurement of gene activity in reverse genetic experiments as well as for the identification of genetic factors that have quantitative effects on gene function in vivo. PMID:10628987

  13. Quantitative analysis of multiple sclerosis: a feasibility study

    NASA Astrophysics Data System (ADS)

    Li, Lihong; Li, Xiang; Wei, Xinzhou; Sturm, Deborah; Lu, Hongbing; Liang, Zhengrong

    2006-03-01

    Multiple Sclerosis (MS) is an inflammatory and demyelinating disorder of the central nervous system with a presumed immune-mediated etiology. For treatment of MS, the measurements of white matter (WM), gray matter (GM), and cerebral spinal fluid (CSF) are often used in conjunction with clinical evaluation to provide a more objective measure of MS burden. In this paper, we apply a new unifying automatic mixture-based algorithm for segmentation of brain tissues to quantitatively analyze MS. The method takes into account the following effects that commonly appear in MR imaging: 1) The MR data is modeled as a stochastic process with an inherent inhomogeneity effect of smoothly varying intensity; 2) A new partial volume (PV) model is built in establishing the maximum a posterior (MAP) segmentation scheme; 3) Noise artifacts are minimized by a priori Markov random field (MRF) penalty indicating neighborhood correlation from tissue mixture. The volumes of brain tissues (WM, GM) and CSF are extracted from the mixture-based segmentation. Experimental results of feasibility studies on quantitative analysis of MS are presented.

  14. Quantitative PCR analysis of laryngeal muscle fiber types

    PubMed Central

    Van Daele, Douglas J.

    2013-01-01

    Voice and swallowing dysfunction as a result of recurrent laryngeal nerve paralysis can be improved with vocal fold injections or laryngeal framework surgery. However, denervation atrophy can cause late-term clinical failure. A major determinant of skeletal muscle physiology is myosin heavy chain (MyHC) expression, and previous protein analyses have shown changes in laryngeal muscle fiber MyHC isoform with denervation. RNA analyses in this setting have not been performed, and understanding RNA levels will allow interventions better designed to reverse processes such as denervation in the future. Total RNA was extracted from bilateral rat thyroarytenoid (TA), posterior cricoarytenoid (PCA), and cricothyroid (CT) muscles in rats. Primers were designed using published MyHC isoform sequences. SYBR Green real time reverse transcription-polymerase chain reaction (SYBR-RT-PCR) was used for quantification. The electropherogram showed a clear separation of total RNA to 28S and 18S subunits. Melting curves illustrated single peaks for all type MyHC primers. All MyHC isoforms were identified in all muscles with various degrees of expression. Quantitative PCR is a sensitive method to detect MyHC isoforms in laryngeal muscle. Isoform expression using mRNA analysis was similar to previous analyses but showed some important differences. This technique can be used to quantitatively assess response to interventions targeted to maintain muscle bulk after denervation. PMID:20430402

  15. Quantitative analysis of the polarization characteristics of atherosclerotic plaques

    NASA Astrophysics Data System (ADS)

    Gubarkova, Ekaterina V.; Kirillin, Michail Y.; Dudenkova, Varvara V.; Kiseleva, Elena B.; Moiseev, Alexander A.; Gelikonov, Grigory V.; Timofeeva, Lidia B.; Fiks, Ilya I.; Feldchtein, Felix I.; Gladkova, Natalia D.

    2016-04-01

    In this study we demonstrate the capability of cross-polarization optical coherence tomography (CP OCT) to assess collagen and elastin fibers condition in atherosclerotic plaques basing on ratio of the OCT signal levels in cross- and co- polarizations. We consider the depolarization factor (DF) and the effective birefringence (Δn) as quantitative characteristics of CP OCT images. We revealed that calculation of both DF and Δn in the region of interest (fibrous cap) yields a statistically significant difference between stable and unstable plaques (0.46+/-0.21 vs 0.09+/-0.04 for IDF; (4.7+/-1.0)•10-4 vs (2.5+/-0.7)•10-4 for Δn p<0.05). In parallel with CP OCT we used the nonlinear microscopy for analysis of thin cross-section of atherosclerotic plaque, revealing the different average isotropy index of collagen and elastin fibers for stable and unstable plaques (0.30 +/- 0.10 vs 0.70 +/- 0.08; p<0.001). The proposed approach for quantitative assessment of CP OCT images allows cross-scattering and birefringence characterization of stable and unstable atherosclerotic plaques.

  16. Bayesian robust analysis for genetic architecture of quantitative traits

    PubMed Central

    Yang, Runqing; Wang, Xin; Li, Jian; Deng, Hongwen

    2009-01-01

    Motivation: In most quantitative trait locus (QTL) mapping studies, phenotypes are assumed to follow normal distributions. Deviations from this assumption may affect the accuracy of QTL detection and lead to detection of spurious QTLs. To improve the robustness of QTL mapping methods, we replaced the normal distribution for residuals in multiple interacting QTL models with the normal/independent distributions that are a class of symmetric and long-tailed distributions and are able to accommodate residual outliers. Subsequently, we developed a Bayesian robust analysis strategy for dissecting genetic architecture of quantitative traits and for mapping genome-wide interacting QTLs in line crosses. Results: Through computer simulations, we showed that our strategy had a similar power for QTL detection compared with traditional methods assuming normal-distributed traits, but had a substantially increased power for non-normal phenotypes. When this strategy was applied to a group of traits associated with physical/chemical characteristics and quality in rice, more main and epistatic QTLs were detected than traditional Bayesian model analyses under the normal assumption. Contact: runqingyang@sjtu.edu.cn; dengh@umkc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18974168

  17. Quantitative analysis of incipient mineral loss in hard tissues

    NASA Astrophysics Data System (ADS)

    Matvienko, Anna; Mandelis, Andreas; Hellen, Adam; Jeon, Raymond; Abrams, Stephen; Amaechi, Bennett

    2009-02-01

    A coupled diffuse-photon-density-wave and thermal-wave theoretical model was developed to describe the biothermophotonic phenomena in multi-layered hard tissue structures. Photothermal Radiometry was applied as a safe, non-destructive, and highly sensitive tool for the detection of early tooth enamel demineralization to test the theory. Extracted human tooth was treated sequentially with an artificial demineralization gel to simulate controlled mineral loss in the enamel. The experimental setup included a semiconductor laser (659 nm, 120 mW) as the source of the photothermal signal. Modulated laser light generated infrared blackbody radiation from teeth upon absorption and nonradiative energy conversion. The infrared flux emitted by the treated region of the tooth surface and sub-surface was monitored with an infrared detector, both before and after treatment. Frequency scans with a laser beam size of 3 mm were performed in order to guarantee one-dimensionality of the photothermal field. TMR images showed clear differences between sound and demineralized enamel, however this technique is destructive. Dental radiographs did not indicate any changes. The photothermal signal showed clear change even after 1 min of gel treatment. As a result of the fittings, thermal and optical properties of sound and demineralized enamel were obtained, which allowed for quantitative differentiation of healthy and non-healthy regions. In conclusion, the developed model was shown to be a promising tool for non-invasive quantitative analysis of early demineralization of hard tissues.

  18. Analysis of generalized interictal discharges using quantitative EEG.

    PubMed

    da Silva Braga, Aline Marques; Fujisao, Elaine Keiko; Betting, Luiz Eduardo

    2014-12-01

    Experimental evidence from animal models of the absence seizures suggests a focal source for the initiation of generalized spike-and-wave (GSW) discharges. Furthermore, clinical studies indicate that patients diagnosed with idiopathic generalized epilepsy (IGE) exhibit focal electroencephalographic abnormalities, which involve the thalamo-cortical circuitry. This circuitry is a key network that has been implicated in the initiation of generalized discharges, and may contribute to the pathophysiology of GSW discharges. Quantitative electroencephalogram (qEEG) analysis may be able to detect abnormalities associated with the initiation of GSW discharges. The objective of this study was to determine whether interictal GSW discharges exhibit focal characteristics using qEEG analysis. In this study, 75 EEG recordings from 64 patients were analyzed. All EEG recordings analyzed contained at least one GSW discharge. EEG recordings were obtained by a 22-channel recorder with electrodes positioned according to the international 10-20 system of electrode placement. EEG activity was recorded for 20 min including photic stimulation and hyperventilation. The EEG recordings were visually inspected, and the first unequivocally confirmed generalized spike was marked for each discharge. Three methods of source imaging analysis were applied: dipole source imaging (DSI), classical LORETA analysis recursively applied (CLARA), and equivalent dipole of independent components with cluster analysis. A total of 753 GSW discharges were identified and spatiotemporally analyzed. Source evaluation analysis using all three techniques revealed that the frontal lobe was the principal source of GSW discharges (70%), followed by the parietal and occipital lobes (14%), and the basal ganglia (12%). The main anatomical sources of GSW discharges were the anterior cingulate cortex (36%) and the medial frontal gyrus (23%). Source analysis did not reveal a common focal source of GSW discharges. However

  19. Quantitative multi-image analysis for biomedical Raman spectroscopic imaging.

    PubMed

    Hedegaard, Martin A B; Bergholt, Mads S; Stevens, Molly M

    2016-05-01

    Imaging by Raman spectroscopy enables unparalleled label-free insights into cell and tissue composition at the molecular level. With established approaches limited to single image analysis, there are currently no general guidelines or consensus on how to quantify biochemical components across multiple Raman images. Here, we describe a broadly applicable methodology for the combination of multiple Raman images into a single image for analysis. This is achieved by removing image specific background interference, unfolding the series of Raman images into a single dataset, and normalisation of each Raman spectrum to render comparable Raman images. Multivariate image analysis is finally applied to derive the contributing 'pure' biochemical spectra for relative quantification. We present our methodology using four independently measured Raman images of control cells and four images of cells treated with strontium ions from substituted bioactive glass. We show that the relative biochemical distribution per area of the cells can be quantified. In addition, using k-means clustering, we are able to discriminate between the two cell types over multiple Raman images. This study shows a streamlined quantitative multi-image analysis tool for improving cell/tissue characterisation and opens new avenues in biomedical Raman spectroscopic imaging. PMID:26833935

  20. Quantitative analysis of the reconstruction performance of interpolants

    NASA Technical Reports Server (NTRS)

    Lansing, Donald L.; Park, Stephen K.

    1987-01-01

    The analysis presented provides a quantitative measure of the reconstruction or interpolation performance of linear, shift-invariant interpolants. The performance criterion is the mean square error of the difference between the sampled and reconstructed functions. The analysis is applicable to reconstruction algorithms used in image processing and to many types of splines used in numerical analysis and computer graphics. When formulated in the frequency domain, the mean square error clearly separates the contribution of the interpolation method from the contribution of the sampled data. The equations provide a rational basis for selecting an optimal interpolant; that is, one which minimizes the mean square error. The analysis has been applied to a selection of frequently used data splines and reconstruction algorithms: parametric cubic and quintic Hermite splines, exponential and nu splines (including the special case of the cubic spline), parametric cubic convolution, Keys' fourth-order cubic, and a cubic with a discontinuous first derivative. The emphasis in this paper is on the image-dependent case in which no a priori knowledge of the frequency spectrum of the sampled function is assumed.

  1. Hydrodynamics Flow and Transport Characterization of a Karstified Physical Model Using Temporal Moment Analysis

    NASA Astrophysics Data System (ADS)

    Anaya, A. A.; Padilla, I. Y.

    2013-12-01

    High productivity of karst groundwater systems is often associated with conduit flow and high matrix permeability. Spatial heterogeneities and anisotropy, among others factors, result in highly complex flow patterns in these systems. The same characteristics that make these aquifers very productive also make them highly vulnerable to contamination and a likely for contaminant exposure. The understanding of contamination fate and transport processes in these complex aquifers demand different statistical and numerical approaches, such as the Temporal Moment Analysis (TMA). TMA of solute breakthrough curves provide qualitative and quantitative results to characterize hydrodynamic variables that affect the release, mobility, persistence, and possible pathways of contaminants in karst groundwater systems. The general objective of this work is to characterize flow and transport processes in conduit and diffusion-dominated flow under low and high flow conditions using TMA in a karstified physical model. A multidimensional, laboratory-scale, Geo-Hydrobed model (GHM) containing a karstified limestone block collected from the karst aquifer formation of northern Puerto Rico are used for this purpose. Experimental work entails injecting dissolved CaCl2 and trichloroethene (TCE) in the upstream boundary of the GHM while monitoring their concentrations spatially and temporally in the limestone under different groundwater flow regimes. Results from the TMA show a highly heterogeneous system resulting in large preferential flow components and specific mass-transfer limitations zones especially in diffuse flow areas. Flow variables like velocity and Reynolds number indicates defined preferential flow paths increasing spatially as flow rate increase. TMA results show to be qualitatively consistent with a previous statistical novel approach developed using mixed models. Comparison between the dissolved CaCl2 tracer and TCE show implications for reactive contaminants in the karst

  2. Temporal coherence and attention in auditory scene analysis

    PubMed Central

    Shamma, Shihab A.; Elhilali, Mounya; Micheyl, Christophe

    2010-01-01

    Humans and other animals can attend to one of multiple sounds, and follow it selectively over time. The neural underpinnings of this perceptual feat remain mysterious. Some studies have concluded that sounds are heard as separate streams when they activate well-separated populations of central auditory neurons, and that this process is largely pre-attentive. Here, we argue instead that stream formation depends primarily on temporal coherence between responses that encode various features of a sound source. Furthermore, we postulate that only when attention is directed towards a particular feature (e.g., pitch) do all other temporally coherent features of that source (e.g., timbre and location) become bound together as a stream that is segregated from the incoherent features of other sources. PMID:21196054

  3. Quantitative image analysis of WE43-T6 cracking behavior

    NASA Astrophysics Data System (ADS)

    Ahmad, A.; Yahya, Z.

    2013-06-01

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

  4. [Accounting for Expected Linkage in Biometric Analysis of Quantitative Traits].

    PubMed

    Mikhailov, M E

    2015-08-01

    The problem of accounting for a genetic estimation of expected linkage in the disposition of random loci was solved for the additive-dominant model. The Comstock-Robinson estimations for the sum of squares of dominant effects, the sum of squares of additive effects, and the average degree of dominance were modified. Also, the Wright's estimation for the number of loci controlling the variation of a quantitative trait was modified and its application sphere was extended. Formulas that should eliminate linkage, on average, were derived for these estimations. Nonbiased estimations were applied to the analysis of maize data. Our result showed that the most likely cause of heterosis is dominance rather than overdominance and that the main part of the heterotic effect is provided by dozens of genes. PMID:26601496

  5. Automated quantitative cytological analysis using portable microfluidic microscopy.

    PubMed

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

    2016-06-01

    In this article, a portable microfluidic microscopy based approach for automated cytological investigations is presented. Inexpensive optical and electronic components have been used to construct a simple microfluidic microscopy system. In contrast to the conventional slide-based methods, the presented method employs microfluidics to enable automated sample handling and image acquisition. The approach involves the use of simple in-suspension staining and automated image acquisition to enable quantitative cytological analysis of samples. The applicability of the presented approach to research in cellular biology is shown by performing an automated cell viability assessment on a given population of yeast cells. Further, the relevance of the presented approach to clinical diagnosis and prognosis has been demonstrated by performing detection and differential assessment of malaria infection in a given sample. PMID:25990413

  6. Quantitative analysis of gallstones using laser-induced breakdown spectroscopy

    SciTech Connect

    Singh, Vivek K.; Singh, Vinita; Rai, Awadhesh K.; Thakur, Surya N.; Rai, Pradeep K.; Singh, Jagdish P

    2008-11-01

    The utility of laser-induced breakdown spectroscopy (LIBS) for categorizing different types of gallbladder stone has been demonstrated by analyzing their major and minor constituents. LIBS spectra of three types of gallstone have been recorded in the 200-900 nm spectral region. Calcium is found to be the major element in all types of gallbladder stone. The spectrophotometric method has been used to classify the stones. A calibration-free LIBS method has been used for the quantitative analysis of metal elements, and the results have been compared with those obtained from inductively coupled plasma atomic emission spectroscopy (ICP-AES) measurements. The single-shot LIBS spectra from different points on the cross section (in steps of 0.5 mm from one end to the other) of gallstones have also been recorded to study the variation of constituents from the center to the surface. The presence of different metal elements and their possible role in gallstone formation is discussed.

  7. Quantitative genetic analysis of injury liability in infants and toddlers

    SciTech Connect

    Phillips, K.; Matheny, A.P. Jr.

    1995-02-27

    A threshold model of latent liability was applied to infant and toddler twin data on total count of injuries sustained during the interval from birth to 36 months of age. A quantitative genetic analysis of estimated twin correlations in injury liability indicated strong genetic dominance effects, but no additive genetic variance was detected. Because interpretations involving overdominance have little research support, the results may be due to low order epistasis or other interaction effects. Boys had more injuries than girls, but this effect was found only for groups whose parents were prompted and questioned in detail about their children`s injuries. Activity and impulsivity are two behavioral predictors of childhood injury, and the results are discussed in relation to animal research on infant and adult activity levels, and impulsivity in adult humans. Genetic epidemiological approaches to childhood injury should aid in targeting higher risk children for preventive intervention. 30 refs., 4 figs., 3 tabs.

  8. Quantitative analysis of forest island pattern in selected Ohio landscapes

    SciTech Connect

    Bowen, G.W.; Burgess, R.L.

    1981-07-01

    The purpose of this study was to quantitatively describe the various aspects of regional distribution patterns of forest islands and relate those patterns to other landscape features. Several maps showing the forest cover of various counties in Ohio were selected as representative examples of forest patterns to be quantified. Ten thousand hectare study areas (landscapes) were delineated on each map. A total of 15 landscapes representing a wide variety of forest island patterns was chosen. Data were converted into a series of continuous variables which contained information pertinent to the sizes, shape, numbers, and spacing of woodlots within a landscape. The continuous variables were used in a factor analysis to describe the variation among landscapes in terms of forest island pattern. The results showed that forest island patterns are related to topography and other environmental features correlated with topography.

  9. Quantitative multielement analysis using high energy particle bombardment

    NASA Technical Reports Server (NTRS)

    Clark, P. J.; Neal, G. F.; Allen, R. O.

    1974-01-01

    Charged particles ranging in energy from 0.8 to 4.0 MeV are used to induce resonant nuclear reactions, Coulomb excitation (gamma X-rays), and X-ray emission in both thick and thin targets. Quantitative analysis is possible for elements from Li to Pb in complex environmental samples, although the matrix can severely reduce the sensitivity. It is necessary to use a comparator technique for the gamma-rays, while for X-rays an internal standard can be used. A USGS standard rock is analyzed for a total of 28 elements. Water samples can be analyzed either by nebulizing the sample doped with Cs or Y onto a thin formvar film or by extracting the sample (with or without an internal standard) onto ion exchange resin which is pressed into a pellet.

  10. Sensitive LC MS quantitative analysis of carbohydrates by Cs+ attachment.

    PubMed

    Rogatsky, Eduard; Jayatillake, Harsha; Goswami, Gayotri; Tomuta, Vlad; Stein, Daniel

    2005-11-01

    The development of a sensitive assay for the quantitative analysis of carbohydrates from human plasma using LC/MS/MS is described in this paper. After sample preparation, carbohydrates were cationized by Cs(+) after their separation by normal phase liquid chromatography on an amino based column. Cesium is capable of forming a quasi-molecular ion [M + Cs](+) with neutral carbohydrate molecules in the positive ion mode of electrospray ionization mass spectrometry. The mass spectrometer was operated in multiple reaction monitoring mode, and transitions [M + 133] --> 133 were monitored (M, carbohydrate molecular weight). The new method is robust, highly sensitive, rapid, and does not require postcolumn addition or derivatization. It is useful in clinical research for measurement of carbohydrate molecules by isotope dilution assay. PMID:16182559